Genome-Wide Overexpression Screen for Activators of Antioxidant Gene Transcription

Abstract Genome-wide transcription factor (TF) binding signal analyses reveal co-localization of TF binding sites, based on which cis-regulatory modules (CRMs) can be inferred. CRMs play a key role in understanding the cooperation of multiple TFs under specific conditions. However, the functions of CRMs and their effects on nearby gene transcription are highly dynamic and context-specific and therefore are challenging to characterize. BICORN (Bayesian Inference of COoperative Regulatory Network) builds a hierarchical Bayesian model and infers context-specific CRMs based on TF-gene binding events and gene expression data for a particular cell type. BICORN automatically searches for a list of candidate CRMs based on the input TF bindings at regulatory regions associated with genes of interest. Applying Gibbs sampling, BICORN iteratively estimates model parameters of CRMs, TF activities, and corresponding regulation on gene transcription, which it models as a sparse network of functional CRMs regulating target genes. The BICORN package is implemented in R (version 3.4 or later) and is publicly available on the CRAN server at https://cran.r-project.org/web/packages/BICORN/index.html.

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Genome-wide DNA methylation profiles in progression to in situand invasive carcinoma of the breast with impact on gene transcription and prognosis

Genome Biology ◽

10.1186/s13059-014-0435-x ◽

2014 ◽

Vol 15 (8) ◽

Cited By ~ 10

Author(s):

Thomas Fleischer ◽

Arnoldo Frigessi ◽

Kevin C Johnson ◽

Hege Edvardsen ◽

Nizar Touleimat ◽

...

Keyword(s):

Dna Methylation ◽

Gene Transcription ◽

Invasive Carcinoma ◽

Carcinoma Of The Breast ◽

Genome Wide

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Genome-Wide Analysis of Cell Type-Specific Gene Transcription during Spore Formation in Clostridium difficile

PLoS Genetics ◽

10.1371/journal.pgen.1003756 ◽

2013 ◽

Vol 9 (10) ◽

pp. e1003756 ◽

Cited By ~ 93

Author(s):

Laure Saujet ◽

Fátima C. Pereira ◽

Monica Serrano ◽

Olga Soutourina ◽

Marc Monot ◽

...

Keyword(s):

Clostridium Difficile ◽

Gene Transcription ◽

Spore Formation ◽

Specific Gene ◽

Cell Type ◽

Genome Wide Analysis ◽

Genome Wide ◽

Cell Type Specific

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Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR

10.1101/353979 ◽

2018 ◽

Author(s):

Gemma Danks ◽

Heloisa Galbiati ◽

Martina Raasholm ◽

Yamila N. Torres Cleuren ◽

Eivind Valen ◽

...

Keyword(s):

Gene Transcription ◽

Growth Regulator ◽

Translational Control ◽

Oikopleura Dioica ◽

Spliced Leader ◽

Animal Density ◽

Genome Wide ◽

Trans Splicing ◽

Initial Recovery ◽

Favorable Conditions

AbstractIn phylogenetically diverse organisms, the 5’ ends of a subset of mRNAs are trans-spliced with a spliced leader (SL) RNA. The functions of SL trans-splicing, however, remain largely enigmatic. Here, we quantified translation genome-wide in the marine chordate, Oikopleura dioica, under inhibition of mTOR, a central growth regulator. Translation of trans-spliced TOP mRNAs was suppressed, showing that the SL sequence permits nutrient-dependent translational control of growth-related mRNAs. Under crowded, nutrient-limiting conditions, O. dioica continues to filter-feed, but arrests growth until favorable conditions return. Upon release from such conditions, initial recovery was independent of nutrient-responsive, trans-spliced genes, suggesting animal density sensing as a first trigger for resumption of development. Our results demonstrate a role for trans-splicing in the coordinated translational down-regulation of nutrient-responsive genes under limiting conditions.

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Steroid hormones regulate genome-wide epigenetic programming and gene transcription in human endometrial cells with marked aberrancies in endometriosis

PLoS Genetics ◽

10.1371/journal.pgen.1008601 ◽

2020 ◽

Vol 16 (6) ◽

pp. e1008601

Author(s):

Sahar Houshdaran ◽

Ashwini B. Oke ◽

Jennifer C. Fung ◽

Kim Chi Vo ◽

Camran Nezhat ◽

...

Keyword(s):

Steroid Hormones ◽

Gene Transcription ◽

Endometrial Cells ◽

Epigenetic Programming ◽

Genome Wide

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Faculty Opinions recommendation of Detecting genome-wide gene transcription profiles associated with high pollution burden in the critically endangered European eel.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718049488.793481239 ◽

2013 ◽

Author(s):

Nico M van Straalen

Keyword(s):

Gene Transcription ◽

Critically Endangered ◽

European Eel ◽

Transcription Profiles ◽

Genome Wide ◽

High Pollution

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Regulation of Gene Transcription by the Histone H2A N-Terminal Domain

Molecular and Cellular Biology ◽

10.1128/mcb.00742-07 ◽

2007 ◽

Vol 27 (21) ◽

pp. 7641-7648 ◽

Cited By ~ 22

Author(s):

Michael A. Parra ◽

John J. Wyrick

Keyword(s):

Gene Transcription ◽

Microarray Data ◽

Transcriptional Repression ◽

Dna Microarrays ◽

Reporter Genes ◽

Histone H2a ◽

Terminal Domain ◽

Genome Wide ◽

Genome Wide Expression

ABSTRACT Histone N-terminal domains play critical roles in regulating chromatin structure and gene transcription. Relatively little is known, however, about the role of the histone H2A N-terminal domain in transcription regulation. We have used DNA microarrays to characterize the changes in genome-wide expression caused by mutations in the N-terminal domain of histone H2A. Our results indicate that the N-terminal domain of histone H2A functions primarily to repress the transcription of a large subset of the Saccharomyces cerevisiae genome and that most of the H2A-repressed genes are also repressed by the histone H2B N-terminal domain. Using the histone H2A microarray data, we selected three reporter genes (BNA1, BNA2, and GCY1), which we subsequently used to map regions in the H2A N-terminal domain responsible for this transcriptional repression. These studies revealed that a small subdomain in the H2A N-terminal tail, comprised of residues 16 to 20, is required for the transcriptional repression of these reporter genes. Deletion of either the entire histone H2A N-terminal domain or just this small subdomain imparts sensitivity to UV irradiation. Finally, we show that two residues in this H2A subdomain, serine-17 and arginine-18, are specifically required for the transcriptional repression of the BNA2 reporter gene.

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