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 …

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 …

Large-scale map** and mutagenesis of human transcriptional effector domains

N DelRosso, J Tycko, P Suzuki, C Andrews, Aradhana… - Nature, 2023 - nature.com
Human gene expression is regulated by more than 2,000 transcription factors and chromatin
regulators,. Effector domains within these proteins can activate or repress transcription …

[HTML][HTML] Hox genes in development and beyond

KA Hubert, DM Wellik - Development, 2023 - journals.biologists.com
Hox genes encode evolutionarily conserved transcription factors that are essential for the
proper development of bilaterian organisms. Hox genes are unique because they are …

Absence of a simple code: how transcription factors read the genome

M Slattery, T Zhou, L Yang, ACD Machado… - Trends in biochemical …, 2014 - cell.com
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …

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 …

Low affinity binding site clusters confer hox specificity and regulatory robustness

J Crocker, N Abe, L Rinaldi, AP McGregor, N Frankel… - Cell, 2015 - cell.com
In animals, Hox transcription factors define regional identity in distinct anatomical domains.
How Hox genes encode this specificity is a paradox, because different Hox proteins bind …

Origins of specificity in protein-DNA recognition

R Rohs, X **, SM West, R Joshi… - Annual review of …, 2010 - annualreviews.org
Specific interactions between proteins and DNA are fundamental to many biological
processes. In this review, we provide a revised view of protein-DNA interactions that …

[HTML][HTML] Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins

M Slattery, T Riley, P Liu, N Abe, P Gomez-Alcala… - Cell, 2011 - cell.com
Members of transcription factor families typically have similar DNA binding specificities yet
execute unique functions in vivo. Transcription factors often bind DNA as multiprotein …

Hox genes: choreographers in neural development, architects of circuit organization

P Philippidou, JS Dasen - Neuron, 2013 - cell.com
The neural circuits governing vital behaviors, such as respiration and locomotion, are
comprised of discrete neuronal populations residing within the brainstem and spinal cord …