Premium
Unusual semi‐extractability as a hallmark of nuclear body‐associated architectural noncoding RNA s
Author(s) -
Chujo Takeshi,
Yamazaki Tomohiro,
Kawaguchi Tetsuya,
Kurosaka Satoshi,
Takumi Toru,
Nakagawa Shinichi,
Hirose Tetsuro
Publication year - 2017
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.15252/embj.201695848
Subject(s) - rna , biology , rna extraction , lysis , microbiology and biotechnology , non coding rna , cell nucleus , extraction (chemistry) , biochemistry , biophysics , nucleus , chromatography , chemistry , gene
NEAT 1_2 long noncoding RNA (lnc RNA ) is the molecular scaffold of paraspeckle nuclear bodies. Here, we report an improved RNA extraction method: extensive needle shearing or heating of cell lysate in RNA extraction reagent improved NEAT 1_2 extraction by 20‐fold (a property we term “semi‐extractability”), whereas using a conventional method NEAT 1_2 was trapped in the protein phase. The improved extraction method enabled us to estimate that approximately 50 NEAT 1_2 molecules are present in a single paraspeckle. Another architectural lnc RNA , IGS 16 , also exhibited similar semi‐extractability. A comparison of RNA ‐seq data from needle‐sheared and control samples revealed the existence of multiple semi‐extractable RNA s, many of which were localized in subnuclear granule‐like structures. The semi‐extractability of NEAT 1_2 correlated with its association with paraspeckle proteins and required the prion‐like domain of the RNA ‐binding protein FUS . This observation suggests that tenacious RNA –protein and protein–protein interactions, which drive nuclear body formation, are responsible for semi‐extractability. Our findings provide a foundation for the discovery of the architectural RNA s that constitute nuclear bodies.