ArticleCell2023
A transcription factor atlas of directed differentiation.
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Article in Cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 153 papers.
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153citing papers in PubMed
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153 citing papers in PubMed.
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- Generation of synthetic vascular organoids via orthogonal programming of human pluripotent stem cells.Cell regeneration (London, England) · 2026Article
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- Synthetic developmental engineering of human liver organogenesis.Development (Cambridge, England) · 2026Review
- Protocol for identifying cellular reprogramming minimal networks using combinatorial transcription factor screening.STAR protocols · 2026Article
- Sgf29 regulates pluripotency by maintaining chromatin accessibility and promoting the expression of core transcription factors.Science China. Life sciences · 2026Article
- Highly Constrained Kinetic Models for Single-Cell Gene Expression Analysis.bioRxiv : the preprint server for biology · 2026Article
- Combinatorial transcription factor interactions drive modular gene regulatory networks.bioRxiv : the preprint server for biology · 2026Article
- Probing transcription factor subsets in gene regulatory networks.Algorithms for molecular biology : AMB · 2026Article
- Functional chromatin signatures premark future lineage-specific enhancers.Cell genomics · 2026Article
- BART-spatial unravels biologically significant transcriptional regulators from spatial omics data.bioRxiv : the preprint server for biology · 2026Article
- Comparative theranostic efficacy ofEuropean journal of nuclear medicine and molecular imaging · 2026Article
- Tissue-specific I-Smad mechanisms revealed by structure-function analysis inLife science alliance · 2026Article
- TxPert: using multiple knowledge graphs for prediction of transcriptomic perturbation effects.Nature biotechnology · 2026Article
93 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
18 authors.
Julia JoungDepartment of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
Sai MaDepartment of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Tristan TayDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Kathryn R Geiger-SchullerDepartment of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Paul C KirchgattererDepartment of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
Vanessa K VerdineDepartment of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
Baolin GuoMcGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Mario A Arias-GarciaMcGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
William E AllenDepartment of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA; Society of Fellows, Harvard University, Cambridge, MA, USA.
Ankita SinghDepartment of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
Olena KuksenkoDepartment of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Omar O AbudayyehDepartment of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
Jonathan S GootenbergDepartment of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
Zhanyan FuMcGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Rhiannon K MacraeDepartment of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
Jason D BuenrostroDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Aviv RegevDepartment of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Feng ZhangDepartment of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA. Electronic address: zhang@broadinstitute.org.
Funding
Center for Cell CircuitsRM1HG006193 · NHGRI · BROAD INSTITUTE, INC. · PI BLAINEY, PAUL CLARK, HACOHEN, NIR · 2016 to 2020
$14.9MProgrammable RNA-targeting toolsR01HG009761 · NHGRI · BROAD INSTITUTE, INC. · PI ZHANG, FENG · 2017 to 2024
$7.5MExploration of Diverse Mobile Genetic Elements for Precision Genome ManipulationDP1HL141201 · NHLBI · BROAD INSTITUTE, INC. · PI ZHANG, FENG · 2017 to 2021
$6.2MSingle-cell epigenomic and cellular plasticityDP2HL151353 · NHLBI · HARVARD UNIVERSITY · PI BUENROSTRO, JASON DANIEL · 2019 to 2019
$2.5MCharacterization of structure-function relationships in distinct thalamic reticular nucleus networksR01MH127085 · NIMH · BROAD INSTITUTE, INC. · PI FU, ZHANYAN · 2021 to 2025
$2.0MGenome-scale transcription factor screen for neural differentiationF31MH117886 · NIMH · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI JOUNG, JULIA · 2018 to 2019
$90kNHGRI NIH HHS R01 HG009761NHGRI NIH HHS RM1 HG006193NHLBI NIH HHS DP1 HL141201NHLBI NIH HHS DP2 HL151353NIMH NIH HHS F31 MH117886NIMH NIH HHS R01 MH127085
Abstract
Transcription factors (TFs) regulate gene programs, thereby controlling diverse cellular processes and cell states. To comprehensively understand TFs and the programs they control, we created a barcoded library of all annotated human TF splice isoforms (>3,500) and applied it to build a TF Atlas charting expression profiles of human embryonic stem cells (hESCs) overexpressing each TF at single-cell resolution. We mapped TF-induced expression profiles to reference cell types and validated candidate TFs for generation of diverse cell types, spanning all three germ layers and trophoblasts. Targeted screens with subsets of the library allowed us to create a tailored cellular disease model and integrate mRNA expression and chromatin accessibility data to identify downstream regulators. Finally, we characterized the effects of combinatorial TF overexpression by developing and validating a strategy for predicting combinations of TFs that produce target expression profiles matching reference cell types to accelerate cellular engineering efforts.
Indexed as
Cell DifferentiationTranscription FactorsAtlases as TopicChromatinGene Expression RegulationHuman Embryonic Stem CellsHumansChromatinTranscription Factorscell engineeringcellular disease modelingcombinatorial perturbationgene regulationgenetic screeningneural progenitorORF overexpressionpluripotent stem cellsingle cell profilingtranscription factor
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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.