메뉴 건너뛰기




Volumn 16, Issue 1, 2015, Pages

EWS and FUS bind a subset of transcribed genes encoding proteins enriched in RNA regulatory functions

Author keywords

Amyotrophic lateral sclerosis; ChIP sequencing; Fronto temporal lobar degeneration; Gene expression; RNA binding; RNA processing; Transcription factors; Transcriptional regulation

Indexed keywords

FUSED IN SARCOMA PROTEIN; RNA; RNA BINDING PROTEIN EWS; RNA POLYMERASE II; CHROMATIN; FUS PROTEIN, HUMAN; PROTEIN BINDING; RNA BINDING PROTEIN FUS;

EID: 84959138906     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-2125-9     Document Type: Article
Times cited : (19)

References (79)
  • 1
    • 0029812470 scopus 로고    scopus 로고
    • hTAF(II)68, a novel RNA/ssDNA-binding protein with homology to the pro-oncoproteins TLS/FUS and EWS is associated with both TFIID and RNA polymerase II
    • Bertolotti A, Lutz Y, Heard DJ, Chambon P, Tora L. hTAF(II)68, a novel RNA/ssDNA-binding protein with homology to the pro-oncoproteins TLS/FUS and EWS is associated with both TFIID and RNA polymerase II. EMBO J. 1996;15(18):5022-31.
    • (1996) EMBO J , vol.15 , Issue.18 , pp. 5022-5031
    • Bertolotti, A.1    Lutz, Y.2    Heard, D.J.3    Chambon, P.4    Tora, L.5
  • 2
    • 0033598946 scopus 로고    scopus 로고
    • The N-terminal domain of human TAFII68 displays transactivation and oncogenic properties
    • Bertolotti A, Bell B, Tora L. The N-terminal domain of human TAFII68 displays transactivation and oncogenic properties. Oncogene. 1999;18(56):8000-10.
    • (1999) Oncogene , vol.18 , Issue.56 , pp. 8000-8010
    • Bertolotti, A.1    Bell, B.2    Tora, L.3
  • 3
    • 0027970712 scopus 로고
    • A novel effector domain from the RNA-binding protein TLS or EWS is required for oncogenic transformation by CHOP
    • Zinszner H, Albalat R, Ron D. A novel effector domain from the RNA-binding protein TLS or EWS is required for oncogenic transformation by CHOP. Genes Dev. 1994;8(21):2513-26.
    • (1994) Genes Dev , vol.8 , Issue.21 , pp. 2513-2526
    • Zinszner, H.1    Albalat, R.2    Ron, D.3
  • 4
    • 79251573834 scopus 로고    scopus 로고
    • Dr. Jekyll and Mr. Hyde: The Two Faces of the FUS/EWS/TAF15 Protein Family
    • Kovar H. Dr. Jekyll and Mr. Hyde: The Two Faces of the FUS/EWS/TAF15 Protein Family. Sarcoma. 2011;2011:837474.
    • (2011) Sarcoma , vol.2011 , pp. 837474
    • Kovar, H.1
  • 7
    • 61349156118 scopus 로고    scopus 로고
    • Mutations in the FUS/TLS gene on chromosome 16 cause familial amyotrophic lateral sclerosis
    • Kwiatkowski Jr TJ, Bosco DA, Leclerc AL, Tamrazian E, Vanderburg CR, Russ C, et al. Mutations in the FUS/TLS gene on chromosome 16 cause familial amyotrophic lateral sclerosis. Science. 2009;323(5918):1205-8.
    • (2009) Science , vol.323 , Issue.5918 , pp. 1205-1208
    • Kwiatkowski, T.J.1    Bosco, D.A.2    Leclerc, A.L.3    Tamrazian, E.4    Vanderburg, C.R.5    Russ, C.6
  • 8
    • 61349162349 scopus 로고    scopus 로고
    • Mutations in FUS, an RNA processing protein, cause familial amyotrophic lateral sclerosis type 6
    • Vance C, Rogelj B, Hortobagyi T, De Vos KJ, Nishimura AL, Sreedharan J, et al. Mutations in FUS, an RNA processing protein, cause familial amyotrophic lateral sclerosis type 6. Science. 2009;323(5918):1208-11.
    • (2009) Science , vol.323 , Issue.5918 , pp. 1208-1211
    • Vance, C.1    Rogelj, B.2    Hortobagyi, T.3    Vos, K.J.4    Nishimura, A.L.5    Sreedharan, J.6
  • 11
    • 48249083430 scopus 로고    scopus 로고
    • The multifunctional FUS, EWS and TAF15 proto-oncoproteins show cell type-specific expression patterns and involvement in cell spreading and stress response
    • Andersson MK, Stahlberg A, Arvidsson Y, Olofsson A, Semb H, Stenman G, et al. The multifunctional FUS, EWS and TAF15 proto-oncoproteins show cell type-specific expression patterns and involvement in cell spreading and stress response. BMC Cell Biol. 2008;9:37.
