Annotation of nuclear lncRNAs based on chromatin interactions
<p dir="ltr">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...
محفوظ في:
| المؤلف الرئيسي: | |
|---|---|
| مؤلفون آخرون: | , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| منشور في: |
2024
|
| الموضوعات: | |
| الوسوم: |
إضافة وسم
لا توجد وسوم, كن أول من يضع وسما على هذه التسجيلة!
|
| _version_ | 1864513509307449344 |
|---|---|
| author | Saumya Agrawal (3441386) |
| author2 | Andrey Buyan (18510102) Jessica Severin (178475) Masaru Koido (14059995) Tanvir Alam (638619) Imad Abugessaisa (627440) Howard Y. Chang (215450) Josée Dostie (262897) Masayoshi Itoh (15728) Juha Kere (11900) Naoto Kondo (32868) Yunjing Li (644191) Vsevolod J. Makeev (7592954) Mickaël Mendez (3864016) Yasushi Okazaki (3100) Jordan A. Ramilowski (2259964) Andrey I. Sigorskikh (18510105) Lisa J. Strug (8293947) Ken Yagi (246069) Kayoko Yasuzawa (18510108) Chi Wai Yip (15068455) Chung Chau Hon (4520500) Michael M. Hoffman (5846618) Chikashi Terao (137128) Ivan V. Kulakovskiy (7592957) Takeya Kasukawa (3041) Jay W. Shin (9030986) Piero Carninci (3015) Michiel J. L. de Hoon (11434447) |
| author2_role | author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| author_facet | Saumya Agrawal (3441386) Andrey Buyan (18510102) Jessica Severin (178475) Masaru Koido (14059995) Tanvir Alam (638619) Imad Abugessaisa (627440) Howard Y. Chang (215450) Josée Dostie (262897) Masayoshi Itoh (15728) Juha Kere (11900) Naoto Kondo (32868) Yunjing Li (644191) Vsevolod J. Makeev (7592954) Mickaël Mendez (3864016) Yasushi Okazaki (3100) Jordan A. Ramilowski (2259964) Andrey I. Sigorskikh (18510105) Lisa J. Strug (8293947) Ken Yagi (246069) Kayoko Yasuzawa (18510108) Chi Wai Yip (15068455) Chung Chau Hon (4520500) Michael M. Hoffman (5846618) Chikashi Terao (137128) Ivan V. Kulakovskiy (7592957) Takeya Kasukawa (3041) Jay W. Shin (9030986) Piero Carninci (3015) Michiel J. L. de Hoon (11434447) |
| author_role | author |
| dc.creator.none.fl_str_mv | Saumya Agrawal (3441386) Andrey Buyan (18510102) Jessica Severin (178475) Masaru Koido (14059995) Tanvir Alam (638619) Imad Abugessaisa (627440) Howard Y. Chang (215450) Josée Dostie (262897) Masayoshi Itoh (15728) Juha Kere (11900) Naoto Kondo (32868) Yunjing Li (644191) Vsevolod J. Makeev (7592954) Mickaël Mendez (3864016) Yasushi Okazaki (3100) Jordan A. Ramilowski (2259964) Andrey I. Sigorskikh (18510105) Lisa J. Strug (8293947) Ken Yagi (246069) Kayoko Yasuzawa (18510108) Chi Wai Yip (15068455) Chung Chau Hon (4520500) Michael M. Hoffman (5846618) Chikashi Terao (137128) Ivan V. Kulakovskiy (7592957) Takeya Kasukawa (3041) Jay W. Shin (9030986) Piero Carninci (3015) Michiel J. L. de Hoon (11434447) |
| dc.date.none.fl_str_mv | 2024-05-06T03:00:00Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pone.0295971 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/journal_contribution/Annotation_of_nuclear_lncRNAs_based_on_chromatin_interactions/26508307 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biological sciences Genetics Human Genome Long Non-Coding RNAs (lncRNAs) RNA-Chromatin Interaction Hi-C Chromatin Conformation Chromatin 3D Conformation Gene Regulation RNA-Protein Interactions |
| dc.title.none.fl_str_mv | Annotation of nuclear lncRNAs based on chromatin interactions |
| dc.type.none.fl_str_mv | Text Journal contribution info:eu-repo/semantics/publishedVersion text contribution to journal |
