Genomes and Genes
nuclear matrix associated proteins
Summary: A broad category of nuclear proteins that are components of or participate in the formation of the NUCLEAR MATRIX.
- Murphy R, Watkins J, Wente S. GLE2, a Saccharomyces cerevisiae homologue of the Schizosaccharomyces pombe export factor RAE1, is required for nuclear pore complex structure and function. Mol Biol Cell. 1996;7:1921-37 pubmed..We propose that Gle2p has a novel role in mediating nuclear transport. ..
- Maekawa T, Kuriyama R. Primary structure and microtubule-interacting domain of the SP-H antigen: a mitotic MAP located at the spindle pole and characterized as a homologous protein to NuMA. J Cell Sci. 1993;105 ( Pt 2):589-600 pubmed
- Le Hir H, Moore M, Maquat L. Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon-exon junctions. Genes Dev. 2000;14:1098-108 pubmed..Such proteins could influence downstream metabolic events in vivo such as mRNA transport, translation, and nonsense-mediated decay. ..
- Banerjee S, Lohia A. Molecular analysis of repetitive DNA elements from Entamoeba histolytica, which encode small RNAs and contain matrix/scaffold attachment recognition sequences. Mol Biochem Parasitol. 2003;126:35-42 pubmed..Thus, two unique sequences-Eh MRS1 and Eh MRS2-demonstrate very similar properties, suggesting that they belong to a superfamily of genomic elements, which may function as scaffold or matrix attachment sites in Entamoeba...
- Goetze S, Gluch A, Benham C, Bode J. Computational and in vitro analysis of destabilized DNA regions in the interferon gene cluster: potential of predicting functional gene domains. Biochemistry. 2003;42:154-66 pubmed..Together, these data emphasize the relevance of SIDD calculations as a valid approach for the localization of structural, regulatory, and coding regions in the eukaryotic genome. ..
- Bowman S, Neumüller R, Novatchkova M, Du Q, Knoblich J. The Drosophila NuMA Homolog Mud regulates spindle orientation in asymmetric cell division. Dev Cell. 2006;10:731-42 pubmed..Our data suggest a model in which asymmetrically localized Pins-G alphai complexes regulate spindle orientation by directly binding to Mud. ..
- Blencowe B, Issner R, Nickerson J, Sharp P. A coactivator of pre-mRNA splicing. Genes Dev. 1998;12:996-1009 pubmed..The results suggest that a complex of the nuclear matrix proteins SRm160 and SRm300 functions as a coactivator of pre-mRNA splicing. ..
- Wu X, Yoo Y, Okuhama N, Tucker P, Liu G, Guan J. Regulation of RNA-polymerase-II-dependent transcription by N-WASP and its nuclear-binding partners. Nat Cell Biol. 2006;8:756-63 pubmed..Based on these results, we propose a nuclear function for N-WASP in transcriptional regulation. ..
- Amelio A, Miraglia L, Conkright J, Mercer B, Batalov S, Cavett V, et al. A coactivator trap identifies NONO (p54nrb) as a component of the cAMP-signaling pathway. Proc Natl Acad Sci U S A. 2007;104:20314-9 pubmed..These data demonstrate the utility of the coactivator trap by identification of a component of cAMP-mediated transcription. ..
- Proteau A, Blier S, Albert A, Lavoie S, Traish A, Vincent M. The multifunctional nuclear protein p54nrb is multiphosphorylated in mitosis and interacts with the mitotic regulator Pin1. J Mol Biol. 2005;346:1163-72 pubmed..Our results also showed that Pin1 binding was favored when at least two of the three threonine residues were phosphorylated, suggesting a regulation mechanism based on multisite phosphorylation. ..
- Pritchard C, Fornerod M, Kasper L, van Deursen J. RAE1 is a shuttling mRNA export factor that binds to a GLEBS-like NUP98 motif at the nuclear pore complex through multiple domains. J Cell Biol. 1999;145:237-54 pubmed..Together, our data suggest that RAE1 is a shuttling transport factor that directly contributes to nuclear export of mRNAs through its ability to anchor to a specific NUP98 motif at the NPC. ..
- Le Hir H, Izaurralde E, Maquat L, Moore M. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J. 2000;19:6860-9 pubmed..Possible functions for this complex in nucleocytoplasmic transport of spliced mRNA, as well as the nonsense-mediated mRNA decay pathway, are discussed. ..
- Kraemer D, Blobel G. mRNA binding protein mrnp 41 localizes to both nucleus and cytoplasm. Proc Natl Acad Sci U S A. 1997;94:9119-24 pubmed
- Hallier M, Tavitian A, Moreau Gachelin F. The transcription factor Spi-1/PU.1 binds RNA and interferes with the RNA-binding protein p54nrb. J Biol Chem. 1996;271:11177-81 pubmed..Altogether, these results raise the intriguing possibility that the functional interference observed between Spi-1/PU.1 and RNA-binding proteins might represent a novel mechanism in malignant erythropoiesis. ..
