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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 …
Saccharomyces cerevisiae. Many fundamental gene regulatory mechanisms have been …
Determining the specificity of protein–DNA interactions
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 …
essential for the proper regulation of gene expression. Identifying the specific sequences …
Base-resolution models of transcription-factor binding reveal soft motif syntax
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 …
cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that …
EP300 Selectively Controls the Enhancer Landscape of MYCN-Amplified Neuroblastoma
Gene expression is regulated by promoters and enhancers marked by histone H3 lysine 27
acetylation (H3K27ac), which is established by the paralogous histone acetyltransferases …
acetylation (H3K27ac), which is established by the paralogous histone acetyltransferases …
Determination and inference of eukaryotic transcription factor sequence specificity
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 …
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 …
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 …
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
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 …
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
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 …
for their genomic targets. However, eukaryotic cells often express, at the same time, TFs with …
Disentangling the many layers of eukaryotic transcriptional regulation
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 …
review, we break down several critical steps, emphasizing new data and techniques that …