m⁶ A 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 (m⁶ A) RNA modification. 11% of the first adenosine in the repetitive HSATIII sequence were m⁶ A-modified. nSBs sequester the m⁶ A writer complex to methylate HSATIII, leading to subsequent sequestration of the nuclear m⁶ A reader, YTHDC1. Sequestration of these factors from the nucleoplasm represses m⁶ A modification of pre-mRNAs, leading to repression of m⁶ A-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 m⁶ A-modified architectural lncRNAs.