The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets

Laperle, Jonathan; Hébert-Deschamps, Simon; Raby, Joanny; Morais, David Anderson de Lima; Barrette, M.; Bujold, David; Bastin, Charlotte; Robert, Marc-Antoine; Nadeau, Jean-François; Harel, Marie; Nordell-Markovits, Alexei; Veilleux, Alain; Bourque, Guillaume; Jacques, Pierre-Étienne

doi:10.1093/bioinformatics/bty655

Cited by 6 publications

(5 citation statements)

References 6 publications

(6 reference statements)

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“…Visual inspection of the data was performed using an Assem-blyHub on the UCSC Genome Browser (Casper et al, 2018). Genome-wide Pearson's correlation coefficients were calculated using the epiGeEC tool version 1.0 (Laperle et al, 2019). 131 isolated tRNA and 35 isolated 5S rRNA were used for the VAP analyses.…”

Section: Chip-seq Data Analysismentioning

confidence: 99%

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Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription

et al. 2019

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R‐loop disassembly by the human helicase Senataxin contributes to genome integrity and to proper transcription termination at a subset of RNA polymerase II genes. Whether Senataxin also contributes to transcription termination at other classes of genes has remained unclear. Here, we show that Sen1, one of two fission yeast homologues of Senataxin, promotes efficient termination of RNA polymerase III (RNAP3) transcription in vivo. In the absence of Sen1, RNAP3 accumulates downstream of RNAP3‐transcribed genes and produces long exosome‐sensitive 3′‐extended transcripts. Importantly, neither of these defects was affected by the removal of R‐loops. The finding that Sen1 acts as an ancillary factor for RNAP3 transcription termination in vivo challenges the pre‐existing view that RNAP3 terminates transcription autonomously. We propose that Sen1 is a cofactor for transcription termination that has been co‐opted by different RNA polymerases in the course of evolution.

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Section: Chip-seq Data Analysismentioning

confidence: 99%

“…We used the 3 0 one reference point mode to generate the graph values and identified the average 5 0 start using the 5 0 one reference point mode (both graphs overlapped perfectly for all curves). Genome-wide Pearson's correlation coefficients were calculated using the epiGeEC tool version 1.0 (Laperle et al, 2019).…”

Section: Chip-seq Data Analysismentioning

confidence: 99%

Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription

et al. 2019

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Section: Discussionmentioning

confidence: 99%

“…It is suitable for elucidating the mechanisms of action of multiple chemical components and molecular targets [ 23 ], and hence, it is a credible approach for modern research in TCM. The GEO database provides a critical online resource for researchers to deeply mine gene expression data [ 24 , 25 ]. Compared with ordinary gene expression profiling studies, multimicroarray conjoint analysis integrates the raw data of multiple microarrays to augment the accuracy and reliability of results.…”

Section: Discussionmentioning

confidence: 99%

Potential Therapeutic Mechanism of Scutellaria baicalensis Georgi against Ankylosing Spondylitis Based on a Comprehensive Pharmacological Model

Liu

Fang

et al. 2022

BioMed Research International

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Background. Scutellaria baicalensis Georgi (SBG) has significant anti-inflammatory and immune-modulating activities and is widely used in the treatment of inflammatory and autoimmune diseases. However, the mechanism of SBG in the treatment of ankylosing spondylitis (AS) remains to be elucidated. Methods. Differentially expressed genes (DEGs) related to AS were analyzed based on two GEO gene chips. The DEGs were merged with the data derived from OMIM, GeneCards, and PharmGKB databases to ascertain AS-related targets. Active components of SBG and their targets were acquired from the TCMSP database. After overlapping the targets of AS and SBG, the action targets were acquired. Subsequently, protein-protein interaction (PPI) network and core target screening were conducted using the STRING database and Cytoscape software. Moreover, the DAVID platform was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of action targets. Finally, the affinity of major active components and core targets was validated with molecular docking. Results. A total of 36 active components of SBG were acquired from TCMSP database. Among these, the main active components were baicalein, wogonin, and oroxylin A. The PPI network and screening showed TNF, IL-6, CXCL8, PTGS2, and VEGFA as core targets associated SBG against AS. GO and KEGG analyses indicated that SBG participated in various biological processes, via regulating IL-17, TNF, and NF-κB signaling pathways. Molecular docking results confirmed a strong binding activity between the main active components and the core targets. Conclusion. The therapeutic mechanism of SBG associated with AS can be characterized as a multicomponent, multitarget, and multipathway mechanism. SBG may be a promising therapeutic candidate for AS.

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“…We used the 3' one reference point mode to generate the graph values and identified the average 5' start using the 5' one reference point mode (both graphs overlapped perfectly for all curves). Genome-wide Pearson correlation coefficients were calculated using the epiGeEC tool version 1.0 (Laperle et al, 2018).…”

Section: Transcription Termination Assaymentioning

confidence: 99%

Sen1 is required for RNA Polymerase III transcription termination in an R-loop independent manner

Rivosecchi

Larochelle

Teste

et al. 2019

Preprint

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R-loop disassembly by the human helicase Senataxin contributes to genomestability and to proper transcription termination at a subset of RNA polymerase II genes. Whether Senataxin-mediated R-loop disassembly also contributes to transcription termination at other classes of genes has remained unclear. Here we show in fission yeast that Senataxin Sen1 promotes efficient termination of RNA Polymerase III (RNAP3) transcription in vivo. In the absence of Senataxin Sen1 , RNAP3 accumulates downstream of the primary terminator at RNAP3-transcribed genes and produces long exosome-sensitive 3'-extended transcripts. Importantly, neither of these defects was affected by the removal of R-loops. The finding that Senataxin Sen1 acts as an ancillary factor for RNAP3 transcription termination in vivo challenges the pre-existing view that RNAP3 terminates transcription autonomously. We propose that Senataxin is a cofactor for transcription termination that has been co-opted by different RNA polymerases in the course of evolution. KEYWORDS R-loops/ RNA Polymerase III/ Senataxin/ Transcription termination

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The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 6 publications

References 6 publications

Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription

Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription

Potential Therapeutic Mechanism of Scutellaria baicalensis Georgi against Ankylosing Spondylitis Based on a Comprehensive Pharmacological Model

Sen1 is required for RNA Polymerase III transcription termination in an R-loop independent manner

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