Evidence map›Paper›PMID 37425940›Full record

ArticlebioRxiv : the preprint server for biology2023

Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis.

Rinaldo Catta-Preta, Susan Lindtner, Athena Ypsilanti, James Price, Armen Abnousi, Linda Su-Feher, Yurong Wang, Ivan Juric, Ian R Jones, Jennifer A Akiyama and 7 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 3 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

17 authors at 5 institutions in 1 country.

Rinaldo Catta-PretaDepartment of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA.
Susan LindtnerNina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
Athena YpsilantiNina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
James PriceNina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
Armen AbnousiDepartment of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA.
Linda Su-FeherDepartment of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA.
Yurong WangDepartment of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA.
Ivan JuricDepartment of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA.
Ian R JonesInstitute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA.
Jennifer A AkiyamaEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Ming HuDepartment of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44106, USA.
Yin ShenInstitute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA.
Axel ViselEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Len A PennacchioEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Diane DickelEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
John L R RubensteinNina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
Alex S NordDepartment of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA.
University of California, San Francisco · USLawrence Berkeley National Laboratory · USCleveland Clinic · USUniversity of California, Davis · USHarvard University · US

Funding

Generation of an In Vivo Human Genome Transcriptional Enhancer DatasetR01HG003988 · NHGRI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI Len Alexander Pennacchio · 2006 to 2026
$24.1M
Genetic Control of Basal Telencephalic DevelopmentR01MH081880 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI RUBENSTEIN, JOHN L. R. · 2009 to 2023
$8.1M
Genetic Regulation of Telencephalon DevelopmentR37MH049428 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI RUBENSTEIN, JOHN L. R. · 2008 to 2017
$5.9M
STRUCTURE, EXPRESSION &FUNCTION OF THE DLX GENE FAMILYR01MH049428 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI RUBENSTEIN, JOHN L. R. · 1992 to 2022
$5.8M
A Single-Cell Resolution Enhancer Atlas of Craniofacial DevelopmentR01DE028599 · NIDCR · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI VISEL, AXEL · 2019 to 2023
$4.2M
Functional Elucidation of the Sequence-Encoded Regulatory Activity of Enhancers in Vivo in the BrainR35GM119831 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI Alexander Nord · 2016 to 2026
$3.9M
Linking Psychiatric Genetics to Cell-Type Specific Enhancer FunctionR01MH117106 · NIMH · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI VISEL, AXEL · 2018 to 2022
$3.6M
Charting the 3D epigenome in human brain development and diseasesU01DA052713 · NIDA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KRIEGSTEIN, ARNOLD, SHEN, YIN · 2020 to 2024
$3.4M
Training Program in Biomolecular TechnologyT32GM008799 · NIGMS · UNIVERSITY OF CALIFORNIA DAVIS · PI LEACH, J. KENT · 2002 to 2016
$2.4M
A High-Resolution Enhancer Atlas of the Developing ForebrainR01NS062859 · NINDS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI PENNACCHIO, LEN ALEXANDER · 2008 to 2010
$1.7M
NHGRI NIH HHS R01 HG003988NIDA NIH HHS U01 DA052713NIDCR NIH HHS R01 DE028599NIGMS NIH HHS R35 GM119831NIGMS NIH HHS T32 GM008799NIMH NIH HHS R01 MH049428NIMH NIH HHS R01 MH081880NIMH NIH HHS R01 MH117106NIMH NIH HHS R37 MH049428NINDS NIH HHS R01 NS062859
6 · The paper itself

Abstract

Transcription factors (TFs) bind combinatorially to genomic cis-regulatory elements (cREs), orchestrating transcription programs. While studies of chromatin state and chromosomal interactions have revealed dynamic neurodevelopmental cRE landscapes, parallel understanding of the underlying TF binding lags. To elucidate the combinatorial TF-cRE interactions driving mouse basal ganglia development, we integrated ChIP-seq for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and transcriptional state, and transgenic enhancer assays. We identified TF-cREs modules with distinct chromatin features and enhancer activity that have complementary roles driving GABAergic neurogenesis and suppressing other developmental fates. While the majority of distal cREs were bound by one or two TFs, a small proportion were extensively bound, and these enhancers also exhibited exceptional evolutionary conservation, motif density, and complex chromosomal interactions. Our results provide new insights into how modules of combinatorial TF-cRE interactions activate and repress developmental expression programs and demonstrate the value of TF binding data in modeling gene regulatory wiring.

Identifiers

PMID37425940
PMCPMC10327028
OpenAlexW4382560064

What OpenQuestion holds

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Registered trials

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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.