Generating specificity in genome regulation through transcription factor sensitivity to chromatin
Cell type-specific gene expression relies on transcription factors (TFs) binding DNA
sequence motifs embedded in chromatin. Understanding how motifs are accessed in …
sequence motifs embedded in chromatin. Understanding how motifs are accessed in …
Regulatory SNPs: altered transcription factor binding sites implicated in complex traits and diseases
AO Degtyareva, EV Antontseva… - International journal of …, 2021 - mdpi.com
The vast majority of the genetic variants (mainly SNPs) associated with various human traits
and diseases map to a noncoding part of the genome and are enriched in its regulatory …
and diseases map to a noncoding part of the genome and are enriched in its regulatory …
Wilds: A benchmark of in-the-wild distribution shifts
Distribution shifts—where the training distribution differs from the test distribution—can
substantially degrade the accuracy of machine learning (ML) systems deployed in the wild …
substantially degrade the accuracy of machine learning (ML) systems deployed in the wild …
Readout of histone methylation by Trim24 locally restricts chromatin opening by p53
The genomic binding sites of the transcription factor (TF) and tumor suppressor p53 are
unusually diverse with regard to their chromatin features, including histone modifications …
unusually diverse with regard to their chromatin features, including histone modifications …
ZNF410 uniquely activates the NuRD component CHD4 to silence fetal hemoglobin expression
Metazoan transcription factors typically regulate large numbers of genes. Here we identify
via a CRISPR-Cas9 genetic screen ZNF410, a pentadactyl DNA-binding protein that in …
via a CRISPR-Cas9 genetic screen ZNF410, a pentadactyl DNA-binding protein that in …
Mechanisms governing target search and binding dynamics of hypoxia-inducible factors
Transcription factors (TFs) are classically attributed a modular construction, containing well-
structured sequence-specific DNA-binding domains (DBDs) paired with disordered …
structured sequence-specific DNA-binding domains (DBDs) paired with disordered …
Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes
I Zhu, D Landsman - Genome Research, 2023 - genome.cshlp.org
Housekeeping genes are considered to be regulated by common enhancers across different
tissues. Here we report that most of the commonly expressed mouse or human genes across …
tissues. Here we report that most of the commonly expressed mouse or human genes across …
Deciphering cell types by integrating scATAC-seq data with genome sequences
Y Zeng, M Luo, N Shangguan, P Shi, J Feng… - Nature Computational …, 2024 - nature.com
The single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq)
technology provides insight into gene regulation and epigenetic heterogeneity at single-cell …
technology provides insight into gene regulation and epigenetic heterogeneity at single-cell …
Domain-adaptive neural networks improve cross-species prediction of transcription factor binding
The intrinsic DNA sequence preferences and cell type–specific cooperative partners of
transcription factors (TFs) are typically highly conserved. Hence, despite the rapid …
transcription factors (TFs) are typically highly conserved. Hence, despite the rapid …
Computational prediction and characterization of cell-type-specific and shared binding sites
Motivation Cell-type-specific gene expression is maintained in large part by transcription
factors (TFs) selectively binding to distinct sets of sites in different cell types. Recent …
factors (TFs) selectively binding to distinct sets of sites in different cell types. Recent …