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Database for Plant Transcription Factor Binding Sites
Reconstruction of gene regulatory networks is a very important but difficult issue in plant sciences. Recently, numerous high-throughput techniques,...
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DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts
BackgroundDNA methylation is an important epigenetic modification which has numerous roles in modulating genome function. Its levels are spatially...
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Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq
Transcription factor binding across the genome is regulated by DNA sequence and chromatin features. However, it is not yet possible to quantify the...
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SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions
MotivationAberrant DNA methylation in transcription factor binding sites has been shown to lead to anomalous gene regulation that is strongly...
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Identification of Plant Transcription Factor DNA-Binding Sites Using seq-DAP-seq
The identification of genome-wide transcription factor binding sites (TFBS) is a critical step in deciphering gene and transcriptional regulatory...
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H3.3 contributes to chromatin accessibility and transcription factor binding at promoter-proximal regulatory elements in embryonic stem cells
BackgroundThe histone variant H3.3 is enriched at active regulatory elements such as promoters and enhancers in mammalian genomes. These regions are...
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Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans
BackgroundTranscription factors (TFs) exhibit heterogeneous DNA-binding specificities in individual cells and whole organisms under natural...
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Transcription factor activating enhancer-binding protein 2ε (AP2ε) modulates phenotypic plasticity and progression of malignant melanoma
Malignant melanoma, the most aggressive form of skin cancer, is often incurable once metastatic dissemination of cancer cells to distant organs has...
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Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
BackgroundTranscription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription...
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Prediction of Transcription Factor Regulators and Gene Regulatory Networks in Tomato Using Binding Site Information
Gene regulatory networks (GRNs) represent the regulatory links between transcription factors (TF) and their target genes. In plants, they are...
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Protein-intrinsic properties and context-dependent effects regulate pioneer factor binding and function
Chromatin is a barrier to the binding of many transcription factors. By contrast, pioneer factors access nucleosomal targets and promote chromatin...
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TFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors
Characterizing the binding preferences of transcription factors (TFs) in different cell types and conditions is key to understand how they...
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Assessing the Activity of Transcription Factor FoxO1
The transcription factor FoxO1 (forkhead box O1) regulates genes that are involved in development, metabolism, cellular innovation, longevity, and...
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Deciphering the roles of subcellular distribution and interactions involving the MEF2 binding region, the ankyrin repeat binding motif and the catalytic site of HDAC4 in Drosophila neuronal morphogenesis
BackgroundDysregulation of nucleocytoplasmic shuttling of histone deacetylase 4 (HDAC4) is associated with several neurodevelopmental and...
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Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize
BackgroundGenetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity....
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A context-dependent and disordered ubiquitin-binding motif
Ubiquitin is a small, globular protein that is conjugated to other proteins as a posttranslational event. A palette of small, folded domains...
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MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions
BackgroundThe microrchidia (MORC) proteins are a family of evolutionarily conserved GHKL-type ATPases involved in chromatin compaction and gene...
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Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing
RNA-binding proteins (RBPs) regulate diverse cellular processes by dynamically interacting with RNA targets. However, effective methods to capture...
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Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome
Existing methods for computational prediction of transcription factor (TF) binding sites evaluate genomic regions with similarity to known TF...
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Modeling binding specificities of transcription factor pairs with random forests
BackgroundTranscription factors (TFs) bind regulatory DNA regions with sequence specificity, form complexes and regulate gene expression. In...
