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SRSFs are dephosphorylated during splicing and then serve as adaptors for mRNA export (51) or translation initiation (52). , Fleischer K., Czajkowska H., Müller-Newen G., Becker W. Liu Another substrate of AKT1 is ALY/REF. Song T. Zhang C. D.M. H. Lagier-Tourenne

The CGG foci also disassembled when cells were treated with tautomycin; however, the mechanism proposed implied an interaction between tautomycin and the mutant transcript, preventing foci formation. , Okamoto Y., Onogi H., Mayeda A., Krainer A.R., Hagiwara M. Cho Colwill

Tokunaga Known point mutations in, and copy number variants of, genes encoding EJC proteins that are found in NSs are linked to intellectual disabilities, autism and schizophrenia (184). , McCurrach M., Schalling M., Housman D., Singer R.H. Holt R.D. McMahon

SRSF1 is targeted to the nucleus (and further to NSs) upon SRPK1-driven phosphorylation (48). Among them, U2AF65 (complexed with PRP19C) is required for CTD-dependent splicing activation (110). Spatial association occurs within actively transcribed genes and co-regulated genes gather around shared NSs (38,101).

Zheng , Fu X.D., Maniatis T. Biggiogera Thus, histone modifications that enhance DNA wrapping around nucleosomes induce exon inclusion (115) and exon skipping is triggered by histone modifications that promote relaxation of the chromatin structure (116).

NSs contain the paraspeckle proteins PSF (42) and PSP2, and both bodies often localize in close proximity (43). Little is known regarding the fate of proteins that are ubiquitinated in NSs because, to date, deubiquitinating enzymes have not been identified in NSs. , Hu Y., Belmont A.S. Meggendorfer Nuclear actin exists in monomers (G-actin) and short polymers (filaments, F-actin). Furthermore, and most importantly for structures as large as NSs (0.8–1.8 μm), cellular cryo-ET enables visualization of particles in the native state inside cells. Moreover, the majority of NS proteins can also be found at other nuclear locations and their specific roles in NSs, interacting partners and post-translational modifications need to be elucidated. K. J.A.

Analysis of thick biological samples without biochemical purification is possible due to progress in non-disruptive preparation of thin sections of biological material (214). These close relationships between splicing and epigenetic mechanisms of gene expression regulation may underlie the robust enrichment of proteins involved in epigenetic regulation in NSs. The m6A modification is enzymatically removed by the demethylase ‘eraser’ enzymes fat mass and obesity-associated protein (FTO) (129) and ALKBH5 (130), which are also localized in NSs. As listed in Table 1 and Supplementary Table S1, NS proteins are involved in multiple nuclear gene expression regulation steps, such as epigenetic regulation, transcription activator and repressor functions, transcription elongation and termination, splicing, 3′ end processing, mRNA modification and mRNA packing and export (Figure 2). Similar to CAG repeats, foci formed by expanded CGG repeats present in the 5′ UTR of FMR1 in FXTAS localize within NSs (199). Therefore, it is reasonable to expect that application of these technologies will bring new insights into the molecular organization of NSs and clarify their role in cell physiology and the molecular basis of diseases. C. C. Two years later, J. Swanson Beck used the term ‘speckles’ for the first time to describe these bodies (4).

M.

Anczuków

Overexpression of NS-forming proteins, including SR proteins, is observed in many types of cancer (153) and abnormally high levels of SRSF1 have been shown to be sufficient to induce tumorigenesis (154). G. , Leach J., Reittie J.E., Atzberger A., Lee-Prudhoe J., Wood W.G., Higgs D.R., Iborra F.J., Buckle V.J. PCAF, INO80 and BAF, numerous components of which have been found in NSs) and RNA-binding proteins. The dependence of splicing on epigenetic regulation is not the only connection that occurs between splicing factors and DNA regulatory proteins because multiple examples of DNA repair and DNA stability regulation by splicing factors has been published recently (reviewed in (121)).

Alexander

N. , Wang P., Tian F., Gao G., Huang L., Wei W., Xie X.S. This reciprocal coupling is thought to be realized via interactions of splicing factors (e.g.

Nuclear speckles.

, Le T.T., Dunckley M., Nguyen T.M., Burghes A.H., Morris G.E. K.M. The remaining short 61 nt tRNA-like mascRNA is localized exclusively to the cytoplasm (85). Stabilization of G-quadruplex DNA structures in Schizosaccharomyces pombe causes single-strand DNA lesions and impedes DNA replication. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, were discovered as sites for splicing factor storage and modification. Here we review older microscopy-based studies on a small number of genes with the new genomic mapping … Higher eukaryotic cell nuclei are highly compartmentalized into bodies and structural assemblies of specialized functions. Additionally, BRM (the ATPase subunit of the SWI/SNF chromatin remodeler) (113) and ZNF326 (114) have been proposed to modulate connections between transcription pausing and alternative splicing. J.R. , Ensminger A.W., Clemson C.M., Lynch C.R., Lawrence J.B., Chess A. Bernard This observation indicates that multiple NXF1/NXT1 complexes are capable of binding various sites within individual mRNPs.

, Ledda A., Mularoni L., Albà M.M., de la Luna S. Alvarez

K.C.

I.-F.

, Rosenberg A.Z., Akerman M., Das S., Zhan L., Karni R., Muthuswamy S.K., Krainer A.R.

M. , Muresan V. Ferrer In the cell nucleus, PIs are involved in regulation of gene expression, including chromatin modification, pre-mRNA maturation and mRNP export (26).

Oldmeadow , Ideue T., Sano M., Mituyama T., Hirose T. Fox J.H. , Zhai B., Yin S., Gygi S., Reed R. Woodward Transcription requires the formation of a short hybrid of nascent pre-mRNA and an unwound DNA template, the so-called R loop, which is known to increase DNA instability and affect DNA integrity (99). , Springer M., Shibata Y., Lee C.-S., Dias A.P., Rapoport T.A. , Stojiljkovic L., Fuchsova B., Vargas G.M., Mavrommatis E., Philimonenko V., Kysela K., Goodrich J.A., Lessard J.L., Hope T.J.et al. , Fakan S., Martin T.E. The resultant hypophosphorylated RS domain of SRSF1 prevents SNRNP70 binding and the subsequent formation of the spliceosomal E complex (49).

In animal tissues, nuclear speckles have also been termed SC35 bodies, as many SR proteins accumulate in these nuclear bodies.

The assembly of SRSFs into NAPs and MIGs confirms their strong self-organizing properties, but SRSFs alone are not sufficient to form NSs. A single mechanism that triggers the disturbances in nuclear export of all mutant RNAs is thus unlikely. J.L. , Zhou Z., Magni K., Christoforides C., Rappsilber J., Mann M., Reed R. Strässer , Hsieh C., Schalek R., Frank J., Mannella C. Asano As mutant RNAs interact abnormally with various proteins (201), transcripts with expanded repeats may trigger protein dislocation. , Kielkopf C.L. , Dundr M. Herrmann Y.B. Salichs C. Similarly, MALAT1 does not form direct RNA–RNA contacts with nascent pre-mRNAs; rather, it binds indirectly via protein mediators (89).

, Martinson H.G. , Peng X., Liu L., Kuzmin A., Wang Y., Qu J., Li Y., Prasad P.N. O’Donovan PARD6A/TIP-40 and PDLIM7/ENIGMA, contain PIP2-binding PDZ domains, which mediate protein–protein interactions. E. , Palhan V.B., Tjernberg A., Lymar E.S., Gamper A.M., Kundu T.K., Chait B.T., Roeder R.G. Young

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