Piwi interacts with chromatin at nuclear pores and promiscuously binds nuclear transcripts in Drosophila ovarian somatic cells

Ilyin, Artem A.; Ryazansky, Sergei; Doronin, Semen A.; Olenkina, Oxana M.; Mikhaleva, Elena A.; Yakushev, E. Y.; Abramov, Yuri; Belyakin, Stepan N.; Ivankin, Anton V.; Pindyurin, Alexey V.; Гвоздев, В. А.; Klenov, Mikhail S.; Shevelyov, Yuri Y.

doi:10.1093/nar/gkx355

Cited by 34 publications

(47 citation statements)

References 67 publications

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“…12). Dam-ID showed that both Piwi and NPCs contacts chromatin at the same regions 31 . In this regard, dNxf1 can localize to nuclear peripheries in which most constitutive heterochromatin resides 13,32–34 .…”

Section: Figurementioning

confidence: 99%

A Pandas complex adapted for piRNA-guided transposon silencing

Zhao

Cheng

Miao

et al. 2019

Preprint

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40The repression of transposons by the Piwi-interacting RNA (piRNA) pathway is essential to 41 protect animal germ cells. In Drosophila ovaries, Panoramix (Panx) enforces transcriptional 42 silencing by binding to the target-engaged Piwi-piRNA complex, although the precise 43 mechanisms by which this occur remain elusive. Here, we show that Panx functions 44 together with a germline specific paralogue of a nuclear export factor, dNxf2, and its 45 cofactor dNxt1 (p15) as a ternary complex to suppress transposon expression. Structural 46 and functional analysis demonstrate that dNxf2 binds Panx via its UBA domain and play an 47 important role in transposon silencing through binding to transposon transcripts directly. 48Unexpectedly, dNxf2 interacts directly with dNxf1 (TAP), which is also essential for 49 transposon silencing. Transient tethering of dNxf2 to nascent transcripts leads to their 50 nuclear retention. Therefore, we propose that dNxf2 may function as a Pandas (Panoramix-51 dNxf2 dependent TAP/p15 silencing) complex, which counteracts the canonical RNA 52 exporting machinery (TAP/p15) and restricts transposons to nuclear peripheries. Our 53 findings may have broader implications for understanding how RNA metabolism modulates 54 epigenetic gene silencing and heterochromatin formation. 55 56Transposons are highly abundant in eukaryotes, which make up nearly half of human genome. To 57 maintain eukaryotic genome integrity, nascent transcripts of transposons are often targeted by 58 nuclear Argonaute proteins for transcriptional gene silencing (TGS) 1-5 . In animal gonads, the PIWI-59 clade Argonautes guided by piRNAs (PIWI-interacting RNA) are thought to recognize nascent 60 transposon transcripts and direct sequence-specific heterochromatin formation 3 . As a critical 61 cofactor of Drosophila nuclear Piwi, Panoramix (Panx, also known as Silencio) links the target-62 engaged Piwi-piRNA complex to the general silencing machinery 6,7 . Enforced tethering of Panx to 63 nascent transcripts leads to cotranscriptional silencing and correlates with deposition of histone H3 64 lysine 9 trimethylation (H3K9me3) marks 6,7 . However, the mechanism by which Panx mediates the 65 repression remains unknown. An equally important question is why H3K9me3 marks are not always 66 sufficient for transposon silencing 8 . 67 68To understand this fundamental question, we cross-examined proteins that co-69 immunoprecipitated with Panx (Extended Data Fig. 1a) with piRNA pathway candidate genes from 70 RNA interference (RNAi) screens 9-12 . Unexpectedly, dNxf2 was identified as a potential cofactor of 71 Panx (Extended Data Fig.1a-c). dNxf2 belongs to an evolutionarily conserved NXF (nuclear export 72 factor) family of proteins, yet depletion of dNxf2 had no effect on polyadenylated mRNA export 13,14 . 73Instead, dNxf2 and its cofactor dNxt1 (also known as p15) were both identified in two published 74RNAi screens as being essential for transposon silencing 9,10 . Similar to Panx, dNxf2 is specifically 75 expressed in female gonads...

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Section: Figurementioning

confidence: 99%

A Pandas complex adapted for piRNA-guided transposon silencing

Zhao

Cheng

Miao

et al. 2019

Preprint

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“…Later, it was established that ELYS recruits Nup107 complex to kinetochores and hence helps in regulation of Nup107 complex mediated microtubule formation at kinetochores (Gillespie et al, 2007;Mishra et al, 2010;Yokoyama et al, 2014). Importantly, ELYS binds with promoter regions in chromatin and interacts with Mcm-7 helicase to exert control during DNA replication as well as interacts with Piwi for transcriptional regulation (Gillespie et al, 2007;Ilyin et al, 2017). Loss of ELYS induces severe defects in organism development like skeleton loss in Zebrafish, embryonic lethality in mouse, tissue differentiation defects and aging phenotypes (Cerveny et al, 2010;Davuluri et al, 2008;de Jong-Curtain et al, 2009;Gao et al, 2011;Okita et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