    • (2008) BMC Cell Biol , vol.9 , pp. 37
    • Andersson, M.K.1    Stahlberg, A.2    Arvidsson, Y.3    Olofsson, A.4    Semb, H.5    Stenman, G.6
  • 12
    • 0032561520 scopus 로고    scopus 로고
    • Genomic structure of the human RBP56/hTAFII68 and FUS/TLS genes
    • Morohoshi F, Ootsuka Y, Arai K, Ichikawa H, Mitani S, Munakata N, et al. Genomic structure of the human RBP56/hTAFII68 and FUS/TLS genes. Gene. 1998;221(2):191-8.
    • (1998) Gene , vol.221 , Issue.2 , pp. 191-198
    • Morohoshi, F.1    Ootsuka, Y.2    Arai, K.3    Ichikawa, H.4    Mitani, S.5    Munakata, N.6
  • 14
    • 77957867303 scopus 로고    scopus 로고
    • Mutant FUS proteins that cause amyotrophic lateral sclerosis incorporate into stress granules
    • Bosco DA, Lemay N, Ko HK, Zhou H, Burke C, Kwiatkowski Jr TJ, et al. Mutant FUS proteins that cause amyotrophic lateral sclerosis incorporate into stress granules. Hum Mol Genet. 2010;19(21):4160-75.
    • (2010) Hum Mol Genet , vol.19 , Issue.21 , pp. 4160-4175
    • Bosco, D.A.1    Lemay, N.2    Ko, H.K.3    Zhou, H.4    Burke, C.5    Kwiatkowski, T.J.6
  • 15
    • 77955792022 scopus 로고    scopus 로고
    • ALS-associated fused in sarcoma (FUS) mutations disrupt Transportin-mediated nuclear import
    • Dormann D, Rodde R, Edbauer D, Bentmann E, Fischer I, Hruscha A, et al. ALS-associated fused in sarcoma (FUS) mutations disrupt Transportin-mediated nuclear import. EMBO J. 2010;29(16):2841-57.
    • (2010) EMBO J , vol.29 , Issue.16 , pp. 2841-2857
    • Dormann, D.1    Rodde, R.2    Edbauer, D.3    Bentmann, E.4    Fischer, I.5    Hruscha, A.6
  • 16
    • 80053646130 scopus 로고    scopus 로고
    • Nuclear localization sequence of FUS and induction of stress granules by ALS mutants
    • Gal J, Zhang J, Kwinter DM, Zhai J, Jia H, Jia J, et al. Nuclear localization sequence of FUS and induction of stress granules by ALS mutants. Neurobiol Aging. 2011;32(12):2323. e2327-2340.
    • (2011) Neurobiol Aging , vol.32 , Issue.12 , pp. 2323
    • Gal, J.1    Zhang, J.2    Kwinter, D.M.3    Zhai, J.4    Jia, H.5    Jia, J.6
  • 17
    • 84866671948 scopus 로고    scopus 로고
    • Gene expression responses to FUS, EWS, and TAF15 reduction and stress granule sequestration analyses identifies FET-protein non-redundant functions
    • Blechingberg J, Luo Y, Bolund L, Damgaard CK, Nielsen AL. Gene expression responses to FUS, EWS, and TAF15 reduction and stress granule sequestration analyses identifies FET-protein non-redundant functions. PLoS One. 2012;7(9):e46251.
    • (2012) PLoS One , vol.7 , Issue.9 , pp. e46251
    • Blechingberg, J.1    Luo, Y.2    Bolund, L.3    Damgaard, C.K.4    Nielsen, A.L.5
  • 18
    • 0030746523 scopus 로고    scopus 로고
    • TLS (FUS) binds RNA in vivo and engages in nucleo-cytoplasmic shuttling
    • Zinszner H, Sok J, Immanuel D, Yin Y, Ron D. TLS (FUS) binds RNA in vivo and engages in nucleo-cytoplasmic shuttling. J Cell Sci. 1997;110(Pt 15):1741-50.
    • (1997) J Cell Sci , vol.110 , pp. 1741-1750
    • Zinszner, H.1    Sok, J.2    Immanuel, D.3    Yin, Y.4    Ron, D.5
  • 19
    • 0035378344 scopus 로고    scopus 로고
    • Exposure on cell surface and extensive arginine methylation of ewing sarcoma (EWS) protein
    • Belyanskaya LL, Gehrig PM, Gehring H. Exposure on cell surface and extensive arginine methylation of ewing sarcoma (EWS) protein. J Biol Chem. 2001;276(22):18681-7.
