Relevant bibliographies by topics / Gene coregulation

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Gene coregulation'

Author: Grafiati
Published: 25 May 2024

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Journal articles on the topic "Gene coregulation"

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Reja, Rohit, Vinesh Vinayachandran, Sujana Ghosh, and B. Franklin Pugh. "Molecular mechanisms of ribosomal protein gene coregulation." Genes & Development 29, no. 18 (September 15, 2015): 1942–54. http://dx.doi.org/10.1101/gad.268896.115.

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Györy, Ildikó, and Janos Minarovits. "Epigenetic regulation of lymphoid specific gene sets." Biochemistry and Cell Biology 83, no. 3 (June 1, 2005): 286–95. http://dx.doi.org/10.1139/o05-020.

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Coregulation of lymphoid-specific gene sets is achieved by a series of epigenetic mechanisms. Association with higher-order chromosomal structures (nuclear subcompartments repressing or favouring gene expression) and locus control regions affects recombination and transcription of clonotypic antigen receptors and expression of a series of other lymphoid-specific genes. Locus control regions can regulate DNA methylation patterns in their vicinity. They may induce tissue- and site-specific DNA demethylation and affect, thereby, accessibility to recombination-activating proteins, transcription factors, and enzymes involved in histone modifications. Both DNA methylation and the Polycomb group of proteins (PcG) function as alternative systems of epigenetic memory in lymphoid cells. Complexes of PcG proteins mark their target genes by covalent histone tail modifications and influence lymphoid development and rearrangement of IgH genes. Ectopic expression of protein noncoding microRNAs may affect the generation of B-lineage cells, too, by guiding effector complexes to sites of heterochromatin assembly. Coregulation of lymphoid and viral promoters is also possible. EBNA 2, a nuclear protein encoded by episomal Epstein-Barr virus genomes, binds to the cellular protein CBF1 (C promoter binding factor 1) and operates, thereby, a regulatory network to activate latent viral promoters and cellular promoters associated with CBF1 binding sites.Key words : lymphoid cells, coregulation of gene batteries, epigenetic regulation, nuclear subcompartment switch, locus control region, DNA methylation, Polycomb group of proteins, histone modifications, microRNA, Epstein-Barr virus, EBNA 2, regulatory network.
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Isaac, R. Stefan, Erik McShane, and L. Stirling Churchman. "The Multiple Levels of Mitonuclear Coregulation." Annual Review of Genetics 52, no. 1 (November 23, 2018): 511–33. http://dx.doi.org/10.1146/annurev-genet-120417-031709.

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Together, the nuclear and mitochondrial genomes encode the oxidative phosphorylation (OXPHOS) complexes that reside in the mitochondrial inner membrane and enable aerobic life. Mitochondria maintain their own genome that is expressed and regulated by factors distinct from their nuclear counterparts. For optimal function, the cell must ensure proper stoichiometric production of OXPHOS subunits by coordinating two physically separated and evolutionarily distinct gene expression systems. Here, we review our current understanding of mitonuclear coregulation primarily at the levels of transcription and translation. Additionally, we discuss other levels of coregulation that may exist but remain largely unexplored, including mRNA modification and stability and posttranslational protein degradation.
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Perco, Paul, Alexander Kainz, Gert Mayer, Arno Lukas, Rainer Oberbauer, and Bernd Mayer. "Detection of coregulation in differential gene expression profiles." Biosystems 82, no. 3 (December 2005): 235–47. http://dx.doi.org/10.1016/j.biosystems.2005.08.001.

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Arnone, James T., Jeffrey R. Arace, Anand R. Soorneedi, Teryn T. Citino, Tadashi L. Kamitaki, and Michael A. McAlear. "Dissecting thecisandtransElements That Regulate Adjacent-Gene Coregulation in Saccharomyces cerevisiae." Eukaryotic Cell 13, no. 6 (April 4, 2014): 738–48. http://dx.doi.org/10.1128/ec.00317-13.

