메뉴 건너뛰기




Volumn 42, Issue 5, 2014, Pages

Quantitative analysis of genomic element interactions by molecular colony technique

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; DODECYL SULFATE SODIUM; HEMOGLOBIN BETA CHAIN; POLYACRYLAMIDE GEL;

EID: 84899006108     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1322     Document Type: Article
Times cited : (23)

References (50)
  • 2
    • 34249307315 scopus 로고    scopus 로고
    • Nuclear organization of the genome and the potential for gene regulation
    • DOI 10.1038/nature05916, PII NATURE05916
    • Fraser, P. and Bickmore, W. (2007) Nuclear organization of the genome and the potential for gene regulation. Nature, 447, 413-417. (Pubitemid 46816747
    • (2007) Nature , vol.447 , Issue.7143 , pp. 413-417
    • Fraser, P.1    Bickmore, W.2
  • 3
    • 67649766870 scopus 로고    scopus 로고
    • Transcription factories: Gene expression in unions?
    • Sutherland, H. and Bickmore, W.A. (2009) Transcription factories: Gene expression in unions? Nat. Rev. Genet., 10, 457-466.
    • (2009) Nat Rev. Genet. , vol.10 , pp. 457-466
    • Sutherland, H.1    Bickmore, W.A.2
  • 4
    • 33847077659 scopus 로고    scopus 로고
    • Beyond the sequence: Cellular organization of genome function
    • DOI 10.1016/j.cell.2007.01.028, PII S0092867407001262
    • Misteli, T. (2007) Beyond the sequence: Cellular organization of genome function. Cell, 128, 787-800. (Pubitemid 46273571
    • (2007) Cell , vol.128 , Issue.4 , pp. 787-800
    • Misteli, T.1
  • 7
    • 79953162695 scopus 로고    scopus 로고
    • Locking the genome: Nuclear organization and cell fate
    • Meister, P., Mango, S.E. and Gasser, S.M. (2011) Locking the genome: Nuclear organization and cell fate. Curr. Opin. Genet. Dev., 21, 167-174.
    • (2011) Curr. Opin. Genet. Dev. , vol.21 , pp. 167-174
    • Meister, P.1    Mango, S.E.2    Gasser, S.M.3
  • 10
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S. and Ren, B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380.
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1    Selvaraj, S.2    Yue, F.3    Kim, A.4    Li, Y.5    Shen, Y.6    Hu, M.7    Liu, J.S.8    Ren, B.9
  • 11
    • 84875190221 scopus 로고    scopus 로고
    • Genome architecture: Domain organization of interphase chromosomes
    • Bickmore, W.A. and van Steensel, B. (2013) Genome architecture: Domain organization of interphase chromosomes. Cell, 152, 1270-1284.
    • (2013) Cell , vol.152 , pp. 1270-1284
    • Bickmore, W.A.1    Van Steensel, B.2
  • 12
    • 84878953434 scopus 로고    scopus 로고
    • Communication of genome regulatory elements in a folded chromosome
    • Razin, S.V., Gavrilov, A.A., Ioudinkova, E.S. and Iarovaia, O.V. (2013) Communication of genome regulatory elements in a folded chromosome. FEBS Lett., 587, 1840-1847.
    • (2013) FEBS Lett. , vol.587 , pp. 1840-1847
    • Razin, S.V.1    Gavrilov, A.A.2    Ioudinkova, E.S.3    Iarovaia, O.V.4
  • 13
    • 0033215443 scopus 로고    scopus 로고
    • Looping versus linking: Toward a model for long-distance gene activation
    • DOI 10.1101/gad.13.19.2465
    • Bulger, M. and Groudine, M. (1999) Looping versus linking: Toward a model of long distance gene activation. Genes Dev., 13, 2465-2477. (Pubitemid 29489638
    • (1999) Genes and Development , vol.13 , Issue.19 , pp. 2465-2477
    • Bulger, M.1    Groudine, M.2
  • 14
    • 53249121024 scopus 로고    scopus 로고
    • Long range chromatin interactions involved in gene regulation
    • Bartkuhn, M. and Renkawitz, R. (2008) Long range chromatin interactions involved in gene regulation. Biochim. Biophys. Acta, 1783, 2161-2166.
