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Landscape of semi-extractable RNAs across five human cell lines

Phase-separated membraneless organelles often contain RNAs that exhibit unusual semi-extractability upon 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, 1,325 semi-extractable RNAs were identified across five humancell lines, including NEAT1, TRIO, EXT1, ZCCHC7, and FTX, which exhibited stable semi-extractability. Semi-extractable RNAs tend to be distributed in the nucleolus 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. Consistently, 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.