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ABSTRACTThe relative positions that genes occupy on their respective chromosomes can play a critical role in determining how they are regulated at the transcriptional level. For example, a significant fraction of the genes from a variety of coregulated gene sets, including the ribosomal protein (RP) and the rRNA and ribosome biogenesis (RRB) regulons, exist as immediate, adjacent gene pairs. These gene pairs occur in all possible divergent, tandem, and convergent orientations. Adjacent-gene pairing in these regulons is associated with a tighter transcriptional coregulation than is observed for nonpaired genes of the same regulons. In order to define thecisandtransfactors that regulate adjacent-gene coregulation (AGC), we conducted a mutational analysis of the convergently oriented RRB gene pairMPP10-YJR003C. We observed that coupled corepression of the gene pair under heat shock was abrogated when the two genes were separated by an actively expressed RNA polymerase (Pol) II transcription unit (theLEU2gene) but not when the insertedLEU2gene was repressed. In contrast, the insertion of an RNA Pol III-transcribed tRNA (Thr) gene did not disrupt the coregulated repression ofMPP10andYJR003C. A targeted screen of mutants defective in regulating chromosome architecture revealed that the Spt20, Snf2, and Chd1 proteins were required for coupling the repression ofYJR003Cto that ofMPP10. Nucleosome occupancy assays performed across theMPP10andYJR003Cpromoter regions revealed that the mechanism of corepression of the gene pair was not related to the repositioning of nucleosomes across the respective gene promoters.
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Zuo, Yu-Ling, Di-Ping Gong, Bi-Ze Li, Juan Zhao, Ling-Yue Zhou, Fang-Yang Shao, Zhao Jin, and Yuan He. "The TF-miRNA Coregulation Network in Oral Lichen Planus." BioMed Research International 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/731264.

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Oral lichen planus (OLP) is a chronic inflammatory disease that affects oral mucosa, some of which may finally develop into oral squamous cell carcinoma. Therefore, pinpointing the molecular mechanisms underlying the pathogenesis of OLP is important to develop efficient treatments for OLP. Recently, the accumulation of the large amount of omics data, especially transcriptome data, provides opportunities to investigate OLPs from a systematic perspective. In this paper, assuming that the OLP associated genes have functional relationships, we present a new approach to identify OLP related gene modules from gene regulatory networks. In particular, we find that the gene modules regulated by both transcription factors (TFs) and microRNAs (miRNAs) play important roles in the pathogenesis of OLP and many genes in the modules have been reported to be related to OLP in the literature.
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Medini, Hadar, Tal Cohen, and Dan Mishmar. "Mitochondria Are Fundamental for the Emergence of Metazoans: On Metabolism, Genomic Regulation, and the Birth of Complex Organisms." Annual Review of Genetics 54, no. 1 (November 23, 2020): 151–66. http://dx.doi.org/10.1146/annurev-genet-021920-105545.

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Out of many intracellular bacteria, only the mitochondria and chloroplasts abandoned their independence billions of years ago and became endosymbionts within the host eukaryotic cell. Consequently, one cannot grow eukaryotic cells without their mitochondria, and the mitochondria cannot divide outside of the cell, thus reflecting interdependence. Here, we argue that such interdependence underlies the fundamental role of mitochondrial activities in the emergence of metazoans. Several lines of evidence support our hypothesis: ( a) Differentiation and embryogenesis rely on mitochondrial function; ( b) mitochondrial metabolites are primary precursors for epigenetic modifications (such as methyl and acetyl), which are critical for chromatin remodeling and gene expression, particularly during differentiation and embryogenesis; and ( c) mitonuclear coregulation adapted to accommodate both housekeeping and tissue-dependent metabolic needs. We discuss the evolution of the unique mitochondrial genetic system, mitochondrial metabolites, mitonuclear coregulation, and their critical roles in the emergence of metazoans and in human disorders.
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Warrell, Jonathan, and Musa Mhlanga. "Stability and structural properties of gene regulation networks with coregulation rules." Journal of Theoretical Biology 420 (May 2017): 304–17. http://dx.doi.org/10.1016/j.jtbi.2016.10.020.

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Anda-Jáuregui, Guillermo de, Cristobal Fresno, Diana García-Cortés, Jesús Espinal Enríquez, and Enrique Hernández-Lemus. "Intrachromosomal regulation decay in breast cancer." Applied Mathematics and Nonlinear Sciences 4, no. 1 (June 28, 2019): 223–30. http://dx.doi.org/10.2478/amns.2019.1.00020.

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AbstractBiological systems exhibit unique phenotypes as the result of the expression of a genomic program. The regulation of this program is a complex phenomenon, wherein different regulatory mechanisms are involved. The deregulation of this program is at the centre of the emergence of diseases such as breast cancer. In particular, it has been observed that coregulation patterns between physically distant genes are lost in breast cancer.In this work, we present a systematic study of chromosome-wide gene coregulation patterns in breast cancer as inferred by information theoretical measures over large (whole-genome expression in several hundred transcriptomes) experimental data corpora. We analyzed the chromosomal distance decay of correlations and found it to be with fat-tail distribution in breast cancer while being fundamentally constant in nontumour samples.After model discrimination analyses, we concluded that the behaviour of the breast cancer distributions belongs to an intermediate regime between power law and Weibull distributions, with distinctive contributions corresponding to different chromosomes. This behaviour may have biological implications in terms of the organization of the gene regulatory program, and the changes found in this program between health and disease.
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Brych, Annika, Fabian B. Haas, Katharina Parzefall, Sabine Panzer, Jeanette Schermuly, Janine Altmüller, Timo Engelsdorf, et al. "Coregulation of gene expression by White collar 1 and phytochrome in Ustilago maydis." Fungal Genetics and Biology 152 (July 2021): 103570. http://dx.doi.org/10.1016/j.fgb.2021.103570.