    • (2008) Biochim. Biophys. Acta , vol.1783 , pp. 2161-2166
    • Bartkuhn, M.1    Renkawitz, R.2
  • 15
    • 79551655285 scopus 로고    scopus 로고
    • Functional and mechanistic diversity of distal transcription enhancers
    • Bulger, M. and Groudine, M. (2010) Functional and mechanistic diversity of distal transcription enhancers. Cell, 144, 327-339.
    • (2010) Cell , vol.144 , pp. 327-339
    • Bulger, M.1    Groudine, M.2
  • 16
    • 0042880630 scopus 로고    scopus 로고
    • Spatial organization of gene expression: The active chromatin hub
    • DOI 10.1023/A:1024922626726
    • de Laat, W. and Grosveld, F. (2003) Spatial organization of gene expression: The active chromatin hub. Chromosome Res., 11, 447-459. (Pubitemid 37041205
    • (2003) Chromosome Research , vol.11 , Issue.5 , pp. 447-459
    • De Laat, W.1    Grosveld, F.2
  • 17
    • 0036923833 scopus 로고    scopus 로고
    • Looping and interaction between hypersensitive sites in the active beta-globin locus
    • Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F. and de Laat, W. (2002) Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol. Cell, 10, 1453-1465.
    • (2002) Mol. Cell , vol.10 , pp. 1453-1465
    • Tolhuis, B.1    Palstra, R.J.2    Splinter, E.3    Grosveld, F.4    De Laat, W.5
  • 18
    • 33745436025 scopus 로고    scopus 로고
    • Active chromatin hub of the mouse alpha-globin locus forms in a transcription factory of clustered housekeeping genes
    • Zhou, G.L., Xin, L., Song, W., Di, L.J., Liu, G., Wu, X.S., Liu, D.P. and Liang, C.C. (2006) Active chromatin hub of the mouse alpha-globin locus forms in a transcription factory of clustered housekeeping genes. Mol. Cell. Biol., 26, 5096-5105.
    • (2006) Mol. Cell. Biol. , vol.26 , pp. 5096-5105
    • Zhou, G.L.1    Xin, L.2    Song, W.3    Di, L.J.4    Liu, G.5    Wu, X.S.6    Liu, D.P.7    Liang, C.C.8
  • 19
    • 34447536151 scopus 로고    scopus 로고
    • Beta-globin active chromatin Hub formation in differentiating erythroid cells and in p45 NF-E2 knock-out mice
    • Kooren, J., Palstra, R.J., Klous, P., Splinter, E., von Lindern, M., Grosveld, F. and de Laat, W. (2007) Beta-globin active chromatin Hub formation in differentiating erythroid cells and in p45 NF-E2 knock-out mice. J. Biol. Chem., 282, 16544-16552.
    • (2007) J. Biol. Chem. , vol.282 , pp. 16544-16552
    • Kooren, J.1    Palstra, R.J.2    Klous, P.3    Splinter, E.4    Von Lindern, M.5    Grosveld, F.6    De Laat, W.7
  • 20
    • 39049092286 scopus 로고    scopus 로고
    • Beta-globin regulation and long-range interactions
    • Palstra, R.J., de Laat, W. and Grosveld, F. (2008) Beta-globin regulation and long-range interactions. Adv. Genet., 61, 107-142.
