Relationship between histone modifications and transcription factor binding is protein family specific

Abstract

The very small fraction of putative binding sites (BSs) TFs displayed protein family-specific preferences for HM patterns surrounding BSs, with high agreement among cell lines. Moreover, compared to models based on DNA sequence and shape at flanking regions of BSs, HM-augmented quantitative machine-learning methods resulted in increased performance in a TF family-specific manner. Analysis of the relative importance of features in these models indicated that TFs, displaying larger HM pattern differences between BSs and non-BSs, bound DNA in an HM-specific manner on a protein family-specific basis. We propose that TF family-specific HM preferences reveal distinct mechanisms that assist in guiding TFs to their cognate BSs by altering chromatin structure and accessibility.

Integrated requirement of non-specific and sequence-specific DNA binding in MYC-driven transcription

“…Unlike pioneer factors that can access DNA in closed chromatin (Kim et al, 2008, Soufi et al, 2012, Myc and other bHLH proteins depend upon a pre-existing active chromatin state (Guccione et al, 2006, Guo et al, 2014, Kim et al, 2008, Soufi et al, 2012, Xin & Rohs, 2018. Moreover, while recognizing specific DNA sequence motifs, all of these transcription factors are also endowed with generic, non-specific DNA-binding activities: how these features are integrated to determine genomic binding profiles and transcriptional outputs remains largely unresolved.…”

Transcription factors and evolution: An integral part of gene expression (Review)

“…Histone proteins have tails which include residues that can be post-translationally modified and influence transcription. This effect on transcription is regulated by changes in histone modification patterns that surround TF binding motifs (45). It is speculated that TFs with evolutionary related DNA binding domains sample putative binding sites with similar histone modification pattern environments (45).…”

Cancer Treatment: An Epigenetic View

“…There are two basic biological outcomes as follows: (1) modifications of histone-DNA interactions because of the lysine losing a positive charge in the procedure, and (2) modification of the binding sites of a chromatin-interacting transcription factor. 13 The level of histone acetylation is correlated with the exact balance among the effect of HATs and histone deacetylases (HDACs).…”

“…Histone methylation is associated with transcriptional activation and repression of interest gene. 13 Histone methylation is catalyzed by histone methyltransferases (HMTs) which is an enzyme group. The methyl group can also be removed by histone demethylases (HDMs).…”