    • (2001) J Biol Chem , vol.276 , Issue.22 , pp. 18681-18687
    • Belyanskaya, L.L.1    Gehrig, P.M.2    Gehring, H.3
  • 20
    • 80052959701 scopus 로고    scopus 로고
    • FET proteins TAF15 and EWS are selective markers that distinguish FTLD with FUS pathology from amyotrophic lateral sclerosis with FUS mutations
    • Neumann M, Bentmann E, Dormann D, Jawaid A, Dejesus-Hernandez M, Ansorge O, et al. FET proteins TAF15 and EWS are selective markers that distinguish FTLD with FUS pathology from amyotrophic lateral sclerosis with FUS mutations. Brain. 2011;134(Pt 9):2595-609.
    • (2011) Brain , vol.134 , pp. 2595-2609
    • Neumann, M.1    Bentmann, E.2    Dormann, D.3    Jawaid, A.4    Dejesus-Hernandez, M.5    Ansorge, O.6
  • 21
    • 0035794162 scopus 로고    scopus 로고
    • Identification of an RNA binding specificity for the potential splicing factor TLS
    • Lerga A, Hallier M, Delva L, Orvain C, Gallais I, Marie J, et al. Identification of an RNA binding specificity for the potential splicing factor TLS. J Biol Chem. 2001;276(9):6807-16.
    • (2001) J Biol Chem , vol.276 , Issue.9 , pp. 6807-6816
    • Lerga, A.1    Hallier, M.2    Delva, L.3    Orvain, C.4    Gallais, I.5    Marie, J.6
  • 22
    • 79952317624 scopus 로고    scopus 로고
    • Characterization of a Family of RanBP2-Type Zinc Fingers that Can Recognize Single-Stranded RNA
    • Nguyen CD, Mansfield RE, Leung W, Vaz PM, Loughlin FE, Grant RP, et al. Characterization of a Family of RanBP2-Type Zinc Fingers that Can Recognize Single-Stranded RNA. J Mol Biol. 2011;407(2):273-83.
    • (2011) J Mol Biol , vol.407 , Issue.2 , pp. 273-283
    • Nguyen, C.D.1    Mansfield, R.E.2    Leung, W.3    Vaz, P.M.4    Loughlin, F.E.5    Grant, R.P.6
  • 23
    • 0028074607 scopus 로고
    • The EWS gene, involved in Ewing family of tumors, malignant melanoma of soft parts and desmoplastic small round cell tumors, codes for an RNA binding protein with novel regulatory domains
    • Ohno T, Ouchida M, Lee L, Gatalica Z, Rao VN, Reddy ES. The EWS gene, involved in Ewing family of tumors, malignant melanoma of soft parts and desmoplastic small round cell tumors, codes for an RNA binding protein with novel regulatory domains. Oncogene. 1994;9(10):3087-97.
    • (1994) Oncogene , vol.9 , Issue.10 , pp. 3087-3097
    • Ohno, T.1    Ouchida, M.2    Lee, L.3    Gatalica, Z.4    Rao, V.N.5    Reddy, E.S.6
  • 24
    • 84859986072 scopus 로고    scopus 로고
    • TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements
    • Tan AY, Riley TR, Coady T, Bussemaker HJ, Manley JL. TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements. Proc Natl Acad Sci U S A. 2012;109(16):6030-5.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , Issue.16 , pp. 6030-6035
    • Tan, A.Y.1    Riley, T.R.2    Coady, T.3    Bussemaker, H.J.4    Manley, J.L.5
  • 25
    • 84890309470 scopus 로고    scopus 로고
    • FUS-mediated alternative splicing in the nervous system: consequences for ALS and FTLD
    • Orozco D, Edbauer D. FUS-mediated alternative splicing in the nervous system: consequences for ALS and FTLD. J Mol Med (Berl). 2013;91(12):1343-54.
    • (2013) J Mol Med (Berl) , vol.91 , Issue.12 , pp. 1343-1354
    • Orozco, D.1    Edbauer, D.2
  • 27
    • 84930705294 scopus 로고    scopus 로고
    • Biochemical Properties and Biological Functions of FET Proteins
    • Schwartz JC, Cech TR, Parker RR. Biochemical Properties and Biological Functions of FET Proteins. Annu Rev Biochem. 2015;84:355-79.
    • (2015) Annu Rev Biochem , vol.84 , pp. 355-379
    • Schwartz, J.C.1    Cech, T.R.2    Parker, R.R.3
  • 28
    • 0031935157 scopus 로고    scopus 로고
    • EWS, but not EWS-FLI-1, is associated with both TFIID and RNA polymerase II: interactions between two members of the TET family, EWS and hTAFII68, and subunits of TFIID and RNA polymerase II complexes
    • Bertolotti A, Melot T, Acker J, Vigneron M, Delattre O, Tora L. EWS, but not EWS-FLI-1, is associated with both TFIID and RNA polymerase II: interactions between two members of the TET family, EWS and hTAFII68, and subunits of TFIID and RNA polymerase II complexes. Mol Cell Biol. 1998;18(3):1489-97.
