Actin is a key regulator of RNA polymerase (pol) II transcription. In complex with specific hnRNPs, it has been proposed that actin functions to recruit pol II coactivators during the elongation of nascent transcripts. Here, we show by affinity chromatography, protein-protein interaction assays, and biochemical fractionation of nuclear extracts that the histone acetyltransferase (HAT) PCAF associates with actin and hnRNP U. PCAF and the nuclear actin-associated HAT activity detected in the DNase I-bound protein fraction could be released by disruption of the actin-hnRNP U complex. In addition, actin, hnRNP U, and PCAF were found to be associated with the Ser2/5-and Ser2-phosphorylated pol II carboxy-terminal domain construct. Chromatin and RNA immunoprecipitation assays demonstrated that actin, hnRNP U, and PCAF are present at the promoters and coding regions of constitutively expressed pol II genes and that they are associated with ribonucleoprotein complexes. Finally, disruption of the actin-hnRNP U interaction repressed bromouridine triphosphate incorporation in living cells, suggesting that actin and hnRNP U cooperate with PCAF in the regulation of pol II transcription elongation.Eukaryotic gene transcription requires dynamic alterations of chromatin structure that are mediated by chromatin remodeling complexes and histone modifying enzymes (23, 28).For transcription competence, histone acetylation allows the switch between repressive and permissive chromatin structures through direct effects on nucleosome stability and through establishment of binding sites for regulatory proteins. Considerable progress in understanding the role of histone acetylation came from the discovery that the Saccharomyces cerevisiae transcription coactivator GCN5 and, more recently, other yeast and metazoan transcription cofactors are histone acetyltransferases (HATs). Mammalian homologs of the yeast cofactor GCN5 include PCAF and GCN5L (2,27,32,33,35). PCAF and GCN5L are encoded by distinct genes, and their expressions are differential and complementary in various tissues (33,35). Moreover, GCN5L is essential for mouse development, whereas PCAF is dispensable (33, 34). Human GCN5L and PCAF form parts of distinct multiprotein HAT complexes, namely the PCAF complex (17), the TFTC complex (1), and the STAGA complex (12). While these mammalian HAT complexes are still incompletely characterized, they have related but not identical subunit compositions.PCAF/GCN5, together with the p300/CREB-binding protein, is among the best-studied transcriptional coactivators (11). PCAF has been proposed to facilitate long-distance transcriptional enhancement by direct association with enhancer sequences (7). PCAF is also known to acetylate free histones or nucleosomes, primarily on lysine 14 of histone H3 (28), and its requirement as coactivator or HAT has been demonstrated for myogenesis and nuclear receptor-mediated and growth factor-signaled activation (28). However, it is presently unclear whether PCAF is also involved in the maintenance of effic...

In mammals actin contributes to transcription elongation by facilitating establishment of permissive chromatin. Here we report that the F-actin severing protein cofilin-1 is part of the same complex with actin and phosphorylated RNA polymerase (pol) II. In chromatin immunoprecipitation assays cofilin-1 was found selectively associated with transcribed regions of active genes, its occupancy being influenced by the polymerization state of actin. Cofilin-1 gene silencing led to a drop in FUrd incorporation into nascent transcripts. In cofilin-1 silenced cells chromatin immunoprecipitations showed that active genes were devoid of actin, phosphorylated pol II and displayed low histone H3 acetylation levels on K9. These findings suggest that cofilin-1 plays a major role in pol II transcription, facilitating association of elongating pol II and actin with active genes. We speculate that cofilin-1 performs its function in pol II transcription by regulating polymerization of gene-associated actin.

In mammals actin contributes to transcription elongation by facilitating establishment of permissive chromatin. Here we report that the F-actin severing protein cofilin-1 is part of the same complex with actin and phosphorylated RNA polymerase (pol) II. In chromatin immunoprecipitation assays cofilin-1 was found selectively associated with transcribed regions of active genes, its occupancy being influenced by the polymerization state of actin. Cofilin-1 gene silencing led to a drop in FUrd incorporation into nascent transcripts. In cofilin-1 silenced cells chromatin immunoprecipitations showed that active genes were devoid of actin, phosphorylated pol II and displayed low histone H3 acetylation levels on K9. These findings suggest that cofilin-1 plays a major role in pol II transcription, facilitating association of elongating pol II and actin with active genes. We speculate that cofilin-1 performs its function in pol II transcription by regulating polymerization of gene-associated actin.

N6-methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are two abundant modifications found in mRNAs and ncRNAs that can regulate multiple aspects of RNA biology. They function mainly by regulating interactions with specific RNA-binding proteins. Both modifications are linked to development, disease and stress response. To date, three methyltransferases and two demethylases have been identified that modify adenosines in mammalian mRNAs. Here, we present a comprehensive analysis of the interactomes of these enzymes. PCIF1 protein network comprises mostly factors involved in nascent RNA synthesis by RNA polymerase II, whereas ALKBH5 is closely linked with most aspects of pre-mRNA processing and mRNA export to the cytoplasm. METTL16 resides in subcellular compartments co-inhabited by several other RNA modifiers and processing factors. FTO interactome positions this demethylase at a crossroad between RNA transcription, RNA processing and DNA replication and repair. Altogether, these enzymes share limited spatial interactomes, pointing to specific molecular mechanisms of their regulation.

