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INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis

Yadav, Vikash Kumar and Santos-Gonzalez, Juan and Köhler, Claudia (2021). INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis. Nucleic Acids Research. 49 , 4371-4385
[Research article]

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Abstract

Higher-order chromatin structure undergoes striking changes in response to various developmental and environmental signals, causing distinct cell types to adopt specific chromatin organization. High throughput chromatin conformation capture (Hi-C) allows studying higher-order chromatin structure; however, this technique requires substantial amounts of starting material, which has limited the establishment of cell type-specific higher-order chromatin structure in plants. To overcome this limitation, we established a protocol that is applicable to a limited amount of nuclei by combining the INTACT (isolation of nuclei tagged in specific cell types) method and Hi-C (INT-Hi-C). Using this INT-Hi-C protocol, we generated Hi-C data from INTACT purified endosperm and leaf nuclei. Our INT-Hi-C data from leaf accurately reiterated chromatin interaction patterns derived from conventional leaf Hi-C data. We found that the higher-order chromatin organization of mixed leaf tissues and endosperm differs and that DNA methylation and repressive histone marks positively correlate with the chromatin compaction level. We furthermore found that self-looped interacting genes have increased expression in leaves and endosperm and that interacting intergenic regions negatively impact on gene expression in the endosperm. Last, we identified several imprinted genes involved in long-range and trans interactions exclusively in endosperm. Our study provides evidence that the endosperm adopts a distinct higher-order chromatin structure that differs from other cell types in plants and that chromatin interactions influence transcriptional activity.

Authors/Creators:Yadav, Vikash Kumar and Santos-Gonzalez, Juan and Köhler, Claudia
Title:INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis
Series Name/Journal:Nucleic Acids Research
Year of publishing :2021
Volume:49
Page range:4371-4385
Number of Pages:15
Publisher:OXFORD UNIV PRESS
ISSN:0305-1048
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution-Noncommercial 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Developmental Biology
URN:NBN:urn:nbn:se:slu:epsilon-p-112242
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-112242
Additional ID:
Type of IDID
DOI10.1093/nar/gkab191
Web of Science (WoS)000654670600018
ID Code:24508
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Plant Biology and Forest Genetics (until 131231)
Deposited By: SLUpub Connector
Deposited On:11 Jun 2021 06:43
Metadata Last Modified:11 Jun 2021 06:51

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