Dissertations / Theses on the topic 'Transcription Start Sites'
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1
Down, T. "Computational localization of promoters and transcription start sites in mammalian genomes." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.598623.
Full textAbstract:
Here, I investigate the question of identifying and annotating promoters, one of the most important regulatory signals in the genome, which mark the points where transcription is initiated, and regulate the transcription of genes. I present a new computational method, EponineTSS, which can predict transcription start sites in bulk genomic sequence data with excellent sensitivity and specificity. Unlike the existing methods, it gives an indication of the actual location of the transcription start site. Comparisons with available experimental data suggest that the positional accuracy of these predictions is very good. Results form this method are included as part of the Ensembl human genome annotation. Having located transcription start sites for genes, I also discuss the use of results from comparative genomics the estimate the extent of the fundamental promoter region upstream of the start site. I show that the extent of promoters is very variable, and that promoter size is correlated with the function of the gene for whose regulation it is responsible. Genes associated with developmental processes tend to have particularly large, and thus presumably complex, promoters, with the homeobox transcription factors among the most extreme examples. I also introduce sparse Bayesian learning, a recently developed approach to supervised machine learning which can be applied to the training of a wide range of model types, and embodies the principle of selecting the simplest possible model to explain the observed data. I demonstrate a new technique which makes sparse Bayesian learning much more scaleable, allowing it to be applied to very large and complex problems, and present a convenient, freely available Java library which provides a general-purpose implementation of this technique. This library was used here in the training of the transcription start site predictor, but has a wide range of applications in computational biology and beyond.
2
Schroeder, Diane Irene. "Two stories of human transcription regulation : bidirectional promoters and the multiple transcription start sites of FOXP2 /." May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
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Van, Jaarsveld Ida CecIlia. "Basal promoter landscape in Eucalyptus grandis : annotation of distal transcription start sites and core promoter usage." Diss., University of Pretoria, 2014. http://hdl.handle.net/2263/79196.
Full textAbstract:
Transcription is a complex biological phenomenon, whereby RNA is transcribed from single
stranded template DNA by assembling targeted regulatory inputs at the promoter region.
Transcription is regulated through many hierarchically organised mechanisms, including
chromosome positioning and organisation, the binding of transcription factors, and DNA’s
secondary and tertiary structures at the region of transcription initiation. The core promoter is
the distinct functional unit of DNA overlapping the transcription start site, which possesses
linear regulator capacity and renders DNA permissive to transcription. In plants, core
promoter and enhancer studies are of particularly high impact for those traits which under
strong transcriptional control. Cellulose biosynthesis in immature xylem, the tissue which
forms wood, is one such trait, and is studied extensively in the herbaceous model plant
organism, Arabidopsis thaliana, and the economically important woody perennial,
Eucalyptus grandis. The release of the E. grandis genome sequence has provided a muchneeded
reference to study transcriptional control, not only for those traits that make it a
dominant fibre crop, but genome-wide. We aimed to use empirical transcript evidence to
perform a high-throughput genome-wide curation of the 5’ UTR annotations and empirically
infer transcription start sites (TSSs) of the nascent E. grandis genome annotation. We then
aimed to use the curated TSSs to define core promoter classes based on their sequence
Magister composition and to determine the putative expression profiles and functional associations of each.
We used deep E. grandis mRNA sequencing data across seven diverse tissues and PASA
assembled E. grandis ESTs to empirically curate 5’ UTR annotations. We improved 17,085
annotations, added 7,596 for which there was no previous annotation and retained 3,675 that
possessed only a predicted TSS without empirical evidence. These complementary data were
used to define distal transcription start sites (dTSS) by a novel, prioritising, computational
rule-based method. From these dTSS annotations, we extracted the core promoters (from
-100 to +50) and described the core promoter landscape by hexamer positional overrepresentation
analysis. We found three types of hexamer over-representation in the core
promoter, that being broad, spiked and low. Broad hexamers were classified into 5 distinct
core promoter classes, including TA, CT, GA, W and S. These were further assessed for
putative expression profiles (specificity and level) and functional associations. TA resembles
the conserved TATA-box core promoter, although displays a bimodal distribution, low
expression levels and the greatest tissue specificity. CT and GA are over-represented both up
and downstream of the dTSS and show narrow windows of greater enrichment with phasic
constraint. W and S occur in close proximity to the dTSS, with S displaying the most
constitutive and highest expression profile. Spiked hexamers occur in close proximity to the
dTSS and low hexamers are enriched for those pyrimidine-rich hexamers found in
Arabidopsis thaliana and Oryza sativa core promoters as the Y Patch. We found that E.
grandis core promoters include those such as the TATA-box class which is conserved across
kingdoms, the CT and GA classes, which are conserved in Arabidopsis, and a number of
classes which, thus far, appear unique to Eucalyptus. We postulate possible underlying
mechanisms of each core promoter class based on their sequence composition and suggest
regulation by TBP binding (TA), nucleosome positioning (W), DNA stability (S), and non-BDNA
conformation (CT and GA). This research provides a basal understanding of cistranscriptional
regulation at the core promoter in this economically important woody plant
species and provides insight into the mechanisms of permissive transcription across plant
species.Dissertation (MSc)--University of Pretoria, 2014.
Biochemistry
MSc
Unrestricted
4
Li, Xiaomeng. "Human Promoter Recognition Based on Principal Component Analysis." Thesis, The University of Sydney, 2008. http://hdl.handle.net/2123/3656.
Full textAbstract:
This thesis presents an innovative human promoter recognition model HPR-PCA. Principal component analysis (PCA) is applied on context feature selection DNA sequences and the prediction network is built with the artificial neural network (ANN). A thorough literature review of all the relevant topics in the promoter prediction field is also provided. As the main technique of HPR-PCA, the application of PCA on feature selection is firstly developed. In order to find informative and discriminative features for effective classification, PCA is applied on the different n-mer promoter and exon combined frequency matrices, and principal components (PCs) of each matrix are generated to construct the new feature space. ANN built classifiers are used to test the discriminability of each feature space. Finally, the 3 and 5-mer feature matrix is selected as the context feature in this model. Two proposed schemes of HPR-PCA model are discussed and the implementations of sub-modules in each scheme are introduced. The context features selected by PCA are III used to build three promoter and non-promoter classifiers. CpG-island modules are embedded into models in different ways. In the comparison, Scheme I obtains better prediction results on two test sets so it is adopted as the model for HPR-PCA for further evaluation. Three existing promoter prediction systems are used to compare to HPR-PCA on three test sets including the chromosome 22 sequence. The performance of HPR-PCA is outstanding compared to the other four systems.
5
Li, Xiaomeng. "Human Promoter Recognition Based on Principal Component Analysis." University of Sydney, 2008. http://hdl.handle.net/2123/3656.
