Robust Hi-C chromatin loop maps in human neurogenesis and brain tissues at high-resolution
By
Leina Lu,
Xiaoxiao Liu,
Wei-Kai Huang,
Paola Giusti-Rodríguez,
Jian Cui,
Shanshan Zhang,
Wanying Xu,
Zhexing Wen,
Shufeng Ma,
Jonathan D Rosen,
Zheng Xu,
Cynthia Bartels,
Riki Kawaguchi,
Ming Hu,
Peter Scacheri,
Zhili Rong,
Yun Li,
Patrick F Sullivan,
Hongjun Song,
Guo-li Ming,
Yan Li,
Fulai Jin
Posted 22 Aug 2019
bioRxiv DOI: 10.1101/744540
Genome-wide mapping of chromatin interactions at high resolution remains experimentally and computationally challenging. Here we used a low-input “easy Hi-C” (eHi-C) protocol to map the 3D genome architecture in neurogenesis and brain tissues, and also developed an improved Hi-C bias-correction pipeline enabling better identification of enhancer loops or aggregates at sub-TAD level. We compared ultra-deep 3D genome maps from 10 human tissue- or cell types, with a focus on stem cells and neural development. We found several large loci in skin-derived human iPSC lines showing recurrent 3D compartmental memory of somatic heterochromatin. Chromatin loop interactions, but not genome compartments, are hallmarks of neural differentiation. Interestingly, we observed many cell type- or differentiation-specific enhancer aggregates spanning large neighborhoods, supporting a phase-separation mechanism that stabilizes enhancer contacts during development. Finally, we demonstrated that chromatin loop outperforms eQTL in explaining neurological GWAS results, revealing a unique value of high-resolution 3D genome maps in elucidating the disease etiology.
Download data
- Downloaded 1,305 times
- Download rankings, all-time:
- Site-wide: 14,159
- In genomics: 1,497
- Year to date:
- Site-wide: 13,189
- Since beginning of last month:
- Site-wide: 16,361
Altmetric data
Downloads over time
Distribution of downloads per paper, site-wide
PanLingua
News
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!