Evidence map›Paper›PMID 25180570›Full record

ArticleTranslational psychiatry2014

Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.

N Oksenberg, G D E Haliburton, W L Eckalbar, I Oren, S Nishizaki, K Murphy, K S Pollard, R Y Birnbaum, N Ahituv

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Translational psychiatry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.

0numbers the graph read from it
0cells of the map it votes in
36citing papers in PubMed
2.1field-weighted citation impact, top 13% of its field
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

36 citing papers in PubMed, 62 citations in OpenAlex.

  1. Article
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  9. Article
  10. Review
  11. Article
  12. Cells · 2022
    Article
  13. AUTS2 Syndrome: Molecular Mechanisms and Model Systems.Frontiers in molecular neuroscience · 2022
    Review
  14. Cells · 2021
    Review
  15. Article
  16. Review
  17. Article
  18. Article
  19. Review
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 2 institutions in 2 countries.

N Oksenberg1] Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA [2] Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
G D E Haliburton1] Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA [2] Gladstone Institutes, San Francisco, CA, USA.
W L Eckalbar1] Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA [2] Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
I OrenDepartment of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.
S Nishizaki1] Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA [2] Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
K Murphy1] Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA [2] Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
K S Pollard1] Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA [2] Gladstone Institutes, San Francisco, CA, USA [3] Division of Biostatistics, University of California San Francisco, San Francisco, CA, USA.
R Y Birnbaum1] Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA [2] Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA [3] Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel.
N Ahituv1] Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA [2] Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
University of California, San Francisco · USBen-Gurion University of the Negev · IL

Funding

PHARMACOGENETICS OF MEMBRANE TRANSPORTERSU01GM061390 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GIACOMINI, KATHLEEN M · 2000 to 2009
$29.2M
Pharmacogenomics of Membrane TransportersU19GM061390 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI WITTE, JOHN S. · 2010 to 2014
$16.3M
The Epigenetic Landscape of Heart DevelopmentU01HL098179 · NHLBI · J. DAVID GLADSTONE INSTITUTES · PI BOYER, LAURIE A, BRUNEAU, BENOIT GAETAN · 2009 to 2014
$10.0M
BMI Bioinformatics Training GrantsT32GM067547 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HERNANDEZ, RYAN D. · 2003 to 2022
$6.6M
The Epigenetic Landscape of Heart DevelopmentUM1HL098179 · NHLBI · J. DAVID GLADSTONE INSTITUTES · PI BRUNEAU, BENOIT GAETAN, POLLARD, KATHERINE S. · 2015 to 2019
$4.7M
Characterization of regulatory elements leading to human limb malformationsR01HD059862 · NICHD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV, BEJERANO, GILL · 2009 to 2013
$2.2M
Integrative interpretation of the organismal consequences of non-coding variationR01CA197139 · NCI · UNIVERSITY OF WASHINGTON · PI COOPER, GREGORY MICHAEL, SHENDURE, JAY ASHOK · 2015 to 2017
$1.9M
Massively parallel, in vivo functional testing of regulatory elementsR01HG006768 · NHGRI · UNIVERSITY OF WASHINGTON · PI AHITUV, NADAV, SHENDURE, JAY ASHOK · 2012 to 2014
$1.8M
Computational & Functional Annotation of the Zebrafish Genome Regulatory ToolboxR01HG005058 · NHGRI · STANFORD UNIVERSITY · PI AHITUV, NADAV, BEJERANO, GILL · 2009 to 2012
$1.6M
Identification & functional characterization of SIM1 obesity-associated variantsR01DK090382 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV, VAISSE, CHRISTIAN · 2012 to 2015
$1.3M
Characterization of neuronal gene regulatory elements associated with epilepsyR01NS079231 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV · 2012 to 2015
$1.2M
NCI NIH HHS R01 CA197139NHGRI NIH HHS R01 HG005058NHGRI NIH HHS R01HG005058NHGRI NIH HHS R01 HG006768NHGRI NIH HHS R01HG006768NHLBI NIH HHS HL098179NHLBI NIH HHS U01 HL098179NHLBI NIH HHS UM1 HL098179NICHD NIH HHS R01 HD059862NICHD NIH HHS R01HD059862NIDDK NIH HHS 1R01DK090382NIDDK NIH HHS R01 DK090382NIGMS NIH HHS T32 GM067547NIGMS NIH HHS U01 GM061390NIGMS NIH HHS U19 GM061390NINDS NIH HHS 1R01NS079231NINDS NIH HHS R01 NS079231
6 · The paper itself

Abstract

The autism susceptibility candidate 2 gene (AUTS2) has been associated with multiple neurological diseases including autism spectrum disorders (ASDs). Previous studies showed that AUTS2 has an important neurodevelopmental function and is a suspected master regulator of genes implicated in ASD-related pathways. However, the regulatory role and targets of Auts2 are not well known. Here, by using ChIP-seq (chromatin immunoprecipitation followed by deep sequencing) and RNA-seq on mouse embryonic day 16.5 forebrains, we elucidated the gene regulatory networks of Auts2. We find that the majority of promoters bound by Auts2 belong to genes highly expressed in the developing forebrain, suggesting that Auts2 is involved in transcriptional activation. Auts2 non-promoter-bound regions significantly overlap developing brain-associated enhancer marks and are located near genes involved in neurodevelopment. Auts2-marked sequences are enriched for binding site motifs of neurodevelopmental transcription factors, including Pitx3 and TCF3. In addition, we characterized two functional brain enhancers marked by Auts2 near NRXN1 and ATP2B2, both ASD-implicated genes. Our results implicate Auts2 as an active regulator of important neurodevelopmental genes and pathways and identify novel genomic regions that could be associated with ASD and other neurodevelopmental diseases.

Indexed as

Genome-Wide Association StudyAnimalsCalcium-Binding ProteinsChild Development Disorders, PervasiveCytoskeletal ProteinsFemaleGene Expression RegulationGenetic Predisposition to DiseaseMiceMice, Inbred StrainsNeural Cell Adhesion MoleculesNuclear ProteinsPlasma Membrane Calcium-Transporting ATPasesPregnancyProsencephalonTranscriptional ActivationAtp2b2 protein, mouseAuts2 protein, mouseCalcium-Binding ProteinsCytoskeletal ProteinsNeural Cell Adhesion MoleculesNrxn1 protein, mouseNuclear ProteinsPlasma Membrane Calcium-Transporting ATPasesTranscription Factors

Identifiers

PMID25180570
PMCPMC4199417
OpenAlexW1995250928

What OpenQuestion holds

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LicenceCC BY-NC-ND
Read underepoch 390

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.