TY - JOUR AU - Lemon, B. AU - Tjian, R. PY - 2000 DA - 2000// TI - Orchestrated response: a symphony of transcription factors for gene control JO - Genes Dev VL - 14 UR - https://doi.org/10.1101/gad.831000 DO - 10.1101/gad.831000 ID - Lemon2000 ER - TY - JOUR AU - Levitsky, V. G. AU - Podkolodnaya, O. A. AU - Kolchanov, N. A. AU - Podkolodny, N. L. PY - 2001 DA - 2001// TI - Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.11.998 DO - 10.1093/bioinformatics/17.11.998 ID - Levitsky2001 ER - TY - JOUR AU - Bode, J. AU - Benham, C. AU - Knopp, A. AU - Mielke, C. PY - 2000 DA - 2000// TI - Transcriptional augmentation: modulation of gene expression by scaffold/matrix-attached regions (S/MAR elements) JO - Crit Rev Eukaryot Gene Expr VL - 10 UR - https://doi.org/10.1615/CritRevEukarGeneExpr.v10.i1.90 DO - 10.1615/CritRevEukarGeneExpr.v10.i1.90 ID - Bode2000 ER - TY - JOUR AU - Grewal, S. I. AU - Moazed, D. PY - 2003 DA - 2003// TI - Heterochromatin and epigenetic control of gene expression JO - Science VL - 301 UR - https://doi.org/10.1126/science.1086887 DO - 10.1126/science.1086887 ID - Grewal2003 ER - TY - JOUR AU - Boeger, H. AU - Griesenbeck, J. AU - Strattan, J. S. AU - Kornberg, R. D. PY - 2003 DA - 2003// TI - Nucleosomes unfold completely at a transcriptionally active promoter JO - Mol Cell VL - 11 UR - https://doi.org/10.1016/S1097-2765(03)00231-4 DO - 10.1016/S1097-2765(03)00231-4 ID - Boeger2003 ER - TY - JOUR AU - Wolffe, A. P. PY - 1994 DA - 1994// TI - Transcriptional activation. Switched-on chromatin JO - Curr Biol VL - 4 UR - https://doi.org/10.1016/S0960-9822(00)00114-7 DO - 10.1016/S0960-9822(00)00114-7 ID - Wolffe1994 ER - TY - JOUR AU - Glazko, G. V. AU - Rogozin, I. B. AU - Glazkov, M. V. PY - 2001 DA - 2001// TI - Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix JO - Biochim Biophys Acta VL - 1517 UR - https://doi.org/10.1016/S0167-4781(00)00297-9 DO - 10.1016/S0167-4781(00)00297-9 ID - Glazko2001 ER - TY - JOUR AU - Glazko, G. V. AU - Koonin, E. V. AU - Rogozin, I. B. AU - Shabalina, S. A. PY - 2003 DA - 2003// TI - A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions JO - Trends Genet VL - 19 UR - https://doi.org/10.1016/S0168-9525(03)00016-7 DO - 10.1016/S0168-9525(03)00016-7 ID - Glazko2003 ER - TY - JOUR AU - Versteeg, R. AU - van Schaik, B. D. AU - van Batenburg, M. F. AU - Roos, M. AU - Monajemi, R. AU - Caron, H. AU - Bussemaker, H. J. AU - van Kampen, A. H. PY - 2003 DA - 2003// TI - The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1649303 DO - 10.1101/gr.1649303 ID - Versteeg2003 ER - TY - JOUR AU - Lercher, M. J. AU - Urrutia, A. O. AU - Hurst, L. D. PY - 2002 DA - 2002// TI - Clustering of housekeeping genes provides a unified model of gene order in the human genome JO - Nat Genet VL - 31 UR - https://doi.org/10.1038/ng887 DO - 10.1038/ng887 ID - Lercher2002 ER - TY - JOUR AU - de Laat, W. AU - Grosveld, F. PY - 2003 DA - 2003// TI - Spatial organisation of gene expression: the active chromatin hub JO - Chromosome Res VL - 11 UR - https://doi.org/10.1023/A:1024922626726 DO - 10.1023/A:1024922626726 ID - de Laat2003 ER - TY - JOUR AU - Byrd, K. AU - Corces, V. G. PY - 2003 DA - 2003// TI - Visualization of chromatin domains created by the gypsy insulator of Drosophila JO - J Cell Biol VL - 162 UR - https://doi.org/10.1083/jcb.200305013 DO - 10.1083/jcb.200305013 ID - Byrd2003 ER - TY - JOUR AU - Nabirochkin, S. AU - Ossokina, M. AU - Heidmann, T. PY - 1998 DA - 1998// TI - A nuclear matrix/scaffold attachment region co-localizes with the gypsy retrotransposon insulator sequence JO - J Biol Chem VL - 273 UR - https://doi.org/10.1074/jbc.273.4.2473 DO - 10.1074/jbc.273.4.2473 ID - Nabirochkin1998 ER - TY - JOUR AU - Kim, J. M. AU - Kim, J. S. AU - Park, D. H. AU - Kang, H. S. AU - Yoon, J. AU - Baek, K. AU - Yoon, Y. PY - 2004 DA - 2004// TI - Improved recombinant gene expression in CHO cells using matrix attachment regions JO - J Biotechnol VL - 107 UR - https://doi.org/10.1016/j.jbiotec.2003.09.015 DO - 10.1016/j.jbiotec.2003.09.015 ID - Kim2004 ER - TY - JOUR AU - Bonifer, C. AU - Yannoutsos, N. AU - Kruger, G. AU - Grosveld, F. AU - Sippel, A. E. PY - 1994 DA - 1994// TI - Dissection of the locus control function located on the chicken lysozyme gene domain in transgenic mice JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.20.4202 DO - 10.1093/nar/22.20.4202 ID - Bonifer1994 ER - TY - JOUR AU - Yusufzai, T. M. AU - Felsenfeld, G. PY - 2004 DA - 2004// TI - The 5'-HS4 chicken beta-globin insulator is a CTCF-dependent nuclear matrix-associated element JO - Proc Natl Acad Sci U S A VL - 101 UR - https://doi.org/10.1073/pnas.0402938101 DO - 10.1073/pnas.0402938101 ID - Yusufzai2004 ER - TY - JOUR AU - Khorasanizadeh, S. PY - 2004 DA - 2004// TI - The nucleosome: from genomic organisation to genomic regulation JO - Cell VL - 116 UR - https://doi.org/10.1016/S0092-8674(04)00044-3 DO - 10.1016/S0092-8674(04)00044-3 ID - Khorasanizadeh2004 ER - TY - JOUR AU - Suter, B. AU - Schnappauf, G. AU - Thoma, F. PY - 2000 DA - 2000// TI - Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.21.4083 DO - 10.1093/nar/28.21.4083 ID - Suter2000 ER - TY - JOUR AU - Koch, K. A. AU - Thiele, D. J. PY - 1999 DA - 1999// TI - Functional analysis of a homopolymeric (dA-dT) element that provides nucleosomal access to yeast and mammalian transcription factors JO - J Biol Chem VL - 274 UR - https://doi.org/10.1074/jbc.274.34.23752 DO - 10.1074/jbc.274.34.23752 ID - Koch1999 ER - TY - JOUR AU - Wang, Y. H. AU - Griffith, J. D. PY - 1996 DA - 1996// TI - The [(G/C)3NN]n motif: a common DNA repeat that excludes nucleosomes JO - Proc Natl Acad Sci U S A VL - 93 UR - https://doi.org/10.1073/pnas.93.17.8863 DO - 10.1073/pnas.93.17.8863 ID - Wang1996 ER - TY - JOUR AU - Iyer, V. AU - Struhl, K. PY - 1995 DA - 1995// TI - Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure JO - Embo J VL - 14 ID - Iyer1995 ER - TY - JOUR AU - Kirkpatrick, D. T. AU - Wang, Y. H. AU - Dominska, M. AU - Griffith, J. D. AU - Petes, T. D. PY - 1999 DA - 1999// TI - Control of meiotic recombination and gene expression in yeast by a simple repetitive DNA sequence that excludes nucleosomes JO - Mol Cell Biol VL - 19 ID - Kirkpatrick1999 ER - TY - JOUR AU - Grover, D. AU - Mukerji, M. AU - Bhatnagar, P. AU - Kannan, K. AU - Brahmachari, S. K. PY - 2004 DA - 2004// TI - Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth005 DO - 10.1093/bioinformatics/bth005 ID - Grover2004 ER - TY - JOUR AU - Jordan, I. K. AU - Rogozin, I. B. AU - Glazko, G. V. AU - Koonin, E. V. PY - 2003 DA - 2003// TI - Origin of a substantial fraction of human regulatory sequences from transposable elements JO - Trends Genet VL - 19 UR - https://doi.org/10.1016/S0168-9525(02)00006-9 DO - 10.1016/S0168-9525(02)00006-9 ID - Jordan2003 ER - TY - JOUR AU - Brahmachari, S. K. AU - Meera, G. AU - Sarkar, P. S. AU - Balagurumoorthy, P. AU - Tripathi, J. AU - Raghavan, S. AU - Shaligram, U. AU - Pataskar, S. PY - 1995 DA - 1995// TI - Simple repetitive sequences in the genome: structure and functional significance JO - Electrophoresis VL - 16 UR - https://doi.org/10.1002/elps.11501601283 DO - 10.1002/elps.11501601283 ID - Brahmachari1995 ER - TY - JOUR AU - Grover, D. AU - Majumder, P. P. AU - Rao, C. B. AU - Brahmachari, S. K. AU - Mukerji, M. PY - 2003 DA - 2003// TI - Nonrandom distribution of alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22 JO - Mol Biol Evol VL - 20 UR - https://doi.org/10.1093/molbev/msg153 DO - 10.1093/molbev/msg153 ID - Grover2003 ER - TY - JOUR AU - Vijaya, S. AU - Steffen, D. L. AU - Robinson, H. L. PY - 1986 DA - 1986// TI - Acceptor sites for retroviral integrations map near DNase I-hypersensitive sites in chromatin JO - J Virol VL - 60 ID - Vijaya1986 ER - TY - JOUR AU - Eisenberg, E. AU - Levanon, E. Y. PY - 2003 DA - 2003// TI - Human housekeeping genes are compact JO - Trends Genet VL - 19 UR - https://doi.org/10.1016/S0168-9525(03)00140-9 DO - 10.1016/S0168-9525(03)00140-9 ID - Eisenberg2003 ER - TY - JOUR AU - Vinogradov, A. E. PY - 2004 DA - 2004// TI - Compactness of human housekeeping genes: selection for economy or genomic design? JO - Trends Genet VL - 20 UR - https://doi.org/10.1016/j.tig.2004.03.006 DO - 10.1016/j.tig.2004.03.006 ID - Vinogradov2004 ER - TY - JOUR AU - Oei, S. L. AU - Babich, V. S. AU - Kazakov, V. I. AU - Usmanova, N. M. AU - Kropotov, A. V. AU - Tomilin, N. V. PY - 2004 DA - 2004// TI - Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters JO - Genomics VL - 83 UR - https://doi.org/10.1016/j.ygeno.2003.11.001 DO - 10.1016/j.ygeno.2003.11.001 ID - Oei2004 ER - TY - JOUR AU - Nemeth, A. AU - Langst, G. PY - 2004 DA - 2004// TI - Chromatin higher order structure: opening up chromatin for transcription JO - Brief Funct Genomic Proteomic VL - 2 UR - https://doi.org/10.1093/bfgp/2.4.334 DO - 10.1093/bfgp/2.4.334 ID - Nemeth2004 ER - TY - JOUR AU - Pennisi, E. PY - 2003 DA - 2003// TI - Human genome. A low number wins the GeneSweep Pool JO - Science VL - 300 UR - https://doi.org/10.1126/science.300.5625.1484b DO - 10.1126/science.300.5625.1484b ID - Pennisi2003 ER - TY - CHAP AU - Brahmachari, S. K. AU - Ramesh, N. AU - Shouche, Y. S. AU - Mishra, R. K. AU - Bagga, R. AU - Meera, G. ED - Sarma, R. H. ED - Sarma, M. H. PY - 1990 DA - 1990// TI - Unusual DNA Structures: Sequence Requirements and Role in Transcriptional Control BT - Structure and Methods PB - Adenine Press CY - New York ID - Brahmachari1990 ER - TY - JOUR AU - Conrad, M. AU - Brahmachari, S. K. AU - Sasisekharan, V. PY - 1986 DA - 1986// TI - DNA structural variability as a factor in gene expression and evolution JO - Biosystems VL - 19 UR - https://doi.org/10.1016/0303-2647(86)90024-9 DO - 10.1016/0303-2647(86)90024-9 ID - Conrad1986 ER - TY - JOUR AU - Gilbert, N. AU - Boyle, S. AU - Fiegler, H. AU - Woodfine, K. AU - Carter, N. P. AU - Bickmore, W. A. PY - 2004 DA - 2004// TI - Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers JO - Cell VL - 118 UR - https://doi.org/10.1016/j.cell.2004.08.011 DO - 10.1016/j.cell.2004.08.011 ID - Gilbert2004 ER - TY - STD TI - List of housekeeping genes[http://www.compugen.co.il/supp_info/Housekeeping_genes.html] UR - http://www.compugen.co.il/supp_info/Housekeeping_genes.html ID - ref36 ER - TY - JOUR AU - Singh, G. B. AU - Kramer, J. A. AU - Krawetz, S. A. PY - 1997 DA - 1997// TI - Mathematical model to predict regions of chromatin attachment to the nuclear matrix JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.7.1419 DO - 10.1093/nar/25.7.1419 ID - Singh1997 ER - TY - STD TI - MAR Finder[http://futuresoft.org/MAR-Wiz/] UR - http://futuresoft.org/MAR-Wiz/ ID - ref38 ER - TY - JOUR AU - Rogozin, I. B. AU - Glazko, G. V. AU - Glazkov, M. V. PY - 2000 DA - 2000// TI - Computer prediction of sites associated with various elements of the nuclear matrix JO - Brief Bioinform VL - 1 UR - https://doi.org/10.1093/bib/1.1.33 DO - 10.1093/bib/1.1.33 ID - Rogozin2000 ER - TY - STD TI - ChrClass[http://ftp.bionet.nsc.ru/pub/biology/chrclass/chrclass.zip] UR - http://ftp.bionet.nsc.ru/pub/biology/chrclass/chrclass.zip ID - ref40 ER - TY - STD TI - Recon[http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/] UR - http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/ ID - ref41 ER - TY - STD TI - RepeatMasker[http://www.repeatmasker.org/] UR - http://www.repeatmasker.org/ ID - ref42 ER -