Gotowe bibliografie tematyczne / Transcription Start Sites

Gotowa bibliografia na temat „Transcription Start Sites”

Autor: Grafiati

Data publikacji: 4 czerwca 2021

Data aktualizacji: 20 lutego 2023

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Artykuły w czasopismach na temat "Transcription Start Sites"

Stamatoyannopoulos, John A. "Illuminating eukaryotic transcription start sites". Nature Methods 7, nr 7 (lipiec 2010): 501–3. http://dx.doi.org/10.1038/nmeth0710-501.

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Nielsen, Mathias, Ryan Ard, Xueyuan Leng, Maxim Ivanov, Peter Kindgren, Vicent Pelechano i Sebastian Marquardt. "Transcription-driven chromatin repression of Intragenic transcription start sites". PLOS Genetics 15, nr 2 (1.02.2019): e1007969. http://dx.doi.org/10.1371/journal.pgen.1007969.

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Li, W. Z., i F. Sherman. "Two types of TATA elements for the CYC1 gene of the yeast Saccharomyces cerevisiae". Molecular and Cellular Biology 11, nr 2 (luty 1991): 666–76. http://dx.doi.org/10.1128/mcb.11.2.666-676.1991.

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Functional TATA elements in the 5' untranslated region of the CYC1 gene in the yeast Saccharomyces cerevisiae have been defined by transcriptional analysis of site-directed mutations. Five sites previously suggested to contain functional TATA elements were altered individually and in all possible combinations. The results indicated that only two elements are required for transcription at the normal level and the normal start sites. The two functional TATA elements are located at sites -178 and -123, where the A of the ATG start codon is assigned nucleotide position +1. They direct initiation within windows encompassing -70 to -46 and -46 to -28, respectively. Only when both of the upstream TATA sites were rendered nonfunctional were the third and fourth downstream TATA-like sequences activated, as indicated by the presence of low levels of transcription starting at -28. The two upstream functional TATA elements differed in sequence. The sequence of the most 5' one at site 1, denoted beta-type, was ATATATATAT, whereas that of the second one at site 2, denoted alpha-type, was TATATAAAA. The following rearrangements of the beta-type and alpha-type elements at two sites (1 and 2) were examined: site1 beta-site2 alpha; site 1 alpha-site 2 beta; site1 alpha-site2 alpha; and site1 beta-site2 beta. When different types were at different sites (site1 beta-site2 alpha and site1 alpha-site2 beta), both were used equally. In contrast, when the same type was present at both sites (site1 alpha-site2 alpha and site1 beta-site2 beta), only the upstream element was used. We suggest that the two TATA elements are recognized by different factors of the transcription apparatus.

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Li, W. Z., i F. Sherman. "Two types of TATA elements for the CYC1 gene of the yeast Saccharomyces cerevisiae." Molecular and Cellular Biology 11, nr 2 (luty 1991): 666–76. http://dx.doi.org/10.1128/mcb.11.2.666.

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Frith, M. C. "Evolutionary turnover of mammalian transcription start sites". Genome Research 16, nr 6 (1.06.2006): 713–22. http://dx.doi.org/10.1101/gr.5031006.

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Gordon, J. J., M. W. Towsey, J. M. Hogan, S. A. Mathews i P. Timms. "Improved prediction of bacterial transcription start sites". Bioinformatics 22, nr 2 (15.11.2005): 142–48. http://dx.doi.org/10.1093/bioinformatics/bti771.

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Drysdale, Melissa, Agathe Bourgogne i Theresa M. Koehler. "Transcriptional Analysis of the Bacillus anthracis Capsule Regulators". Journal of Bacteriology 187, nr 15 (1.08.2005): 5108–14. http://dx.doi.org/10.1128/jb.187.15.5108-5114.2005.

