Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes DOI Open Access
Judith F. Kribelbauer, Chaitanya Rastogi, Harmen J. Bussemaker

et al.

Annual Review of Cell and Developmental Biology, Journal Year: 2019, Volume and Issue: 35(1), P. 357 - 379

Published: July 8, 2019

Eukaryotic transcription factors (TFs) from the same structural family tend to bind similar DNA sequences, despite ability of these TFs execute distinct functions in vivo. The cell partly resolves this specificity paradox through combinatorial strategies and use low-affinity binding sites, which are better able distinguish between TFs. However, because sites have low affinity, it is challenging understand how recognize them Here, we summarize recent findings technological advancements that allow for quantification mechanistic interpretation TF recognition across a wide range affinities. We propose model integrates insights fields genetics biology provide further conceptual understanding specificity. argue eukaryotes, target driven by an inhomogeneous 3D nuclear distribution variation affinity such locally elevated concentration allows be functional.

Language: Английский

RNA modifications modulate gene expression during development DOI Open Access
Michaela Frye, Bryan T. Harada, Mikaela Behm

et al.

Science, Journal Year: 2018, Volume and Issue: 361(6409), P. 1346 - 1349

Published: Sept. 28, 2018

RNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programs. They affect diverse eukaryotic biological processes, and the correct deposition many these is required for normal development. Messenger (mRNA) regulate various aspects mRNA metabolism. For example,

Language: Английский

Citations

977

Long-range enhancer–promoter contacts in gene expression control DOI
Stefan Schoenfelder, Peter Fraser

Nature Reviews Genetics, Journal Year: 2019, Volume and Issue: 20(8), P. 437 - 455

Published: May 13, 2019

Language: Английский

Citations

946

Quantitative Proteomics of the Cancer Cell Line Encyclopedia DOI Creative Commons
David P. Nusinow,

John Szpyt,

Mahmoud Ghandi

et al.

Cell, Journal Year: 2020, Volume and Issue: 180(2), P. 387 - 402.e16

Published: Jan. 1, 2020

Language: Английский

Citations

826

Organization and regulation of gene transcription DOI
Patrick Cramer

Nature, Journal Year: 2019, Volume and Issue: 573(7772), P. 45 - 54

Published: Aug. 28, 2019

Language: Английский

Citations

618

Determinants of enhancer and promoter activities of regulatory elements DOI
Robin Andersson, Albin Sandelin

Nature Reviews Genetics, Journal Year: 2019, Volume and Issue: 21(2), P. 71 - 87

Published: Oct. 11, 2019

Language: Английский

Citations

601

The Self-Organizing Genome: Principles of Genome Architecture and Function DOI Creative Commons
Tom Misteli

Cell, Journal Year: 2020, Volume and Issue: 183(1), P. 28 - 45

Published: Sept. 24, 2020

Language: Английский

Citations

553

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding DOI Creative Commons
Tsung-Han S. Hsieh, Claudia Cattoglio, Elena Slobodyanyuk

et al.

Molecular Cell, Journal Year: 2020, Volume and Issue: 78(3), P. 539 - 553.e8

Published: March 25, 2020

Language: Английский

Citations

545

Transcription factors and 3D genome conformation in cell-fate decisions DOI
Ralph Stadhouders, Guillaume J. Filion, Thomas Graf

et al.

Nature, Journal Year: 2019, Volume and Issue: 569(7756), P. 345 - 354

Published: May 15, 2019

Language: Английский

Citations

471

Liquid–liquid phase separation in human health and diseases DOI Creative Commons
Bin Wang, Lei Zhang, Tong Dai

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2021, Volume and Issue: 6(1)

Published: Aug. 1, 2021

Abstract Emerging evidence suggests that liquid–liquid phase separation (LLPS) represents a vital and ubiquitous phenomenon underlying the formation of membraneless organelles in eukaryotic cells (also known as biomolecular condensates or droplets). Recent studies have revealed evidences indicate LLPS plays role human health diseases. In this review, we describe our current understanding summarize its physiological functions. We further development Additionally, review recently developed methods for studying LLPS. Although research is infancy—but fast-growing—it clear an essential pathophysiological conditions. This highlights need overview recent advances field to translate knowledge regarding into therapeutic discoveries.

Language: Английский

Citations

450

Visualizing DNA folding and RNA in embryos at single-cell resolution DOI

Leslie J. Mateo,

Sedona E. Murphy, Antonina Hafner

et al.

Nature, Journal Year: 2019, Volume and Issue: 568(7750), P. 49 - 54

Published: March 18, 2019

Language: Английский

Citations

397