Digital RNase Footprinting of RNA-Protein Complexes and Ribosomes in Mitochondria

Research output: Chapter in Book/Conference paperChapterpeer-review

Abstract

RNA-binding proteins and mitochondrial ribosomes have been found to be linchpins of mitochondrial gene expression in health and disease. The expanding repertoire of proteins that bind and regulate the mitochondrial transcriptome has necessitated the development of new tools and methods to examine their molecular functions. Next-generation sequencing technologies have advanced the RNA biology field through application of high-throughput methods to study RNA-protein interactions. Here we describe a digital RNase footprinting method to analyze protein and ribosome interactions with mitochondrially encoded transcripts that provides insight into their mechanisms and minimal binding sites. We provide details on RNase digestion and next-generation sequencing, along with computational analyses and visualization of the binding targets within the mitochondrial transcriptome.

Original languageEnglish
Title of host publicationThe Mitoribosome
Subtitle of host publicationMethods and Protocols
EditorsAntoni Barrientos, Flavia Fontanesi
Place of PublicationUSA
PublisherHumana Press Inc.
Pages317-328
Number of pages12
ISBN (Electronic)978-1-0716-3171-3
ISBN (Print)978-1-0716-3170-6
DOIs
Publication statusPublished - 2023

Publication series

NameMethods in Molecular Biology
Volume2661
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

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