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Platform-based gene regulation by an endoderm-specific lncRNA via stabilizing nuclear speckles

ABSTRACT: Nuclear speckles (NSs), one of the key non-membrane nuclear bodies, participate in transcription, RNA processing, and chromatin organization, yet their precise functions and mechanisms in vivo remain elusive. Here we show that Falcor, an endoderm-specific long non-coding RNA (lncRNA), is necessary and sufficient for maintaining structural integrity of NSs in mouse liver cells. Disruption and reinstatement of NSs by Falcor coordinately regulate more than one thousand genes, including those related to metabolic processes. Falcor locates in the core of NSs, and interacts with Zinc finger CCCH domain-containing protein 11A (ZC3H11A), thereby facilitating phase separation to maintain NSs' structure. Furthermore, specific knockout of Falcor in the mouse liver uncovered its pivotal role in governing metabolic homeostasis, and its absence affords protection against diet-induced liver steatosis, obesity, and metabolic disorders. Collectively, our study demonstrated essential roles of Falcor in NSs maintenance and regulating metabolic homeostasis, which imply the importance of lineage-specific lncRNAs in “platform-based” gene regulation via NSs during pathophysiological processes.

ORGANISM(S): Mus musculus

PROVIDER: GSE267072 | GEO | 2024/05/13

REPOSITORIES: GEO

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Nuclear speckles as a key regulator for the 3D genome organization [HiC]

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2019-06-30 | GSE131463 | GEO

Nuclear speckles as a key regulator for the 3D genome organization [RNA-Seq]

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ZC3H11A interacts with PABPN1 and alters polyadenylation of viral transcripts

Project description:Nuclear mRNA metabolism is regulated by multiple proteins, which either directly bind to RNA or form multi-protein complexes. The RNA-binding protein ZC3H11A is involved in nuclear mRNA export, and NF-κB signaling and is essential during mouse embryo development. Furthermore, previous studies have shown that ZC3H11A is important for nuclear-replicating viruses. However, detailed biochemical characterization of the ZC3H11A protein has been lacking. In this study, we established the ZC3H11A protein interactome in human and mouse cells. We demonstrate that the nuclear poly(A)-binding protein PABPN1 interacts specifically with the ZC3H11A protein and controls ZC3H11A localization into nuclear speckles. We report that ZC3H11A specifically interacts with the human adenovirus type 5 (HAdV-5) capsid mRNA in a PABPN1-dependent manner. Notably, ZC3H11A uses the same zinc finger motifs to interact with PABPN1 and mRNA, with a single zinc finger motif responsible for these functions. Further, we demonstrate that the lack of ZC3H11A alters the polyadenylation of HAdV-5 capsid mRNA. Taken together, our results suggest that the ZC3H11A protein acts as a novel regulator of polyadenylation of nuclear mRNA.

2023-10-24 | PXD042238 | Pride

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2022-02-06 | GSE196025 | GEO

Project description:ZC3H11A RNAseq data

| PRJNA436744 | ENA

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