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ABSTRACT The poly-d-glutamic acid capsule of Bacillus anthracis is essential for virulence. Control of capsule synthesis occurs at the level of transcription and involves positive regulation of the capsule biosynthetic operon capBCAD by a CO2/bicarbonate signal and three plasmid-borne regulators: atxA, acpA, and acpB. Although the molecular mechanism for control of cap transcription is unknown, atxA affects cap expression via positive control of acpA and acpB, two genes with partial functional similarity. Transcriptional analyses of a genetically complete strain indicate that capB expression is several hundred-fold higher during growth in 5% CO2 compared to growth in air. atxA was expressed appreciably during growth in air and induced only 2.5-fold by CO2. In contrast, expression of acpA and acpB was induced up to 23-fold and 59-fold, respectively, by CO2. The 5′-end mapping of gene transcripts revealed atxA-regulated and atxA-independent apparent transcription start sites for capB, acpA, and acpB. Transcripts mapping to all atxA-regulated start sites were increased during growth in elevated CO2. The acpA gene has one atxA-regulated and one atxA-independent start site. acpB lies downstream of capBCAD. A single atxA-independent start site maps immediately upstream of acpB. atxA-mediated control of acpB appears to occur via transcriptional read-through from atxA-dependent start sites 5′ of capB. One atxA-independent and two atxA-regulated start sites map upstream of capB. Transcription from the atxA-regulated start sites of capBCAD was reduced significantly in an acpA acpB double mutant but unaffected in mutants with deletion of only acpA or acpB, in agreement with the current model for epistatic relationships between the regulators.

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Membrillo-Hernández, Jorge, i E. C. C. Lin. "Regulation of Expression of the adhE Gene, Encoding Ethanol Oxidoreductase in Escherichia coli: Transcription from a Downstream Promoter and Regulation by Fnr and RpoS". Journal of Bacteriology 181, nr 24 (15.12.1999): 7571–79. http://dx.doi.org/10.1128/jb.181.24.7571-7579.1999.

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ABSTRACT The adhE gene of Escherichia coli, located at min 27 on the chromosome, encodes the bifunctional NAD-linked oxidoreductase responsible for the conversion of acetyl-coenzyme A to ethanol during fermentative growth. The expression of adhEis dependent on both transcriptional and posttranscriptional controls and is about 10-fold higher during anaerobic than during aerobic growth. Two putative transcriptional start sites have been reported: one at position −292 and the other at −188 from the translational start codon ATG. In this study we show, by using several different transcriptional and translational fusions to the lacZ gene, that both putative transcriptional start sites can be functional and each site can be redox regulated. Although both start sites are NarL repressible in the presence of nitrate, Fnr activates only the −188 start site and Fis is required for the transcription of only the −292 start site. In addition, it was discovered that RpoS activatesadhE transcription at both start sites. Under all experimental conditions tested, however, only the upstream start site is active. Available evidence indicates that under those conditions, the upstream promoter region acts as a silencer of the downstream transcriptional start site. Translation of the mRNA starting at −292, but not the one starting at −188, requires RNase III. The results support the previously postulated ribosomal binding site (RBS) occlusion model, according to which RNase III cleavage is required to release the RBS from a stem-loop structure in the long transcript.

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Howcroft, T. Kevin, Aparna Raval, Jocelyn D. Weissman, Anne Gegonne i Dinah S. Singer. "Distinct Transcriptional Pathways Regulate Basal and Activated Major Histocompatibility Complex Class I Expression". Molecular and Cellular Biology 23, nr 10 (15.05.2003): 3377–91. http://dx.doi.org/10.1128/mcb.23.10.3377-3391.2003.

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ABSTRACT Transcription of major histocompatibility complex (MHC) class I genes is regulated by both tissue-specific (basal) and hormone/cytokine (activated) mechanisms. Although promoter-proximal regulatory elements have been characterized extensively, the role of the core promoter in mediating regulation has been largely undefined. We report here that the class I core promoter consists of distinct elements that are differentially utilized in basal and activated transcription pathways. These pathways recruit distinct transcription factor complexes to the core promoter elements and target distinct transcription initiation sites. Class I transcription initiates at four major sites within the core promoter and is clustered in two distinct regions: “upstream” (−14 and −18) and “downstream” (+12 and +1). Basal transcription initiates predominantly from the upstream start site region and is completely dependent upon the general transcription factor TAF1 (TAFII250). Activated transcription initiates predominantly from the downstream region and is TAF1 (TAFII250) independent. USF1 augments transcription initiating through the upstream start sites and is dependent on TAF1 (TAFII250), a finding consistent with its role in regulating basal class I transcription. In contrast, transcription activated by the interferon mediator CIITA is independent of TAF1 (TAFII250) and focuses initiation on the downstream start sites. Thus, basal and activated transcriptions of an MHC class I gene target distinct core promoter domains, nucleate distinct transcription initiation complexes and initiate at distinct sites within the promoter. We propose that transcription initiation at the core promoter is a dynamic process in which the mechanisms of core promoter function differ depending on the cellular environment.

