m⁶A modification of HSATIII lncRNAs regulates temperature-dependent splicing

Nuclear stress bodies (nSBs) are nuclear membraneless organelles formed around stress-inducible HSATIII architectural long noncoding RNAs (lncRNAs). nSBs repress splicing of hundreds of introns during thermal stress recovery, which are partly regulated by CLK1 kinase phosphorylation of temperature-dependent Ser/Arg-rich splicing factors (SRSFs). Here, we report a distinct mechanism for this splicing repression through protein sequestration by nSBs. Comprehensive identification of RNA-binding proteins revealed HSATIII association with proteins related to N6-methyladenosine (m6A) RNA modification. 11% of the first adenosine in the repetitive HSATIII sequence were m6A-modified. nSBs sequester the m6A writer complex to methylate HSATIII, leading to subsequent sequestration of the nuclear m6A reader, YTHDC1. Sequestration of these factors from the nucleoplasm represses m6A modification of pre-mRNAs, leading to repression of m6A-dependent splicing during stress recovery phase. Thus, nSBs serve as a common platform for regulation of temperature-dependent splicing through dual mechanisms employing two distinct ribonucleoprotein modules with partially m6A-modified architectural lncRNAs.