Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency

Although many long non-coding RNAs (lncRNAs) exhibit lineage-specific expression, the vast majority remain functionally uncharacterized in the context of development. Here, we report the first described human embryonic stem cell (hESC) lines to repress (CRISPRi) or activate (CRISPRa) transcription d...

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Autores principales:	Jeffrey R. Haswell, Kaia Mattioli, Chiara Gerhardinger, Philipp G. Maass, Daniel J. Foster, Paola Peinado, Xiaofeng Wang, Pedro P. Medina, John L. Rinn, Frank J. Slack
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0eee6775d6e44636ac1a683d2f039c3e
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spelling	oai:doaj.org-article:0eee6775d6e44636ac1a683d2f039c3e2021-11-11T06:44:15ZGenome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency1932-6203https://doaj.org/article/0eee6775d6e44636ac1a683d2f039c3e2021-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8565776/?tool=EBIhttps://doaj.org/toc/1932-6203Although many long non-coding RNAs (lncRNAs) exhibit lineage-specific expression, the vast majority remain functionally uncharacterized in the context of development. Here, we report the first described human embryonic stem cell (hESC) lines to repress (CRISPRi) or activate (CRISPRa) transcription during differentiation into all three germ layers, facilitating the modulation of lncRNA expression during early development. We performed an unbiased, genome-wide CRISPRi screen targeting thousands of lncRNA loci expressed during endoderm differentiation. While dozens of lncRNA loci were required for proper differentiation, most differentially expressed lncRNAs were not, supporting the necessity for functional screening instead of relying solely on gene expression analyses. In parallel, we developed a clustering approach to infer mechanisms of action of lncRNA hits based on a variety of genomic features. We subsequently identified and validated FOXD3-AS1 as a functional lncRNA essential for pluripotency and differentiation. Taken together, the cell lines and methodology described herein can be adapted to discover and characterize novel regulators of differentiation into any lineage.Jeffrey R. HaswellKaia MattioliChiara GerhardingerPhilipp G. MaassDaniel J. FosterPaola PeinadoXiaofeng WangPedro P. MedinaJohn L. RinnFrank J. SlackPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jeffrey R. Haswell Kaia Mattioli Chiara Gerhardinger Philipp G. Maass Daniel J. Foster Paola Peinado Xiaofeng Wang Pedro P. Medina John L. Rinn Frank J. Slack Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency
description	Although many long non-coding RNAs (lncRNAs) exhibit lineage-specific expression, the vast majority remain functionally uncharacterized in the context of development. Here, we report the first described human embryonic stem cell (hESC) lines to repress (CRISPRi) or activate (CRISPRa) transcription during differentiation into all three germ layers, facilitating the modulation of lncRNA expression during early development. We performed an unbiased, genome-wide CRISPRi screen targeting thousands of lncRNA loci expressed during endoderm differentiation. While dozens of lncRNA loci were required for proper differentiation, most differentially expressed lncRNAs were not, supporting the necessity for functional screening instead of relying solely on gene expression analyses. In parallel, we developed a clustering approach to infer mechanisms of action of lncRNA hits based on a variety of genomic features. We subsequently identified and validated FOXD3-AS1 as a functional lncRNA essential for pluripotency and differentiation. Taken together, the cell lines and methodology described herein can be adapted to discover and characterize novel regulators of differentiation into any lineage.
format	article
author	Jeffrey R. Haswell Kaia Mattioli Chiara Gerhardinger Philipp G. Maass Daniel J. Foster Paola Peinado Xiaofeng Wang Pedro P. Medina John L. Rinn Frank J. Slack
author_facet	Jeffrey R. Haswell Kaia Mattioli Chiara Gerhardinger Philipp G. Maass Daniel J. Foster Paola Peinado Xiaofeng Wang Pedro P. Medina John L. Rinn Frank J. Slack
author_sort	Jeffrey R. Haswell
title	Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency
title_short	Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency
title_full	Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency
title_fullStr	Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency
title_full_unstemmed	Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency
title_sort	genome-wide crispr interference screen identifies long non-coding rna loci required for differentiation and pluripotency
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/0eee6775d6e44636ac1a683d2f039c3e
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Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency

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