Genome-wide and cell-type-selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing.

Autor:	Li X; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA., Mills WT 4th; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA., Jin DS; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA., Meffert MK; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: mkm@jhmi.edu.
Jazyk:	angličtina
Zdroj:	Cell reports methods [Cell Rep Methods] 2024 Aug 19; Vol. 4 (8), pp. 100836. Date of Electronic Publication: 2024 Aug 09.
DOI:	10.1016/j.crmeth.2024.100836
Abstrakt:	Small noncoding RNAs (sncRNAs) regulate biological processes by impacting post-transcriptional gene expression through repressing the translation and levels of targeted transcripts. Despite the clear biological importance of sncRNAs, approaches to unambiguously define genome-wide sncRNA:target RNA interactions remain challenging and not widely adopted. We present CIMERA-seq, a robust strategy incorporating covalent ligation of sncRNAs to their target RNAs within the RNA-induced silencing complex (RISC) and direct detection of in vivo interactions by sequencing of the resulting chimeric RNAs. Modifications are incorporated to increase the capacity for processing low-abundance samples and permit cell-type-selective profiling of sncRNA:target RNA interactions, as demonstrated in mouse brain cortex. CIMERA-seq represents a cohesive and optimized method for unambiguously characterizing the in vivo network of sncRNA:target RNA interactions in numerous biological contexts and even subcellular fractions. Genome-wide and cell-type-selective CIMERA-seq enhances researchers' ability to study gene regulation by sncRNAs in diverse model systems and tissue types. Competing Interests: Declaration of interests The authors declare no competing interests. (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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