Understanding 3D genome organization by multidisciplinary methods

Nature Reviews Molecular Cell Biology, Journal Year: 2021, Volume and Issue: 22(8), P. 511 - 528

Published: May 5, 2021

Language: Английский

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Advances in targeting ‘undruggable’ transcription factors with small molecules

Nature Reviews Drug Discovery, Journal Year: 2021, Volume and Issue: 20(9), P. 669 - 688

Published: May 18, 2021

Language: Английский

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Beyond the RNA-dependent function of LncRNA genes

eLife, Journal Year: 2020, Volume and Issue: 9

Published: Oct. 23, 2020

While long non-coding RNA (lncRNA) genes have attracted a lot of attention in the last decade, focus regarding their mechanisms action has been primarily on product these genes. Recent work several lncRNAs demonstrates that not only is produced species important, but also transcription lncRNA locus alone can regulatory functions. Like functions transcripts, underlie genome-based are varied. Here we highlight some examples and provide an outlook how functional gene be determined.

Language: Английский

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Biomarkers of aging

Science China Life Sciences, Journal Year: 2023, Volume and Issue: 66(5), P. 893 - 1066

Published: April 11, 2023

Language: Английский

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Nuclear compartmentalization as a mechanism of quantitative control of gene expression

Nature Reviews Molecular Cell Biology, Journal Year: 2021, Volume and Issue: 22(10), P. 653 - 670

Published: Aug. 2, 2021

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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Regulation of single-cell genome organization into TADs and chromatin nanodomains

Nature Genetics, Journal Year: 2020, Volume and Issue: 52(11), P. 1151 - 1157

Published: Oct. 19, 2020

Language: Английский

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Stabilization of chromatin topology safeguards genome integrity

Nature, Journal Year: 2019, Volume and Issue: 574(7779), P. 571 - 574

Published: Oct. 23, 2019

Language: Английский

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Machine learning for multi-omics data integration in cancer

iScience, Journal Year: 2022, Volume and Issue: 25(2), P. 103798 - 103798

Published: Jan. 22, 2022

Multi-omics data analysis is an important aspect of cancer molecular biology studies and has led to ground-breaking discoveries. Many efforts have been made develop machine learning methods that automatically integrate omics data. Here, we review tools categorized as either general-purpose or task-specific, covering both supervised unsupervised for integrative multi-omics We benchmark the performance five approaches using from Cancer Cell Line Encyclopedia, reporting accuracy on type classification mean absolute error drug response prediction, evaluating runtime efficiency. This provides recommendations researchers regarding suitable method selection their specific applications. It should also promote development novel methodologies integration, which will be essential discovery, clinical trial design, personalized treatments.

Language: Английский

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Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers

Cell Reports, Journal Year: 2020, Volume and Issue: 32(3), P. 107929 - 107929

Published: July 1, 2020

It is currently assumed that 3D chromosomal organization plays a central role in transcriptional control. However, depletion of cohesin and CTCF affects the steady-state levels only minority transcripts. Here, we use high-resolution Capture Hi-C to interrogate dynamics contacts all annotated human gene promoters upon degradation CTCF. We show majority promoter-anchored are lost these conditions, but many with distinct properties maintained, some new ones gained. The rewiring between active enhancers associates rapid changes target transcription as detected by SLAM sequencing (SLAM-seq). These results provide mechanistic explanation for limited, consistent, effects on suggest existence both cohesin-dependent -independent mechanisms enhancer-promoter pairing.

Language: Английский

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