    • (1998) Mol Cell Biol , vol.18 , Issue.3 , pp. 1489-1497
    • Bertolotti, A.1    Melot, T.2    Acker, J.3    Vigneron, M.4    Delattre, O.5    Tora, L.6
  • 29
    • 0344407006 scopus 로고    scopus 로고
    • Proto-oncoprotein TLS/FUS is associated to the nuclear matrix and complexed with splicing factors PTB, SRm160, and SR proteins
    • Meissner M, Lopato S, Gotzmann J, Sauermann G, Barta A. Proto-oncoprotein TLS/FUS is associated to the nuclear matrix and complexed with splicing factors PTB, SRm160, and SR proteins. Exp Cell Res. 2003;283(2):184-95.
    • (2003) Exp Cell Res , vol.283 , Issue.2 , pp. 184-195
    • Meissner, M.1    Lopato, S.2    Gotzmann, J.3    Sauermann, G.4    Barta, A.5
  • 31
    • 84929584026 scopus 로고    scopus 로고
    • Position-specific binding of FUS to nascent RNA regulates mRNA length
    • Masuda A, Takeda J, Okuno T, Okamoto T, Ohkawara B, Ito M, et al. Position-specific binding of FUS to nascent RNA regulates mRNA length. Genes Dev. 2015;29(10):1045-57.
    • (2015) Genes Dev , vol.29 , Issue.10 , pp. 1045-1057
    • Masuda, A.1    Takeda, J.2    Okuno, T.3    Okamoto, T.4    Ohkawara, B.5    Ito, M.6
  • 32
    • 84937125225 scopus 로고    scopus 로고
    • FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1 snRNP
    • Yu Y, Reed R. FUS functions in coupling transcription to splicing by mediating an interaction between RNAP II and U1 snRNP. Proc Natl Acad Sci U S A. 2015;112(28):8608-13.
    • (2015) Proc Natl Acad Sci U S A , vol.112 , Issue.28 , pp. 8608-8613
    • Yu, Y.1    Reed, R.2
  • 34
    • 36048958883 scopus 로고    scopus 로고
    • Nucleolar localization of DGCR8 and identification of eleven DGCR8-associated proteins
    • Shiohama A, Sasaki T, Noda S, Minoshima S, Shimizu N. Nucleolar localization of DGCR8 and identification of eleven DGCR8-associated proteins. Exp Cell Res. 2007;313(20):4196-207.
    • (2007) Exp Cell Res , vol.313 , Issue.20 , pp. 4196-4207
    • Shiohama, A.1    Sasaki, T.2    Noda, S.3    Minoshima, S.4    Shimizu, N.5
  • 35
    • 0033968408 scopus 로고    scopus 로고
    • Fus deficiency in mice results in defective B-lymphocyte development and activation, high levels of chromosomal instability and perinatal death
    • Hicks GG, Singh N, Nashabi A, Mai S, Bozek G, Klewes L, et al. Fus deficiency in mice results in defective B-lymphocyte development and activation, high levels of chromosomal instability and perinatal death. Nat Genet. 2000;24(2):175-9.
    • (2000) Nat Genet , vol.24 , Issue.2 , pp. 175-179
    • Hicks, G.G.1    Singh, N.2    Nashabi, A.3    Mai, S.4    Bozek, G.5    Klewes, L.6
  • 36
    • 0034142209 scopus 로고    scopus 로고
    • Male sterility and enhanced radiation sensitivity in TLS(-/-) mice
    • Kuroda M, Sok J, Webb L, Baechtold H, Urano F, Yin Y, et al. Male sterility and enhanced radiation sensitivity in TLS(-/-) mice. EMBO J. 2000;19(3):453-62.
    • (2000) EMBO J , vol.19 , Issue.3 , pp. 453-462
    • Kuroda, M.1    Sok, J.2    Webb, L.3    Baechtold, H.4    Urano, F.5    Yin, Y.6
  • 37
    • 34248203558 scopus 로고    scopus 로고
    • Ewing sarcoma gene EWS is essential for meiosis and B lymphocyte development
    • Li H, Watford W, Li C, Parmelee A, Bryant MA, Deng C, et al. Ewing sarcoma gene EWS is essential for meiosis and B lymphocyte development. J Clin Invest. 2007;117(5):1314-23.
    • (2007) J Clin Invest , vol.117 , Issue.5 , pp. 1314-1323
    • Li, H.1    Watford, W.2    Li, C.3    Parmelee, A.4    Bryant, M.A.5    Deng, C.6
  • 38
    • 41549137834 scopus 로고    scopus 로고
    • Ewing sarcoma protein ewsr1 maintains mitotic integrity and proneural cell survival in the zebrafish embryo
    • Azuma M, Embree LJ, Sabaawy H, Hickstein DD. Ewing sarcoma protein ewsr1 maintains mitotic integrity and proneural cell survival in the zebrafish embryo. PLoS One. 2007;2(10):e979.
