The Self-Organizing Genome: Principles of Genome Architecture and Function

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

Published: Sept. 24, 2020

Language: Английский

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Mechanisms of enhancer action: the known and the unknown

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: April 15, 2021

Abstract Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic phylogenetic diversity of cell types. A key regulator differential programs are the enhancers, gene-distal cis -regulatory sequences that govern spatiotemporal quantitative dynamics target genes. Enhancers widely believed physically contact promoters effect transcriptional activation. However, our understanding full complement regulatory proteins definitive mechanics enhancer action is incomplete. Here, we review recent findings present some emerging concepts on also outline a set outstanding questions.

Language: Английский

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Structure and mechanism of the RNA polymerase II transcription machinery

Genes & Development, Journal Year: 2020, Volume and Issue: 34(7-8), P. 465 - 488

Published: April 1, 2020

RNA polymerase II (Pol II) transcribes all protein-coding genes and many noncoding RNAs in eukaryotic genomes. Although Pol is a complex, 12-subunit enzyme, it lacks the ability to initiate transcription cannot consistently transcribe through long DNA sequences. To execute these essential functions, an array of proteins protein complexes interact with regulate its activity. In this review, we detail structure mechanism over dozen factors that govern initiation (e.g., TFIID, TFIIH, Mediator), pausing, elongation DSIF, NELF, PAF, P-TEFb). The structural basis for regulation has advanced rapidly past decade, largely due technological innovations cryoelectron microscopy. Here, summarize wealth functional data have enabled deeper understanding mechanisms; also highlight mechanistic questions remain unanswered or controversial.

Language: Английский

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Transcription in Living Cells: Molecular Mechanisms of Bursting

Annual Review of Biochemistry, Journal Year: 2020, Volume and Issue: 89(1), P. 189 - 212

Published: March 25, 2020

Transcription in several organisms from certain bacteria to humans has been observed be stochastic nature: toggling between active and inactive states. Periods of nascent RNA synthesis known as bursts represent individual gene activation events which multiple polymerases are initiated. Therefore, bursting is the single locus illustration both repression. Although transcriptional was originally decades ago, only recently have technological advances enabled field begin elucidating regulation at single-locus level. In this review, we focus on how biochemical, genomic, single-cell data describe regulatory steps bursts.

Language: Английский

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The Mediator complex as a master regulator of transcription by RNA polymerase II

Nature Reviews Molecular Cell Biology, Journal Year: 2022, Volume and Issue: 23(11), P. 732 - 749

Published: June 20, 2022

Language: Английский

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What Is a Transcriptional Burst?

Trends in Genetics, Journal Year: 2020, Volume and Issue: 36(4), P. 288 - 297

Published: Feb. 5, 2020

Language: Английский

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An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors

Molecular Cell, Journal Year: 2021, Volume and Issue: 81(7), P. 1484 - 1498.e6

Published: Feb. 8, 2021

Language: Английский

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“Structure”-function relationships in eukaryotic transcription factors: The role of intrinsically disordered regions in gene regulation

Molecular Cell, Journal Year: 2022, Volume and Issue: 82(21), P. 3970 - 3984

Published: Oct. 19, 2022

Language: Английский

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Illuminating RNA biology through imaging

Nature Cell Biology, Journal Year: 2022, Volume and Issue: 24(6), P. 815 - 824

Published: June 1, 2022

Language: Английский

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Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions

Molecular Cell, Journal Year: 2023, Volume and Issue: 83(8), P. 1251 - 1263.e6

Published: March 29, 2023

Language: Английский

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