Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function
Sign Up to like & getrecommendations! Published in 2018 at "Cell"
DOI: 10.1016/j.cell.2018.04.018
Abstract: Non-coding genetic variation is a major driver of phenotypic diversity and allows the investigation of mechanisms that control gene expression. Here, we systematically investigated the effects of >50 million variations from five strains of mice… read more here.
Keywords: transcription factor; factor binding; mechanisms control; transcription ... See more keywords
Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells
Sign Up to like & getrecommendations! Published in 2020 at "Cell"
DOI: 10.1016/j.cell.2020.06.037
Abstract: Cellular heterogeneity confounds in situ assays of transcription factor (TF) binding. Single-cell RNA sequencing (scRNA-seq) deconvolves cell types from gene expression, but no technology links cell identity to TF binding sites (TFBS) in those cell… read more here.
Keywords: transcription factor; factor binding; cell; gene expression ... See more keywords
ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-18035-1
Abstract: While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread application… read more here.
Keywords: transcription factor; factor binding; zygotic genome; atac seq ... See more keywords
Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites
Sign Up to like & getrecommendations! Published in 2022 at "Scientific Reports"
DOI: 10.1038/s41598-022-08645-8
Abstract: Endothelial cells (ECs) lining blood vessels are exposed to mechanical forces, such as shear stress. These forces control many aspects of EC biology, including vascular tone, cell migration and proliferation. Despite a good understanding of… read more here.
Keywords: transcription factor; shear stress; klf transcription; stress ... See more keywords
NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac569
Abstract: Motivation Machine learning models for predicting cell-type-specific transcription factor (TF) binding sites have become increasingly more accurate thanks to the increased availability of next-generation sequencing data and more standardized model evaluation criteria. However, knowledge transfer… read more here.
Keywords: cell; prediction; transcription factor; factor binding ... See more keywords
PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes.
Sign Up to like & getrecommendations! Published in 2022 at "Database : the journal of biological databases and curation"
DOI: 10.1093/database/baac024
Abstract: More accurate and more complete predictions of cis-regulatory modules (CRMs) and constituent transcription factor (TF) binding sites (TFBSs) in genomes can facilitate characterizing functions of regulatory sequences. Here, we developed a database predicted cis-regulatory modules… read more here.
Keywords: factor binding; database; constituent transcription; transcription factor ... See more keywords
DOP07 Ulcerative Colitis associated single nucleotide polymorphisms found in transcription factor binding sites effect key pathogenesis pathways and facilitate patient stratification
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Crohn's and Colitis"
DOI: 10.1093/ecco-jcc/jjab073.046
Abstract: Ulcerative Colitis (UC) associated single nucleotide polymorphisms (SNP) are mostly in non-coding regions of the genome. Because of that, it has been challenging to determine their role in the disease onset and severity. We have… read more here.
Keywords: colitis; binding sites; factor binding; factor ... See more keywords
Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs)
Sign Up to like & getrecommendations! Published in 2018 at "Genome Biology and Evolution"
DOI: 10.1093/gbe/evy073
Abstract: Abstract Transposable elements are one of the main drivers of plant genome evolution. Transposon insertions can modify the gene coding capacity or the regulation of their expression, the latter being a more subtle effect, and… read more here.
Keywords: transcription; miniature inverted; transcription factor; factor binding ... See more keywords
Evolutionary Potential of Cis-Regulatory Mutations to Cause Rapid Changes in Transcription Factor Binding
Sign Up to like & getrecommendations! Published in 2019 at "Genome Biology and Evolution"
DOI: 10.1093/gbe/evy269
Abstract: Abstract Transcriptional regulation is crucial for all biological processes and well investigated at the molecular level for a wide range of organisms. However, it is quite unclear how innovations, such as the activity of a… read more here.
Keywords: transcription factor; factor binding; rapid changes; evolutionary potential ... See more keywords
Variable interplay of UV-induced DNA damage and repair at transcription factor binding sites
Sign Up to like & getrecommendations! Published in 2020 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkaa1219
Abstract: Abstract An abnormally high rate of UV-light related mutations appears at transcription factor binding sites (TFBS) across melanomas. The binding of transcription factors (TFs) to the DNA impairs the repair of UV-induced lesions and certain… read more here.
Keywords: transcription factor; binding sites; rate; factor binding ... See more keywords
Quantitative analysis of transcription factor binding and expression using calling cards reporter arrays
Sign Up to like & getrecommendations! Published in 2020 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkaa141
Abstract: Abstract We report a tool, Calling Cards Reporter Arrays (CCRA), that measures transcription factor (TF) binding and the consequences on gene expression for hundreds of synthetic promoters in yeast. Using Cbf1p and MAX, we demonstrate… read more here.
Keywords: calling cards; cards reporter; reporter arrays; transcription factor ... See more keywords