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Volumn 20, Issue 1, 2013, Pages 45-53

Using chimaeric expression sequence tag as the reference to identify three-dimensional chromosome contacts

Author keywords

chimaeric expression sequence tag (EST); chromatin; chromatin loop; inter and intrachromosomal interaction; transcription factory

Indexed keywords

ARTICLE; CHIMERIC EXPRESSION SEQUENCE TAG; CHROMOSOME; EXPRESSED SEQUENCE TAG; GENE INTERACTION; GENE LOCUS; GENETIC SCREENING;

EID: 84874480162     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dss032     Document Type: Article
Times cited : (2)

References (30)
  • 1
    • 30044431810 scopus 로고    scopus 로고
    • Transcription-mediated gene fusion in the human genome
    • Akiva, P., Toporik, A., Edelheit, S., et al. 2006, Transcription-mediated gene fusion in the human genome, Genome Res., 16, 30-6.
    • (2006) Genome Res. , vol.16 , pp. 30-36
    • Akiva, P.1    Toporik, A.2    Edelheit, S.3
  • 2
    • 26444468532 scopus 로고    scopus 로고
    • Pre-mRNA trans-splicing: From kinetoplastids to mammals, an easy language for life diversity
    • Mayer, M.G. and Floeter-Winter, L.M. 2005, Pre-mRNA trans-splicing: from kinetoplastids to mammals, an easy language for life diversity, Mem. Inst. Oswaldo Cruz, 100, 501-13.
    • (2005) Mem. Inst. Oswaldo Cruz , vol.100 , pp. 501-513
    • Mayer, M.G.1    Floeter-Winter, L.M.2
  • 3
    • 0026911111 scopus 로고
    • Trans-splicing in protozoa and helminths
    • Nilsen, T.W. 1992, Trans-splicing in protozoa and helminths, Infect. Agents Dis., 1, 212-8.
    • (1992) Infect. Agents Dis. , vol.1 , pp. 212-218
    • Nilsen, T.W.1
  • 4
    • 0023659440 scopus 로고
    • A trans-spliced leader sequence on actin mRNA in C. elegans
    • Krause, M. and Hirsh, D. 1987, A trans-spliced leader sequence on actin mRNA in C. elegans, Cell, 49, 753-61.
    • (1987) Cell , vol.49 , pp. 753-761
    • Krause, M.1    Hirsh, D.2
  • 5
    • 33746207803 scopus 로고    scopus 로고
    • Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis
    • Satou, Y., Hamaguchi, M., Takeuchi, K., Hastings, K.E. and Satoh, N. 2006, Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis, Nucleic Acids Res., 34, 3378-88.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 3378-3388
    • Satou, Y.1    Hamaguchi, M.2    Takeuchi, K.3    Hastings, K.E.4    Satoh, N.5
  • 6
    • 0036235138 scopus 로고    scopus 로고
    • Trans-splicing as a novel mechanism to explain interallelic complementation in Drosophila
    • Mongelard, F., Labrador, M., Baxter, E.M., Gerasimova, T.I. and Corces, V.G. 2002, Trans-splicing as a novel mechanism to explain interallelic complementation in Drosophila, Genetics, 160, 1481-7.
    • (2002) Genetics , vol.160 , pp. 1481-1487
    • Mongelard, F.1    Labrador, M.2    Baxter, E.M.3    Gerasimova, T.I.4    Corces, V.G.5
  • 7
    • 0038235237 scopus 로고    scopus 로고
    • A candidate chimeric mammalian mRNA transcript is derived from distinct chromosomes and is associated with nonconsensus splice junction motifs
    • Zhang, C., Xie, Y., Martignetti, J.A., Yeo, T.T., Massa, S.M. and Longo, F.M. 2003, A candidate chimeric mammalian mRNA transcript is derived from distinct chromosomes and is associated with nonconsensus splice junction motifs, DNA Cell Biol., 22, 303-15.
    • (2003) DNA Cell Biol. , vol.22 , pp. 303-315
    • Zhang, C.1    Xie, Y.2    Martignetti, J.A.3    Yeo, T.T.4    Massa, S.M.5    Longo, F.M.6
  • 8
    • 59849091728 scopus 로고    scopus 로고
    • Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes
    • Li, X., Zhao, L., Jiang, H. and Wang, W. 2009, Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes, J. Mol. Evol., 68, 56-65.
