Poly(ADP-ribosyl)ation of heterogeneous nuclear ribonucleoproteins modulates splicing

Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
Nucleic Acids Research (Impact Factor: 9.11). 05/2009; 37(11):3501-13. DOI: 10.1093/nar/gkp218
Source: PubMed


The biological functions of poly(ADP-ribosyl)ation of heterogeneous nuclear ribonucleoproteins (hnRNPs) are not well understood.
However, it is known that hnRNPs are involved in the regulation of alternative splicing for many genes, including the Ddc gene in Drosophila. Therefore, we first confirmed that poly(ADP-ribose) (pADPr) interacts with two Drosophila hnRNPs, Squid/hrp40 and Hrb98DE/hrp38, and that this function is regulated by Poly(ADP-ribose) Polymerase 1 (PARP1) and Poly(ADP-ribose) Glycohydrolase (PARG) in vivo. These findings then provided a basis for analyzing the role of pADPr binding to these two hnRNPs in terms of alternative
splicing regulation. Our results showed that Parg null mutation does cause poly(ADP-ribosyl)ation of Squid and hrp38 protein, as well as their dissociation from active chromatin.
Our data also indicated that pADPr binding to hnRNPs inhibits the RNA-binding ability of hnRNPs. Following that, we demonstrated
that poly(ADP-ribosyl)ation of Squid and hrp38 proteins inhibits splicing of the intron in the Hsrω-RC transcript, but enhances splicing of the intron in the Ddc pre-mRNA. Taken together, these findings suggest that poly(ADP-ribosyl)ation regulates the interaction between hnRNPs and
RNA and thus modulates the splicing pathways.