Full textAbstract:
Master of EngineeringThis thesis presents an innovative human promoter recognition model HPR-PCA. Principal component analysis (PCA) is applied on context feature selection DNA sequences and the prediction network is built with the artificial neural network (ANN). A thorough literature review of all the relevant topics in the promoter prediction field is also provided. As the main technique of HPR-PCA, the application of PCA on feature selection is firstly developed. In order to find informative and discriminative features for effective classification, PCA is applied on the different n-mer promoter and exon combined frequency matrices, and principal components (PCs) of each matrix are generated to construct the new feature space. ANN built classifiers are used to test the discriminability of each feature space. Finally, the 3 and 5-mer feature matrix is selected as the context feature in this model. Two proposed schemes of HPR-PCA model are discussed and the implementations of sub-modules in each scheme are introduced. The context features selected by PCA are III used to build three promoter and non-promoter classifiers. CpG-island modules are embedded into models in different ways. In the comparison, Scheme I obtains better prediction results on two test sets so it is adopted as the model for HPR-PCA for further evaluation. Three existing promoter prediction systems are used to compare to HPR-PCA on three test sets including the chromosome 22 sequence. The performance of HPR-PCA is outstanding compared to the other four systems.
6
Zehentner, Barbara Katrin [Verfasser], Siegfried [Akademischer Betreuer] Scherer, Wolfgang [Gutachter] Liebl, Siegfried [Gutachter] Scherer, and Lindsay [Gutachter] Hall. "Experimental characterization of overlapping genes in enterohemorrhagic E. coli: Overexpression phenotypes and high-throughput NGS analysis of transcription start sites / Barbara Katrin Zehentner ; Gutachter: Wolfgang Liebl, Siegfried Scherer, Lindsay Hall ; Betreuer: Siegfried Scherer." München : Universitätsbibliothek der TU München, 2020. http://d-nb.info/1233427962/34.
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7
Moos, Abdul Ragmaan. "A case-control approach to assess variability in distribution of distance between transcription factor binding site and transcription start site." Thesis, Rhodes University, 2017. http://hdl.handle.net/10962/5315.
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Using the in-silico approach, with ENCODE ChIP-seq data for various transcription factors and different cell types; we systematically compared the distance between the transcription factor binding site (TFBS) and the transcription start (TSS). Our aim was to determine if the same transcription factor binds at a different position relative to the TSS in a normal and an abnormal cell type. We compare distribution of distance of binding sites from the TSS; to make description less verbose we call this “distance” where there is no possibility of confusion. We used a case-control methodology where the distance between the TFBS and the TSS in the normal, non-cancerous or untreated cell type is the control. The distance between the TFBS and the TSS in the cancerous or treated cell type is the case. We use the distance between the TFBS and the TSS in the control as the standard. We compared the distance between the TFBS and the TSS in the case and the control. If the distance between the TFBS and the TSS in the control was greater than the distance between the TFBS and the TSS in the case, we can infer the following. The transcription factor in the case binds closer to the TSS compared to the control. If the distance between the TFBS and the TSS in the control is smaller than the distance between the TFBS and the TSS in the case, we can infer the following. The TF in the case binds further away from the TSS compared to the control. Our method is a screening method whereby we compare ChIP-seq data to determine if there is a difference in the distribution distance between the TFBS and the TSS for normal and abnormal cell types. We used the R package ChIP-Enrich to compare the distribution of distance between ChIP-seq peak and the nearest TSS. ChIP-Enrich produces a histogram with the number of ChIP-seq peaks at a certain distance from the TSS. The results indicate for some transcription factors like GM12878-cMyc and K562-cMyc there is a difference between the distribution of distance between the TFBS and the nearest TSS. cMyc has more binding sites within a distance of 1kb from the TSS in GM12878 when compared to K562. GM12878-CTCF and K562-CTCF have slight differences when comparing their distribution of distance from the TSS. This means CTCF binds almost the same distance from the TSS in both GM12878 and K562. A549-gr treated with dexamethasone is interesting because with increase dose of dexamethasone the distribution of distance from the TSS changes as well.
8
CARSON, DANIEL J. "DECIPHERING THE ROLE OF TFIIB IN TRANSCRIPTIONAL ACTIVATION AND START SITE DETERMINATION." University of Cincinnati / OhioLINK, 2002. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1022683318.
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Raborn, R. Taylor. "Genome-wide analysis of transcription initiation and promoter architecture in eukaryotes." Diss., University of Iowa, 2012. https://ir.uiowa.edu/etd/4728.
Full textAbstract:
The transcriptome represents the entirety of RNA molecules within a cell or tissue at a given time. Recent advances have facilitated the production of large-scale, global interrogations of transcriptomes, finding that genomes are extensively transcribed and contain diverse classes of RNAs (Dinger et al., 2009). Information generated by high-throughput analyses of mRNA transcription start sites (TSSs) such as CAGE (Cap Analysis of Gene Expression) indicate that eukaryotic genomes have complex landscapes of transcription initiation. The TSS is important for the annotation of cis-regulatory sequences, because it provides a link between the mRNA transcript and the promoter. The patterns of TSS distributions observed within mRNA 5' end profiling studies prevent straightforward annotation of putative promoters.
To address this challenge, we developed a method to identify- on a genome-wide basis- the putative promoter, which we define by TSS distributions and designate the transcription start region (TSR). We applied a clustering method to identify and annotate TSRs within the budding yeast Saccharomyces cerevisiae using a full-length cDNA dataset (Miura et al., 2006). To validate these TSR annotations, we performed an integrative genomic analysis using multiple datasets. Our method identified TSRs at positions consistent with bona fide promoters in S. cerevisiae. In addition, using 5'RACE, we find overall agreement between computationally-defined TSRs and TSSs identified experimentally. From this analysis, we find that a significant proportion of genes exhibiting alternative promoter usage within sporulation are associated with respiration, suggesting that this is regulated on a condition-specific basis in budding yeast.
We further developed our TSS clustering method into a bioinformatics tool called TSRchitect, which identifies and annotates TSRs from large-scale TSS profiling information. TSRchitect is capable of handling both tag and sequence-based TSS information and efficiently computes TSRs from global TSS datasets on a desktop computer. We find support for TSRchitect's annotations in human from a CAGE experiment from the ENCODE (Encyclopedia of DNA Elements) project.
Finally, we use TSRchitect to identify TSRs from the transcriptomes of diverse eukaryotes. We investigated the conservation of TSRs among orthologous genes. We frequently identify multiple TSRs for a given gene, suggesting that alternative promoter usage is widespread. Overall, using TSS profiling data derived from separate tissues within mouse and human, we find that the positions of TSRs are relatively stable across tissues surveyed; however, a small fraction of genes exhibit tissue-specific differences in TSR use.
As transcriptome profiling information continues to be generated at an rapid pace, computational approaches are increasingly important. It is anticipated that the method and approach we describe within this dissertation will contribute to an improved of gene regulation and promoter architecture in eukaryotes.