- Jeganathan K, Malureanu L, van Deursen J. The Rae1-Nup98 complex prevents aneuploidy by inhibiting securin degradation. Nature. 2005;438:1036-9 pubmed..Together, our results suggest that Rae1 and Nup98 are temporal regulators of APC(Cdh1) that maintain euploidy by preventing unscheduled degradation of securin. ..
- Dong B, Horowitz D, Kobayashi R, Krainer A. Purification and cDNA cloning of HeLa cell p54nrb, a nuclear protein with two RNA recognition motifs and extensive homology to human splicing factor PSF and Drosophila NONA/BJ6. Nucleic Acids Res. 1993;21:4085-92 pubmed
- Emili A, Shales M, McCracken S, Xie W, Tucker P, Kobayashi R, et al. Splicing and transcription-associated proteins PSF and p54nrb/nonO bind to the RNA polymerase II CTD. RNA. 2002;8:1102-11 pubmed..PSF and p54nrb/NonO may therefore provide a direct physical link between the pol II CTD and pre-mRNA processing components, at both the initiation and elongation phases of transcription. ..
- Siller K, Cabernard C, Doe C. The NuMA-related Mud protein binds Pins and regulates spindle orientation in Drosophila neuroblasts. Nat Cell Biol. 2006;8:594-600 pubmed..We propose that Mud is a functional orthologue of mammalian NuMA and Caenorhabditis elegans Lin-5, and that Mud coordinates spindle orientation with cortical polarity to promote asymmetric cell division. ..
- Whalen W, Bharathi A, Danielewicz D, Dhar R. Advancement through mitosis requires rae1 gene function in fission yeast. Yeast. 1997;13:1167-79 pubmed..We propose a model where rae1 functions in cell cycle progression through trafficking of proteins required for mitosis. ..
- Basu A, Dong B, Krainer A, Howe C. The intracisternal A-particle proximal enhancer-binding protein activates transcription and is identical to the RNA- and DNA-binding protein p54nrb/NonO. Mol Cell Biol. 1997;17:677-86 pubmed..Based on the close sequence relatedness of this protein to PSF, which is required for pre-mRNA splicing in vitro, we discuss the possibility that p54nrb has dual roles in transcription and splicing. ..
- Zhang Z, Carmichael G. The fate of dsRNA in the nucleus: a p54(nrb)-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. Cell. 2001;106:465-75 pubmed..We provide evidence that one function of the complex identified here is to anchor hyperedited RNAs to the nuclear matrix, while allowing selectively edited mRNAs to be exported. ..
- Longman D, McGarvey T, McCracken S, Johnstone I, Blencowe B, Caceres J. Multiple interactions between SRm160 and SR family proteins in enhancer-dependent splicing and development of C. elegans. Curr Biol. 2001;11:1923-33 pubmed..Our results provide biochemical and genetic evidence indicating that interactions between SRm160 and multiple SR family proteins are important for both optimal splicing activity and for proper development. ..
- Haren L, Merdes A. Direct binding of NuMA to tubulin is mediated by a novel sequence motif in the tail domain that bundles and stabilizes microtubules. J Cell Sci. 2002;115:1815-24 pubmed..Our results suggest that NuMA organises the poles by stable crosslinking of the microtubule fibers. ..
- Sabri N, Visa N. The Ct-RAE1 protein interacts with Balbiani ring RNP particles at the nuclear pore. RNA. 2000;6:1597-609 pubmed
- Yasumi M, Sakisaka T, Hoshino T, Kimura T, Sakamoto Y, Yamanaka T, et al. Direct binding of Lgl2 to LGN during mitosis and its requirement for normal cell division. J Biol Chem. 2005;280:6761-5 pubmed..NuMA complex. These results indicate that Lgl2 forms a Lgl2.Par-6.aPKC.LGN complex, which responds to mitotic signaling to establish normal cell division. ..
- Brown J, Bharathi A, Ghosh A, Whalen W, Fitzgerald E, Dhar R. A mutation in the Schizosaccharomyces pombe rae1 gene causes defects in poly(A)+ RNA export and in the cytoskeleton. J Biol Chem. 1995;270:7411-9 pubmed..The rae1 gene was isolated by complementation and encodes a predicted protein of 352 amino acids with four beta-transducin/WD40 repeats. ..
- Dong X, Sweet J, Challis J, Brown T, Lye S. Transcriptional activity of androgen receptor is modulated by two RNA splicing factors, PSF and p54nrb. Mol Cell Biol. 2007;27:4863-75 pubmed..These data demonstrated that PSF and p54nrb complex with AR and play a key role in modulating AR-mediated gene transcription. ..
