Joint profiling of DNA methylation and chromatin architecture in single cells.

Nature Methods
Guoqiang LiBing Ren

Abstract

We report a molecular assay, Methyl-HiC, that can simultaneously capture the chromosome conformation and DNA methylome in a cell. Methyl-HiC reveals coordinated DNA methylation status between distal genomic segments that are in spatial proximity in the nucleus, and delineates heterogeneity of both the chromatin architecture and DNA methylome in a mixed population. It enables simultaneous characterization of cell-type-specific chromatin organization and epigenome in complex tissues.

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Citations

May 13, 2020·Science China. Life Sciences·Yan Zhang, Guoliang Li
Nov 7, 2019·Nature Structural & Molecular Biology·Chenxu ZhuBing Ren
Jun 26, 2020·Genome Medicine·Florian ErgerJanine Altmüller
Jan 8, 2020·Nature Methods·Chenxu ZhuBing Ren
Nov 6, 2020·Transcription·Nahyun Kong, Inkyung Jung
Nov 28, 2020·Nature Reviews. Genetics·Benjamin Carter, Keji Zhao
Jan 8, 2021·Neuron·Ethan J ArmandEran A Mukamel
Oct 28, 2020·Computational and Structural Biotechnology Journal·Geyang LuoBo Yan
Jul 10, 2020·Methods : a Companion to Methods in Enzymology·Yuanyuan Li
Nov 27, 2020·Journal of Molecular and Cellular Cardiology·Alessandro Bertero, Manuel Rosa-Garrido
Dec 18, 2020·Frontiers in Genetics·Tingting GuoXuyu Cai
Dec 18, 2020·Nature Reviews. Urology·Michael C HaffnerSrinivasan Yegnasubramanian
Feb 13, 2021·Bioinformatics·Dejun LinWilliam Stafford Noble
Feb 10, 2021·The New Phytologist·Liuling PeiMaojun Wang
Mar 7, 2021·Briefings in Functional Genomics·Anastasia Labudina, Julia A Horsfield
Feb 24, 2021·Nature Reviews. Molecular Cell Biology·Haofei WangLi Qian
Mar 26, 2021·Genome Biology·Roy RabbieDavid J Adams
Mar 30, 2021·Frontiers in Genetics·Xuefei YuanMichael D Wilson
Aug 21, 2020·Trends in Biotechnology·Anjun MaQin Ma
Apr 25, 2021·Trends in Genetics : TIG·Arnaud R Krebs
May 7, 2021·Nature Reviews. Molecular Cell Biology·Ivana Jerkovic, Giacomo Cavalli
May 11, 2021·Briefings in Functional Genomics·Xianjun DongMikhail Dozmorov
May 14, 2021·Developmental Cell·Erin Aboelnour, Boyan Bonev
May 19, 2021·The Plant Journal : for Cell and Molecular Biology·Leonie Verhage
May 18, 2021·Frontiers in Cell and Developmental Biology·Wojciech J SzlachcicMalgorzata Borowiak
Jul 11, 2021·Nature Protocols·Hongcang GuAndreas Gnirke
Aug 10, 2021·Frontiers in Cell and Developmental Biology·Mahya MehrmohamadiMohammad Reza Norouzi
Aug 19, 2021·Briefings in Bioinformatics·Aleksandra A Galitsyna, Mikhail S Gelfand
Aug 29, 2021·Pharmaceuticals·Marcin JanowskiAleksandra Pękowska
Aug 25, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Daijing SunYan Jiang
Mar 17, 2021·Annual Review of Genomics and Human Genetics·Gilad D EvronyChongyuan Luo
Sep 2, 2021·Annual Review of Biomedical Data Science·Tianming ZhouJian Ma
Aug 31, 2021·RSC Chemical Biology·Dongsheng BaiChengqi Yi
Oct 13, 2021·Nature Biotechnology·Ruochi ZhangJian Ma
Nov 5, 2021·Scientific Reports·Jordi AbanteJohn Goutsias
Oct 9, 2021·Bioinformatics·Yang XuRachel Patton McCord
Nov 26, 2021·Immunological Reviews·Zewen Kelvin TuongMenna R Clatworthy

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Methods Mentioned

BETA
WGBS
Hi-C
Methyl-HiC
proximity ligation
scMethyl-HiC
single-cell Hi-C
FACS
PCR

Software Mentioned

Rtsne package
BWA
GREAT genomic regions enrichment of annotations
HiCCUPS
R package ‘ cocor ’
HiC
tSNE
scMethyl
Picard
R

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