10
Mwangi, Sarah Wambui. "In silico investigation of glossina morsitans promoters." University of the Western Cape, 2013. http://hdl.handle.net/11394/3990.
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Philosophiae Doctor - PhDTsetse flies (Glossina spp) are the biological vectors for Trypanosomes, the causative magents of Human African Trypanosomiasis (HAT). HAT is a debilitating disease that continues to present a major public health problem and a key factor limiting rural development in vast regions of tropical Africa. To augment vector control efforts, the International Glossina Genome Initiative (IGGI) was established in 2004 with the ultimate goal of generating a fully annotated whole genome sequence for Glossina morsitans. A working draft genome of Glossina morsitans was availed in 2011. In this thesis, transcriptional regulatory features in Glossina morsitans were analysed using the draft genome. A method for TSS identification in the newly sequenced Glossina morsitans genome was developed using TSS-seq tags sampled from two developmental stages of Glossina morsitans. High throughput next generation sequencing reads obtained from Glossina morsitans larvae and pupae were used to locate transcription start sites (TSS) in the Glossina morsitans genome. TSS-seq tag clusters, defined as a minimum number of reads at the 5’ predicted UTR or first coding exon, were used to define transcription start sites. A total of 3134 tag clusters were identified on the Glossina genome. Approximately 45.4% (1424) of the tag clusters mapped to the first coding exons or their proximal predicted 5’UTR regions and include 31 tag clusters that mapped to transposons. A total of 1101 (35.1%) tag clusters mapped outside the genic region and/or scaffolds without gene predictions and may correspond to previously un-annotated transcripts or noncoding RNA TSS. The core promoter regions were classified as narrow or broad based on the number of TSS positions within a TSS-seq cluster. Majority (95%) of the core promoters analysed in this study were of the broad type while only 5% were of the narrow type. Comparison of canonical core promoter motif occurences between random and bona fide core promoters showed that, generally, the number of motifs in biologically functional genomic windows in the true dataset exceeded those in the random dataset (p <= 0.00164, 0.00135, 0.00185 for the narrow, broad with peak and broad without peak categories respectively). Frequency of motif co-occurrence in core promoter was found to be fundamentally different across various initiation patterns. Narrow core promoters recorded higher frequency of the TATA-box and INR motifs and two-way motif co-occurrence showed that the TATA-box-INR pair is over-represented in the narrow category. Broad core promoters showed higher frequency of the BREd and MTE motifs and two-way motif co-occurrence showed that the MTE-DPE pair is over-represented in broad core promoters. TATA-less promoters account for 77% of the core promoters in this analysis. TATA-less core promoters showed a higher frequency of the MTE and INR motifs in contrast to observations in Drosophila where the DPE motif has been reported to occur frequently in TATA-less promoters. These motif combinations suggest their equal importance to transcription in their corresponding promoter classes in Glossina morsitans.
11
Xia, Yu. "Molecular cloning and characterization of the human [alpha]-synuclein (SNCA) gene : genomic structure, transcription start site, promoter region and polymorphisms /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1998. http://wwwlib.umi.com/cr/ucsd/fullcit?p9835292.
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Beder, Thomas [Verfasser], Hans Peter [Gutachter] Saluz, Rainer [Gutachter] König, and Nicole [Gutachter] Borel. "Differential RNA-Seq and transcription start site annotation in Chlamydia / Thomas Beder ; Gutachter: Hans Peter Saluz, Rainer König, Nicol Borel." Jena : Friedrich-Schiller-Universität Jena, 2019. http://d-nb.info/1210026996/34.
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Grech, Brian James. "Bioinformatic prediction of conserved promoters across multiple whole genomes of Chlamydia." Thesis, Queensland University of Technology, 2007. https://eprints.qut.edu.au/16521/1/Brian_James_Grech_Thesis.pdf.
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The genome sequencing projects have generated a wealth of genomic data and the analysis of this data has provided many interesting findings. However, genome wide analysis of bacteria for promoters has lagged behind, because it has been difficult to accurately predict the promoters with so much background noise that are found in bacterial genomes. One approach to overcome this problem is to predict phylogenetically conserved promoters across multiple genomes of different bacteria, thus filtering out many of the false positives, which are predicted by the current methods. However, there are no programmes capable of doing this. Therefore, the work presented in this thesis has developed a position weight matrix (PWM) based programme called Multiscan that predicts conserved promoters across multiple bacterial genomes. Since Chlamydia is one of the most sequenced bacterial genera and has a high level of conservation of genes and large-scale conservation of gene order between species, Multiscan was developed and tested on Chlamydia. When Multiscan analysed a genome wide dataset of equivalent non-coding regions (NCRs) upstream of genes, from Chlamydia trachomatis, Chlamydia pneumoniae and Chlamydia caviae for σ66 promoters that are phylogenetically conserved, Multiscan predicted 42 promoters. Since only one of the 42 promoters predicted by Multiscan had previously available biological data to confirm its prediction, an additional subset of 10 of the remaining 41 σ66 promoters were analysed in C. trachomatis by mapping the 5' end of the transcripts. The primer extension assay synthesised cDNA products of the correct length for seven of the 10 genes chosen. When the performance of Multiscan was compared to one of the accepted method for genome wide prediction of promoters in bacteria, the "standard PWM method", Multiscan predicted 32 more promoters than the "standard PWM method" in Chlamydia. Furthermore, the promoters predicted by Multiscan were up to three more mismatches from the Escherichia coli σ70 consensus sequence than the promoters predicted by the standard PWM method. Although Multiscan predicted 42 promoters that were well conserved across the three chlamydial species, the analysis was unable to identify the 14 known σ66 promoters in C. trachomatis. These promoters were missed (1) because they were dissimilar to the E. coli σ70 consensus sequence and/or (2) because the promoters were poorly conserved across the three chlamydial species. To address the second possibility, the 14 false negatives were analysed by another phylogenetic footprinting method. Fourteen sets of equivalent NCRs located upstream of the homologous genes from the three chlamydiae were aligned with the computer programme Clustal W and the alignment analysed "by eye" for evidence of phylogenetic footprints containing the 14 false negatives. The analysis identified that seven of the 14 false negatives were poorly conserved across the chlamydial species. Analysis of two of the seven promoters that could not be footprinted, the promoters of ltuA and ltuB, by mapping the transcriptional start sites in C. caviae, confirmed their poor conservation across C. trachomatis and C. caviae. This analysis showed that substantial differences exist in chlamydial σ66 promoters from equivalent NCRs upstream of genes. This study has developed a new computer programme for genome wide prediction of promoters that are phylogenetically conserved and has shown the value of this programme by identifying seven new well conserved promoters and seven candidate poorly conserved promoters in Chlamydia.
14
Grech, Brian James. "Bioinformatic prediction of conserved promoters across multiple whole genomes of Chlamydia." Queensland University of Technology, 2007. http://eprints.qut.edu.au/16521/.
