Simultaneous profiling of chromatin-associated RNA at targeted DNA loci and RNA-RNA Interactions through TaDRIM-seq
文献类型： 外文期刊
作者： Ding, Cheng 1 ; Chen, Guoting 1 ; Luan, Shiping 1 ; Gao, Runxin 1 ; Fan, Yudong 1 ; Zhang, Ying 1 ; Wang, Xiaoting 1 ; Li, Guoliang 1 ; Foda, Mohamed F. 1 ; Yan, Jiapei 1 ; Li, Xingwang 1 ;
作者机构： 1.Huazhong Agr Univ, Natl Key Lab Crop Genet Improvement, Hubei Hongshan Lab, Wuhan, Peoples R China
2.Huazhong Agr Univ, Hubei Key Lab Agr Bioinformat, Wuhan, Peoples R China
3.Huazhong Agr Univ, Hubei Engn Technol Res Ctr Agr Big Data, Genom Res Ctr 3D, Wuhan, Peoples R China
4.Benha Univ, Fac Agr, Dept Biochem, Banha 13736, Egypt
5.Huazhong Agr Univ, Shenzhen Inst Nutr & Hlth, Wuhan, Peoples R China
6.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch,Genome Anal Lab Minist Agr, Guangdong Lab Lingnan Modern Agr, Shenzhen, Peoples R China
期刊名称：NATURE COMMUNICATIONS （ 影响因子：15.7； 五年影响因子：17.2 ）
ISSN：
年卷期： 2025 年 16 卷 1 期
页码：
收录情况： SCI
摘要： Eukaryotic genomes are extensively transcribed into various types of RNAs, many of which are physically associated with chromatin in cis at their transcription sites or in trans to other genomic loci. Emerging roles have been uncovered for these chromatin-associated RNAs (caRNAs) in gene regulation and genome organization, yet they remain challenging to interrogate. Here, we present TaDRIM-seq, a technique employing Protein G (PG)-Tn5-targeted DNA elements and in situ proximity ligation to concurrently probe caRNAs across diverse genomic regions as well as global RNA-RNA interactions within intact nuclei. Notably, this approach diminishes required cell inputs, minimizes hands-on time compared to established methodologies, and is compatible in both mammalian cells and plants. Using this technique, we identify extensive caRNAs at DNA anchor regions associated with chromatin loops and reveal diurnal variation in RNA-DNA and RNA-RNA connectivity networks within rice.
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