Deciphering the multi-scale, quantitative cis-regulatory code
S Kim, J Wysocka - Molecular cell, 2023 - cell.com
Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …
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 …
Evolutionary constraint and innovation across hundreds of placental mammals
Zoonomia is the largest comparative genomics resource for mammals produced to date. By
aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect …
aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect …
Potent and uniform fetal hemoglobin induction via base editing
Inducing fetal hemoglobin (HbF) in red blood cells can alleviate β-thalassemia and sickle
cell disease. We compared five strategies in CD34+ hematopoietic stem and progenitor …
cell disease. We compared five strategies in CD34+ hematopoietic stem and progenitor …
Expanded encyclopaedias of DNA elements in the human and mouse genomes
The human and mouse genomes contain instructions that specify RNAs and proteins and
govern the timing, magnitude, and cellular context of their production. To better delineate …
govern the timing, magnitude, and cellular context of their production. To better delineate …
A stromal Integrated Stress Response activates perivascular cancer-associated fibroblasts to drive angiogenesis and tumour progression
II Verginadis, H Avgousti, J Monslow, G Skoufos… - Nature cell …, 2022 - nature.com
Bidirectional signalling between the tumour and stroma shapes tumour aggressiveness and
metastasis. ATF4 is a major effector of the Integrated Stress Response, a homeostatic …
metastasis. ATF4 is a major effector of the Integrated Stress Response, a homeostatic …
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 …
cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that …
Global reference mapping of human transcription factor footprints
J Vierstra, J Lazar, R Sandstrom, J Halow, K Lee… - Nature, 2020 - nature.com
Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation
in all organisms. Genetic variation in regulatory regions has been connected with diseases …
in all organisms. Genetic variation in regulatory regions has been connected with diseases …
hTFtarget: a comprehensive database for regulations of human transcription factors and their targets
Transcription factors (TFs) as key regulators play crucial roles in biological processes. The
identification of TF–target regulatory relationships is a key step for revealing functions of TFs …
identification of TF–target regulatory relationships is a key step for revealing functions of TFs …
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
There is pressing urgency to understand the pathogenesis of the severe acute respiratory
syndrome coronavirus clade 2 (SARS-CoV-2), which causes the disease COVID-19. SARS …
syndrome coronavirus clade 2 (SARS-CoV-2), which causes the disease COVID-19. SARS …