Full textAbstract:
The genome sequencing projects have generated a wealth of genomic data and the analysis of this data has provided many interesting findings. However, genome wide analysis of bacteria for promoters has lagged behind, because it has been difficult to accurately predict the promoters with so much background noise that are found in bacterial genomes. One approach to overcome this problem is to predict phylogenetically conserved promoters across multiple genomes of different bacteria, thus filtering out many of the false positives, which are predicted by the current methods. However, there are no programmes capable of doing this. Therefore, the work presented in this thesis has developed a position weight matrix (PWM) based programme called Multiscan that predicts conserved promoters across multiple bacterial genomes. Since Chlamydia is one of the most sequenced bacterial genera and has a high level of conservation of genes and large-scale conservation of gene order between species, Multiscan was developed and tested on Chlamydia. When Multiscan analysed a genome wide dataset of equivalent non-coding regions (NCRs) upstream of genes, from Chlamydia trachomatis, Chlamydia pneumoniae and Chlamydia caviae for σ66 promoters that are phylogenetically conserved, Multiscan predicted 42 promoters. Since only one of the 42 promoters predicted by Multiscan had previously available biological data to confirm its prediction, an additional subset of 10 of the remaining 41 σ66 promoters were analysed in C. trachomatis by mapping the 5' end of the transcripts. The primer extension assay synthesised cDNA products of the correct length for seven of the 10 genes chosen. When the performance of Multiscan was compared to one of the accepted method for genome wide prediction of promoters in bacteria, the "standard PWM method", Multiscan predicted 32 more promoters than the "standard PWM method" in Chlamydia. Furthermore, the promoters predicted by Multiscan were up to three more mismatches from the Escherichia coli σ70 consensus sequence than the promoters predicted by the standard PWM method. Although Multiscan predicted 42 promoters that were well conserved across the three chlamydial species, the analysis was unable to identify the 14 known σ66 promoters in C. trachomatis. These promoters were missed (1) because they were dissimilar to the E. coli σ70 consensus sequence and/or (2) because the promoters were poorly conserved across the three chlamydial species. To address the second possibility, the 14 false negatives were analysed by another phylogenetic footprinting method. Fourteen sets of equivalent NCRs located upstream of the homologous genes from the three chlamydiae were aligned with the computer programme Clustal W and the alignment analysed "by eye" for evidence of phylogenetic footprints containing the 14 false negatives. The analysis identified that seven of the 14 false negatives were poorly conserved across the chlamydial species. Analysis of two of the seven promoters that could not be footprinted, the promoters of ltuA and ltuB, by mapping the transcriptional start sites in C. caviae, confirmed their poor conservation across C. trachomatis and C. caviae. This analysis showed that substantial differences exist in chlamydial σ66 promoters from equivalent NCRs upstream of genes. This study has developed a new computer programme for genome wide prediction of promoters that are phylogenetically conserved and has shown the value of this programme by identifying seven new well conserved promoters and seven candidate poorly conserved promoters in Chlamydia.
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Taylor, Russell Haywood. "A guanine to adenine mutation -76bp from the transcriptional start site decreases constitutive CYP1A2 expression in a novel mouse strain." Thesis, University of Ottawa (Canada), 2007. http://hdl.handle.net/10393/27924.
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Variations in the expression of drug metabolizing enzymes of the Cytochrome P450 superfamily are a principal cause of atypical reactions to therapeutics. The molecular mechanisms by which the metabolizing enzymes of the drug are regulated, and the effects of genetic variation on this regulation, are not completely understood. Cytochrome P450 1A2 (CYP1A2) is one such enzyme. The APN mouse strain has low expression of the CYP1A2 enzyme, relative to the C3H/HeJ strain. It was hypothesized that this difference in expression of the CYP1A2 was occurring as a result of a single nucleotide polymorphism at the Cyp1a2 locus. This work has demonstrated that this variation in CYP1A2 expression occurs at the level of transcription and that a single nucleotide change 76 base pairs upstream of the transcriptional start site was critical for promoter function. The mechanism of constitutive CYP1A2 expression involves a previously unidentified cis-acting element in this region.
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Almeida, João Paulo Pereira de. "O transcritoma antisense primário de Halobacterium salinarum NRC-1." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/17/17131/tde-15012019-101127/.
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Em procariotos, RNAs antisense (asRNAs) constituem a classe de RNAs não codificantes (ncRNAs) mais numerosa detectada por métodos de avaliação de transcritoma em larga escala. Apesar da grande abundância, pouco se sabe sobre mecanismos regulatórios e aspectos da conservação evolutiva dessas moléculas, principalmente em arquéias, onde o mecanismo de degradação de RNAs dupla fita (dsRNAs) é um fenômeno pouco conhecido. No presente estudo, utilizando dados de dRNA-seq, identificamos 1626 inícios de transcrição primários antisense (aTSSs) no genoma de Halobacterium salinarum NRC-1, importante organismo modelo para estudos de regulação gênica no domínio Archaea. Integrando dados de expressão gênica obtidos a partir de 18 bibliotecas de RNA-seq paired-end, anotamos 846 asRNAs a partir dos aTSSs mapeados. Encontramos asRNAs em ~21% dos genes anotados, alguns desses relacionados a importantes características desse organismo como: codificadores de proteínas que constituem vesículas de gás e da proteína bacteriorodopsina, além de vários genes relacionados a maquinaria de tradução e transposases. Além desses, encontramos asRNAs em genes pertencentes a sistemas de toxinas-antitoxinas do tipo II e utilizando dados públicos de dRNA-seq, evidenciamos que esse é um fenômeno que ocorre em bactérias e arquéias. A interação de um ncRNA com seu RNA alvo pode ser dependente de proteínas, em arquéias, a proteína LSm é uma chaperona de RNA homóloga a Hfq de bactérias, implicada no controle pós-transcricional. Utilizamos dados de RIP-seq de RNAs imunoprecipitados com LSm e identificamos 91 asRNAs interagindo com essa proteína, para 81 desses, o mRNA do gene sense também foi encontrado interagindo. Buscando por aTSSs presentes nas mesmas regiões de genes ortólogos, identificamos 160 aTSSs que dão origem a asRNAs em H. salinarum possivelmente conservados em Haloferax volcanii. A expressão dos asRNAs anotados foi avaliada ao longo de uma curva de crescimento e em uma linhagem knockout de um gene que codifica uma RNase R, possível degradadora de dsRNAs em arquéias. Encontramos um total de 144 asRNAs diferencialmente expressos ao longo da curva de crescimento, para 56 desses o gene sense também está diferencialmente expresso, caracterizando possíveis mecanismos de regulação em cis por esses RNAs. Na linhagem knockout, encontramos cinco asRNAs diferencialmente expressos e apenas para um desses o gene sense também está diferencialmente expresso, resultado que não nos permitiu inferir um possível papel de degradação de dsRNAs da RNAse R em H. salinarum NRC-1. Nesse trabalho apresentamos um mapeamento completo do transcritoma antisense primário de H. salinarum NRC-1 com resultados que consistem em um importante passo na direção da compreensão do envolvimento da transcrição antisense na regulação gênica pós-transcricional desse organismo modelo do terceiro domínio da vida.Antisense RNAs (asRNAs) constitute the most numerous class of non-coding RNAs (ncRNAs) detected by transcriptome highthroughput methods in prokaryotes. Despite this abundance, little is known about regulatory mechanisms and evolutionary aspects of these molecules, mainly in archaea, where the mechanism of double-strand RNA (dsRNA) degradation remains poorly understood. In this study, using dRNA-seq data, we identified 1626 antisense transcription start sites (aTSSs) in the genome of Halobacterium salinarum NRC-1, an important model organism for gene expression regulation studies in Archaea. By integrating gene expression data from 18 RNA-seq paired-end libraries, we were able to annotate 846 asRNAs from mapped aTSSs. We found asRNAs in ~21% of annotated genes including genes related to important characteristics of this organism, such as: gas vesicle proteins, bacteriorhodopsin, translation machinery and transposases. We also found asRNAs in type II toxin-antitoxin systems and using public dRNA-seq data, we show evidences that this phenomenon might be conserved in archaea and bacteria. The interaction of a ncRNA with its target may depend on intermediary proteins action. In archaea, the LSm protein is a RNA chaperone homologous to bacterial Hfq, involved in post-transcriptional regulation. We used RIP-seq data from RNAs immunoprecipitated with LSm and identified 91 asRNAs interacting with this protein, for 81 of these the mRNA of the sense gene is also interacting. We searched for aTSSs present in the same region of orthologous genes in the Haloferax volcanii. We found 160 aTSSs that originated asRNAs in H. salinarum NRC-1 that might be conserved in this two archaea. The expression of annotated asRNAs was analyzed over a growth curve and in a knockout strain for RNase R gene. We found 144 asRNA differentially expressed over the growth curve, for 56 of these the sense gene was also differentially expressed, characterizing possible cis regulators asRNAs. In the knockout strain we found five differentially expressed asRNAs and only one asRNA/gene pair, this result does not allow us to infer a dsRNA degradation in vivo activity for this RNase in H. salinarum NRC- 1. This work contributes to the discovery of the antisense transcriptome in H. salinarum NRC- 1 a relevant step to uncover the post-transcriptional gene regulatory network in this archaeon.
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Lloyd, Amanda Lian. "Cloning, characterisation and sequencing of promoters of Helicobacter pylori 4187E." University of Western Australia. Microbiology Discipline Group, 2005. http://theses.library.uwa.edu.au/adt-WU2005.0112.
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Published information on the structure and regulation of H. pylori promoters is limited. The work presented in this thesis describes the cloning and characterisation of promoter regions from a clinical isolate of H. pylori, and the development of an alternative, non-radioactive method for verifying the location of transcriptional start sites of bacterial promoters. H. pylori 4187E promoters were randomly cloned into the promoter-trap vector pKK232-8 in Escherichia coli DH5α using two sets of restriction enzymes. Vector pKK232-8 contains a promoterless chloramphenicol acetyltransferase (CAT) gene. Seventy-four promoter-containing clones were isolated from selective media based on their resistance to chloramphenicol. The strength of each promoter was analysed qualitatively, using chloramphenicol minimum inhibitory concentrations, and quantitatively, using CAT assays following exposure of the clones to pH 4 and pH 7. Selected promoter fragments were subcloned into the GFP reporter vector pFPV25, containing a promoterless gfp gene. The subclones were exposed to buffered LB broth at pH 4, 5, 6, 7 and 8, for varying lengths of time, to study acid-induced regulation of gene expression. Subclones were examined qualitatively, using visual examination of GFP fluorescence and fluorescence microscopy, and quantitatively, using flow cytometry following acid shock. DNA sequences were determined for 61 of the 74 H. pylori promoters, and sequence alignments with the published H. pylori strains (26695 and J99) were performed. The transcriptional start site of 27 H. pylori promoter fragments was experimentally mapped using a fluorescence-based primer extension protocol developed by our group. Potential -35 and -10 sequences were identified for each promoter, and a new consensus sequence for H. pylori promoters was proposed based upon these results. This study has considerably expanded knowledge of H. pylori promoter sequences and transcriptional start sites based on those which also function in E. coli. It has also revealed several H. pylori promoters which appear to respond to acid stress
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Millán, Ariño Lluís 1984. "Genomic distribution and functional specificity of human histone H1 subtypes." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/292370.
Full textAbstract:
Seven linker histone H1 variants exist in human somatic cells with distinct prevalence among
cell types and during differentiation. Despite being key chromatin structural components, it
remains elusive how they participate in the regulation of nuclear processes. Moreover, it is
not well understood whether the different variants have specific roles or are differentially
distributed along the genome. By taking advantage of specific antibodies for H1 variants and
HA-tagged recombinant H1s expressed in breast cancer cells, the distribution of somatic
variants H1.2 to H1.5, H1.0 and H1X has been investigated by combining ChIP-qPCR, ChIP-chip,
and ChIP-seq analysis. All H1 variants bind gene promoters and are depleted from the TSS in
active genes, and also from regulatory sites. The extension of H1 depletion at promoters is
dependent on the transcriptional status of the gene and differs between variants. Analyses
show that histone H1 is not uniformly distributed along the genome and differences among
variants exist, being H1.2 the variant showing a more specific pattern and a strongest
correlation with gene repression in breast cancer cells. Results suggest that different variants
may be present at different chromatin types, and this may depend on the cell type,
differentiation state, and whether cells are originated from a neoplastic process. In a second
part of the thesis, it is shown that a previously reported H1.4 knock-down cell line presents
and off-target effect against lamin B2. Therefore, it has been developed a new inducible
knock-down cell line specifically inhibiting H1.4, which resembles previously characterized
H1.2 knock-down. Finally, combined depletion of H1.4/lamin B2 and H1.2/H1.4 causes similar
effects in T47D breast cancer cell line.Fins a set variants de la histona H1 s han identificat en mamífers, les quals mostres una prevalença diferent entre tipus cel lulars i durant el procés de diferenciació. Tot i que la histona H1 juga un paper clau en l estructuració de la cromatina, no s acaba d entendre encara com participa exactament en els diferent processos cel lulars. A més a més, encara no està clar si les diferents variants tenen funcions específiques ni si es distribueixen igual al llarg del genoma. Mitjançant anticossos específics per algunes variants d H1 i de línies cel lulars de càncer de mama que expressen H1s recombinant fusionades a un pèptid HA, s ha estudiat la distribució genòmica de H1.2 a H1.5, H1.0 i H1X, combinant ChIP-qPCR, ChIP-chip i ChIP-seq. Totes les H1s es troben a promotors gènics i empobrides a l inici de transcripció dels gens actius, i també a les regions reguladores. El grau de disminució d H1 al promotor depèn de l estat transcripcional del gen i presenta diferències entre variants. Els anàlisis mostren que la histona H1 no es distribueix uniformement al genoma i que hi ha diferències entre variants, essent H1.2 la variant que presenta un patró més específic i una correlació més forta amb repressió gènica a cèl lules de càncer de mama. Aquests resultats suggereixen que variants d H1 diferents es troben presents als diversos tipus de cromatina, i aquest fet podria dependre de la línia cel lular, l estat de diferenciació, o de si les cèl lules s han originat durant un procés neoplàsic. En una segona part de la tesi, es mostra que una línia cel lular anteriorment descrita que inhibeix H1.4 presenta un efecte inespecífic contra lamina B2. Així, s ha desenvolupat una altra línia que inhibeix H1.4 específicament, la qual s assembla a un mutant anteriorment caracteritzat que inhibeix H1.2. Finalment, la inhibició combinada de H1.4/lamina B2 i H1.2/H1.4 provoca efectes fenotípics semblants a cèl lules de càncer de mama T47D.