- Xu X, Rose A, Muthuswamy S, Jeong S, Venkatakrishnan S, Zhao Q, et al. NUCLEAR PORE ANCHOR, the Arabidopsis homolog of Tpr/Mlp1/Mlp2/megator, is involved in mRNA export and SUMO homeostasis and affects diverse aspects of plant development. Plant Cell. 2007;19:1537-48 pubmed
- Jiang S, Meyer R, Kang K, Osborne C, Wong J, Oesterreich S. Scaffold attachment factor SAFB1 suppresses estrogen receptor alpha-mediated transcription in part via interaction with nuclear receptor corepressor. Mol Endocrinol. 2006;20:311-20 pubmed..The coexpression of these proteins in breast cancer specimens, and the combined recruitment (and release) of SAFB1/2 and N-CoR furthermore suggests that this interaction has functional relevance. ..
- McCracken S, Longman D, Johnstone I, Caceres J, Blencowe B. An evolutionarily conserved role for SRm160 in 3'-end processing that functions independently of exon junction complex formation. J Biol Chem. 2003;278:44153-60 pubmed..Our combined results provide evidence for an evolutionarily conserved interaction between SRm160 and the 3'-end cleavage machinery that functions independently of EJC formation. ..
- Rosonina E, Ip J, Calarco J, Bakowski M, Emili A, McCracken S, et al. Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo. Mol Cell Biol. 2005;25:6734-46 pubmed..Collectively, these results suggest that the recruitment of PSF to activated promoters and the pol II CTD provides a mechanism by which transcription and pre-mRNA processing are coordinated within the cell. ..
- Krauss S, Spence J, Bahmanyar S, Barth A, Go M, Czerwinski D, et al. Downregulation of protein 4.1R, a mature centriole protein, disrupts centrosomes, alters cell cycle progression, and perturbs mitotic spindles and anaphase. Mol Cell Biol. 2008;28:2283-94 pubmed publisher..1R makes crucial contributions to the structural integrity of centrosomes and mitotic spindles which normally enable mitosis and anaphase to proceed with the coordinated precision required to avoid pathological events. ..
- Peng R, Dye B, Pérez I, Barnard D, Thompson A, Patton J. PSF and p54nrb bind a conserved stem in U5 snRNA. RNA. 2002;8:1334-47 pubmed..Sedimentation analyses show that both proteins associate with spliceosomes and with U4/U6.U5 tri-snPNP. ..
- Larsen N, Harrison S. Crystal structure of the spindle assembly checkpoint protein Bub3. J Mol Biol. 2004;344:885-92 pubmed..Comparison of the Bub3 sequence to the WD40 protein, Rae1, shows high sequence conservation along the same surfaces. Rae1 interaction with Bub1 is, therefore, likely to involve a similar mode of binding. ..
- Qi H, Rath U, Wang D, Xu Y, Ding Y, Zhang W, et al. Megator, an essential coiled-coil protein that localizes to the putative spindle matrix during mitosis in Drosophila. Mol Biol Cell. 2004;15:4854-65 pubmed
- Oesterreich S. Scaffold attachment factors SAFB1 and SAFB2: Innocent bystanders or critical players in breast tumorigenesis?. J Cell Biochem. 2003;90:653-61 pubmed..The possibility that SAFB1 and SAFB2 are novel breast tumor suppressor genes, and how they might function in this role, are discussed. ..
- Peters U, Haberhausen G, Kostrzewa M, Nolte D, Muller U. AFX1 and p54nrb: fine mapping, genomic structure, and exclusion as candidate genes of X-linked dystonia parkinsonism. Hum Genet. 1997;100:569-72 pubmed..AFX1 and p54nrb were excluded as candidates of DYT3 by sequencing of the exons and the flanking intronic sequences in an XDP patient and a control, and by Northern blot analysis. ..
- Wagner S, Chiosea S, Nickerson J. The spatial targeting and nuclear matrix binding domains of SRm160. Proc Natl Acad Sci U S A. 2003;100:3269-74 pubmed..Sequences from the N-terminal domain localized proteins to the nuclear lamina near sites where mRNA leaves the nucleus. ..
- Bailer S, Siniossoglou S, Podtelejnikov A, Hellwig A, Mann M, Hurt E. Nup116p and nup100p are interchangeable through a conserved motif which constitutes a docking site for the mRNA transport factor gle2p. EMBO J. 1998;17:1107-19 pubmed..Thus, the in vivo function of Gle2p is strictly coupled to the short GLEBS within Nup116p which links this putative mRNA transport factor to the nuclear pores. ..
- Clark J, Lu Y, Sidhar S, Parker C, Gill S, Smedley D, et al. Fusion of splicing factor genes PSF and NonO (p54nrb) to the TFE3 gene in papillary renal cell carcinoma. Oncogene. 1997;15:2233-9 pubmed..These observations suggest the possibility of intriguing links between the processes of RNA splicing, DNA transcription and oncogenesis. ..
