Annotation of nuclear lncRNAs based on chromatin interactions

Saumya Agrawal; Andrey Buyan; Jessica Severin; Masaru Koido; Tanvir Alam; Imad Abugessaisa; Howard Y. Chang; Josee Dostie; Masayoshi Itoh; Juha Kere; Naoto Kondo; Yunjing Li; Vsevolod J. Makeev; Mickael Mendez; Yasushi Okazaki; Jordan A. Ramilowski; Andrey I. Sigorskikh; Lisa J. Strug; Ken Yagi; Kayoko Yasuzawa; Chi Wai Yip; Chung Chau Hon; Michael M. Hoffman; Chikashi Terao; Ivan V. Kulakovskiy; Takeya Kasukawa; Jay W. Shin; Piero Carninci; Michiel J. L. de Hoon

doi:10.1371/journal.pone.0295971

Annotation of nuclear lncRNAs based on chromatin interactions

Saumya Agrawal, Andrey Buyan, Jessica Severin, Masaru Koido, Tanvir Alam, Imad Abugessaisa, Howard Y. Chang, Josee Dostie, Masayoshi Itoh, Juha Kere, Naoto Kondo, Yunjing Li, Vsevolod J. Makeev, Mickael Mendez, Yasushi Okazaki, Jordan A. Ramilowski, Andrey I. Sigorskikh, Lisa J. Strug, Ken Yagi, Kayoko YasuzawaChi Wai Yip, Chung Chau Hon, Michael M. Hoffman, Chikashi Terao, Ivan V. Kulakovskiy, Takeya Kasukawa, Jay W. Shin, Piero Carninci, Michiel J. L. de Hoon

CSE Information & Computing Technology

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA.

Original language	English
Article number	e0295971
Number of pages	24
Journal	PLoS ONE
Volume	19
Issue number	5
DOIs	https://doi.org/10.1371/journal.pone.0295971
Publication status	Published - 6 May 2024

Keywords

Long noncoding rnas
Set enrichment analysis
Susceptibility loci
Gene-expression
Transcription
Reveals
Binding
Database
Architecture
Genomics

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10.1371/journal.pone.0295971

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Agrawal, S., Buyan, A., Severin, J., Koido, M., Alam, T., Abugessaisa, I., Chang, H. Y., Dostie, J., Itoh, M., Kere, J., Kondo, N., Li, Y., Makeev, V. J., Mendez, M., Okazaki, Y., Ramilowski, J. A., Sigorskikh, A. I., Strug, L. J., Yagi, K., ... de Hoon, M. J. L. (2024). Annotation of nuclear lncRNAs based on chromatin interactions. PLoS ONE, 19(5), Article e0295971. https://doi.org/10.1371/journal.pone.0295971

@article{8d19f3cda71e4b758fc35e2cef5468b4,

title = "Annotation of nuclear lncRNAs based on chromatin interactions",

abstract = "The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/\#F6\_3D\_lncRNA.",

keywords = "Long noncoding rnas, Set enrichment analysis, Susceptibility loci, Gene-expression, Transcription, Reveals, Binding, Database, Architecture, Genomics",

author = "Saumya Agrawal and Andrey Buyan and Jessica Severin and Masaru Koido and Tanvir Alam and Imad Abugessaisa and Chang, \{Howard Y.\} and Josee Dostie and Masayoshi Itoh and Juha Kere and Naoto Kondo and Yunjing Li and Makeev, \{Vsevolod J.\} and Mickael Mendez and Yasushi Okazaki and Ramilowski, \{Jordan A.\} and Sigorskikh, \{Andrey I.\} and Strug, \{Lisa J.\} and Ken Yagi and Kayoko Yasuzawa and Yip, \{Chi Wai\} and Hon, \{Chung Chau\} and Hoffman, \{Michael M.\} and Chikashi Terao and Kulakovskiy, \{Ivan V.\} and Takeya Kasukawa and Shin, \{Jay W.\} and Piero Carninci and \{de Hoon\}, \{Michiel J. L.\}",

note = "Publisher Copyright: Copyright: {\textcopyright} 2024 Agrawal et al.",

year = "2024",

month = may,

day = "6",

doi = "10.1371/journal.pone.0295971",

language = "English",

volume = "19",

journal = "PLoS ONE",

issn = "1932-6203",

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Agrawal, S, Buyan, A, Severin, J, Koido, M, Alam, T, Abugessaisa, I, Chang, HY, Dostie, J, Itoh, M, Kere, J, Kondo, N, Li, Y, Makeev, VJ, Mendez, M, Okazaki, Y, Ramilowski, JA, Sigorskikh, AI, Strug, LJ, Yagi, K, Yasuzawa, K, Yip, CW, Hon, CC, Hoffman, MM, Terao, C, Kulakovskiy, IV, Kasukawa, T, Shin, JW, Carninci, P & de Hoon, MJL 2024, 'Annotation of nuclear lncRNAs based on chromatin interactions', PLoS ONE, vol. 19, no. 5, e0295971. https://doi.org/10.1371/journal.pone.0295971

TY - JOUR

T1 - Annotation of nuclear lncRNAs based on chromatin interactions

AU - Agrawal, Saumya

AU - Buyan, Andrey

AU - Severin, Jessica

AU - Koido, Masaru

AU - Alam, Tanvir

AU - Abugessaisa, Imad

AU - Chang, Howard Y.

AU - Dostie, Josee

AU - Itoh, Masayoshi

AU - Kere, Juha

AU - Kondo, Naoto

AU - Li, Yunjing

AU - Makeev, Vsevolod J.

AU - Mendez, Mickael

AU - Okazaki, Yasushi

AU - Ramilowski, Jordan A.

AU - Sigorskikh, Andrey I.

AU - Strug, Lisa J.

AU - Yagi, Ken

AU - Yasuzawa, Kayoko

AU - Yip, Chi Wai

AU - Hon, Chung Chau

AU - Hoffman, Michael M.

AU - Terao, Chikashi

AU - Kulakovskiy, Ivan V.

AU - Kasukawa, Takeya

AU - Shin, Jay W.

AU - Carninci, Piero

AU - de Hoon, Michiel J. L.

PY - 2024/5/6

Y1 - 2024/5/6

N2 - The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA.

AB - The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA.

KW - Long noncoding rnas

KW - Set enrichment analysis

KW - Susceptibility loci

KW - Gene-expression

KW - Transcription

KW - Reveals

KW - Binding

KW - Database

KW - Architecture

KW - Genomics

UR - https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=hbku_researchportal&SrcAuth=WosAPI&KeyUT=WOS:001219428600010&DestLinkType=FullRecord&DestApp=WOS_CPL

U2 - 10.1371/journal.pone.0295971

DO - 10.1371/journal.pone.0295971

M3 - Article

C2 - 38709794

SN - 1932-6203

VL - 19

JO - PLoS ONE

JF - PLoS ONE

IS - 5

M1 - e0295971

ER -

Annotation of nuclear lncRNAs based on chromatin interactions

Abstract

Keywords

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