TY  - JOUR
TI  - Simultaneous Capture of Chromatin-Associated RNA and Global RNA–RNA Interactions With Reduced Input Requirements
AU  - Ding, Cheng 
AU  - Chen, Guoting 
AU  - Luan, Shiping 
AU  - Gong, Yuanyuan 
AU  - Gui, Cuilin 
AU  - Yang, Chen 
AU  - Xiang, Zihe 
AU  - Du, Junjie 
AU  - Foda, Mohamed F.
AU  - Yan, Jiapei 
AU  - Li, Xingwang  
VL  - 15
IS  - 17
PY  - 2025
DA  - 2025/09/05
SP  - e5430
C1  - Bio-protocol 2025;15:e5430
DO  - 10.21769/BioProtoc.5430
UR  - https://doi.org/10.21769/BioProtoc.5430
AB  - Chromatin-associated RNAs (caRNAs) have been increasingly recognized as key regulators of gene expression and genome architecture. A few technologies, such as ChRD-PET and RedChIP, have emerged to assess protein-mediated RNA–chromatin interactions, but each has limitations. Here, we describe the TaDRIM-seq (targeted DNA-associated RNA and RNA–RNA interaction mapping by sequencing) technique, which combines Protein G (PG)-Tn5-targeted DNA tagmentation with in situ proximity ligation to simultaneously profile caRNAs across genomic regions and capture global RNA–RNA interactions within intact nuclei. This approach reduces the required cell input, shortens the experimental duration compared to existing protocols, and is applicable to both mammalian and plant systems.
KW  - Chromatin-associated RNAs (caRNAs)
KW  - Multi-omics
KW  - RNA–DNA interactomes
KW  - RNA–RNA interactomes
KW  - DNA element
KW  - TaDRIM-seq
KW  - Low-input requirement
JF  - Bio-protocol
SN  - 2331-8325
PB  - Bio-protocol LLC.
BIO101  - False