    • (2007) PLoS One , vol.2 , Issue.10 , pp. e979
    • Azuma, M.1    Embree, L.J.2    Sabaawy, H.3    Hickstein, D.D.4
  • 39
    • 0033527059 scopus 로고    scopus 로고
    • Human POMp75 is identified as the pro-oncoprotein TLS/FUS: both POMp75 and POMp100 DNA homologous pairing activities are associated to cell proliferation
    • Bertrand P, Akhmedov AT, Delacote F, Durrbach A, Lopez BS. Human POMp75 is identified as the pro-oncoprotein TLS/FUS: both POMp75 and POMp100 DNA homologous pairing activities are associated to cell proliferation. Oncogene. 1999;18(31):4515-21.
    • (1999) Oncogene , vol.18 , Issue.31 , pp. 4515-4521
    • Bertrand, P.1    Akhmedov, A.T.2    Delacote, F.3    Durrbach, A.4    Lopez, B.S.5
  • 40
    • 33845188648 scopus 로고    scopus 로고
    • An in vitro enzymatic assay coupled to proteomics analysis reveals a new DNA processing activity for Ewing sarcoma and TAF(II)68 proteins
    • Guipaud O, Guillonneau F, Labas V, Praseuth D, Rossier J, Lopez B, et al. An in vitro enzymatic assay coupled to proteomics analysis reveals a new DNA processing activity for Ewing sarcoma and TAF(II)68 proteins. Proteomics. 2006;6(22):5962-72.
    • (2006) Proteomics , vol.6 , Issue.22 , pp. 5962-5972
    • Guipaud, O.1    Guillonneau, F.2    Labas, V.3    Praseuth, D.4    Rossier, J.5    Lopez, B.6
  • 41
    • 0033607753 scopus 로고    scopus 로고
    • Human 75-kDa DNA-pairing protein is identical to the pro-oncoprotein TLS/FUS and is able to promote D-loop formation
    • Baechtold H, Kuroda M, Sok J, Ron D, Lopez BS, Akhmedov AT. Human 75-kDa DNA-pairing protein is identical to the pro-oncoprotein TLS/FUS and is able to promote D-loop formation. J Biol Chem. 1999;274(48):34337-42.
    • (1999) J Biol Chem , vol.274 , Issue.48 , pp. 34337-34342
    • Baechtold, H.1    Kuroda, M.2    Sok, J.3    Ron, D.4    Lopez, B.S.5    Akhmedov, A.T.6
  • 42
    • 84883136968 scopus 로고    scopus 로고
    • The RNA-binding Protein Fused in Sarcoma (FUS) Functions Downstream of Poly(ADP-ribose) Polymerase (PARP) in Response to DNA Damage
    • Mastrocola AS, Kim SH, Trinh AT, Rodenkirch LA, Tibbetts RS. The RNA-binding Protein Fused in Sarcoma (FUS) Functions Downstream of Poly(ADP-ribose) Polymerase (PARP) in Response to DNA Damage. J Biol Chem. 2013;288(34):24731-41.
    • (2013) J Biol Chem , vol.288 , Issue.34 , pp. 24731-24741
    • Mastrocola, A.S.1    Kim, S.H.2    Trinh, A.T.3    Rodenkirch, L.A.4    Tibbetts, R.S.5
  • 43
    • 46649093597 scopus 로고    scopus 로고
    • Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription
    • Wang X, Arai S, Song X, Reichart D, Du K, Pascual G, et al. Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature. 2008;454(7200):126-30.
    • (2008) Nature , vol.454 , Issue.7200 , pp. 126-130
    • Wang, X.1    Arai, S.2    Song, X.3    Reichart, D.4    Du, K.5    Pascual, G.6
  • 44
    • 84864448921 scopus 로고    scopus 로고
    • Position-dependent FUS-RNA interactions regulate alternative splicing events and transcriptions
    • Ishigaki S, Masuda A, Fujioka Y, Iguchi Y, Katsuno M, Shibata A, et al. Position-dependent FUS-RNA interactions regulate alternative splicing events and transcriptions. Sci Rep. 2012;2:529.
    • (2012) Sci Rep , vol.2 , pp. 529
    • Ishigaki, S.1    Masuda, A.2    Fujioka, Y.3    Iguchi, Y.4    Katsuno, M.5    Shibata, A.6
  • 46
    • 0030596083 scopus 로고    scopus 로고
    • Molecular cloning and subcellular localisation of the snRNP-associated protein 69KD, a structural homologue of the proto-oncoproteins TLS and EWS with RNA and DNA-binding properties
    • Hackl W, Luhrmann R. Molecular cloning and subcellular localisation of the snRNP-associated protein 69KD, a structural homologue of the proto-oncoproteins TLS and EWS with RNA and DNA-binding properties. J Mol Biol. 1996;264(5):843-51.
