PT  - JOURNAL ARTICLE
AU  - Riccardo Calandrelli
AU  - Xingzhao Wen
AU  - John L Charles Richard
AU  - Zhifei Luo
AU  - Tri C. Nguyen
AU  - Chien-Ju Chen
AU  - Zhijie Qi
AU  - Shuanghong Xue
AU  - Weizhong Chen
AU  - Zhangming Yan
AU  - Weixin Wu
AU  - Kathia Zaleta-Rivera
AU  - Rong Hu
AU  - Miao Yu
AU  - Yuchuan Wang
AU  - Wenbo Li
AU  - Jian Ma
AU  - Bing Ren
AU  - Sheng Zhong
TI  - Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells
AID  - 10.1101/2021.06.10.447969
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2021.06.10.447969
4099  - http://biorxiv.org/content/early/2022/09/07/2021.06.10.447969.short
4100  - http://biorxiv.org/content/early/2022/09/07/2021.06.10.447969.full
AB  - Chromatin-associated RNA (caRNA) is a vital component of the interphase nucleus; yet its distribution and role in the three-dimensional (3D) genome organization and function remain poorly understood. Here, we map caRNA’s spatial distribution on the 3D genome in human embryonic stem cells, fibroblasts, and myelogenous leukemia cells. These maps reveal several characteristics of caRNA distribution. caRNA is preferentially associated with its transcription site and up to several megabases of flanking genomic sequence. Furthermore, topologically associating domain (TAD) boundaries insulate RNA-DNA contacts. Abolishment or creation of a TAD boundary by genomic editing changed the boundary’s ability to insulate RNA-DNA contacts, demonstrating an impact of the 3D genome structure on the distribution of caRNA. Conversely, depletion of caRNA weakens TAD boundaries. We characterize caRNA based on their target genomic sequence into loop-anchor-associated RNA and those associated with any genomic sequence between loop anchors (between-anchor caRNA). Between-anchor caRNA suppresses chromatin loops, especially those with convergent CTCF binding sites in their loop anchors. These data suggest the indispensable roles of caRNA in the 3D genome organization.Competing Interest StatementThe authors have declared no competing interest.