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Lai, Cheng-Kuo, and 賴政國. "Comparative studies of microRNA transcription start sites between human and chimpanzee." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/86666970495841783343.
Full textAbstract:
碩士國立中興大學
基因體暨生物資訊學研究所
103
Identifying the transcription start sites (TSSs) of microRNA (miRNA) genes is essential for understanding the regulation of miRNA transcription which is extremely important for determining the specific roles that miRNAs play in regulatory pathways. Because humans and chimpanzees share most of genes, comparative studies of the two species are the ways often used to comprehend humans more. In the past, most studies are focused on the divergence of proteins, genes and miRNAs. However, the divergence of the regulation of miRNA transcription between humans and chimpanzees seems still not to be addressed yet. In this study, 86 global-run-on-sequencing (GRO-Seq) validated TSSs of 125 human miRNAs were collected to search their homologous regions in the chimpanzee genome. An un-annotated homologous miRNA region was considered to be a putative chimpanzee miRNA if the sequence of the region can be folded into a hairpin structure. In addition, a homologous TSS location was then confirmed as a putative chimpanzee miRNA TSS if it was able to be identified by a semi-supervised statistical model trained on Pol II ChIP-sequencing data of chimpanzee and several sequence-associated features. From the result, most of the human TSS-miRNA pairs are still kept in chimpanzees. We identified 33 un-annotated chimpanzee miRNAs and 48 putative chimpanzee miRNA TSSs of 69 chimpanzee miRNAs. Interestingly, a number of human TSS-miRNA pairs were missing; we found that 18 miRNAs were lost in chimpanzee during evolution and another missing miRNA, mir-659, might be human specific. We studied the regulatory pathway of mir-659 and found that mir-659 could be involved in neurodevelopmental. These divergence of the regulation of miRNA transcription might be, at least in part, the molecular footprint of speciation events in the human and chimpanzee lineages.
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Sung, Tsai-Jung, and 宋采蓉. "Identification of Chlorocebus sabaeus microRNAs and prediction of the microRNA transcription start sites." Thesis, 2019. http://ndltd.ncl.edu.tw/cgi-bin/gs32/gsweb.cgi/login?o=dnclcdr&s=id=%22107NCHU5105029%22.&searchmode=basic.
Full textAbstract:
碩士國立中興大學
基因體暨生物資訊學研究所
107
The Vero cell is a renal epithelial cell line (kidney epithelial cells from a female African green monkey, Chlorocebus sabaeus), and has the cellular characteristics of interferon manufacturing defects. That causes a faster rate of virus spread, compared to the normal cells. Vero cells have been used as a host for mammalian viruses, and play an important role in vaccine manufacturing industry. Many studies have pointed out that the interaction between viruses and hosts may be related to non-coding RNA (ncRNAs, such as microRNAs, miRNAs). For example, siRNA-100, one small interfering RNA (siRNA) of Poliovirus (PV) can indirectly increase the concentration of miR-7 in the host, thereby inhibit the replication rate of poliovirus. Knowledge of the regulation of Vero cell miRNAs and their upstream and downstream will help to identify the factors related to the speed and quality of viral replication in Vero cells, and to achieve the purposes of reducing the cost and uncertainty of the experiment, improving the effectiveness of the vaccine and stabilizing the production quality and yield. However, there is no complete database related to Vero cells miRNA at present. Therefore, we try to identify the corresponding homologous miRNAs of the green monkey based on the Macaca mulatta and Homo sapiens precursor miRNAs. A total of 742 green monkey miRNAs were obtained from the Next Generation Sequencing (NGS) data of the green monkey. At the same time, in order to understand the upstream promoter regulation of miRNAs. The transcription start sites of 236 miRNAs were predicted by using the support vector machine (SVM) combined with the published next generation transcript sequencing data and sequence characteristics (including CpG content and DNA structural properties). This study identified 742 miRNAs, and 49 of these miRNAs have been shown to be involved in the regulation of viral replication in African green monkey cells. At the same time, the transcription start site was also predicted. It is expected that there will be a further understanding of the regulation network of African green monkeys and virus replication. And make vaccine production more stable yield and quality.
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Yang, Shang-Teng, and 楊翔騰. "Identification of microRNA Transcription Start Sites of Vertebrates Using Transcriptome Data and Sequence Features." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/69723278750184061681.
Full textAbstract:
碩士國立中興大學
基因體暨生物資訊學研究所
104
To identify microRNA (miRNA) transcription start sites (TSSs) is still difficult. Some studies utilized machine learning methods as well as the TSS-related data, such as CAGE (cap analysis gene expression) data, histone modification site data and TSS-seq data, and some sequence features to predict miRNA TSSs. However, at present, the TSS-related data are available only for human or mouse. In this study, we would like to develop a method that can be applied to more species; we predict miRNA TSSs using the technique of SVM (support vector machine) trained on RNA-seq data and some sequence features like CpG content and sequence conservation. Our results are comparable to that of the other studies on human and mouse. In addition, we applied our method to some other species, such as opossum, chicken, xenopus, zebrafish and Arabidopsis, and found that the accuracy of the proposed method is decreasing from opossum to Arabidopsis; the accuracy of the proposed method is about 70% for opossum and zebrafish but less than 70% for Arabidopsis. We then studied the sequences around TSSs and found that the animal promoter regions become CG-rich during evolution. Our method is able to predict miRNA TSSs in vertebrates and has higher prediction accuracy in placental mammals.
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Hsiao, Yu-Ming, and 蕭鈺銘. "Sequence-based prediction of microRNA transcription start sites from transcriptome data using DNA structural properties." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/57u4de.
