Ever-changing landscapes: transcriptional enhancers in development and evolution
HK Long, SL Prescott, J Wysocka - Cell, 2016 - cell.com
A class of cis-regulatory elements, called enhancers, play a central role in orchestrating
spatiotemporally precise gene-expression programs during development. Consequently …
spatiotemporally precise gene-expression programs during development. Consequently …
Transcription factor–DNA binding: beyond binding site motifs
S Inukai, KH Kock, ML Bulyk - Current opinion in genetics & development, 2017 - Elsevier
Sequence-specific transcription factors (TFs) regulate gene expression by binding to cis-
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …
G-quadruplexes are transcription factor binding hubs in human chromatin
Background The binding of transcription factors (TF) to genomic targets is critical in the
regulation of gene expression. Short, double-stranded DNA sequence motifs are routinely …
regulation of gene expression. Short, double-stranded DNA sequence motifs are routinely …
[HTML][HTML] Structural basis for Cas9 off-target activity
The target DNA specificity of the CRISPR-associated genome editor nuclease Cas9 is
determined by complementarity to a 20-nucleotide segment in its guide RNA. However …
determined by complementarity to a 20-nucleotide segment in its guide RNA. However …
Homeodomain proteins: an update
TR Bürglin, M Affolter - Chromosoma, 2016 - Springer
Here, we provide an update of our review on homeobox genes that we wrote together with
Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have …
Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have …
Low-affinity binding sites and the transcription factor specificity paradox in eukaryotes
JF Kribelbauer, C Rastogi… - Annual review of cell …, 2019 - annualreviews.org
Eukaryotic transcription factors (TFs) from the same structural family tend to bind similar DNA
sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell …
sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell …
Quantum annealing versus classical machine learning applied to a simplified computational biology problem
Transcription factors regulate gene expression, but how these proteins recognize and
specifically bind to their DNA targets is still debated. Machine learning models are effective …
specifically bind to their DNA targets is still debated. Machine learning models are effective …
Order through disorder: The role of intrinsically disordered regions in transcription factor binding specificity
Transcription factors (TFs) must bind at specific genomic locations to accurately regulate
gene expression. The ability of TFs to recognize specific DNA sequence motifs arises from …
gene expression. The ability of TFs to recognize specific DNA sequence motifs arises from …
Predicting DNA structure using a deep learning method
Understanding the mechanisms of protein-DNA binding is critical in comprehending gene
regulation. Three-dimensional DNA structure, also described as DNA shape, plays a key …
regulation. Three-dimensional DNA structure, also described as DNA shape, plays a key …
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo
Chromatin endogenous cleavage (ChEC) uses fusion of a protein of interest to micrococcal
nuclease (MNase) to target calcium-dependent cleavage to specific genomic loci in vivo …
nuclease (MNase) to target calcium-dependent cleavage to specific genomic loci in vivo …