Satellite RNAs: emerging players in subnuclear architecture and gene regulation

Abstract

Satellite DNA is characterized by long, tandemly repeated sequences mainly found in centromeres and pericentromeric chromosomal regions. The recent advent of telomere-to-telomere sequencing data revealed the complete sequences of satellite regions, including centromeric α-satellites and pericentromeric HSat1-3, which together comprise ~ 5.7% of the human genome. Despite possessing constitutive heterochromatin features, these regions are transcribed to produce long noncoding RNAs with highly repetitive sequences that associate with specific sets of proteins to play various regulatory roles. In certain stress or pathological conditions, satellite RNAs are induced to assemble mesoscopic membraneless organelles. Specifically, under heat stress, nuclear stress bodies (nSBs) are scaffolded by HSat3 lncRNAs, which sequester hundreds of RNA-binding proteins. Upon removal of the stressor, nSBs recruit additional regulatory proteins, including protein kinases and RNA methylases, which modify the previously sequestered nSB components. The sequential recruitment of substrates and enzymes enables nSBs to efficiently regulate the splicing of hundreds of pre-mRNAs under limited temperature conditions. This review discusses the structural features and regulatory roles of satellite RNAs in intracellular architecture and gene regulation.

Keywords: T2T genome; membraneless organelle; noncoding RNA; satellite DNA; stress response.

Figure 1. Summary of satellite DNAs and RNAs in human cells

(A) Representative illustration of satellite DNAs in human chromosomes. Four types of satellite DNAs, namely αSat, HSat1, HSat2, and HSat3, are shown. Triangles represent repeat sequences comprising each satellite DNA. The αSat arrays are composed of HORs with different monomer repeat sequences repeated > 1,000 times. (B) Overview of satellite RNA functions. αSat RNAs are transcribed from centromeric αSat DNAs in all chromosomes. Intracellular localization of αSat lncRNAs is reported to be retained at the centromere, but another study reported the nucleolar localization of αSat lncRNAs, which relocate to the centromere at the beginning of mitosis. A further study also reported the centromeric localization of the minor population and the cytoplasmic localization of the major population. (B) HSat1A lncRNAs are thought to be mainly transcribed from the large HSat1A DNA and they are reported to colocalize with fibrillarin in the nucleolar periphery but not in the centromere. HSat2 lncRNAs are transcribed from HSat2 DNA, which includes large satellite regions in chr1 and chr16, particularly in cancer cells. HSat2 lncRNAs sequester proteins including MeCP and assemble MLOs termed CAST bodies. HSat3 lncRNAs are transcribed from HSat3 DNA, which includes a large satellite region in chr 9, under various stress conditions including heat stress. HSat3 lncRNAs sequester more than 100 proteins including SRSF1 and SAFB and assemble stress‐inducible MLOs termed nuclear stress bodies (nSBs).

Figure 2. Schematic presentation of HSat3 induction and nSB assembly

HSat3 regions are in the form of heterochromatin under normal conditions and euchromatin upon heat stress. Transcription factors accumulate at HSat3 regions, and HSat3 lncRNAs are thereby transcribed and recruit specific RBPs. After stress removal, remodeling of nSB components occurs (see also Table 2). The green and yellow circles indicate constitutive nSB proteins and the purple and beige circles indicate recovery phase‐specific nSB proteins.

Figure 3. Two modes of nSB action for regulating splicing

(A) Overview of biochemical modifications within nSBs. HSat3 lncRNAs concentrate dephosphorylated SRSFs within nSBs during heat stress and recruit CLK1 kinase into nSBs after stress removal to rapidly rephosphorylate SRSFs (reaction crucible). HSat3 lncRNAs also recruit m⁶A writer complex after stress removal to undergo RNA m⁶A modification, thereby sequestering an m⁶A reader protein, YTHDC1 (molecular sponge). (B) Through the action as the reaction crucible, nSBs rapidly normalize the heat stress‐induced dephosphorylation of SRSFs and splicing alterations after stress removal. (C) As molecular sponges, nSBs sequester m⁶A factors, resulting in inhibition of the m⁶A modification of other pre‐mRNAs and their m⁶A‐dependent splicing.

Figure 4. Comparison of SAC31 foci and nSBs

(A, B) Schematic illustration of SCA31 foci (A) and nSB (B). (C) List of features of HSat3 and SCA31 RNA. The common binding proteins are shown in bold.