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Ishihara, Satoru, Yohei Sasagawa, Takeru Kameda, Hayato Yamashita, Mana Umeda, Naoe Kotomura, Masayuki Abe, Yohei Shimono i Itoshi Nikaido. "Local states of chromatin compaction at transcription start sites control transcription levels". Nucleic Acids Research 49, nr 14 (7.07.2021): 8007–23. http://dx.doi.org/10.1093/nar/gkab587.

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Abstract The ‘open’ and ‘compact’ regions of chromatin are considered to be regions of active and silent transcription, respectively. However, individual genes produce transcripts at different levels, suggesting that transcription output does not depend on the simple open-compact conversion of chromatin, but on structural variations in chromatin itself, which so far have remained elusive. In this study, weakly crosslinked chromatin was subjected to sedimentation velocity centrifugation, which fractionated the chromatin according to its degree of compaction. Open chromatin remained in upper fractions, while compact chromatin sedimented to lower fractions depending on the level of nucleosome assembly. Although nucleosomes were evenly detected in all fractions, histone H1 was more highly enriched in the lower fractions. H1 was found to self-associate and crosslinked to histone H3, suggesting that H1 bound to H3 interacts with another H1 in an adjacent nucleosome to form compact chromatin. Genome-wide analyses revealed that nearly the entire genome consists of compact chromatin without differences in compaction between repeat and non-repeat sequences; however, active transcription start sites (TSSs) were rarely found in compact chromatin. Considering the inverse correlation between chromatin compaction and RNA polymerase binding at TSSs, it appears that local states of chromatin compaction determine transcription levels.

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Rozprawy doktorskie na temat "Transcription Start Sites"

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.

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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.

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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.

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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

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Li, Xiaomeng. "Human Promoter Recognition Based on Principal Component Analysis". Thesis, The University of Sydney, 2008. http://hdl.handle.net/2123/3656.

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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.

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Li, Xiaomeng. "Human Promoter Recognition Based on Principal Component Analysis". University of Sydney, 2008. http://hdl.handle.net/2123/3656.

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Master of Engineering
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.

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Zehentner, Barbara Katrin [Verfasser], Siegfried [Akademischer Betreuer] Scherer, Wolfgang [Gutachter] Liebl, Siegfried [Gutachter] Scherer i 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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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.

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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.

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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.

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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 - PhD
Tsetse 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.

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Części książek na temat "Transcription Start Sites"

Georgakilas, Georgios, Nikos Perdikopanis i Artemis G. Hatzigeorgiou. "Identifying Pri-miRNA Transcription Start Sites". W Methods in Molecular Biology, 11–31. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8624-8_2.

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Harbers, Matthias, Mitchell S. Dushay i Piero Carninci. "DeepCAGE: Genome-Wide Mapping of Transcription Start Sites". W Tag-Based Next Generation Sequencing, 23–46. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527644582.ch2.

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Gordon, James, i Michael Towsey. "SVM Based Prediction of Bacterial Transcription Start Sites". W Lecture Notes in Computer Science, 448–53. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/11508069_58.

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Wang, Jia, Chuang Ma, Dao Zhou, Libin Zhang i Yanhong Zhou. "Accurately Predicting Transcription Start Sites Using Logitlinear Model and Local Oligonucleotide Frequencies". W Bio-Inspired Computing and Applications, 107–14. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-24553-4_16.

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Pachganov, Stepan, Khalimat Murtazalieva, Alexei Zarubin, Tatiana Taran, Duane Chartier i Tatiana V. Tatarinova. "Prediction of Rice Transcription Start Sites Using TransPrise: A Novel Machine Learning Approach". W Methods in Molecular Biology, 261–74. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1068-8_17.

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Han, Yanping. "Determination of Transcription Start Sites (TSSs) in Yersinia pestis with a Primer Extension Assay". W Springer Protocols Handbooks, 89–98. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-7947-4_9.

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Makita, Yuko, Yukio Kurihara, Nyok-Sean Lau, Mika Kawashima, Ahmad Sofiman Othman i Minami Matsui. "Genome-Wide Analysis of Transcription Start Sites and Core Promoter Elements in Hevea brasiliensis". W The Rubber Tree Genome, 81–91. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-42258-5_6.

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Singh, Navjot, i Joseph T. Wade. "Identification of Regulatory RNA in Bacterial Genomes by Genome-Scale Mapping of Transcription Start Sites". W Methods in Molecular Biology, 1–10. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-730-3_1.

