Evidence map›Paper›PMID 35704185›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2022

Identification of RNA-DNA Hybrids Associated with R-Loops at the IgH Switch Sequence in Activated B Cells.

Junghyun Lim, Brice Laffleur, Uttiya Basu, Kefei Yu

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

Article in Methods in molecular biology (Clifton, N.J.), 2022. 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
1.4field-weighted citation impact, top 23% 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

0 citing papers in PubMed, 1 citations in OpenAlex.

No citing paper in PubMed yet.

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

4 authors at 3 institutions in 3 countries.

Junghyun LimDepartment of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
Brice LaffleurDepartment of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
Uttiya BasuDepartment of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA. ub2121@cumc.columbia.edu.
Kefei YuDepartment of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA. yuke@msu.edu.
Columbia University · USInserm · FRMichigan State University · US

Funding

Role of ncRNA Surveillance Complex "RNA Exosome" in Class Switch Recombination and Somatic HypermutationR01AI099195 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Uttiya Basu · 2012 to 2026
$9.8M
Long noncoding RNA expressing genomic element that control antibody diversification and chromosomal integrity in B cellsR01AI134988 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Uttiya Basu · 2018 to 2026
$4.7M
The role of N6-methyladenosine RNA modification in programmed and aberrant DNA mutagenesis in B cellsR01AI143897 · NIAID · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Uttiya Basu · 2020 to 2026
$3.4M
DNA Structure Directed AID Deamination During Immunoglobulin Isotype SwitchingR01AI139039 · NIAID · MICHIGAN STATE UNIVERSITY · PI YU, KEFEI · 2018 to 2022
$1.5M
NIAID NIH HHS R01 AI099195NIAID NIH HHS R01 AI134988NIAID NIH HHS R01 AI139039NIAID NIH HHS R01 AI143897
6 · The paper itself

Abstract

During transcription and replication, R-loops that contain RNA-DNA hybrids are generated across numerous genomic loci and contribute to many biological events. Using S9.6, a monoclonal antibody against RNA-DNA hybrids, accelerated the study of R-loop biology. An outpouring of recent studies has implicated various contributions of R-loop in physiological cellular functions. Earlier studies using nondenaturing sodium bisulfite probing also supported existence of DNA-RNA hybrids formation in mammalian cells. In activated B cells, RNA-DNA hybrids formation at IgH gene locus of B cells is crucial for class switch recombination that ensure the proper effector function of the antibody. Here, we describe the identification of R-loops associated with the IgH locus using RNA-DNA hybrid immunoprecipitation sequencing and nondenaturing sodium bisulfite probing. This will be helpful for future studies of R-loops status on whole genome as well as on IgH locus in B cells.

Indexed as

R-Loop StructuresRNAAnimalsDNAImmunoglobulin Class SwitchingImmunoprecipitationMammalsDNARNAB cellsClass switch recombinationDRIP-seqNondenaturing sodium bisulfite probing

Identifiers

PMID35704185
PMCPMC9261291
OpenAlexW4285059715

What OpenQuestion holds

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Read underepoch 390

Registered trials

None linked

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.