Chrom-seq identifies RNAs at chromatin marks

Ligang Fan; Wei Sun; Yitong Lyu; Furong Ju; Wenju Sun; Jie Chen; Haiqian Ma; Shifei Yang; Xiaomin Zhou; Nan Wu; Wenkai Yi; Erfei Chen; Rodrigo Villaseñor; Tuncay Baubec; Jian Yan

doi:10.1126/sciadv.adn1397

Chrom-seq identifies RNAs at chromatin marks

Ligang Fan (Co-first Author), Wei Sun (Co-first Author), Yitong Lyu, Furong Ju, Wenju Sun, Jie Chen, Haiqian Ma, Shifei Yang, Xiaomin Zhou, Nan Wu, Wenkai Yi, Erfei Chen, Rodrigo Villaseñor, Tuncay Baubec, Jian Yan^*

^*Corresponding author for this work

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

7 Citations (Scopus)

25 Downloads (CityUHK Scholars)

Abstract

Chromatin marks are associated with transcriptional regulatory activities. However, very few lncRNAs have been characterized with the role in regulating epigenetic marks, largely due to the technical difficulty in identifying chromatin-associating RNA. Current methods are largely limited by the availability of ChIP-grade antibody and the crosslinking, which generates high noise. Here, we developed a method termed Chrom-seq to efficiently capture RNAs associated with various chromatin marks in living cells. Chrom-seq jointly applies highly specific chromatin mark reader with APEX2, which catalyzes the oxidation of biotin-aniline to label the adjacent RNAs for isolation by streptavidin-coated beads. Using the readers of mCBX7/dPC, mCBX1, and mTAF3, we detected RNA species significantly associated with H3K27me3, H3K9me3, and H3K4me3, respectively. We demonstrated that Chrom-seq outperformed other equivalent methods in terms of sensitivity, efficiency, and cost of practice. It provides an antibody-free approach to systematically map RNAs at chromatin marks with potential regulatory roles in epigenetic events. Copyright © 2024 The Authors, some rights reserved

Original language	English
Article number	eadn1397
Number of pages	13
Journal	Science Advances
Volume	10
Issue number	31
Online published	31 Jul 2024
DOIs	https://doi.org/10.1126/sciadv.adn1397
Publication status	Published - Aug 2024

Funding

This work was supported by the National Natural Science Foundation of China (32070596, 32100468, and 32270634), Shenzhen Medical Research Fund (B2302027), the Research Grants Council of Hong Kong (21100420 and 11101022), the Innovation and Technology Commission of Hong Kong (ITS/087/22), the Shaanxi Academy of Fundamental Sciences (Chemistry & Biology) (22JHZ009), and City University of Hong Kong (9610618, 9667240, and 7006043).

Research Keywords

Chromatin/metabolism
Humans
Histones/metabolism
RNA/metabolism
Epigenesis, Genetic
Sequence Analysis, RNA/methods

Publisher's Copyright Statement

This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/

RGC Funding Information

RGC-funded

Access Output

10.1126/sciadv.adn1397

232063819.pdfFinal Published version, 1.46 MBLicence: CC BY

Other Access Options

Check CityUHK Library

Permanent Link

Right click to copy link

Cite this

@article{3ac64a8b4aca43e481fb9478b22a5e83,

title = "Chrom-seq identifies RNAs at chromatin marks",

abstract = "Chromatin marks are associated with transcriptional regulatory activities. However, very few lncRNAs have been characterized with the role in regulating epigenetic marks, largely due to the technical difficulty in identifying chromatin-associating RNA. Current methods are largely limited by the availability of ChIP-grade antibody and the crosslinking, which generates high noise. Here, we developed a method termed Chrom-seq to efficiently capture RNAs associated with various chromatin marks in living cells. Chrom-seq jointly applies highly specific chromatin mark reader with APEX2, which catalyzes the oxidation of biotin-aniline to label the adjacent RNAs for isolation by streptavidin-coated beads. Using the readers of mCBX7/dPC, mCBX1, and mTAF3, we detected RNA species significantly associated with H3K27me3, H3K9me3, and H3K4me3, respectively. We demonstrated that Chrom-seq outperformed other equivalent methods in terms of sensitivity, efficiency, and cost of practice. It provides an antibody-free approach to systematically map RNAs at chromatin marks with potential regulatory roles in epigenetic events. Copyright {\textcopyright} 2024 The Authors, some rights reserved",

keywords = "Chromatin/metabolism, Humans, Histones/metabolism, RNA/metabolism, Epigenesis, Genetic, Sequence Analysis, RNA/methods",

author = "Ligang Fan and Wei Sun and Yitong Lyu and Furong Ju and Wenju Sun and Jie Chen and Haiqian Ma and Shifei Yang and Xiaomin Zhou and Nan Wu and Wenkai Yi and Erfei Chen and Rodrigo Villase{\~n}or and Tuncay Baubec and Jian Yan",