    • (2009) J. Mol. Evol. , vol.68 , pp. 56-65
    • Li, X.1    Zhao, L.2    Jiang, H.3    Wang, W.4
  • 9
    • 84863512195 scopus 로고    scopus 로고
    • Novel domain combinations in proteins encoded by chimeric transcripts
    • Frenkel-Morgenstern, M. and Valencia, A. 2012, Novel domain combinations in proteins encoded by chimeric transcripts, Bioinformatics, 28, i67-74.
    • (2012) Bioinformatics , vol.28
    • Frenkel-Morgenstern, M.1    Valencia, A.2
  • 10
    • 84863011366 scopus 로고    scopus 로고
    • Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription
    • Patel, M., Simon, J.M., Iglesia, M.D., et al. 2011, Tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription, Genome Res., 22, 259-70.
    • (2011) Genome Res. , vol.22 , pp. 259-270
    • Patel, M.1    Simon, J.M.2    Iglesia, M.D.3
  • 11
    • 51149114001 scopus 로고    scopus 로고
    • A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells
    • Li, H., Wang, J., Mor, G. and Sklar, J. 2008, A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells, Science, 321, 1357-61.
    • (2008) Science , vol.321 , pp. 1357-1361
    • Li, H.1    Wang, J.2    Mor, G.3    Sklar, J.4
  • 13
    • 33744542916 scopus 로고    scopus 로고
    • Close encounters between active genes in the nucleus
    • Chuang, C.H. and Belmont, A.S. 2005, Close encounters between active genes in the nucleus, Genome Biol., 6, 237.
    • (2005) Genome Biol. , vol.6 , pp. 237
    • Chuang, C.H.1    Belmont, A.S.2
  • 14
    • 33646729244 scopus 로고    scopus 로고
    • Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations
    • Branco, M.R. and Pombo, A. 2006, Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations, PLoS Biol., 4, e138.
    • (2006) PLoS Biol. , vol.4
    • Branco, M.R.1    Pombo, A.2
  • 15
    • 0346492907 scopus 로고    scopus 로고
    • Fractal and statistical properties of large compact polymers: A computational study
    • Lua, R., Borovinskiy, A.L. and Grosberg, A.Y. 2004, Fractal and statistical properties of large compact polymers: a computational study, Polymer, 45, 717-31.
    • (2004) Polymer , vol.45 , pp. 717-731
    • Lua, R.1    Borovinskiy, A.L.2    Grosberg, A.Y.3
  • 16
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden, E., van Berkum, L.N., Williams, L., et al. 2009, Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, 326, 289-93.
    • (2009) Science , vol.326 , pp. 289-293
    • Lieberman-Aiden, E.1    Van Berkum, L.N.2    Williams, L.3
  • 18
    • 62649137535 scopus 로고    scopus 로고
    • Spatially confined folding of chromatin in the interphase nucleus
    • Mateos-Langerak, J., Bohn, M., de Leeuw, W., et al. 2009, Spatially confined folding of chromatin in the interphase nucleus, Proc. Natl. Acad. Sci. USA, 106, 3812-7.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 3812-3817
    • Mateos-Langerak, J.1    Bohn, M.2    De Leeuw, W.3
  • 19
    • 75749147065 scopus 로고    scopus 로고
    • Topological interactions between ring polymers: Implications for chro-matin loops
    • Bohn, M. and Heermann, D.W. 2010, Topological interactions between ring polymers: implications for chro-matin loops, J. Chem. Phys., 132, 044904.
    • (2010) J. Chem. Phys. , vol.132 , pp. 044904
    • Bohn, M.1    Heermann, D.W.2
  • 20
    • 52449116694 scopus 로고    scopus 로고
    • Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data
    • Unneberg, P. and Claverie, M.J. 2007, Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data, PLoS One, 2, e254.
    • (2007) PLoS One , vol.2
    • Unneberg, P.1    Claverie, M.J.2
  • 21
    • 80054984337 scopus 로고    scopus 로고
    • Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
    • Yaffe, E. and Tanay, A. 2011, Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture, Nat. Genet., 43, 1059-65.
    • (2011) Nat. Genet. , vol.43 , pp. 1059-1065
    • Yaffe, E.1    Tanay, A.2
  • 22
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent, W.J. 2002, BLAT-the BLAST-like alignment tool, Genome Res., 12, 656-64.
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 24
    • 0037327027 scopus 로고    scopus 로고
    • A novel algorithm for computational identification of contaminated EST libraries
    • Sorek, R. and Safer, H.M. 2003, A novel algorithm for computational identification of contaminated EST libraries, Nucleic Acids Res., 31, 1067-74.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1067-1074
    • Sorek, R.1    Safer, H.M.2
  • 25
    • 0031027131 scopus 로고    scopus 로고
    • Review: Proximity effects in the production of chromosome aberrations by ionizing radiation
    • Sachs, R.K., Chen, A.M. and Brenner, D.J. 1997, Review: proximity effects in the production of chromosome aberrations by ionizing radiation, Int. J. Radiat. Biol., 71, 1-19.
    • (1997) Int. J. Radiat. Biol. , vol.71 , pp. 1-19
    • Sachs, R.K.1    Chen, A.M.2    Brenner, D.J.3
  • 26
    • 4444280219 scopus 로고    scopus 로고
    • Finding fusion genes resulting from chromosome rearrangement by analyzing the expressed sequence databases
    • Hahn, Y., Bera, T.K., Gehlhaus, K., Kirsch, I.R., Pastan, I.H. and Lee, B. 2004, Finding fusion genes resulting from chromosome rearrangement by analyzing the expressed sequence databases, Proc. Natl. Acad. Sci. USA, 101, 13257-61.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 13257-13261
    • Hahn, Y.1    Bera, T.K.2    Gehlhaus, K.3    Kirsch, I.R.4    Pastan, I.H.5    Lee, B.6
  • 27
    • 34250334695 scopus 로고    scopus 로고
    • Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using paired-end ditags (PETs)
    • Ruan, Y., Ooi, H.S., Choo, S.W., et al. 2007, Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using paired-end ditags (PETs), Genome Res., 17, 828-38.
    • (2007) Genome Res. , vol.17 , pp. 828-838
    • Ruan, Y.1    Ooi, H.S.2    Choo, S.W.3
  • 28
    • 69249234735 scopus 로고    scopus 로고
    • A probabilistic model for the arrangement of a subset of human chromosome territories in WI38 human fibroblasts
    • Zeitz, M.J., Mukherjee, L., Bhattacharya, S., Xu, J. and Berezney, R. 2009, A probabilistic model for the arrangement of a subset of human chromosome territories in WI38 human fibroblasts, J. Cell Physiol., 221, 120-9.
    • (2009) J. Cell Physiol. , vol.221 , pp. 120-129
    • Zeitz, M.J.1    Mukherjee, L.2    Bhattacharya, S.3    Xu, J.4    Berezney, R.5
  • 29
    • 69249238070 scopus 로고    scopus 로고
    • Cell type specific chromosome territory organization in the interphase nuclus of normal and cancer cells
    • Marella, N.V., Bhattacharya, S., Mukherjee, L., Xu, J. and Berezney, R. 2009, Cell type specific chromosome territory organization in the interphase nuclus of normal and cancer cells, J. Cell Physiol., 221, 130-8.
    • (2009) J. Cell Physiol. , vol.221 , pp. 130-138
    • Marella, N.V.1    Bhattacharya, S.2    Mukherjee, L.3    Xu, J.4    Berezney, R.5
  • 30
    • 77957867310 scopus 로고    scopus 로고
    • Diffusion-driven looping provides a consistent framework for chromatin organization
    • Bohn, M. and Heermann, D.W. 2010, Diffusion-driven looping provides a consistent framework for chromatin organization, PLoS One, 5, e12218.
    • (2010) PLoS One , vol.5
    • Bohn, M.1    Heermann, D.W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.