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Morioka, Masaki Suimye, Hideya Kawaji, Hiromi Nishiyori-Sueki, Mitsuyoshi Murata, Miki Kojima-Ishiyama, Piero Carninci i Masayoshi Itoh. "Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites". W Bioinformatics for Cancer Immunotherapy, 277–301. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0327-7_20.

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Binder, Stefan, i Kristina Kühn. "Determining Mitochondrial Transcript Termini for the Study of Transcription Start Sites and Transcript 5′ End Maturation". W Methods in Molecular Biology, 13–30. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2639-8_2.

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Streszczenia konferencji na temat "Transcription Start Sites"

Zheng, Hansi, Xiaoman Li i Haiyan Hu. "Deep Learning to Identify Transcription Start Sites from CAGE Data". W 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2020. http://dx.doi.org/10.1109/bibm49941.2020.9313267.

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Wang, Xi, Sanghamitra Bandyopadhya, Zhenyu Xuan, Xiaoyue Zhao, Michael Q. Zhang i Xuegong Zhang. "PREDICTION OF TRANSCRIPTION START SITES BASED ON FEATURE SELECTION USING AMOSA". W Proceedings of the CSB 2007 Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2007. http://dx.doi.org/10.1142/9781860948732_0021.

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Lanlieng, Phirayu, Chatchawit Aporntewan i Monnat Pongpanich. "Identification of transcription start sites via distribution of A/T-singletons". W 2015 International Computer Science and Engineering Conference (ICSEC). IEEE, 2015. http://dx.doi.org/10.1109/icsec.2015.7401407.

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Ni, Chung-En, Duy-Phuong Doan, Yen-Jung Chiu i Yen-Hua Huang. "TSSNet – A Deep Neural Network Model for Predicting Prokaryotic Transcription Start Sites". W 2022 IEEE 22nd International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2022. http://dx.doi.org/10.1109/bibe55377.2022.00054.

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Collins, Corolyn J., Richard B. Levene, Christina P. Ravera, Marker J. Dombalagian, David M. Livingston i Dennis C. Lynch. "MOLECULAR CLONING OF THE HUMAN GENE FOR VON WILLEBRAND FACTOR AND IDENTIFICATION OF THE TRANSCRIPTION INITIATION SITE". W XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642830.

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Most patients with von Willebrand's disease appear to have a defect affecting the level of expression of the von Willebrand factor (vWf) gene. Thus, an understanding of the pathogenesis of von Willebrand's disease will require an analysis of the structure and function of the vWf gene in normals and in patients. To begin such analyses, we have screened a human genomic cosmid library with probes obtained from vWf cDNA and isolated a colinear segment spanning ≈175 kb in five overlapping clones. This segment extends ≈25 kb upstream and ≈5 kb downstream of the transcription start and stop sites for vWf mRNA, implying the vWf gene has a length of ≈150 kb. Within one of these clones, the vWf transcription initiation sites have been mapped. A portion of the promoter region has been sequenced, revealing a typical TATA box, a downstream CCAAT box, and a perfect downstream repeat of the 8 base pairs containing the major transcription start site. Primer extension analysis suggests that sequences contained within the downstream repeat of the transcription start site may be used as minor initiation sites in endothelial cells. Transfection studies are underway to evaluate the role of sequences within this promoter region in gene regulatory activity. Comparative restriction analyses of cloned and chromosomal DNA segments strongly suggests that no major alterations ocurred during cloning and that there is only one complete copy of the vWf gene in the human haploid genome. Similar analyses of DNA from vWf-expressing endothelial cells and non-expressing white blood cells suggests that no major rearrangements are associated with vWf gene expression. Finally, cross hybridization patterns among seven mammalian species suggests a strong conservation of genomic sequences encoding the plasma portion of vWf, but a lower degree of conservation of sequences encoding the N terminal region of provWf.

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Jun Cai Huang, Feng Bi Wang, Huan Zhang Mao i Ming Tian Zhou. "A self-training semi-supervised support vector machine method for recognizing transcription start sites". W 2010 International Conference on Apperceiving Computing and Intelligence Analysis (ICACIA). IEEE, 2010. http://dx.doi.org/10.1109/icacia.2010.5709922.

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"Alternative transcription start sites contribute to acute-stressinduced transcriptome response in human skeletal muscle". W Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-040.

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Juncai, Huang, Wang Fengbi, Mao Huanzhang i Zhou Mingtian. "A Markov Chain Monte Carlo Sampling Relevance Vector Machine Model for Recognizing Transcription Start Sites". W 2010 International Conference on Artificial Intelligence and Computational Intelligence (AICI). IEEE, 2010. http://dx.doi.org/10.1109/aici.2010.277.