Full textAbstract:
碩士國立中興大學
基因體暨生物資訊學研究所
106
microRNAs (miRNAs) are important small non-coding RNAs, mainly regulating gene expression in cells. Understanding upstream promoter regions of miRNAs is also an important issue. Current developed methods to identify miRNA transcription start sites (TSSs) all require specifically designed experiments or integrated multiple data. Therefore, we want to construct a more generic method. We use standard RNA sequencing (RNA-seq) data and sequence features (including conservation score, CpG content, and structural properties), and utilize the Support Vector Machine (SVM) maching learning algorithm to predict miRNA TSSs. Based on the method we have established before, this time we incorporate the structural properties into models, which improve the performance of the models. Comparison of our prediction results with experimentally validated TSS data shows that our method can identify miRNA TSSs. Moreover, this prediction system is not limited to human or mouse. It can be applied to more species because of its generic characteristics in sequence features. We hope these predicted TSSs can compensate for the lack of experimentally validated TSS data or provide TSS candidate sites for further experimental verification, to comprehensively understand the role of miRNAs in regulatory network.
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Liu, Hsiang-Hua, and 劉湘華. "Integration of experimental data of human microRNA transcription start sites and comparative studies of microRNA promoter regions between human and chimpanzee." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/54492480172777603249.
Full textAbstract:
碩士國立中興大學
基因體暨生物資訊學研究所
105
MicroRNAs (miRNAs) are small non-coding RNAs of ~20-24 nucleotides (nt) that participate the regulation of expression of protein coding genes in multicellular eukaryotes. Although there have been many studies on the mechanism of miRNA target gene regulation and the methods of target gene prediction, little is known regarding the regulation of miRNA genes themselves. Even though both miRNA genes and protein coding genes are transcribed by RNA polymerase II, it is still very difficult to identify miRNA transcription start sites (TSSs) or promoter regions with a common sequencing method because the distances between miRNAs and their TSSs vary a lot and the primary miRNA transcripts will be sliced and degraded by enzyme quickly after they are transcribed. In this study, we integrated three sets of experimentally validated human miRNA TSS data and found that most TSSs from different sets for a specific miRNA were located within regions of approximately 100 nt in length. We then utilized the alignment tool to search 199 precursor miRNAs and their corresponding promoters obtained from the human integration data against the chimpanzee genome. There were 192 (97%) miRNAs and the corresponding promoters that could be found in the chimpanzee genome. In order to examine the miRNA and promoter candidates found in the chimpanzee genome, we further checked some sequence and structure properties of the candidates as well as their expression. Finally, we found that 7 human TSS-miRNA pairs were missing and 1 human miRNA might lose function in chimpanzee. We further tried to date the missing events in evolution by using some primate out group data and found that mir-4717 and mir-5091 may play important roles in human. In this study, we propose a homology search approach to identify miRNAs and their promoter regions in closely related species by using precursor miRNA sequences and experimentally validated miRNA TSSs.
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Tompkins, Leslie Meredith. "Identification of novel transcription start sites and distinct proximal promoter regions for pregnane X receptor (PXR) isoforms PXR 1 and PXR 2." 2007. http://www.lib.ncsu.edu/theses/available/etd-08152007-133052/unrestricted/etd.pdf.
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Wang, Ting-Yuan, and 王定遠. "Identification of MicroRNA Transcriptional Start Sites in Human Genome." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/26407504225695503774.
Full textAbstract:
碩士國立交通大學
生物資訊研究所
96
The miRNAs are ~21nt single-strand short nucleotide that can induce RNAi mechanism through complete or partial complementarities. Most of the miRNAs are transcribed by RNA polymerase II [1]. The pri-miRNA transcribed by RNA polymerase II contained 5’cap and 3’poly-A tail [2]. For those intergenic miRNA, non-gene-overlap miRNA, they have their own promoter. It is important to understand those promoters of intergenic miRNA gene to facilitated understanding the regulation of intergenic miRNA. Because of the nature of the enzymatic reaction the probability of retrieving the sequence of extreme 5’ end region was very low with traditional PCR technology. Here, we use 5’RACE [3, 4] to ensure that the 5’end region of pri-miRNAs was obtained. In addition, we incorporate miRNA expression profile [5] to filter out those lower-expressed miRNA. With a series of computational promoter prediction, we could choose the putative TSS that has many support evidences. In order to identify whether putative TSS is true or false, the putative TSS specific primer was designed. Finally, the RT-PCT results were used to confirm the putative promoter regions.
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Hsu, Yu-Pin, and 許郁彬. "Identification of human microRNA transcriptional start sites from transcriptome." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/e7794f.
Full textAbstract:
碩士國立中興大學
基因體暨生物資訊學研究所
101
Identifying gene transcription start sites (TSSs) is the basis for determining gene upstream regulatory region. With the progress of the next generation sequencing (NGS) technologies, many kinds of NGS data have been utilized to identify TSSs. For example, RNA PolⅡChIP-seq (Chromatin immunoprecipitation sequencing) is used to recognize RNA PolⅡbinding sites and therefore is a direct way to identify TSSs. In addition, some other kinds of data like nucleosome-seq, DNase-seq (DNase I hypersensitive sites sequencing) and FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements sequencing), which are associated with histone modification sites, hyper-sensitive sites and regulatory activity, respectively, are alone or combined to determine TSSs. Several statistical or machine learning methods have been developed for finding and characterizing TSSs. These datasets and methods can be also used to locate miRNA TSSs because it is believed that most miRNA genes, like protein coding genes, require RNA Pol II for expression. In this thesis, we utilized RNA-seq data, i.e. transcriptome sequencing data, to locate miRNA TSSs. We observed that there are signals of RNA-seq sequences near the TSS of well-annotated protein coding genes so we proposed that the miRNA TSSs may also have similar pattern. We then located splice junction region and tried to complete primary transcripts of miRNAs (i.e. pri-miRNAs) and then miRNA TSSs were identified. This approach can not only locate miRNA TSSs but also give information to characterize TSSs of other gene types. Information obtained from transcriptome sequencing data could be a new feature for predicting gene TSSs and analyzing gene regulation. KEY WORDS MicroRNA, Transcription Start Site, TSS, Transcription Factor Binding Site, TFBS, upstream regulation
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"Promoter Identification in Daphnia Populations Revealed by Transcription Start Site Profiling." Master's thesis, 2020. http://hdl.handle.net/2286/R.I.62809.
