Understanding 3D genome organization by multidisciplinary methods

Nature Reviews Molecular Cell Biology, Год журнала: 2021, Номер 22(8), С. 511 - 528

Опубликована: Май 5, 2021

Язык: Английский

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Advances in targeting ‘undruggable’ transcription factors with small molecules

Nature Reviews Drug Discovery, Год журнала: 2021, Номер 20(9), С. 669 - 688

Опубликована: Май 18, 2021

Язык: Английский

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Beyond the RNA-dependent function of LncRNA genes

eLife, Год журнала: 2020, Номер 9

Опубликована: Окт. 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.

Язык: Английский

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Biomarkers of aging

Science China Life Sciences, Год журнала: 2023, Номер 66(5), С. 893 - 1066

Опубликована: Апрель 11, 2023

Язык: Английский

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Nuclear compartmentalization as a mechanism of quantitative control of gene expression

Nature Reviews Molecular Cell Biology, Год журнала: 2021, Номер 22(10), С. 653 - 670

Опубликована: Авг. 2, 2021

Язык: Английский

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

Nature Reviews Molecular Cell Biology, Год журнала: 2022, Номер 23(11), С. 732 - 749

Опубликована: Июнь 20, 2022

Язык: Английский

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

Nature Genetics, Год журнала: 2020, Номер 52(11), С. 1151 - 1157

Опубликована: Окт. 19, 2020

Язык: Английский

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Stabilization of chromatin topology safeguards genome integrity

Nature, Год журнала: 2019, Номер 574(7779), С. 571 - 574

Опубликована: Окт. 23, 2019

Язык: Английский

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Machine learning for multi-omics data integration in cancer

iScience, Год журнала: 2022, Номер 25(2), С. 103798 - 103798

Опубликована: Янв. 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.

Язык: Английский

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

Cell Reports, Год журнала: 2020, Номер 32(3), С. 107929 - 107929

Опубликована: Июль 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.

Язык: Английский

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