Detection of Nuclear RNA Decay Intermediates Using a Modified Oxford Nanopore RNA Sequencing Strategy.

Kevin He, Guillaume F Chanfreau

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. 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

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1 · What the graph read from it

What it found

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3 · Its place in the literature

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0 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

2 authors.

Kevin HeDepartment of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA.

Guillaume F ChanfreauDepartment of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA. guillom@chem.ucla.edu.

Funding

The Control of Gene Expression by Eukaryotic RibonucleasesR35GM130370 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Guillaume F Chanfreau · 2019 to 2026

$3.3M

NIGMS NIH HHS R35 GM130370

6 · The paper itself

Abstract

The nuclear RNA exosome complex is crucial for noncoding RNA processing and RNA quality control in the nucleus. Identifying substrates and intermediates of RNA decay pathways, such as those mediated by the exosome complex using Oxford Nanopore sequencing can be difficult in part because a simple method to detect them has been lacking and also because some of these RNAs lack abundant poly(A) tails which are required for Oxford Nanopore-based sequencing. Here we describe an Oxford nanopore-based approach which can be used to identify long reads corresponding to precursors and products of nuclear exosome processing. We are able to observe accumulation of unprocessed snoRNAs, cleavage products of the yeast nuclear RNase III endonuclease Rnt1p when the nuclear exosome component Rrp6p is inactivated.

Indexed as

Exosome Multienzyme Ribonuclease ComplexNanopore SequencingRNA StabilityRNA, NuclearRNA, Small NucleolarSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence Analysis, RNAExosome Multienzyme Ribonuclease ComplexRNA, NuclearRNA, Small NucleolarRRP6 protein, S cerevisiaeSaccharomyces cerevisiae ProteinsOxford Nanopore sequencingRNA degradationRNA exosomeRnt1Rrp6Saccharomyces cerevisiaeSlu7

Identifiers

PMID39535719

DOI10.1261/rna.079505.122

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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.