- Wells R, Catzavelos C, Kamel Reid S. Fusion of retinoic acid receptor alpha to NuMA, the nuclear mitotic apparatus protein, by a variant translocation in acute promyelocytic leukaemia. Nat Genet. 1997;17:109-13 pubmed
- Zolotukhin A, Michalowski D, Bear J, Smulevitch S, Traish A, Peng R, et al. PSF acts through the human immunodeficiency virus type 1 mRNA instability elements to regulate virus expression. Mol Cell Biol. 2003;23:6618-30 pubmed..Thus, p54nrb and PSF have properties of key factors mediating INS function and likely define a novel mRNA regulatory pathway that is hijacked by HIV-1. ..
- Le Hir H, Gatfield D, Izaurralde E, Moore M. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay. EMBO J. 2001;20:4987-97 pubmed..Finally, we show that the composition of the EJC is dynamic in vivo and is subject to significant evolution upon mRNA export to the cytoplasm. ..
- Wang X, Babu J, Harden J, Jablonski S, Gazi M, Lingle W, et al. The mitotic checkpoint protein hBUB3 and the mRNA export factor hRAE1 interact with GLE2p-binding sequence (GLEBS)-containing proteins. J Biol Chem. 2001;276:26559-67 pubmed..Our findings demonstrate that GLEBS motifs reside in mammalian nucleoporins and mitotic checkpoint proteins and apparently serve as specific binding sites for either BUB3, RAE1, or both. ..
- Gordon M, Howard L, Compton D. Chromosome movement in mitosis requires microtubule anchorage at spindle poles. J Cell Biol. 2001;152:425-34 pubmed..These results demonstrate that anchorage of microtubule minus ends at spindle poles mediated by overlapping mechanisms involving both NuMA and HSET is essential for chromosome movement during mitosis. ..
- Blencowe B, Baurén G, Eldridge A, Issner R, Nickerson J, Rosonina E, et al. The SRm160/300 splicing coactivator subunits. RNA. 2000;6:111-20 pubmed..The results indicate that SRm160 may be the more critical component of the SRm160/300 coactivator in the splicing of SRm160/300-dependent pre-mRNAs. ..
- Johansen K, Johansen J. Cell and molecular biology of the spindle matrix. Int Rev Cytol. 2007;263:155-206 pubmed..However, as reviewed here multiple studies spanning the evolutionary spectrum from lower eukaryotes to vertebrates have provided new and intriguing evidence that a spindle matrix may be a general feature of mitosis. ..
- Eldridge A, Li Y, Sharp P, Blencowe B. The SRm160/300 splicing coactivator is required for exon-enhancer function. Proc Natl Acad Sci U S A. 1999;96:6125-30 pubmed..The results suggest a model for ESE function in which the SRm160/300 splicing coactivator promotes critical interactions between ESE-bound "activators" and the snRNP machinery of the spliceosome. ..
- Hata K, Nishimura R, Muramatsu S, Matsuda A, Matsubara T, Amano K, et al. Paraspeckle protein p54nrb links Sox9-mediated transcription with RNA processing during chondrogenesis in mice. J Clin Invest. 2008;118:3098-108 pubmed publisher..These data suggest that p54nrb plays an important role in the regulation of Sox9 function and the formation of paraspeckle bodies during chondrogenesis. ..
- Evans K, Ott S, Hansen A, Koentges G, Wernisch L. A comparative study of S/MAR prediction tools. BMC Bioinformatics. 2007;8:71 pubmed..However, while a number of S/MAR predictors have been proposed, their accuracy has so far not come under scrutiny...
- Fox A, Bond C, Lamond A. P54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in an RNA-dependent manner. Mol Biol Cell. 2005;16:5304-15 pubmed..Thus paraspeckles are the sites where a subset of the total cellular pool of p54nrb is targeted in a RNA Polymerase II-dependent manner. ..
- Myojin R, Kuwahara S, Yasaki T, Matsunaga T, Sakurai T, Kimura M, et al. Expression and functional significance of mouse paraspeckle protein 1 on spermatogenesis. Biol Reprod. 2004;71:926-32 pubmed..Therefore, we conclude that mPSP1 may regulate multiple phases of important nuclear events during spermatogenesis. ..
- Bladen C, Udayakumar D, Takeda Y, Dynan W. Identification of the polypyrimidine tract binding protein-associated splicing factor.p54(nrb) complex as a candidate DNA double-strand break rejoining factor. J Biol Chem. 2005;280:5205-10 pubmed..Based on structural comparison with related proteins, we propose a model where the four RNA recognition motif domains in the heteromeric PSF.p54(nrb) complex cooperate to align separate DNA molecules. ..