    • (2008) Adv. Genet. , vol.61 , pp. 107-142
    • Palstra, R.J.1    De Laat, W.2    Grosveld, F.3
  • 21
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • DOI 10.1126/science.1067799
    • Dekker, J., Rippe, K., Dekker, M. and Kleckner, N. (2002) Capturing chromosome conformation. Science, 295, 1306-1311. (Pubitemid 34157624
    • (2002) Science , vol.295 , Issue.5558 , pp. 1306-1311
    • Dekker, J.1    Rippe, K.2    Dekker, M.3    Kleckner, N.4
  • 22
    • 0029051646 scopus 로고
    • Transcription complex stability and chromatin dynamics in vivo
    • Wijgerde, M., Grosveld, F. and Fraser, P. (1995) Transcription complex stability and chromatin dynamics in vivo. Nature, 377, 209-213.
    • (1995) Nature , vol.377 , pp. 209-213
    • Wijgerde, M.1    Grosveld, F.2    Fraser, P.3
  • 23
    • 0032531694 scopus 로고    scopus 로고
    • Chromatin interaction mechanism of transcriptional control in vivo
    • DOI 10.1093/emboj/17.20.6020
    • Gribnau, J., de Boer, E., Trimborn, T., Wijgerde, M., Milot, E., Grosveld, F. and Fraser, P. (1998) Chromatin interaction mechanism of transcriptional control in vivo. EMBO J., 17, 6020-6027. (Pubitemid 28474795
    • (1998) EMBO Journal , vol.17 , Issue.20 , pp. 6020-6027
    • Gribnau, J.1    De Boer, E.2    Trimborn, T.3    Wijgerde, M.4    Milot, E.5    Grosveld, F.6    Fraser, P.7
  • 24
    • 33750212321 scopus 로고    scopus 로고
    • Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C
    • DOI 10.1038/ng1896, PII NG1896
    • Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B. and de Laat, W. (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C) Nat. Genet., 38, 1348-1354. (Pubitemid 44646300
    • (2006) Nature Genetics , vol.38 , Issue.11 , pp. 1348-1354
    • Simonis, M.1    Klous, P.2    Splinter, E.3    Moshkin, Y.4    Willemsen, R.5    De Wit, E.6    Van Steensel, B.7    De Laat, W.8
  • 25
    • 33750203582 scopus 로고    scopus 로고
    • Circular chromosome conformation capture (4C uncovers extensive networks of epigenetically regulated intra-And interchromosomal interactions
    • Zhao, Z., Tavoosidana, G., Sjolinder, M., Gondor, A., Mariano, P., Wang, S., Kanduri, C., Lezcano, M., Sandhu, K.S., Singh, U. et al. (2006) Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-And interchromosomal interactions. Nat. Genet., 38, 1341-1347.
    • (2006) Nat. Genet. , vol.38 , pp. 1341-1347
    • Zhao, Z.1    Tavoosidana, G.2    Sjolinder, M.3    Gondor, A.4    Mariano, P.5    Wang, S.6    Kanduri, C.7    Lezcano, M.8    Sandhu, K.S.9    Singh, U.10
  • 28
    • 1642453552 scopus 로고    scopus 로고
    • 3C Technology: Analyzing the spatial organization of genomic loci in vivo
    • DOI 10.1016/S0076-6879(03)75030-7
    • Splinter, E., Grosveld, F. and de Laat, W. (2004) 3C technology: Analyzing the spatial organization of genomic loci in vivo. Methods Enzymol., 375, 493-507. (Pubitemid 38124886
    • (2004) Methods in Enzymology , vol.375 , pp. 493-507
    • Splinter, E.1    Grosveld, F.2    De Laat, W.3
  • 31
    • 84859845974 scopus 로고    scopus 로고
    • The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture
    • Markaki, Y., Smeets, D., Fiedler, S., Schmid, V.J., Schermelleh, L., Cremer, T. and Cremer, M. (2012) The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture. Bioessays, 34, 412-426.
