ArticleCell2020
Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells.
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Article in Cell, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53citing papers in PubMed
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53 citing papers in PubMed, 97 citations in OpenAlex.
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- Inducible Calling Cards: Developing Mouse Reagents for Experimentally Controlled Transposon InsertionbioRxiv : the preprint server for biology · 2025Article
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Authors and funding
13 authors at 1 institution in 1 country.
Arnav MoudgilDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
Michael N WilkinsonDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
Xuhua ChenDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
June HeDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
Alexander J CammackDepartment of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
Michael J VasekDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
Tomás LagunasDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
Zongtai QiDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
Matthew A LalliDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
Chuner GuoDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Medical Scientist Training Program, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
Samantha A MorrisDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
Joseph D DoughertyDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
Robi D MitraDepartment of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA; Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA. Electronic address: rmitra@wustl.edu.
Washington University in St. Louis · US
Funding
Washington University Center for Cellular ImagingP30CA091842 · NCI · WASHINGTON UNIVERSITY · PI AIMEE S JAMES · 2001 to 2026
$128.0MWU INSTITUTE OF CLINICAL AND TRANSLATIONAL SCIENCESUL1TR002345 · NCATS · WASHINGTON UNIVERSITY · PI William G. Powderly · 2017 to 2026
$97.8MNATIONAL RESEARCH SERVICE AWARD-MEDICAL SCIENTISTT32GM007200 · NIGMS · WASHINGTON UNIVERSITY · PI YOKOYAMA, WAYNE M. · 1985 to 2024
$59.8MWashington University Institute of Clinical and Translational SciencesUL1TR000448 · NCATS · WASHINGTON UNIVERSITY · PI EVANOFF, BRADLEY A · 2012 to 2016
$41.4MTRAINING PROGRAM IN CELLULAR AND MOLECULAR BIOLOGYT32GM007067 · NIGMS · WASHINGTON UNIVERSITY · PI TRUE-KROB, HEATHER L · 1985 to 2020
$20.4MWUIDDRC Supplement-Supporting the health and well-being of children with intellectual and developmental disability during COVID-19 pandemicP50HD103525 · NICHD · WASHINGTON UNIVERSITY · PI JOSEPH D DOUGHERTY, Natasha Marrus · 2020 to 2026
$15.5MWashington University Center for Translational NeuroscienceP30NS057105 · NINDS · WASHINGTON UNIVERSITY · PI HOLTZMAN, DAVID M. · 2006 to 2011
$8.7MINSTITUTIONAL TRAINING GRANT IN GENOMIC SCIENCET32HG000045 · NHGRI · WASHINGTON UNIVERSITY · PI MICHAEL R BRENT, Barak A Cohen · 1997 to 2026
$8.4MSystems and Molecular Neurobiology Training ProgramT32GM008151 · NIGMS · WASHINGTON UNIVERSITY · PI SNYDER, LAWRENCE H · 1985 to 2019
$6.5MMAXIMIZING STUDENT DIVERSITY IN THE BIOMEDICAL SCIENCES AT WASHINGTON UNIVERSITYR25GM103757 · NIGMS · WASHINGTON UNIVERSITY · PI SKEATH, JAMES BENJAMIN · 2013 to 2022
$4.5MPediatric Cardiovascular and Pulmonary Research Training Program.T32HL125241 · NHLBI · WASHINGTON UNIVERSITY · PI Juliane Bubeck Wardenburg, Kory J. Lavine · 2015 to 2026
$4.1MAN INDUCIBLE MOLECULAR MEMORY SYSTEM TO RECORD TRANSIENT STATES OF CNS CELLSU01MH109133 · NIMH · WASHINGTON UNIVERSITY · PI MITRA, ROBI D · 2015 to 2017
$3.6MNCATS NIH HHS UL1 TR000448NCATS NIH HHS UL1 TR002345NCI NIH HHS P30 CA091842NHGRI NIH HHS F30 HG009986NHGRI NIH HHS R21 HG009750NHGRI NIH HHS T32 HG000045NHLBI NIH HHS T32 HL125241NICHD NIH HHS P50 HD103525NIGMS NIH HHS R01 GM126112NIGMS NIH HHS R25 GM103757NIGMS NIH HHS T32 GM007067NIGMS NIH HHS T32 GM007200NIGMS NIH HHS T32 GM008151NIMH NIH HHS RF1 MH117070NIMH NIH HHS U01 MH109133NINDS NIH HHS F32 NS105363NINDS NIH HHS P30 NS057105
Abstract
Cellular heterogeneity confounds in situ assays of transcription factor (TF) binding. Single-cell RNA sequencing (scRNA-seq) deconvolves cell types from gene expression, but no technology links cell identity to TF binding sites (TFBS) in those cell types. We present self-reporting transposons (SRTs) and use them in single-cell calling cards (scCC), a novel assay for simultaneously measuring gene expression and mapping TFBS in single cells. The genomic locations of SRTs are recovered from mRNA, and SRTs deposited by exogenous, TF-transposase fusions can be used to map TFBS. We then present scCC, which map SRTs from scRNA-seq libraries, simultaneously identifying cell types and TFBS in those same cells. We benchmark multiple TFs with this technique. Next, we use scCC to discover BRD4-mediated cell-state transitions in K562 cells. Finally, we map BRD4 binding sites in the mouse cortex at single-cell resolution, establishing a new method for studying TF biology in situ.
Indexed as
AnimalsBinding SitesBromodomain Containing ProteinsCell Cycle ProteinsCell Line, TumorCerebral CortexChromatin ImmunoprecipitationDNA Transposable ElementsGene ExpressionHepatocyte Nuclear Factor 3-betaHumansMiceProtein BindingSequence Analysis, RNASingle-Cell AnalysisSp1 Transcription FactorBRD4 protein, humanBromodomain Containing ProteinsCell Cycle ProteinsDNA Transposable ElementsFOXA2 protein, humanHepatocyte Nuclear Factor 3-betaSp1 Transcription FactorTranscription Factorsbromodomainscalling cardscell statemouse cortexsingle celltranscription factorstransposons
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