year = "2024",

month = aug,

doi = "10.1126/sciadv.adn1397",

language = "English",

volume = "10",

journal = "Science Advances",

issn = "2375-2548",

publisher = "American Association for the Advancement of Science",

number = "31",

}

TY - JOUR

T1 - Chrom-seq identifies RNAs at chromatin marks

AU - Fan, Ligang

AU - Sun, Wei

AU - Lyu, Yitong

AU - Ju, Furong

AU - Sun, Wenju

AU - Chen, Jie

AU - Ma, Haiqian

AU - Yang, Shifei

AU - Zhou, Xiaomin

AU - Wu, Nan

AU - Yi, Wenkai

AU - Chen, Erfei

AU - Villaseñor, Rodrigo

AU - Baubec, Tuncay

AU - Yan, Jian

PY - 2024/8

Y1 - 2024/8

N2 - Chromatin marks are associated with transcriptional regulatory activities. However, very few lncRNAs have been characterized with the role in regulating epigenetic marks, largely due to the technical difficulty in identifying chromatin-associating RNA. Current methods are largely limited by the availability of ChIP-grade antibody and the crosslinking, which generates high noise. Here, we developed a method termed Chrom-seq to efficiently capture RNAs associated with various chromatin marks in living cells. Chrom-seq jointly applies highly specific chromatin mark reader with APEX2, which catalyzes the oxidation of biotin-aniline to label the adjacent RNAs for isolation by streptavidin-coated beads. Using the readers of mCBX7/dPC, mCBX1, and mTAF3, we detected RNA species significantly associated with H3K27me3, H3K9me3, and H3K4me3, respectively. We demonstrated that Chrom-seq outperformed other equivalent methods in terms of sensitivity, efficiency, and cost of practice. It provides an antibody-free approach to systematically map RNAs at chromatin marks with potential regulatory roles in epigenetic events. Copyright © 2024 The Authors, some rights reserved

AB - Chromatin marks are associated with transcriptional regulatory activities. However, very few lncRNAs have been characterized with the role in regulating epigenetic marks, largely due to the technical difficulty in identifying chromatin-associating RNA. Current methods are largely limited by the availability of ChIP-grade antibody and the crosslinking, which generates high noise. Here, we developed a method termed Chrom-seq to efficiently capture RNAs associated with various chromatin marks in living cells. Chrom-seq jointly applies highly specific chromatin mark reader with APEX2, which catalyzes the oxidation of biotin-aniline to label the adjacent RNAs for isolation by streptavidin-coated beads. Using the readers of mCBX7/dPC, mCBX1, and mTAF3, we detected RNA species significantly associated with H3K27me3, H3K9me3, and H3K4me3, respectively. We demonstrated that Chrom-seq outperformed other equivalent methods in terms of sensitivity, efficiency, and cost of practice. It provides an antibody-free approach to systematically map RNAs at chromatin marks with potential regulatory roles in epigenetic events. Copyright © 2024 The Authors, some rights reserved

KW - Chromatin/metabolism

KW - Humans

KW - Histones/metabolism

KW - RNA/metabolism

KW - Epigenesis, Genetic

KW - Sequence Analysis, RNA/methods

UR - http://www.scopus.com/inward/record.url?scp=85200306058&partnerID=8YFLogxK

UR - https://www.scopus.com/record/pubmetrics.uri?eid=2-s2.0-85200306058&origin=recordpage

U2 - 10.1126/sciadv.adn1397

DO - 10.1126/sciadv.adn1397

M3 - RGC 21 - Publication in refereed journal

C2 - 39083617

SN - 2375-2548

VL - 10

JO - Science Advances

JF - Science Advances

IS - 31

M1 - eadn1397

ER -

Chrom-seq identifies RNAs at chromatin marks

Abstract

Funding

Research Keywords

Publisher's Copyright Statement

RGC Funding Information

Access Output

Other Access Options

Permanent Link

Other Files and Links

Fingerprint

GRF: Unravelling the Molecular Mechanism of DNA Demethylation around CTCF Binding Sites in Mammalian Cells

ITF: Developing A Method for Efficient Detection of Binding Proteins of Specific RNA in Cells and Tissues

ECS: Dissect the Molecular Mechanisms of HERV-H Mediated Shaping of Chromatin 3D Structure in Human Pluripotent Stem Cells

Cite this

Chrom-seq identifies RNAs at chromatin marks

Abstract

Funding

Research Keywords

Publisher's Copyright Statement

RGC Funding Information

Access Output

Other Access Options

Permanent Link

Other Files and Links

Fingerprint

Projects

GRF: Unravelling the Molecular Mechanism of DNA Demethylation around CTCF Binding Sites in Mammalian Cells

ITF: Developing A Method for Efficient Detection of Binding Proteins of Specific RNA in Cells and Tissues

ECS: Dissect the Molecular Mechanisms of HERV-H Mediated Shaping of Chromatin 3D Structure in Human Pluripotent Stem Cells

Cite this