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
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Publicado: Public Library of Science (PLoS) 2021
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Acceso en línea:https://doaj.org/article/0c003e912f964144b90286b77f64afc5
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spelling oai:doaj.org-article:0c003e912f964144b90286b77f64afc52021-12-02T20:04:31ZGenome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency.1932-620310.1371/journal.pone.0252848https://doaj.org/article/0c003e912f964144b90286b77f64afc52021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0252848https://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, p e0252848 (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/0c003e912f964144b90286b77f64afc5
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