Identification of a Xist silencing domain by Tiling CRISPR

Scientific Reports
Yang WangJing Crystal Zhao

Abstract

Despite essential roles played by long noncoding RNAs (lncRNAs) in development and disease, methods to determine lncRNA cis-elements are lacking. Here, we developed a screening method named "Tiling CRISPR" to identify lncRNA functional domains. Using this approach, we identified Xist A-Repeats as the silencing domain, an observation in agreement with published work, suggesting Tiling CRISPR feasibility. Mechanistic analysis suggested a novel function for Xist A-repeats in promoting Xist transcription. Overall, our method allows mapping of lncRNA functional domains in an unbiased and potentially high-throughput manner to facilitate the understanding of lncRNA functions.

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Citations

Aug 29, 2019·EMBO Reports·Aurélie BousardSimão Teixeira da Rocha
Sep 29, 2020·Nucleic Acids Research·Jackson B TrotmanJ Mauro Calabrese
Nov 13, 2019·Wiley Interdisciplinary Reviews. RNA·William Garland, Torben Heick Jensen
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Apr 17, 2021·Wiley Interdisciplinary Reviews. RNA·Jackson B TrotmanJ Mauro Calabrese
Jun 3, 2021·Cancers·Lidia BorkiewiczIlona Telejko
Oct 16, 2021·Nature Biotechnology·Tingting JiangWen Xue
Dec 10, 2021·Biochemical Society Transactions·Ana Cláudia RaposoSimão Teixeira da Rocha

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Methods Mentioned

BETA
biopsy
RSA
PCR
immunoprecipitation
RepA
Genotyping
pull-down
FACS
Assay

Software Mentioned

Redundant siRNA Analysis ( RSA )
SMRT Tools
BWA
Blasr
SAMTools
Tiling

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