Protocol for mapping RNA G-quadruplex for chromatin-bound RNA using d-rG4-seq.

Yong Woo Lee, Vered Levy, Jeannie T Lee

Abstract read

In one paragraph

Article in STAR protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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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.

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2 · The registry

The trial behind it

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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.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

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5 · Who and what money

Authors and funding

3 authors.

Yong Woo LeeDepartment of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.

Vered LevyDepartment of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.

Jeannie T LeeDepartment of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA. Electronic address: lee@molbio.mgh.harvard.edu.

Funding

Spreading of Xist RNA and Polycomb complexes along the inactive X-chromosome.R01HD097665 · NICHD · MASSACHUSETTS GENERAL HOSPITAL · PI LEE, JEANNIE T · 2019 to 2023

$3.5M

NICHD NIH HHS R01 HD097665

6 · The paper itself

Abstract

Here, we present a protocol for using d-rG4-seq, a technique for mapping RNA G-quadruplex (rG4) for chromatin-bound RNA. We describe steps for identifying in vivo rG4 structures based on differential sensitivity of rG4 to dimethyl sulfate (DMS) modification, folding in the presence of monovalent cations, K+ versus Li+, and reverse transcriptase (RT) readthrough when folded. We then detail procedures for isolating RNA from the chromatin-bound fractions to enrich for epigenetic regulators and comparing in vitro versus in vivo profiles. For complete details on the use and execution of this protocol, please refer to Lee et al.

Indexed as

ChromatinG-QuadruplexesRNAHumansSequence Analysis, RNAChromatinRNAGene ExpressionGenomicsMolecular Biology

Identifiers

PMID39643965

DOI10.1016/j.xpro.2024.103471

PMCPMC11656088

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LicenceCC BY-NC-ND

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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.