| description | <p dir="ltr">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.</p><h2>Other Information</h2><p dir="ltr">Published in: PLOS ONE<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1371/journal.pone.0295971" target="_blank">https://dx.doi.org/10.1371/journal.pone.0295971</a></p> |
| eu_rights_str_mv | openAccess |
| id | Manara2_faff2983456af33f2a644a197dd16452 |
| identifier_str_mv | 10.1371/journal.pone.0295971 |
| network_acronym_str | Manara2 |
| network_name_str | Manara2 |
| oai_identifier_str | oai:figshare.com:article/26508307 |
| publishDate | 2024 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Annotation of nuclear lncRNAs based on chromatin interactionsSaumya Agrawal (3441386)Andrey Buyan (18510102)Jessica Severin (178475)Masaru Koido (14059995)Tanvir Alam (638619)Imad Abugessaisa (627440)Howard Y. Chang (215450)Josée Dostie (262897)Masayoshi Itoh (15728)Juha Kere (11900)Naoto Kondo (32868)Yunjing Li (644191)Vsevolod J. Makeev (7592954)Mickaël Mendez (3864016)Yasushi Okazaki (3100)Jordan A. Ramilowski (2259964)Andrey I. Sigorskikh (18510105)Lisa J. Strug (8293947)Ken Yagi (246069)Kayoko Yasuzawa (18510108)Chi Wai Yip (15068455)Chung Chau Hon (4520500)Michael M. Hoffman (5846618)Chikashi Terao (137128)Ivan V. Kulakovskiy (7592957)Takeya Kasukawa (3041)Jay W. Shin (9030986)Piero Carninci (3015)Michiel J. L. de Hoon (11434447)Biological sciencesGeneticsHuman GenomeLong Non-Coding RNAs (lncRNAs)RNA-Chromatin InteractionHi-C Chromatin ConformationChromatin 3DConformation Gene RegulationRNA-Protein Interactions<p dir="ltr">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.</p><h2>Other Information</h2><p dir="ltr">Published in: PLOS ONE<br>License: <a href="http://creativecommons.org/licenses/by/4.0/" target="_blank">http://creativecommons.org/licenses/by/4.0/</a><br>See article on publisher's website: <a href="https://dx.doi.org/10.1371/journal.pone.0295971" target="_blank">https://dx.doi.org/10.1371/journal.pone.0295971</a></p>2024-05-06T03:00:00ZTextJournal contributioninfo:eu-repo/semantics/publishedVersiontextcontribution to journal10.1371/journal.pone.0295971https://figshare.com/articles/journal_contribution/Annotation_of_nuclear_lncRNAs_based_on_chromatin_interactions/26508307CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/265083072024-05-06T03:00:00Z |
| spellingShingle | Annotation of nuclear lncRNAs based on chromatin interactions Saumya Agrawal (3441386) Biological sciences Genetics Human Genome Long Non-Coding RNAs (lncRNAs) RNA-Chromatin Interaction Hi-C Chromatin Conformation Chromatin 3D Conformation Gene Regulation RNA-Protein Interactions |
| status_str | publishedVersion |
| title | Annotation of nuclear lncRNAs based on chromatin interactions |
| title_full | Annotation of nuclear lncRNAs based on chromatin interactions |
| title_fullStr | Annotation of nuclear lncRNAs based on chromatin interactions |
| title_full_unstemmed | Annotation of nuclear lncRNAs based on chromatin interactions |
| title_short | Annotation of nuclear lncRNAs based on chromatin interactions |
| title_sort | Annotation of nuclear lncRNAs based on chromatin interactions |
| topic | Biological sciences Genetics Human Genome Long Non-Coding RNAs (lncRNAs) RNA-Chromatin Interaction Hi-C Chromatin Conformation Chromatin 3D Conformation Gene Regulation RNA-Protein Interactions |