    • (1996) J Mol Biol , vol.264 , Issue.5 , pp. 843-851
    • Hackl, W.1    Luhrmann, R.2
  • 47
    • 0032479980 scopus 로고    scopus 로고
    • TLS/FUS, a pro-oncogene involved in multiple chromosomal translocations, is a novel regulator of BCR/ABL-mediated leukemogenesis
    • Perrotti D, Bonatti S, Trotta R, Martinez R, Skorski T, Salomoni P, et al. TLS/FUS, a pro-oncogene involved in multiple chromosomal translocations, is a novel regulator of BCR/ABL-mediated leukemogenesis. EMBO J. 1998;17(15):4442-55.
    • (1998) EMBO J , vol.17 , Issue.15 , pp. 4442-4455
    • Perrotti, D.1    Bonatti, S.2    Trotta, R.3    Martinez, R.4    Skorski, T.5    Salomoni, P.6
  • 48
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754-60.
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 50
    • 77955368935 scopus 로고    scopus 로고
    • Evaluation of algorithm performance in ChIP-seq peak detection
    • Wilbanks EG, Facciotti MT. Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One. 2010;5(7):e11471.
    • (2010) PLoS One , vol.5 , Issue.7 , pp. e11471
    • Wilbanks, E.G.1    Facciotti, M.T.2
  • 52
    • 84864577725 scopus 로고    scopus 로고
    • Dynamic transitions in RNA polymerase II density profiles during transcription termination
    • Grosso AR, de Almeida SF, Braga J, Carmo-Fonseca M. Dynamic transitions in RNA polymerase II density profiles during transcription termination. Genome Res. 2012;22(8):1447-56.
    • (2012) Genome Res , vol.22 , Issue.8 , pp. 1447-1456
    • Grosso, A.R.1    Almeida, S.F.2    Braga, J.3    Carmo-Fonseca, M.4
  • 53
    • 84871002507 scopus 로고    scopus 로고
    • FUS stimulates microRNA biogenesis by facilitating co-transcriptional Drosha recruitment
    • Morlando M, Dini Modigliani S, Torrelli G, Rosa A, Di Carlo V, Caffarelli E, et al. FUS stimulates microRNA biogenesis by facilitating co-transcriptional Drosha recruitment. EMBO J. 2012;31(24):4502-10.
    • (2012) EMBO J , vol.31 , Issue.24 , pp. 4502-4510
    • Morlando, M.1    Dini Modigliani, S.2    Torrelli, G.3    Rosa, A.4    Carlo, V.5    Caffarelli, E.6
  • 54
    • 70349972615 scopus 로고    scopus 로고
    • Analysis of Ewing sarcoma (EWS)-binding proteins: interaction with hnRNP M, U, and RNA-helicases p68/72 within protein-RNA complexes
    • Pahlich S, Quero L, Roschitzki B, Leemann-Zakaryan RP, Gehring H. Analysis of Ewing sarcoma (EWS)-binding proteins: interaction with hnRNP M, U, and RNA-helicases p68/72 within protein-RNA complexes. J Proteome Res. 2009;8(10):4455-65.
    • (2009) J Proteome Res , vol.8 , Issue.10 , pp. 4455-4465
    • Pahlich, S.1    Quero, L.2    Roschitzki, B.3    Leemann-Zakaryan, R.P.4    Gehring, H.5
  • 55
    • 73549089900 scopus 로고    scopus 로고
    • TLS inhibits RNA polymerase III transcription
    • Tan AY, Manley JL. TLS inhibits RNA polymerase III transcription. Mol Cell Biol. 2010;30(1):186-96.
    • (2010) Mol Cell Biol , vol.30 , Issue.1 , pp. 186-196
    • Tan, A.Y.1    Manley, J.L.2
  • 56
    • 45549096156 scopus 로고    scopus 로고
    • The Ewing sarcoma protein (EWS) binds directly to the proximal elements of the macrophage-specific promoter of the CSF-1 receptor (csf1r) gene
    • Hume DA, Sasmono T, Himes SR, Sharma SM, Bronisz A, Constantin M, et al. The Ewing sarcoma protein (EWS) binds directly to the proximal elements of the macrophage-specific promoter of the CSF-1 receptor (csf1r) gene. J Immunol. 2008;180(10):6733-42.
    • (2008) J Immunol , vol.180 , Issue.10 , pp. 6733-6742
    • Hume, D.A.1    Sasmono, T.2    Himes, S.R.3    Sharma, S.M.4    Bronisz, A.5    Constantin, M.6
  • 57
    • 80053599512 scopus 로고    scopus 로고
    • Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data
    • Malone BM, Tan F, Bridges SM, Peng Z. Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data. PLoS One. 2011;6(9):e25260.
