TY  - JOUR
TI  - Chromatin-RNA in situ Reverse Transcription Sequencing (CRIST-seq) Approach to Profile the Non-coding RNA Interaction Network
AU  - Zhang, Shilin 
AU  - Wen, Xue 
AU  - Zhou, Lei 
AU  - Li, Hui 
AU  - Li, Wei 
AU  - Hoffman, Andrew R
AU  - Hu, Ji- Fan
AU  - Cui, Jiuwei 
VL  - 13
IS  - 14
PY  - 2023
DA  - 2023/07/20
SP  - e4718
C1  - Bio-protocol 2023;13:e4718
DO  - 10.21769/BioProtoc.4718
UR  - https://doi.org/10.21769/BioProtoc.4718
AB  - Non-coding RNAs (ncRNAs) are defined as RNAs that do not encode proteins, but many ncRNAs do have the ability to regulate gene expression. These ncRNAs play a critical role in the epigenetic regulation of various physiological and pathological processes through diverse biochemical mechanisms. However, the existing screening methods to identify regulatory ncRNAs only focus on whole-cell expression levels and do not capture every ncRNA that targets certain genes. We describe a new method, chromatin-RNA in situ reverse transcription sequencing (CRIST-seq), that can identify all the ncRNAs that are associated with the regulation of any given gene. In this article, we targeted the ncRNAs that are associated with pluripotent gene Sox2, allowing us to catalog the ncRNA regulation network of pluripotency maintenance. This methodology is universally applicable for the study of epigenetic regulation of any genes by making simple changes on the CRISPR-dCas9 gRNAs.Key features• This method provides a new technique for screening ncRNAs and establishing chromatin interaction networks.• The target gene for this method can be any gene of interest and any site in the entire genome.• This method can be further extended to detect RNAs, DNAs, and proteins that interact with target genes.Graphical overview
KW  - CRIST-seq
KW  - Noncoding RNA
KW  - RNA-seq
KW  - Regulatory element
KW  - RNA–DNA interaction
KW  - Epigenetics
JF  - Bio-protocol
SN  - 2331-8325
PB  - Bio-protocol LLC.
BIO101  - False