| Journal Title /掲載ジャーナル名 |
Nucleic Acids Research |
| Publication Year and Month /掲載年月 |
July, 2023 |
| Paper Title /論文タイトル |
Landscape of semi-extractable RNAｓacross five human cell lines |
| DOI /論文DOI |
10.1093/nar/gkad567 |
| Author of Waseda University /本学の著者 |
ZENG, Chao(Junior Researcher(Assistant Professor), Faculty of Science and Engineering, Waseda Research Institute for Science and Engineering):First Author |
| Related Websites /関連Web |
– |
| Abstract /抄録 |
Phase-separated membraneless organelles often contain RNAs that exhibit unusual semi-extractability using the conventional RNA extraction method, and can be efficiently retrieved by needle shearing or heating during RNA extraction. Semi-extractable RNAs are promising resources for understanding RNA-centric phase separation. However, limited assessments have been performed to systematically identify and characterize semi-extractable RNAs. In this study, 1074 semi-extractable RNAs, including ASAP1, DANT2, EXT1, FTX, IGF1R, LIMS1, NEAT1, PHF21A, PVT1, SCMH1, STRG.3024.1, TBL1X, TCF7L2, TVP23C-CDRT4, UBE2E2, ZCCHC7, ZFAND3 and ZSWIM6, which exhibited consistent semi-extractability were identified across five human cell lines. By integrating publicly available datasets, we found that semi-extractable RNAs tend to be distributed in the nuclear compartments but are dissociated from the chromatin. Long and repeat-containing semi-extractable RNAs act as hubs to provide global RNA–RNA interactions. Semi-extractable RNAs were divided into four groups based on their k-mer content. The NEAT1 group preferred to interact with paraspeckle proteins, such as FUS and NONO, implying that RNAs in this group are potential candidates of architectural RNAs that constitute nuclear bodies. |