    • (2012) Bioessays , vol.34 , pp. 412-426
    • Markaki, Y.1    Smeets, D.2    Fiedler, S.3    Schmid, V.J.4    Schermelleh, L.5    Cremer, T.6    Cremer, M.7
  • 32
    • 53249124651 scopus 로고    scopus 로고
    • FISH-eyed and genome-wide views on the spatial organisation of gene expression
    • Simonis, M. and de Laat, W. (2008) FISH-eyed and genome-wide views on the spatial organisation of gene expression. Biochim. Biophys. Acta, 1783, 2052-2060.
    • (2008) Biochim. Biophys. Acta , vol.1783 , pp. 2052-2060
    • Simonis, M.1    De Laat, W.2
  • 33
    • 53249107918 scopus 로고    scopus 로고
    • Molecular colony technique: A new tool for biomedical research and clinical practice
    • Chetverin, A.B. and Chetverina, H.V. (2008) Molecular colony technique: A new tool for biomedical research and clinical practice. Prog. Nucleic Acid Res. Mol. Biol., 82, 219-255.
    • (2008) Prog. Nucleic Acid Res. Mol. Biol. , vol.82 , pp. 219-255
    • Chetverin, A.B.1    Chetverina, H.V.2
  • 35
    • 33747886268 scopus 로고    scopus 로고
    • Realtime monitoring of DNA colonies growing in a polyacrylamide gel
    • Samatov, T.R., Chetverina, H.V. and Chetverin, A.B. (2006) Realtime monitoring of DNA colonies growing in a polyacrylamide gel. Anal. Biochem., 356, 300-302.
    • (2006) Anal. Biochem. , vol.356 , pp. 300-302
    • Samatov, T.R.1    Chetverina, H.V.2    Chetverin, A.B.3
  • 36
    • 0036073952 scopus 로고    scopus 로고
    • Molecular colony diagnostics: Detection and quantitation of viral nucleic acids by in-gel PCR
    • 154 156
    • Chetverina, H.V., Samatov, T.R., Ugarov, V.I. and Chetverin, A.B. (2002) Molecular colony diagnostics: Detection and quantitation of viral nucleic acids by in-gel PCR. Biotechniques, 33, 150-152, 154, 156.
    • (2002) Biotechniques , vol.33 , pp. 150-152
    • Chetverina, H.V.1    Samatov, T.R.2    Ugarov, V.I.3    Chetverin, A.B.4
  • 38
    • 0029670262 scopus 로고    scopus 로고
    • Molecular beacons: Probes that fluoresce upon hybridization
    • Tyagi, S. and Kramer, F.R. (1996) Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol., 14, 303-308.
    • (1996) Nat. Biotechnol. , vol.14 , pp. 303-308
    • Tyagi, S.1    Kramer, F.R.2
  • 40
    • 0344826470 scopus 로고    scopus 로고
    • Role of Ras signaling in erythroid differentiation of mouse fetal liver cells: Functional analysis by a flow cytometry-based novel culture system
    • DOI 10.1182/blood-2003-05-1479
    • Zhang, J., Socolovsky, M., Gross, A.W. and Lodish, H.F. (2003) Role of Ras signaling in erythroid differentiation of mouse fetal liver cells: Functional analysis by a flow cytometry-based novel culture system. Blood, 102, 3938-3946. (Pubitemid 37486974
    • (2003) Blood , vol.102 , Issue.12 , pp. 3938-3946
    • Zhang, J.1    Socolovsky, M.2    Gross, A.W.3    Lodish, H.F.4
  • 41
    • 7244259100 scopus 로고    scopus 로고
    • Megabase deletions of gene deserts result in viable mice
    • DOI 10.1038/nature03022
    • Nobrega, M.A., Zhu, Y., Plajzer-Frick, I., Afzal, V. and Rubin, E.M. (2004) Megabase deletions of gene deserts result in viable mice. Nature, 431, 988-993. (Pubitemid 39434420
    • (2004) Nature , vol.431 , Issue.7011 , pp. 988-993
    • Nobrega, M.A.1    Zhu, Y.2    Plajer-Frick, I.3    Afzal, Y.4    Rubin, E.M.5
  • 42
    • 79952294070 scopus 로고    scopus 로고
    • A chromatin insulator driving three-dimensional Polycomb response element (PRE contacts and Polycomb association with the chromatin fiber
    • Comet, I., Schuettengruber, B., Sexton, T. and Cavalli, G. (2011) A chromatin insulator driving three-dimensional Polycomb response element (PRE) contacts and Polycomb association with the chromatin fiber. Proc. Natl Acad. Sci. USA, 108, 2294-2299.