    • (2011) PLoS One , vol.6 , Issue.9 , pp. e25260
    • Malone, B.M.1    Tan, F.2    Bridges, S.M.3    Peng, Z.4
  • 58
    • 66149186985 scopus 로고    scopus 로고
    • Genomic location analysis by ChIP-Seq
    • Barski A, Zhao K. Genomic location analysis by ChIP-Seq. J Cell Biochem. 2009;107(1):11-8.
    • (2009) J Cell Biochem , vol.107 , Issue.1 , pp. 11-18
    • Barski, A.1    Zhao, K.2
  • 59
    • 70449711243 scopus 로고    scopus 로고
    • Computation for ChIP-seq and RNA-seq studies
    • Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods. 2009;6(11 Suppl):S22-32.
    • (2009) Nat Methods , vol.6 , Issue.11 , pp. S22-S32
    • Pepke, S.1    Wold, B.2    Mortazavi, A.3
  • 60
    • 37849036555 scopus 로고    scopus 로고
    • RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes
    • Glover-Cutter K, Kim S, Espinosa J, Bentley DL. RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nat Struct Mol Biol. 2008;15(1):71-8.
    • (2008) Nat Struct Mol Biol , vol.15 , Issue.1 , pp. 71-78
    • Glover-Cutter, K.1    Kim, S.2    Espinosa, J.3    Bentley, D.L.4
  • 61
    • 66149187105 scopus 로고    scopus 로고
    • Transcription termination by nuclear RNA polymerases
    • Richard P, Manley JL. Transcription termination by nuclear RNA polymerases. Genes Dev. 2009;23(11):1247-69.
    • (2009) Genes Dev , vol.23 , Issue.11 , pp. 1247-1269
    • Richard, P.1    Manley, J.L.2
  • 63
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 2008;322(5909):1845-8.
    • (2008) Science , vol.322 , Issue.5909 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 64
    • 80455164573 scopus 로고    scopus 로고
    • Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3' end of human genes
    • Martins SB, Rino J, Carvalho T, Carvalho C, Yoshida M, Klose JM, et al. Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3' end of human genes. Nat Struct Mol Biol. 2011;18(10):1115-23.
    • (2011) Nat Struct Mol Biol , vol.18 , Issue.10 , pp. 1115-1123
    • Martins, S.B.1    Rino, J.2    Carvalho, T.3    Carvalho, C.4    Yoshida, M.5    Klose, J.M.6
  • 65
    • 84876441383 scopus 로고    scopus 로고
    • Making ends meet: coordination between RNA 3'-end processing and transcription initiation
    • Andersen PK, Jensen TH, Lykke-Andersen S. Making ends meet: coordination between RNA 3'-end processing and transcription initiation. Wiley Interdiscip Rev RNA. 2013;4(3):233-46.
    • (2013) Wiley Interdiscip Rev RNA , vol.4 , Issue.3 , pp. 233-246
    • Andersen, P.K.1    Jensen, T.H.2    Lykke-Andersen, S.3
  • 66
    • 0036674269 scopus 로고    scopus 로고
    • Large-scale proteomic analysis of the human spliceosome
    • Rappsilber J, Ryder U, Lamond AI, Mann M. Large-scale proteomic analysis of the human spliceosome. Genome Res. 2002;12(8):1231-45.
    • (2002) Genome Res , vol.12 , Issue.8 , pp. 1231-1245
    • Rappsilber, J.1    Ryder, U.2    Lamond, A.I.3    Mann, M.4
  • 67
    • 77449136874 scopus 로고    scopus 로고
    • The TET family of proteins: functions and roles in disease
    • Tan AY, Manley JL. The TET family of proteins: functions and roles in disease. J Mol Cell Biol. 2009;1(2):82-92.
    • (2009) J Mol Cell Biol , vol.1 , Issue.2 , pp. 82-92
    • Tan, A.Y.1    Manley, J.L.2
  • 68
    • 79960925229 scopus 로고    scopus 로고
    • The Ewing sarcoma protein regulates DNA damage-induced alternative splicing
    • Paronetto MP, Minana B, Valcarcel J. The Ewing sarcoma protein regulates DNA damage-induced alternative splicing. Mol Cell. 2011;43(3):353-68.
    • (2011) Mol Cell , vol.43 , Issue.3 , pp. 353-368
    • Paronetto, M.P.1    Minana, B.2    Valcarcel, J.3
  • 69
    • 84868152371 scopus 로고    scopus 로고
    • Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs
    • Lagier-Tourenne C, Polymenidou M, Hutt KR, Vu AQ, Baughn M, Huelga SC, et al. Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs. Nat Neurosci. 2012;15(11):1488-97.
    • (2012) Nat Neurosci , vol.15 , Issue.11 , pp. 1488-1497
    • Lagier-Tourenne, C.1    Polymenidou, M.2    Hutt, K.R.3    Vu, A.Q.4    Baughn, M.5    Huelga, S.C.6
  • 70
    • 84866126892 scopus 로고    scopus 로고
    • Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain
    • Rogelj B, Easton LE, Bogu GK, Stanton LW, Rot G, Curk T, et al. Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain. Sci Rep. 2012;2:603.