Full textAbstract:
abstract: Regulation of transcription initiation is a critical factor in the emergence of diverse biological phenotypes, including the development of multiple cell types from a single genotype, the ability of organisms to respond to environmental cues, and the rise of heritable diseases. Transcription initiation is regulated in large part by promoter regions of DNA. The identification and characterization of cis-regulatory regions, and understanding how these sequences differ across species, is a question of interest in evolution. To address this topic, I used the model organism Daphnia pulex, a well-characterized microcrustacean with an annotated genome sequence and selected a distribution of well-defined populations geographically located throughout the Midwestern US, Oregon, and Canada. Using isolated total RNA from adult, female Daphnia originating from the selected populations as well as a related taxon, Daphnia pulicaria (200,000 years diverged from D. pulex), I identified an average of over 14,000 (n=14,471) promoter regions using a novel transcription start site (TSS) profiling method, STRIPE-seq. Through the identification of sequence architecture, promoter class, conservation, and transcription start region (TSR) width, of cis-regulatory regions across the aforementioned Daphnia populations, I constructed a system for the study of promoter evolution, enabling a robust interpretation of promoter evolution in the context of the population-genetic environment. The methodology presented, coupled with the generated dataset, provides a foundation for the study of the evolution of promoters across both species and populations.Dissertation/Thesis
Masters Thesis Molecular and Cellular Biology 2020
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Fang, Hao-Yu, and 方浩宇. "Using high-throughput sequencing data to identify the transcriptional start sites of mouse microRNAs." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/32453885381096374336.
Full textAbstract:
碩士國立中興大學
基因體暨生物資訊學研究所
101
MicroRNAs (miRNAs) are non-coding small RNAs that inhibit protein coding gene expression by hybridizing with messenger RNAs (mRNAs). MiRNAs are involved in a lot of diverse biological processes and various diseases. To identify miRNA transcription start sites (TSSs) is important for studying the upstream regulatory networks of miRNAs. Up to now the studies regarding miRNA TSS identification are all focus on human miRNAs. We are interested in other species and our aim in this study is to identify mouse miRNA TSSs and the result would contribute to understanding the evolution of upstream regulatory networks of miRNAs. In this study, we integrated two types of high-throughput sequencing data, i.e. transcription start sites sequencing (TSSseq) and Cap Analysis of Gene Expression (CAGE), as the evidence of miRNA TSSs. A machine-learning-based Support Vector Machine (SVM) was developed to identify mouse miRNA TSSs. In addition, we also incorporated the ESTs (expression sequence tag) and sequence conservation information to provide evidence for mouse miRNA TSSs.
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Dieterich, Christoph, Steffen Grossmann, Andrea Tanzer, Stefan Röpcke, Peter F. Arndt, Peter F. Stadler, and Martin Vingron. "Comparative promoter region analysis powered by CORG." 2005. https://ul.qucosa.de/id/qucosa%3A32449.
Full textAbstract:
Background
Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which largely determines gene expression. In vertebrates, transcription start sites and surrounding regulatory elements are often poorly defined. To support promoter analysis, we present CORG http://corg.molgen.mpg.de, a framework for studying upstream regions including untranslated exons (5' UTR).
Description
The automated annotation of promoter regions integrates information of two kinds. First, statistically significant cross-species conservation within upstream regions of orthologous genes is detected. Pairwise as well as multiple sequence comparisons are computed. Second, binding site descriptions (position-weight matrices) are employed to predict conserved regulatory elements with a novel approach. Assembled EST sequences and verified transcription start sites are incorporated to distinguish exonic from other sequences.
As of now, we have included 5 species in our analysis pipeline (man, mouse, rat, fugu and zebrafish). We characterized promoter regions of 16,127 groups of orthologous genes. All data are presented in an intuitive way via our web site. Users are free to export data for single genes or access larger data sets via our DAS server http://tomcat.molgen.mpg.de:8080/das. The benefits of our framework are exemplarily shown in the context of phylogenetic profiling of transcription factor binding sites and detection of microRNAs close to transcription start sites of our gene set.
Conclusion
The CORG platform is a versatile tool to support analyses of gene regulation in vertebrate promoter regions. Applications for CORG cover a broad range from studying evolution of DNA binding sites and promoter constitution to the discovery of new regulatory sequence elements (e.g. microRNAs and binding sites).
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Hsu, Chen-Wei, and 許承偉. "Modeling Transcription Start Site and Promoter Elements with Dependency Graphs and Their Expanded Bayesian Networks." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/85582533837369657887.
Full textAbstract:
碩士國立清華大學
電機工程學系
92
We have a large amount of raw genomic DNA sequence data now with the completion of the Human Genome Project (HGP). There are hundreds of programs developed to analyze these DNA sequences. Promoter is a region usually located at the 5' flanking end of a gene and encompasses the transcription start site. The promoter plays an important role in gene regulation and the detection of the promoter region could help to improve the accuracy of gene-finding. There are also several in silico approaches to predict promoter region or transcription start site, but the performance of these programs are usually unsatisfactory since the number of false positives is too high. In this thesis, we first develop a dependency graph as the basic model for the transcription start site by chi-square test and then expand this graph with a Bayesian network by allowing nucleotides in each position to appear more than once to catch their inter-dependency but avoid overfitting. In consideration of more than one signals within the promoter region, we also construct dependency graph and it's expanded Bayesian network to model TATA box. The prediction of TATA box will be integrated into the prediction of transcription start site in this thesis. The results show that our method has the best performance comparing with four most famous programs available on the Internet.
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Qiu, Yu. "Microarray-based Escherichia coli functional genomic studies : cold shock and iron starvation responses, and transcription start site identification /." 2006. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Handel, Katherine. "Identification of the promoter and transcription start site of the katE gene, encoding hydroperoxidase HPII, in Escherichia coli." 1995. http://hdl.handle.net/1993/17642.
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Carpio, Farro Ronald Erick [Verfasser]. "Studies on transcriptional regulation in the human retina : mapping of transcriptional start sites of retinal expressed genes and functional characterization of the CNGA3 promoter / vorgelegt von Ronald Erick Carpio Farro." 2009. http://d-nb.info/1007612452/34.
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Suh, Won-Chul. "The interaction of E. Coli RNA polymerase with lambda phage PR promoter evidence for two open complexes and a requirement for Mg²⁺ to open the transcription start site /." 1993. http://catalog.hathitrust.org/api/volumes/oclc/30697555.html.
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Majovski, Robert C. "Structure-function analysis of the Saccharomyces cerevisiae RNA polymerase II active center a functional role for the switch 2 region in transcription start site utilization and abortive initiation /." 2007. http://proquest.umi.com/pqdweb?did=1402170981&sid=15&Fmt=2&clientId=39334&RQT=309&VName=PQD.
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Thesis (Ph.D.)--State University of New York at Buffalo, 2007.Title from PDF title page (viewed on Mar. 06, 2008) Available through UMI ProQuest Digital Dissertations. Thesis adviser: Ponticelli, Alfred S. Includes bibliographical references.
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Wiegand, Sandra. "RNA-Seq and proteomics based analysis of regulatory RNA features and gene expression in Bacillus licheniformis." Doctoral thesis, 2013. http://hdl.handle.net/11858/00-1735-0000-0022-5E88-E.
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