Unveiling Multi‐Scale Architectural Features in Single‐Cell Hi‐C Data Using scCAFE

Advanced Science, Год журнала: 2025, Номер unknown

Опубликована: Апрель 24, 2025

Abstract Single‐cell Hi‐C (scHi‐C) has provided unprecedented insights into the heterogeneity of 3D genome organization. However, its sparse and noisy nature poses challenges for computational analyses, such as chromatin architectural feature identification. Here, scCAFE is introduced, which a deep learning model multi‐scale detection features at single‐cell level. provides unified framework annotating loops, TAD‐like domains (TLDs), compartments across individual cells. This outperforms previous scHi‐C loop calling methods delivers accurate predictions TLDs that are biologically consistent with studies. The resulting annotations also offer measure to characterize different levels cell types. then leveraged identify series marker anchors, demontrating potential data annotate identities without aid simultaneously sequenced omics data. Overall, not only serves useful tool analyzing genomic architecture, but paves way precise cell‐type solely based on features.

Язык: Английский

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Tri-omic single-cell mapping of the 3D epigenome and transcriptome in whole mouse brains throughout the lifespan

Nature Methods, Год журнала: 2025, Номер unknown

Опубликована: Апрель 29, 2025

Язык: Английский

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Reorganization of the heterochromatin-associated gene-dense subcompartment in early neuronal development

Biology Open, Год журнала: 2025, Номер 14(5)

Опубликована: Май 12, 2025

ABSTRACT The 3D organization of the genome has emerged as an important regulator cellular development. Post-mitotic neurons undergo conserved changes in organization, such inward radial repositioning heterochromatin-rich chromosomes they differentiate. Additionally, transcriptionally active but heterochromatin-associated gene-dense (hGD) regions significantly strengthen their long-distance interactions during cerebellar However, specific developmental stages which these nuclear take place have remained poorly defined. Here, we report that hGD relocalize toward interior and chromosomal immature granule transition from cell migration to subsequent neuronal differentiation. During this period, genomic are coordinately repositioned nucleus alongside physically tethered heterochromatic chromocenters. Despite major subcompartment remains distinct other or repressive bodies, including chromocenters, throughout Notably, appear be independent transcriptional occur neuron Together, our results provide insights into timing structural post-mitotic neurons.

Язык: Английский

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Solid phase transitions as a solution to the genome folding paradox

Nature, Год журнала: 2025, Номер unknown

Опубликована: Май 14, 2025

Язык: Английский

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Spatiotemporal 3D chromatin organization across multiple brain regions during human fetal development

Cell Discovery, Год журнала: 2025, Номер 11(1)

Опубликована: Май 16, 2025

Язык: Английский

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