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    • "Armadillo, a transcriptional regulator in the canonical Wnt pathway, required for LTM in Drosophila (Tan et al., 2013 ), was downregulated in Glo-LTMshort . Three genes involved in splice variation were DE in Glo- LTM-long, i.e., Ataxin-2 binding protein 1 (A2bp1), which is involved in splicing of exons in ion channels, receptors and synaptic proteins (Lee et al., 2009), Mushroom-body expressed (Mub) (Park et al., 2004), which is involved in mRNA splicing, and Parg (Poly(ADP-ribose) glycohydrolase), which modulates alternative splicing (Ji and Tulin, 2009). "
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    ABSTRACT: Even though learning and memory are universal traits in the Animal Kingdom, closely related species reveal substantial variation in learning rate and memory dynamics. To determine the genetic background of this natural variation, we studied two congeneric parasitic wasp species, Cotesia glomerata and C. rubecula, which lay their eggs in caterpillars of the large and small cabbage white butterfly. A successful egg laying event serves as an unconditioned stimulus (US) in a classical conditioning paradigm, where plant odors become associated with the encounter of a suitable host caterpillar. Depending on the host species, the number of conditioning trials and the parasitic wasp species, three different types of transcription-dependent long-term memory (LTM) and one type of transcription-independent, anesthesia-resistant memory (ARM) can be distinguished. To identify transcripts underlying these differences in memory formation, we isolated mRNA from parasitic wasp heads at three different time points between induction and consolidation of each of the four memory types, and for each sample three biological replicates, where after strand-specific paired-end 100 bp deep sequencing. Transcriptomes were assembled de novo and differential expression was determined for each memory type and time point after conditioning, compared to unconditioned wasps. Most differentially expressed (DE) genes and antisense transcripts were only DE in one of the LTM types. Among the DE genes that were DE in two or more LTM types, were many protein kinases and phosphatases, small GTPases, receptors and ion channels. Some genes were DE in opposing directions between any of the LTM memory types and ARM, suggesting that ARM in Cotesia requires the transcription of genes inhibiting LTM or vice versa. We discuss our findings in the context of neuronal functioning, including RNA splicing and transport, epigenetic regulation, neurotransmitter/peptide synthesis and antisense transcription. In conclusion, these brain transcriptomes provide candidate genes that may be involved in the observed natural variation in LTM in closely related Cotesia parasitic wasp species.
    Full-text · Article · Sep 2015 · Frontiers in Behavioral Neuroscience
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    • "The hsrr is a developmentally active, heat shock (HS) inducible, noncoding gene in Drosophila (reviewed in Lakhotia, 2011) producing multiple lncRNAs ( Its most extensively studied nucleus limited hsrr-n1 (hsrr-RB) and spliced hsrr-n2 (hsrr-RG) lncRNAs, together referred to as hsrr-n (Mallik and Lakhotia, 2011), interact with variety of RNA processing proteins including Hrb87F/Hrp36, Hrb57A/Bancal, Hrb98DE/Hrp38, Squid/Hrp40, PEP, Rumpelstiltskin/Hrp59, NonA, and Sxl (Prasanth et al., 2000; Jolly and Lakhotia, 2006; Ji and Tulin, 2009; Onorati et al., 2011; Singh and Lakhotia, 2012) to organize the omega speckles. "
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    ABSTRACT: The nucleus limited long-noncoding hsrω-n transcripts, hnRNPs, and some other RNA processing proteins organize nucleoplasmic omega speckles in Drosophila. Unlike other nuclear speckles, omega speckles rapidly disappear following cell stress, while hnRNPs and other associated proteins move away from chromosome sites, nucleoplasm, and the disappearing speckles to get uniquely sequestered at hsrω locus. Omega speckles reappear and hnRNPs get redistributed to normal locations during recovery from stress. With a view to understand the dynamics of omega speckles and their associated proteins, we used live imaging of GFP tagged hnRNPs (Hrb87F, Hrb98DE, or Squid) in unstressed and stressed Drosophila cells. Omega speckles display size dependent mobility in nucleoplasmic domains with significant colocalization with nuclear matrix Tpr/Megator and SAFB proteins, which also accumulate at hsrω gene site after stress. Instead of moving towards the nuclear periphery located hsrω locus following heat shock or colchicine treatment, omega speckles rapidly disappear within nucleoplasm while chromosomal and nucleoplasmic hnRNPs move, stochastically or, more likely, by nuclear matrix-mediated transport to hsrω locus in non-particulate form. Continuing transcription of hsrω during cell stress is essential for sequestering incoming hnRNPs at the site. While recovering from stress, the sequestered hnRNPs are released as omega speckles in ISWI-dependent manner. Photobleaching studies reveal hnRNPs to freely move between nucleoplasm, omega speckles, chromosome regions, and hsrω gene site although their residence periods at chromosomes and hsrω locus are longer. A model for regulation of exchange of hnRNPs between nuclear compartments by hsrω-n transcripts is presented.
    Full-text · Article · Aug 2015 · Chromosoma
    • "Furthermore, the ability of pADPr to bind hnRNPs is also upregulated by heat-shock treatment, indicating that pADPr binding to hnRNPs may play a role in regulating hnRNP upon environmental stresses (Ji and Tulin 2009). Moreover, pADPr seems to be responsible for the relocalization of hnRNPs from chromatin to the nucleoplasm (Ji and Tulin 2009), Recent data have shown that PARylation regulates at least two hnRNPdependent post-transcriptional processes like alternative splicing and translation ( Tulin 2012, 2013). In conclusion, hnRNP regulation by pADPr seems essential to modulate their activity under normal physiological conditions. "
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    ABSTRACT: Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a highly conserved family of RNA-binding proteins able to associate with nascent RNAs in order to support their localization, maturation and translation. Research over this last decade has remarked the importance of gene regulatory processes at post-transcriptional level, highlighting the emerging roles of hnRNPs in several essential biological events. Indeed, hnRNPs are key factors in regulating gene expression, thus, having a number of roles in many biological pathways. Moreover, failure of the activities catalysed by hnRNPs affects various biological processes and may underlie several human diseases including cancer, diabetes and neurodegenerative syndromes. In this review, we summarize some of hnRNPs' roles in the model organism Drosophila melanogaster, particularly focusing on their participation in all aspects of post-transcriptional regulation as well as their conserved role and involvement in the aetiology of human pathologies.
    No preview · Article · Jun 2014 · Chromosoma
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