Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites

被引:123
作者
Wade, JT
Reppas, NB
Church, GM
Struhl, K [1 ]
机构
[1] Harvard Univ, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA
[2] Harvard Univ, Sch Med, Grad Biophys Program, Boston, MA 02115 USA
[3] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA
关键词
LexA; chromatin immunoprecipitation; genome organization; transcription; RNA polymerase;
D O I
10.1101/gad.1355605
中图分类号
Q2 [细胞生物学];
学科分类号
071009 ; 090102 ;
摘要
Genomes of eukaryotic organisms are packaged into nucleosomes that restrict the binding of transcription factors to accessible regions. Bacteria do not contain histones, but they have nucleoid-associated proteins that have been proposed to function analogously. Here, we combine chromatin immunoprecipitation and high-density oligonucleotide microarrays to define the in vivo DNA targets of the LexA transcriptional repressor in Escherichia coli. We demonstrate a near-universal relationship between the presence of a LexA sequence motif, LexA binding in vitro, and LexA binding in vivo, suggesting that a suitable recognition site for LexA is sufficient for binding in vivo. Consistent with this observation, LexA binds comparably to ectopic target sites introduced at various positions in the genome. We also identify similar to 20 novel LexA targets that lack a canonical LexA sequence motif, are not bound by LexA in vitro, and presumably require an additional factor for binding in vivo., Our results indicate that, unlike eukaryotic genomes, the E. coli genome is permissive to transcription factor binding. The permissive nature of the E. coli genome has important consequences for the nature of transcriptional regulatory proteins, biological specificity, and evolution.
引用
收藏
页码:2619 / 2630
页数:12
相关论文
共 49 条
[1]  
Aparicio O, 2004, CURRENT PROTOCOLS MO
[2]  
Bailey T L, 1994, Proc Int Conf Intell Syst Mol Biol, V2, P28
[3]   REGULATED EXPRESSION OF ENDONUCLEASE ECORI IN SACCHAROMYCES-CEREVISIAE - NUCLEAR ENTRY AND BIOLOGICAL CONSEQUENCES [J].
BARNES, G ;
RINE, J .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1985, 82 (05) :1354-1358
[4]   Global nucleosome occupancy in yeast [J].
Bernstein, BE ;
Liu, CL ;
Humphrey, EL ;
Perlstein, EO ;
Schreiber, SL .
GENOME BIOLOGY, 2004, 5 (09)
[5]   Spatial arrangement and macrodomain organization of bacterial chromosomes [J].
Boccard, F ;
Esnault, E ;
Valens, M .
MOLECULAR MICROBIOLOGY, 2005, 57 (01) :9-16
[6]   Removal of promoter nucleosomes by disassembly rather than sliding in vivo [J].
Boeger, H ;
Griesenbeck, J ;
Strattan, JS ;
Kornberg, RD .
MOLECULAR CELL, 2004, 14 (05) :667-673
[7]   Nucleosomes unfold completely at a transcriptionally active promoter [J].
Boeger, H ;
Griesenbeck, J ;
Strattan, JS ;
Kornberg, RD .
MOLECULAR CELL, 2003, 11 (06) :1587-1598
[8]   Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs [J].
Cawley, S ;
Bekiranov, S ;
Ng, HH ;
Kapranov, P ;
Sekinger, EA ;
Kampa, D ;
Piccolboni, A ;
Sementchenko, V ;
Cheng, J ;
Williams, AJ ;
Wheeler, R ;
Wong, B ;
Drenkow, J ;
Yamanaka, M ;
Patel, S ;
Brubaker, S ;
Tammana, H ;
Helt, G ;
Struhl, K ;
Gingeras, TR .
CELL, 2004, 116 (04) :499-509
[9]   ANALYSIS OF THE REGULATORY REGION OF THE PROTEASE-III (PTR) GENE OF ESCHERICHIA-COLI K-12 [J].
CLAVERIEMARTIN, F ;
DIAZTORRES, MR ;
KUSHNER, SR .
GENE, 1987, 54 (2-3) :185-195
[10]  
Courcelle J, 2001, GENETICS, V158, P41