ArticleCell reports2019
Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development.
Article in Cell reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 103 citations in OpenAlex.
- Systematic Dissection of Key Driver Perturbation Signatures in Single Cells via ECCITE-seq.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Benchmarking methods for inferring single-cell transcription factor activity using large-scale perturbation sequencing data.Briefings in bioinformatics · 2026Article
- FOXA2 in cancer: from fundamental biology to clinical translation.Frontiers in oncology · 2026Review
- Review
- Accurate Transcription Factor Activity Inference to Decipher Cell Identity from Single-Cell Transcriptomic Data with MetaTF.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Identification and multi-omics analysis of essential coding and long non-coding genes in colorectal cancer.Biochemistry and biophysics reports · 2025Article
- Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP.Briefings in bioinformatics · 2024Article
- The interferon γ pathway enhances pluripotency and X-chromosome reactivation in iPSC reprogramming.Science advances · 2024Article
- A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data.Nature communications · 2024Article
- Genome-scale CRISPR-Cas9 screening in stem cells: theories, applications and challenges.Stem cell research & therapy · 2024Review
- Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi.iScience · 2024Article
- Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection.Genome biology · 2024Article
- NatD epigenetically activates FOXA2 expression to promote breast cancer progression by facilitating MMP14 expression.iScience · 2024Article
- Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate.Molecular cell · 2024Article
- The Current Situation and Development Prospect of Whole-Genome Screening.International journal of molecular sciences · 2024Review
- The genetics and pathogenesis of CAKUT.Nature reviews. Nephrology · 2023Review
- CRISPR screening in hematology research: from bulk to single-cell level.Journal of hematology & oncology · 2023Review
- Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.Nature communications · 2023Article
- Generation and molecular characterization of human pluripotent stem cell-derived pharyngeal foregut endoderm.Developmental cell · 2023Article
- GiRAFR improves gRNA detection and annotation in single-cell CRISPR screens.Communications biology · 2023Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Studies in vertebrates have outlined conserved molecular control of definitive endoderm (END) development. However, recent work also shows that key molecular aspects of human END regulation differ even from rodents. Differentiation of human embryonic stem cells (ESCs) to END offers a tractable system to study the molecular basis of normal and defective human-specific END development. Here, we interrogated dynamics in chromatin accessibility during differentiation of ESCs to END, predicting DNA-binding proteins that may drive this cell fate transition. We then combined single-cell RNA-seq with parallel CRISPR perturbations to comprehensively define the loss-of-function phenotype of those factors in END development. Following a few candidates, we revealed distinct impairments in the differentiation trajectories for mediators of TGFβ signaling and expose a role for the FOXA2 transcription factor in priming human END competence for human foregut and hepatic END specification. Together, this single-cell functional genomics study provides high-resolution insight on human END development.
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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.