    • (2012) Sci Rep , vol.2 , pp. 603
    • Rogelj, B.1    Easton, L.E.2    Bogu, G.K.3    Stanton, L.W.4    Rot, G.5    Curk, T.6
  • 71
    • 84875421844 scopus 로고    scopus 로고
    • FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns
    • Nakaya T, Alexiou P, Maragkakis M, Chang A, Mourelatos Z. FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns. RNA. 2013;19(4):498-509.
    • (2013) RNA , vol.19 , Issue.4 , pp. 498-509
    • Nakaya, T.1    Alexiou, P.2    Maragkakis, M.3    Chang, A.4    Mourelatos, Z.5
  • 72
    • 80455176999 scopus 로고    scopus 로고
    • CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
    • Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature. 2011;479(7371):74-9.
    • (2011) Nature , vol.479 , Issue.7371 , pp. 74-79
    • Shukla, S.1    Kavak, E.2    Gregory, M.3    Imashimizu, M.4    Shutinoski, B.5    Kashlev, M.6
  • 73
    • 78649289872 scopus 로고    scopus 로고
    • Global analysis of nascent RNA reveals transcriptional pausing in terminal exons
    • Carrillo Oesterreich F, Preibisch S, Neugebauer KM. Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Mol Cell. 2010;40(4):571-81.
    • (2010) Mol Cell , vol.40 , Issue.4 , pp. 571-581
    • Carrillo Oesterreich, F.1    Preibisch, S.2    Neugebauer, K.M.3
  • 74
    • 84857710881 scopus 로고    scopus 로고
    • PRAS40 is a functionally critical target for EWS repression in Ewing sarcoma
    • Huang L, Nakai Y, Kuwahara I, Matsumoto K. PRAS40 is a functionally critical target for EWS repression in Ewing sarcoma. Cancer Res. 2012;72(5):1260-9.
    • (2012) Cancer Res , vol.72 , Issue.5 , pp. 1260-1269
    • Huang, L.1    Nakai, Y.2    Kuwahara, I.3    Matsumoto, K.4
  • 75
    • 84860863883 scopus 로고    scopus 로고
    • TDP-43 and FUS RNA-binding proteins bind distinct sets of cytoplasmic messenger RNAs and differently regulate their post-transcriptional fate in motoneuron-like cells
    • Colombrita C, Onesto E, Megiorni F, Pizzuti A, Baralle FE, Buratti E, et al. TDP-43 and FUS RNA-binding proteins bind distinct sets of cytoplasmic messenger RNAs and differently regulate their post-transcriptional fate in motoneuron-like cells. J Biol Chem. 2012;287(19):15635-47.
    • (2012) J Biol Chem , vol.287 , Issue.19 , pp. 15635-15647
    • Colombrita, C.1    Onesto, E.2    Megiorni, F.3    Pizzuti, A.4    Baralle, F.E.5    Buratti, E.6
  • 76
    • 33847661809 scopus 로고    scopus 로고
    • Protocol for the fast chromatin immunoprecipitation (ChIP) method
    • Nelson JD, Denisenko O, Bomsztyk K. Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nat Protoc. 2006;1(1):179-85.
    • (2006) Nat Protoc , vol.1 , Issue.1 , pp. 179-185
    • Nelson, J.D.1    Denisenko, O.2    Bomsztyk, K.3
  • 78
    • 77958599059 scopus 로고    scopus 로고
    • Analysis of qPCR data by converting exponentially related Ct values into linearly related X0 values
    • Thomsen R, Solvsten CA, Linnet TE, Blechingberg J, Nielsen AL. Analysis of qPCR data by converting exponentially related Ct values into linearly related X0 values. J Bioinform Comput Biol. 2010;8(5):885-900.
    • (2010) J Bioinform Comput Biol , vol.8 , Issue.5 , pp. 885-900
    • Thomsen, R.1    Solvsten, C.A.2    Linnet, T.E.3    Blechingberg, J.4    Nielsen, A.L.5
  • 79
    • 34447273319 scopus 로고    scopus 로고
    • Type III interferon (IFN) induces a type I IFN-like response in a restricted subset of cells through signaling pathways involving both the Jak-STAT pathway and the mitogen-activated protein kinases
    • Zhou Z, Hamming OJ, Ank N, Paludan SR, Nielsen AL, Hartmann R. Type III interferon (IFN) induces a type I IFN-like response in a restricted subset of cells through signaling pathways involving both the Jak-STAT pathway and the mitogen-activated protein kinases. J Virol. 2007;81(14):7749-58.
    • (2007) J Virol , vol.81 , Issue.14 , pp. 7749-7758
    • Zhou, Z.1    Hamming, O.J.2    Ank, N.3    Paludan, S.R.4    Nielsen, A.L.5    Hartmann, R.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.