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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2021
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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) |
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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 |
work_keys_str_mv |
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