CLIP-Seq to identify targets and interactions of RNA binding proteins and RNA modifying enzymes.

Szczegóły
Abstrakt

Tytuł:: CLIP-Seq to identify targets and interactions of RNA binding proteins and RNA modifying enzymes.
Autorzy:: Stoute J; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
Liu KF; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States. Electronic address: .
Źródło:: Methods in enzymology [Methods Enzymol] 2021; Vol. 658, pp. 419-434. Date of Electronic Publication: 2021 Aug 23.
Typ publikacji:: Journal Article; Research Support, N.I.H., Extramural
Język:: English
Imprint Name(s):: Original Publication: New York, Academic Press.
MeSH Terms:: Chromatin Immunoprecipitation Sequencing*
RNA*/genetics
Immunoprecipitation ; RNA-Binding Proteins/genetics ; Sequence Analysis, RNA
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Grant Information:: R35 GM133721 United States GM NIGMS NIH HHS; T32 GM132039 United States GM NIGMS NIH HHS
Contributed Indexing:: Keywords: CLIP-seq; RNA binding protein; RNA modification; RNA modifying enzymes; Sequencing method
Substance Nomenclature:: 0 (RNA-Binding Proteins)
63231-63-0 (RNA)
Entry Date(s):: Date Created: 20210914 Date Completed: 20210922 Latest Revision: 20230519
Update Code:: 20240105
PubMed Central ID:: PMC9073954
DOI:: 10.1016/bs.mie.2021.08.001
PMID:: 34517957
: Czasopismo naukowe

The study of RNA chemical modifications is currently one of the most rapid-growing fields. Many types of RNA modifications in diverse RNA species have been shown to play versatile roles in a wide array of cellular processes. These modifications are installed and erased by writer and eraser enzymes, respectively. Additionally, RNA chemical modifications have downstream biological effects through either influencing changes in the chemistry or structure of RNA molecules or through recognition of the modification; these functions are primarily executed by the modification reader proteins. Reader proteins may bind to the modification site and cause a downstream signal cascade. One of the essential tools for studying erasers, writers, and readers is cross-linking immunoprecipitation followed by high-throughput sequencing (CLIP-seq). This method can detect the sites on endogenous RNAs bound by RNA-binding proteins or RNA modifying enzymes. Essentially, this strategy allows for snapshots of the epitranscriptome and molecular events occurring within the cell. In this article, we go through in detail the various steps involved in CLIP-seq.
(Copyright © 2021 Elsevier Inc. All rights reserved.)

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