Evidence map›Paper›PMID 37503149›Full record

ArticlebioRxiv : the preprint server for biology2023

R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription.

Elizabeth A LaMarca, Atsushi Saito, Amara Plaza-Jennings, Sergio Espeso-Gil, Allyse Hellmich, Michael B Fernando, Behnam Javidfar, Will Liao, Molly Estill, Kayla Townsley and 9 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, 4 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

19 authors at 4 institutions in 1 country.

Elizabeth A LaMarcaGraduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Atsushi SaitoDepartment of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA.
Amara Plaza-JenningsGraduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Sergio Espeso-GilNash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Allyse HellmichNash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Michael B FernandoGraduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Behnam JavidfarNash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Will LiaoNew York Genome Center, New York, NY 10013, USA.
Molly EstillNash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Kayla TownsleyGraduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Anna FlorioDepartment of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA.
James E EthridgeNash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Catherine DoCenter for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA.
Benjamin TyckoCenter for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA.
Li ShenNash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Atsushi KamiyaDepartment of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA.
Nadejda M TsankovaNash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Kristen J BrennandNash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Schahram AkbarianNash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Allen Institute for Brain Science · USJohns Hopkins University · USHackensack Meridian Health · USNew York Genome Center · US

Funding

Project 3P50MH094268 · NIMH · JOHNS HOPKINS UNIVERSITY · PI GALLAGHER, MICHELA · 2011 to 2020
$19.9M
Higher Order Chromatin and Genetic Risk for SchizophreniaR01MH106056 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, BRENNAND, KRISTEN JENNIFER · 2015 to 2023
$6.7M
Functional genomic resource and integrative model of dopaminergic circuitry associated with psychiatric diseaseU01DA048279 · NIDA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, BRENNAND, KRISTEN JENNIFER · 2019 to 2023
$3.5M
Molecular mechanism of astrocytic vulnerability to adolescent cannabis useR01DA041208 · NIDA · JOHNS HOPKINS UNIVERSITY · PI KAMIYA, ATSUSHI, PLETNIKOV, MIKHAIL V · 2016 to 2020
$2.9M
Targeting age and gender-dependent microglia-mediated mechanisms underlying postoperative cognitive impairment for treatment of delirium in the elderlyR01AG065168 · NIA · JOHNS HOPKINS UNIVERSITY · PI KAMIYA, ATSUSHI · 2020 to 2024
$2.1M
Chromatin Plasticity, Transcriptional Activity and Kinetics in Developing and Adult Human Astrocyte and Oligodendroglial LineagesRF1DA048810 · NIDA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI TSANKOVA, NADEJDA MINCHEVA · 2019 to 2019
$1.8M
Modeling the contribution of common variants to schizophrenia riskR56MH101454 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI BRENNAND, KRISTEN JENNIFER, HUCKINS, LAURA MARIANNE · 2018 to 2019
$1.5M
R-loops as Mechanisms Governing Neural Differentiation and Cell Type-Specific TranscriptionF31MH121062 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI LAMARCA, ELIZABETH ANN · 2019 to 2020
$75k
NIA NIH HHS R01 AG065168NIDA NIH HHS R01 DA041208NIDA NIH HHS RF1 DA048810NIDA NIH HHS U01 DA048279NIMH NIH HHS F31 MH121062NIMH NIH HHS P50 MH094268NIMH NIH HHS R01 MH106056NIMH NIH HHS R56 MH101454
6 · The paper itself

Abstract

Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivity

Identifiers

PMID37503149
PMCPMC10370098
OpenAlexW4384828645

What OpenQuestion holds

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LicenceCC BY-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.