ArticlePloS one2021
Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 31 citations in OpenAlex.
- Identification of long non-coding RNAs involved in leukemogenesis and venetoclax response in acute myeloid leukemia through functional CRISPR-dCas9 interference screens.Non-coding RNA research · 2026Article
- Scanning transcriptomes for nonlinear, domain-level similarities using hmSEEKR.bioRxiv : the preprint server for biology · 2026Article
- Antisense oligonucleotides: targeting oncogenic long non-coding RNAs for cancer therapy.Biotechnology letters · 2026Review
- Genetic screening of long non-coding RNAs in human embryonic stem cells reveals novel regulators of pluripotency.Stem cell reports · 2026Article
- CRISPR GENome and epigenome engineering improves loss-of-function genetic-screening approaches.Cell reports methods · 2025Article
- Engineering novel CRISPRi repressors for highly efficient mammalian gene regulation.Genome biology · 2025Article
- Long noncoding RNA as an emerging regulator of endoderm differentiation: progress and perspectives.Cell regeneration (London, England) · 2025Review
- Chemically defined and growth factor-free system for highly efficient endoderm induction of human pluripotent stem cells.Stem cell reports · 2025Article
- Seed sequences mediate off-target activity in the CRISPR-interference system.Cell genomics · 2024Article
- CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant.Cell reports · 2024Article
- Identification and Functional Characterization of lncRNAs involved in Human Monocyte-to-Macrophage Differentiation.bioRxiv : the preprint server for biology · 2024Article
- CRISPRi screens identify the lncRNA,Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Integration of transcription regulation and functional genomic data reveals lncRNA SNHG6's role in hematopoietic differentiation and leukemia.Journal of biomedical science · 2024Article
- The Current Situation and Development Prospect of Whole-Genome Screening.International journal of molecular sciences · 2024Review
- Identification and functional characterization of lncRNAs involved in human monocyte-to-macrophage differentiation.RNA biology · 2024Article
- Reduction of GAS5 and FOXD3-AS1 long non-coding RNAs in patients with bipolar disorder.Scientific reports · 2023Article
- Specific gene expression signatures of low grade meningiomas.Frontiers in oncology · 2023Article
- Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors.eLife · 2022Article
- Emerging Roles and Mechanisms of lncRNA FOXD3-AS1 in Human Diseases.Frontiers in oncology · 2022Review
- CRISPR-Based Approaches for the High-Throughput Characterization of Long Non-Coding RNAs.Non-coding RNA · 2021Review
Corrections and comments
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Authors and funding
10 authors at 7 institutions in 3 countries.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.