Transcriptional Regulation in Saccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and …

S Hahn, ET Young - Genetics, 2011 - academic.oup.com
Here we review recent advances in understanding the regulation of mRNA synthesis in
Saccharomyces cerevisiae. Many fundamental gene regulatory mechanisms have been …

Determining the specificity of protein–DNA interactions

GD Stormo, Y Zhao - Nature Reviews Genetics, 2010 - nature.com
Proteins, such as many transcription factors, that bind to specific DNA sequences are
essential for the proper regulation of gene expression. Identifying the specific sequences …

Base-resolution models of transcription-factor binding reveal soft motif syntax

Ž Avsec, M Weilert, A Shrikumar, S Krueger… - Nature …, 2021 - nature.com
The arrangement (syntax) of transcription factor (TF) binding motifs is an important part of the
cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that …

EP300 Selectively Controls the Enhancer Landscape of MYCN-Amplified Neuroblastoma

AD Durbin, T Wang, VK Wimalasena… - Cancer …, 2022 - aacrjournals.org
Gene expression is regulated by promoters and enhancers marked by histone H3 lysine 27
acetylation (H3K27ac), which is established by the paralogous histone acetyltransferases …

Determination and inference of eukaryotic transcription factor sequence specificity

MT Weirauch, A Yang, M Albu, AG Cote… - Cell, 2014 - cell.com
Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are
currently known for only∼ 1% of eukaryotic TFs. Broadly sampling DNA-binding domain …

Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution

HS Rhee, BF Pugh - Cell, 2011 - cell.com
Chromatin immunoprecipitation (ChIP-chip and ChIP-seq) assays identify where proteins
bind throughout a genome. However, DNA contamination and DNA fragmentation …

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

RC McLeay, TL Bailey - BMC bioinformatics, 2010 - Springer
Background A major goal of molecular biology is determining the mechanisms that control
the transcription of genes. Motif Enrichment Analysis (MEA) seeks to determine which DNA …

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

R Pique-Regi, JF Degner, AA Pai, DJ Gaffney… - Genome …, 2011 - genome.cshlp.org
Accurate functional annotation of regulatory elements is essential for understanding global
gene regulation. Here, we report a genome-wide map of 827,000 transcription factor binding …

[HTML][HTML] Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape

R Gordân, N Shen, I Dror, T Zhou, J Horton, R Rohs… - Cell reports, 2013 - cell.com
DNA sequence is a major determinant of the binding specificity of transcription factors (TFs)
for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with …

Disentangling the many layers of eukaryotic transcriptional regulation

KM Lelli, M Slattery, RS Mann - Annual review of genetics, 2012 - annualreviews.org
Regulation of gene expression in eukaryotes is an extremely complex process. In this
review, we break down several critical steps, emphasizing new data and techniques that …