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Salavati, M., R. Clark, D. Becker, C. Kühn, G. Plastow, G. C. M. Moreira, C. Charlier i E. L. Clark. "554. Comparative analysis of CAGE-Seq across tissues reveals transcription start sites unique to cattle". W World Congress on Genetics Applied to Livestock Production. The Netherlands: Wageningen Academic Publishers, 2022. http://dx.doi.org/10.3920/978-90-8686-940-4_554.

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Huber, P., J. Dalmon, M. Laurent, G. Courtois, D. Thevenon i G. Marguerie. "CHARACTERIZATION OFTHE 5’FLANKING REGION FOR THE HUMAN FIBRINOGEN β GENE". W XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642889.

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Fibrinogen is coded by three separate genes located in a 50kb region of chromosome 4 and organized in a α - β - γ orientation with an inversion of the gene 3- A human genomic library was constructed using the EMBL4 phage and screened with cDNA probes coding for human fibrinogen Aα, Bβ and γ chains. Clones, covering the fibrinogen locus,were identified, and their organization was analyzed by means of hybridization and restriction mapping. Among these clones one recombinant phage containing the β gene and large 5’ and 3’ -flanking sequences was isolated.To identify the regulatory sequences Dpstream from the human β gene, a 1.5 kb fragment of the immediate 5’-flanking region was sequenced. The SI mapping experiments revealed three transcription initiation sites. PotentialTATA and CAAT sequences were identified upstream the initiation start points at the positions -21 and -58 from the first initiation start point.Comparison of this sequence with that previously reported for the same region upstream from the human γ gene revealed no significant homology which suggests that the potential promoting sequences of these genes are different. In contrast, comparison of the 5’flanking regions of human and rat β genes showed more than 80% homology for 142 bp upstream from the gene. This highly conserved region is a potential candidate for a regulatory sequence of the human β gene.To verify this activity, a β fibrinogen minigene was constructed by deletion of the internal part of the normal gene and including 3.4kb of the 5’flanking region and 1.4kb of the 3’flanking region. The minigene was transfected into HepG2, a human hepatoma cell line, to show whether the 5’flanking region of the human fibrinogen gene contains DNA sequences sufficient for efficient transcription in HepG2. Constructions of several parts of the sequenced 5’flanking region of the human β gene with the gene of the chloramphenical acetyl transferase have been also transfected in the HepG2 cells to determine the specificity of the gene expression and to localize the sequences controlling the transcription of the gene.

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Raporty organizacyjne na temat "Transcription Start Sites"

Levy, Avraham A., i Virginia Walbot. Regulation of Transposable Element Activities during Plant Development. United States Department of Agriculture, sierpień 1992. http://dx.doi.org/10.32747/1992.7568091.bard.

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We have studied the regulation of the maize Ac and MuDR transposable elements activities during plant development. Ac was studied in an heterologous system (transgenic tobacco plants and cell suspensions) while MuDR was studied in the native maize background. The focus of this study was on the transcriptional regulation of Ac and MuDR. For Ac, the major achievements were to show that 1-It is autoregulated in a way that the Ac-encoded transposase can repress the activity of its own promoter; 2-It is expressed at low basal level in all the plant organs that were studied, and its activity is stronger in dividing tissues -- a behaviour reminiscent of housekeeping genes; 3- the activity of Ac promoter is cell cycle regulated -- induced at early S-phase and increasing until mitosis; 4- host factor binding sites were identified at both extremities of Ac and may be important for transposition. For MuDR, It was shown that it encodes two genes, mudrA and mudrB, convergently transcribed from near-identical promoters in the terminal inverted repeats. Distinct 5' start sites, alternative splicing, production of antisense RNA and tissue specificity were all shown to be involved in the regulation of MuDR.

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Yaron, Zvi, Abigail Elizur, Martin Schreibman i Yonathan Zohar. Advancing Puberty in the Black Carp (Mylopharyngodon piceus) and the Striped Bass (Morone saxatilis). United States Department of Agriculture, styczeń 2000. http://dx.doi.org/10.32747/2000.7695841.bard.