“…We chose Drosophila melanogaster (fruit flies) to address the importance of ELYS in early developmental processes. Although CG14215 has been reported as ELYS in Drosophila (hereafter as dElys) and shown to be present at the nuclear periphery and in association with promoter region on polytene chromosomes, none of these studies characterized dElys for its role in NPC assembly or other cellular processes in vivo (Ilyin et al, 2017;Pascual-Garcia et al, 2017). Here, through genetic, molecular and cellular characterization we report that the dElys plays important roles in the assembly and dynamics of nuclear pore and nuclear lamina functions.…”

mentioning

confidence: 81%

ELYS coordinates NF-κB pathway dynamics during development inDrosophila

Mehta

Kumar

Mishra

2018

Preprint

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Nuclear pores are the exclusive conduit to facilitate the nucleocytoplasmic transport in a precisely regulated manner. ELYS, a constituent protein of nuclear pores, initiates assembly of nuclear pore complexes (NPCs) into functional nuclear pores towards the end of mitosis. Using cellular, molecular and genetic tools, here, we report that ELYS orthologue (dElys) plays critical roles during Drosophila development. Through in silico analyses, we find all conserved structural features in dElys except for the presence of non-canonical AT-hook motif strongly binding with DNA. dElys localized to nuclear rim in interphase cells, but during mitosis, it was present on chromatin. RNAi mediated depletion of dElys leads to aberrant development and defects in the nuclear lamina and NPCs assembly at the cellular level. Furthermore, we demonstrate that in dElys depletion NF-B is activated and accumulates inside the nucleus which results in illtimed expression of critical molecules. dElys depletion sustains NF-B into the nucleus in post-embryonic stages. Prolonged NF-B inside nucleus induces apoptosis in response to hitherto unknown quality check mechanism and highlights on the underappreciated apoptotic paradigm of NF-B pathway.

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“…Finally, we tested whether Hywi-piRNA complexes physically associate with the somatic RNA targets identified by piRNA mapping, DGE analysis of hywi RNAi animals, and/or degradome sequencing. To this end, we performed RNA-immunoprecipitation (RIP) to isolate Hywi-piRNA-RNA ternary complexes from epithelial Hydra (Ilyin et al 2017). We performed RT-PCR to test for the presence of the following transcripts in our immunoprecipitated complexes: 1) eight TE transcripts that were upregulated in response to hywi knockdown, had a high number of piRNAs mapping, and were identified as targets in the degradome sequencing; 2) seven gene transcripts that were upregulated in response to hywi knockdown and had a high number of piRNAs mapping (one of these was identified as a target in the degradome sequencing) ( Table S3); 3) three gene transcripts that were upregulated in response to hywi knockdown, but did not have a high number of piRNAs mapping; and 4) six gene transcripts that were not affected by hywi knockdown and did not have a high number of piRNAs mapping to act as negative controls.…”

Section: Piwi-pirna Complexes Cleave Te Transcripts In Epithelial Stementioning

confidence: 99%

PIWI-piRNA pathway-mediated transposable element repression inHydrasomatic stem cells

Teefy

Siebert

Cazet

et al. 2019

Preprint

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Transposable elements (TEs) can damage genomes, thus organisms employ a variety of mechanisms to repress TE expression. However, these mechanisms often fail over time leading to de-repression of TEs in aging tissues. The PIWI-piRNA pathway is a small RNA pathway that represses TE expression in the germline of animals. Here we explore the function of the pathway in the epithelial stem cells of Hydra, a long-lived freshwater cnidarian. Hydra have three stem cell populations; endodermal and ectodermal epithelial stem cells are strictly somatic, whereas the interstitial stem cells retain germline competence. In our previous study, we found that the PIWI proteins are expressed in all three Hydra stem cell types. In this study, we focus on the ectodermal and endodermal epithelial stem cells to understand the somatic function of the pathway. We isolated piRNAs from Hydra that lack the interstitial lineage and found that these somatic piRNAs map predominantly to TE transcripts and display the conserved sequence signatures typical of germline piRNAs. Three lines of evidence suggest that the PIWI-piRNA pathway represses TEs in Hydra epithelial stem cells. First, epithelial knockdown of the Hydra PIWI protein hywi resulted in upregulation of TE expression. Second, degradome sequencing revealed evidence of PIWImediated cleavage of TE RNAs in epithelial cells using the ping-pong mechanism. Finally, we demonstrated a direct association between Hywi protein and TE transcripts in epithelial cells using RNA immunoprecipitation. Interestingly, we found that RNAi knockdown of hywi leads to an upregulation of genes involved in innate immunity, which may be in response to TE upregulation; this is consistent with recent studies on TE expression in mammalian cells. Altogether, this study suggests a function for the PIWI-piRNA pathway in maintaining the long-lived somatic cell lineages of Hydra and may point to a broader role for this pathway in protecting somatic tissue from TE-induced damage.

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Piwi interacts with chromatin at nuclear pores and promiscuously binds nuclear transcripts in Drosophila ovarian somatic cells

Cited by 34 publications

References 67 publications

A Pandas complex adapted for piRNA-guided transposon silencing

A Pandas complex adapted for piRNA-guided transposon silencing

ELYS coordinates NF-κB pathway dynamics during development inDrosophila

PIWI-piRNA pathway-mediated transposable element repression inHydrasomatic stem cells

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