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Dissertations / Theses on the topic "Gene coregulation"

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FOUCHET, CLAUDE. "Etude de la coregulation de l'expression des genes xg et mic2 et analyse des bases moleculaires du polymorphisme xg(a+)/xg(a-)." Paris 7, 2000. http://www.theses.fr/2000PA077084.

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La proteine cd99, produit du gene mic2 situe sur les chromosomes x et y, presente un polymorphisme quantitatif erythrocyte specifique coregule avec le polymorphisme xg(a+)/xg(a-) de l'antigene de groupe sanguin xg a, dont le gene xg n'est present dans son integralite que sur le chromosome x. Nous avons montre, en utilisant un systeme cellulaire eucaryote, que l'expression simultanee des genes xg et mic2 n'est vraisemblablement pas regulee au stade proteique, confortant ainsi l'hypothese d'un controle transcriptionnel de leur coexpression. La caracterisation de xg et cd99 par western blot et immunoprecipitation n'a revele aucune association entre ces deux proteines dans la membrane de cellules transfectees ou d'erythrocytes humains. Par analyse en northern blot, nous avons etabli que la transcription de xg n'est pas strictement erythroide et confirme l'expression ubiquitaire de mic2. L'analyse quantitative de xg a et cd99 a la surface des erythrocytes corrobore le modele d'un controle genetique unique de l'expression des deux antigenes. Nous avons etudie les bases moleculaires du polymorphisme xg(a+)/xg(a) et montre que la structure du gene xg est identique entre les deux phenotypes. L'analyse des transcrits de reticulocytes indique l'existence de cinq spliceoformes du messager xg, presentes soit exclusivement soit majoritairement chez les individus xg(a), alors qu'il nous reste a confirmer que le transcrit normal des individus xg(a+) est rarement detecte parmi les arn xg(a). Nous avons montre que la region 5 flanquante de xg possede les caracteristiques d'un promoteur erythroide mais que de nombreux sites potentiels de fixation de facteurs de transcription presentent des divergences avec les sequences consensuelles, en particulier
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Webber, Aaron. "Transcriptional co-regulation of microRNAs and protein-coding genes." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/transcriptional-coregulation-of-micrornas-and-proteincoding-genes(f5b601b2-33f3-4608-9ae8-b7d5a0c6beaf).html.

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This thesis was presented by Aaron Webber on the 4th December 2013 for the degree of Doctor of Philosophy from the University of Manchester. The title of this thesis is ‘Transcriptional co-regulation of microRNAs and protein-coding genes’. The thesis relates to gene expression regulation within humans and closely related primate species. We have investigated the binding site distributions from publically available ChIP-seq data of 117 transcription regulatory factors (TRFs) within the human genome. These were mapped to cis-regulatory regions of two major classes of genes,  20,000 genes encoding proteins and  1500 genes encoding microRNAs. MicroRNAs are short 20 - 24 nt noncoding RNAs which bind complementary regions within target mRNAs to repress translation. The complete collection of ChIP-seq binding site data is related to genomic associations between protein-coding and microRNA genes, and to the expression patterns and functions of both gene types across human tissues. We show that microRNA genes are associated with highly regulated protein-coding gene regions, and show rigorously that transcriptional regulation is greater than expected, given properties of these protein-coding genes. We find enrichment in developmental proteins among protein-coding genes hosting microRNA sequences. Novel subclasses of microRNAs are identified that lie outside of protein-coding genes yet may still be expressed from a shared promoter region with their protein-coding neighbours. We show that such microRNAs are more likely to form regulatory feedback loops with the transcriptional regulators lying in the upstream protein-coding promoter region. We show that when a microRNA and a TRF regulate one another, the TRF is more likely to sometimes function as a repressor. As in many studies, the data show that microRNAs lying downstream of particular TRFs target significantly many genes in common with these TRFs. We then demonstrate that the prevalence of such TRF/microRNA regulatory partnerships relates directly to the variation in mRNA expression across human tissues, with the least variable mRNAs having the most significant enrichment in such partnerships. This result is connected to theory describing the buffering of gene expression variation by microRNAs. Taken together, our study has demonstrated significant novel linkages between the transcriptional TRF and post-transcriptional microRNA-mediated regulatory layers. We finally consider transcriptional regulators alone, by mapping these to genes clustered on the basis of their expression patterns through time, within the context of CD4+ T cells from African green monkeys and Rhesus macaques infected with Simian immunodeficiency virus (SIV). African green monkeys maintain a functioning immune system despite never clearing the virus, while in rhesus macaques, the immune system becomes chronically stimulated leading to pathogenesis. Gene expression clusters were identified characterizing the natural and pathogenic host systems. We map transcriptional regulators to these expression clusters and demonstrate significant yet unexpected co-binding by two heterodimers (STAT1:STAT2 and BATF:IRF4) over key viral response genes. From 34 structural families of TRFs, we demonstrate that bZIPs, STATs and IRFs are the most frequently perturbed upon SIV infection. Our work therefore contributes to the characterization of both natural and pathogenic SIV infections, with longer term implications for HIV therapeutics.
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Venkadakrishnan, Varadha Balaji. "PKN1 is a novel therapeutic target to block serum response factor-dependent androgen receptor action in advanced prostate cancer." Cleveland State University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=csu160140048514005.