In rRNA biogenesis, nuclear myosin 1 (NM1) and actin synergize to activate rRNA gene transcription. Evidence that actin is in preribosomal subunits and NM1 may control rRNA biogenesis post-transcriptionally prompted us to investigate whether NM1 associates with and accompanies rRNA to nuclear pores (NPC). Ultracentrifugation on HeLa nucleolar extracts showed RNA-dependent NM1 coelution with preribosomal subunits. In RNA immunoprecipitations (RIPs), NM1 coprecipitated with pre-rRNAs and 18S, 5.8S, and 28S rRNAs, but failed to precipitate 5S rRNA and 7SL RNA. In isolated nuclei and living HeLa cells, NM1 or actin inhibition and selective alterations in actin polymerization impaired 36S pre-rRNA processing. Immunoelectron microscopy (IEM) on sections of manually isolated Xenopus oocyte nuclei showed NM1 localization at the NPC basket. Field emission scanning IEM on isolated nuclear envelopes and intranuclear content confirmed basket localization and showed that NM1 decorates actin-rich pore-linked filaments. Finally, RIP and successive RIPs (reRIPs) on cross-linked HeLa cells demonstrated that NM1, CRM1, and Nup153 precipitate same 18S and 28S rRNAs but not 5S rRNA. We conclude that NM1 facilitates maturation and accompanies export-competent preribosomal subunits to the NPC, thus modulating export.

In eukaryotes, RNA processing events in the nucleus influence the fate of transcripts in the cytoplasm. The multi-protein exon junction complex (EJC) associates with mRNAs concomitant with splicing in the nucleus and plays important roles in export, translation, surveillance and localization of mRNAs in the cytoplasm. In mammalian cells, the ribosome associated protein PYM (HsPYM) binds the Y14-Mago heterodimer moiety of the EJC core, and disassembles EJCs, presumably during the pioneer round of translation. However, the significance of the association of the EJC with mRNAs in a physiological context has not been tested and the function of PYM in vivo remains unknown. Here we address PYM function in Drosophila, where the EJC core proteins are genetically required for oskar mRNA localization during oogenesis. We provide evidence that the EJC binds oskar mRNA in vivo. Using an in vivo transgenic approach, we show that elevated amounts of the Drosophila PYM (DmPYM) N-terminus during oogenesis cause dissociation of EJCs from oskar RNA, resulting in its mislocalization and consequent female sterility. We find that, in contrast to HsPYM, DmPYM does not interact with the small ribosomal subunit and dismantles EJCs in a translation-independent manner upon over-expression. Biochemical analysis shows that formation of the PYM-Y14-Mago ternary complex is modulated by the PYM C-terminus revealing that DmPYM function is regulated in vivo. Furthermore, we find that whereas under normal conditions DmPYM is dispensable, its loss of function is lethal to flies with reduced y14 or mago gene dosage. Our analysis demonstrates that the amount of DmPYM relative to the EJC proteins is critical for viability and fertility. This, together with the fact that the EJC-disassembly activity of DmPYM is regulated, implicates PYM as an effector of EJC homeostasis in vivo.

Ribosome biogenesis is essential for cell growth and proliferation and is commonly elevated in cancer. Accordingly, numerous oncogene and tumor suppressor signaling pathways target rRNA synthesis. In breast cancer, non-canonical Wnt signaling by Wnt5a has been reported to antagonize tumor growth. Here, we show that Wnt5a rapidly represses rDNA gene transcription in breast cancer cells and generates a chromatin state with reduced transcription of rDNA by RNA polymerase I (Pol I). These effects were specifically dependent on Dishevelled1 (DVL1), which accumulates in nucleolar organizer regions (NORs) and binds to rDNA regions of the chromosome. Upon DVL1 binding, the Pol I transcription activator and deacetylase Sirtuin 7 (SIRT7) releases from rDNA loci, concomitant with disassembly of Pol I transcription machinery at the rDNA promoter. These findings reveal that Wnt5a signals through DVL1 to suppress rRNA transcription. This provides a novel mechanism for how Wnt5a exerts tumor suppressive effects and why disruption of Wnt5a signaling enhances mammary tumor growth in vivo.

Highlights d ipaRt: a method for protein-RNA-binding landscape definition in cells and organisms d Drosophila EJC-bound mRNAs are biased toward differentiation and development d Drosophila EJC assembly on mRNAs favors genes with complex gene architecture d Splice site strength, RNA structure, and CG-rich hexamers enhance EJC binding in flies