However, models trained on genomic sequences often fail to explain why the same transcription factor can activate or repress transcription in different contexts. To address this limitation, we developed an active learning approach to train models that distinguish between enhancers and silencers composed ...
specific transcription factors to higher-order chromatin architecture through chromatin remodelling complexes, chromosomal loops and potentially phase-separated condensates. In this review, we synthesise classic and recent evidence on the organisation and function of enhancers, focusing in particular on the pr...
TFs, often referred to as trans-acting factors, bind to enhancers, SEs, or silencers and control the efficiency by which target genes are transcribed [80]. In 2013, SEs were first identified in ESCs because o ESC-specific TFs such as SOX2, NANOG, and OCT4 were found to be enriched at ...
Super-enhancers (SEs) consist of multiple typical enhancers enriched at high density with transcription factors, histone-modifying enzymes and cofactors. Oncogenic SEs promote tumorigenesis and malignancy by altering protein-coding gene expression and no
J. Cross-talk between site-specific transcription factors and DNA methylation states. J. Biol. Chem. 288, 34287–34294 (2013). CAS PubMed PubMed Central Google Scholar Kolovos, P., Knoch, T. A., Grosveld, F. G., Cook, P. R. & Papantonis, A. Enhancers and silencers: an ...
promoter regions, but also analysis of shared and conserved other DNA motifs such as enhancers and silencers, in mRNA (motifs or regulatory elements e.g. for polyadenylation) and lncRNAs. The tool AIModules presented here is an integrated solution for motif analysis, offered as a Web service ...
Transcriptional silencers—not to be confused with inactive (“silent”) chromatin—are active negative regulatory elements that repress the transcription of otherwise active promoters (Ogbourne and Antalis, 1998). They play crucial roles in contributing to the specification of precise gene expression pat...
Contiguous genomic segments including the enhancer and the E6 promoter of genital as well as non-genital papillomaviruses generally had very low transcriptional activities, presumably due to silencers between enhancer and promoter sequences. This generalization applies to all cell types tested in spite ...
in exons. Depending on whether the sequence elements assist or inhibit the splicing process, they are called exonic splicing enhancers or exonic splicing silencers. Exonic splicing enhancers (ESEs) are usually purine-rich sequences that bind members of the SR protein family (see Figure1). SR ...
TFs TFs, often referred to as trans-acting factors, bind to enhancers, SEs, or silencers and control the efficiency by which target genes are transcribed [80]. In 2013, SEs were first identified in ESCs because o ESC-specific TFs such as SOX2, NANOG, and OCT4 were found to be enriched...