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 2294-2299
    • Comet, I.1    Schuettengruber, B.2    Sexton, T.3    Cavalli, G.4
  • 43
    • 7444260237 scopus 로고    scopus 로고
    • Gene order and dynamic domains
    • DOI 10.1126/science.1103864
    • Kosak, S.T. and Groudine, M. (2004) Gene order and dynamic domains. Science, 306, 644-647. (Pubitemid 39440904
    • (2004) Science , vol.306 , Issue.5696 , pp. 644-647
    • Kosak, S.T.1    Groudine, M.2
  • 44
    • 2942679507 scopus 로고    scopus 로고
    • Form follows function: The genomic organization of cellular differentiation
    • DOI 10.1101/gad.1209304
    • Kosak, S.T. and Groudine, M. (2004) Form follows function: The genomic organization of cellular differentiation. Genes Dev., 18, 1371-1384. (Pubitemid 38780624
    • (2004) Genes and Development , vol.18 , Issue.12 , pp. 1371-1384
    • Kosak, S.T.1    Groudine, M.2
  • 45
    • 84875464666 scopus 로고    scopus 로고
    • Actual ligation frequencies in the chromosome conformation capture procedure
    • Gavrilov, A.A., Golov, A.K. and Razin, S.V. (2013) Actual ligation frequencies in the chromosome conformation capture procedure. PLoS One, 8, e60403.
    • (2013) PLoS One , vol.8
    • Gavrilov, A.A.1    Golov, A.K.2    Razin, S.V.3
  • 46
    • 84870379849 scopus 로고    scopus 로고
    • Hi-C: A comprehensive technique to capture the conformation of genomes
    • Belton, J.M., McCord, R.P., Gibcus, J.H., Naumova, N., Zhan, Y. and Dekker, J. (2012) Hi-C: A comprehensive technique to capture the conformation of genomes. Methods, 58, 268-276.
    • (2012) Methods , vol.58 , pp. 268-276
    • Belton, J.M.1    McCord, R.P.2    Gibcus, J.H.3    Naumova, N.4    Zhan, Y.5    Dekker, J.6
  • 49
    • 1642337153 scopus 로고    scopus 로고
    • Use of bifunctional cross-linking reagents in mapping genomic distribution of chromatin remodeling complexes
    • DOI 10.1016/j.ymeth.2003.10.022, PII S1046202303002974
    • Fujita, N. and Wade, P.A. (2004) Use of bifunctional cross-linking reagents in mapping genomic distribution of chromatin remodeling complexes. Methods, 33, 81-85. (Pubitemid 38369094
    • (2004) Methods , vol.33 , Issue.1 , pp. 81-85
    • Fujita, N.1    Wade, P.A.2
  • 50
    • 34047198759 scopus 로고    scopus 로고
    • In vivo dual cross-linking for identification of indirect DNA-Associated proteins by chromatin immunoprecipitation
    • Zeng, P.Y., Vakoc, C.R., Chen, Z.C., Blobel, G.A. and Berger, S.L. (2006) In vivo dual cross-linking for identification of indirect DNA-Associated proteins by chromatin immunoprecipitation. Biotechniques, 41, 694-698.
    • (2006) Biotechniques , vol.41 , pp. 694-698
    • Zeng, P.Y.1    Vakoc, C.R.2    Chen, Z.C.3    Blobel, G.A.4    Berger, S.L.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.