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Both the genes and cDNA sequences encoding the b-subunits of black carp LH and FSH were isolated, cloned and sequenced. Sequence analysis of the bcFSHb and LHb5'flanking regions revealed that the promoter region of both genes contains canonical TATA sequences, 30 bp and 17 bp upstream of the transcription start site of FSHb and LHb genes, respectively. In addition, they include several sequences of cis-acting motifs, required for inducible and tissue-specific transcriptional regulation: the gonadotropin-specific element (GSE), GnRH responsive element (GRE), half sites of estrogen and androgen response elements, cAMP response element, and AP1. Several methods have been employed by the Israeli team to purify the recombinant b subunits (EtOH precipitation, gel filtration and lentil lectin). While the final objective to produce pure recombinantGtH subunits has not yet been achieved, we have covered much ground towards this goal. The black carp ovary showed a gradual increase in both mass and oocyte diameter. First postvitellogenic oocytes were found in 5 yr old fish. At this age, the testes already contained spermatozoa. The circulating LH levels increased from 0.5 ng/ml in 4 yr old fish to >5ng/ml in 5 yr old fish. In vivo challenge experiments in black carp showed the initial LH response of the pituitary to GnRH in 4 yr old fish. The response was further augmented in 5 yr old fish. The increase in estradiol level in response to gonadotropic stimulation was first noted in 4 yr old fish but this response was much stronger in the following year. In vivo experiments on the FSHb and LHb mRNA levels in response to GnRH were carried out on common carp as a model for synchronom spawning cyprinids. These experiments showed the prevalence of FSHP in maturing fish while LHP mRNA was prevalent in mature fish, especially in females. The gonadal fat-pad was found to originate from the retroperitoneal mesoderm and not from the genital ridge, thus differing from that reported in certain amphibians This tissue possibly serves as the major source of sex steroids in the immature black carp. However, such a function is taken over by the developing gonads in 4 yr old fish. In the striped bass, we described the ontogeny of the neuro-endocrine parameters along the brain-pituitary-gonadal axis during the first four years of life, throughout gonadal development and the onset of puberty. We also described the responsiveness of the reproductive axis to long-term hormonal manipulations at various stages of gonadal development. Most males reached complete sexual maturity during the first year of life. Puberty was initiated during the third year of life in most females, but this first reproductive cycle did not lead to the acquisition of full sexual maturity. This finding indicates that more than one reproductive cycle may be required before adulthood is reached. Out of the three native GnRHs present in striped bass, only sbGnRH and cGnRH II increased concomitantly with the progress of gonadal development and the onset of puberty. This finding, together with data on GtH synthesis and release, suggests that while sbGnRH and cGnRH II may be involved in the regulation of puberty in striped bass, these neuropeptides are not limiting factors to the onset of puberty. Plasma LH levels remained low in all fish, suggesting that LH plays only a minor role in early gonadal development. This hypothesis was further supported by the finding that experimentally elevated plasma LH levels did not result in the induction of complete ovarian and testicular development. The acquisition of complete puberty in 4 yr old females was associated with a rise in the mRNA levels of all GtH subunit genes, including a 218-fold increase in the mRNA levels of bFSH. mRNA levels of the a and PLH subunits increased only 11- and 8-fold, respectively. Although data on plasma FSH levels are unavailable, the dramatic increase in bFSH mRNA suggests a pivotal role for this hormone in regulating the onset and completion of puberty in striped bass. The hormonal regulation of the onset of puberty and of GtH synthesis and release was studied by chronic administration of testosterone (T) and/or an analog of gonadotropin-releasing hormone (G). Sustained administration of T+G increased the mRNA levels of the PLH subunit to the values characteristic of sexually mature fish, and also increased the plasma levels of LH. However, these changes did not result in the acceleration of sexual maturation. The mRNA levels of the bFSH subunit were slightly stimulated, but remained about 1/10 of the values characteristic of sexually mature fish. It is concluded that the stimulation of FSH gene expression and release does not lead to the acceleration of sexual maturity, and that the failure to sufficiently stimulate the bFSH subunit gene expression may underlie the inability of the treatments to advance sexual maturity. Consequently, FSH is suggested to be the key hormone to the initiation and completion of puberty in striped bass. Future efforts to induce precocious puberty in striped bass should focus on understanding the regulation of FSH synthesis and release and on developing technologies to induce these processes. Definite formulation of hormonal manipulation to advance puberty in the striped bass and the black carp seems to be premature at this stage. However, the project has already yielded a great number of experimental tools of DNA technology, slow-release systems and endocrine information on the process of puberty. These systems and certain protocols have been already utilized successfully to advance maturation in other fish (e.g. grey mullet) and will form a base for further study on fish puberty.

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