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Book chapters on the topic "Gene coregulation"

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Bhar, Anirban, Martin Haubrock, Anirban Mukhopadhyay, Ujjwal Maulik, Sanghamitra Bandyopadhyay, and Edgar Wingender. "δ-TRIMAX: Extracting Triclusters and Analysing Coregulation in Time Series Gene Expression Data." In Lecture Notes in Computer Science, 165–77. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-33122-0_13.

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Mooi, Frits R. "Genes for the Filamentous Hemagglutinin and Fimbriae of Bordetella pertussis: Colocation, Coregulation, and Cooperation?" In Molecular Genetics of Bacterial Pathogenesis, 145–55. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818340.ch10.

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Taguchi, Y. H. "Possible miRNA Coregulation of Target Genes in Brain Regions by Both Differential miRNA Expression and miRNA-Targeting-Specific Promoter Methylation." In Communications in Computer and Information Science, 225–30. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-39678-6_38.

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Kumar, Vijay. "rDNA gene structure, transcription, and its coregulation." In Emerging Concepts in Ribosome Structure, Biogenesis, and Function, 33–45. Elsevier, 2021. http://dx.doi.org/10.1016/b978-0-12-816364-1.00010-x.

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Roforth, Matthew M., Sundeep Khosla, and David G. Monroe. "Changes in Nuclear Receptor and Coregulator Gene Expression during Osteoblastic Differentiation." In BASIC/TRANSLATIONAL - Actions of Adrenal Steroid Receptors & Other Nuclear Receptors, P3–16—P3–16. The Endocrine Society, 2011. http://dx.doi.org/10.1210/endo-meetings.2011.part3.p16.p3-16.

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Park, SH, SY Yoon, Y. Zhao, L. Liao, Z. Liu, J. Xu, JP Lydon, et al. "Altering Coregulator Concentration by Conditional Genetic Modification: Gene Dosage of REA Is Critical for Fertility and Uterine Function." In The Endocrine Society's 92nd Annual Meeting, June 19–22, 2010 - San Diego, P3–349—P3–349. Endocrine Society, 2010. http://dx.doi.org/10.1210/endo-meetings.2010.part3.p7.p3-349.

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Madak-Erdogan, Zeynep, and Benita S. Katzenellenbogen. "Aryl Hydrocarbon Receptor Modulation of Estrogen Receptor-alpha-Mediated Gene Regulation by a Multimeric Chromatin Complex Involving the Two Receptors and the Coregulator RIP140." In TRANSLATIONAL - Steroidal Regulation of Breast & Prostate Cancer, OR06–1—OR06–1. The Endocrine Society, 2011. http://dx.doi.org/10.1210/endo-meetings.2011.part1.or7.or06-1.

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Conference papers on the topic "Gene coregulation"

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Munoz, Matthew, and Alexander Zambon. "InSilico-ChIP: A Coregulation and Evolutionary Conservation Based Transcription Factor and Target Gene Predictor." In 2012 IEEE Second International Conference on Healthcare Informatics, Imaging and Systems Biology (HISB). IEEE, 2012. http://dx.doi.org/10.1109/hisb.2012.47.

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Paul, Amit, and Jaya Sil. "Missing value estimation in microarray data using coregulation and similarity of genes." In 2011 World Congress on Information and Communication Technologies (WICT). IEEE, 2011. http://dx.doi.org/10.1109/wict.2011.6141332.

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