Genome Research cityscape

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

Published online before print January 13, 2003, 10.1101/gr.207502. Article published online before print in January 2002
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental Research Data
Right arrow All Versions of this Article:
GR-2075Rv1
12/2/298    most recent
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Rajewsky, N.
Right arrow Articles by Siggia, E. D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rajewsky, N.
Right arrow Articles by Siggia, E. D.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 12, Issue 2, 298-308, February 2002

LETTER
The Evolution of DNA Regulatory Regions for Proteo-Gamma Bacteria by Interspecies Comparisons

Nikolaus Rajewsky, Nicholas D. Socci, Martin Zapotocky, and Eric D. Siggia1

Center for Studies in Physics and Biology, Rockefeller University, New York, New York 10021, USA

The comparison of homologous noncoding DNA for organisms a suitable evolutionary distance apart is a powerful tool for the identification of cis regulatory elements for transcription and translation and for the study of how they assemble into functional modules. We have fit the three parameters of an affine global probabilistic alignment algorithm to establish the background mutation rate of noncoding seqeunce between E. coli and a series of gamma proteobacteria ranging from Salmonella to Vibrio. The lower bound we find to the neutral mutation rate is sufficiently high, even for Salmonella, that most of the conservation of noncoding sequence is indicative of selective pressures rather than of insufficient time to evolve. We then use a local version of the alignment algorithm combined with our inferred background mutation rate to assign a significance to the degree of local sequence conservation between orthologous genes, and thereby deduce a probability profile for the upstream regulatory region of all E. coli protein-coding genes. We recover 75%-85% (depending on significance level) of all regulatory sites from a standard compilation for E. coli, and 66%-85% of sigma sites.

We also trace the evolution of known regulatory sites and the groups associated with a given transcription factor. Furthermore, we find that approximately one-third of paralogous gene pairs in E. coli have a significant degree of correlation in their regulatory sequence. Finally, we demonstrate an inverse correlation between the rate of evolution of transcription factors and the number of genes they regulate. Our predictions are available at http://www.physics.rockefeller.edu/~siggia.
[Online supplemental material available at http://www.genome.org.]

1 Corresponding author.

12:298-308 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Genome Res.Home page
N. Molina and E. van Nimwegen
Universal patterns of purifying selection at noncoding positions in bacteria
Genome Res., January 1, 2008; 18(1): 148 - 160.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Pachkov, I. Erb, N. Molina, and E. van Nimwegen
SwissRegulon: a database of genome-wide annotations of regulatory sites
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D127 - D131.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
D. M. Nanavati, K. Thirangoon, and K. M. Noll
Several Archaeal Homologs of Putative Oligopeptide-Binding Proteins Encoded by Thermotoga maritima Bind Sugars
Appl. Envir. Microbiol., February 1, 2006; 72(2): 1336 - 1345.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
K. Tan, L. A. McCue, and G. D. Stormo
Making connections between novel transcription factors and their DNA motifs
Genome Res., February 1, 2005; 15(2): 312 - 320.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. D. Gonzalez, V. Espinosa, A. T. Vasconcelos, E. Perez-Rueda, and J. Collado-Vides
TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D98 - D102.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
G. Mazon, I. Erill, S. Campoy, P. Cortes, E. Forano, and J. Barbe
Reconstruction of the evolutionary history of the LexA-binding sequence
Microbiology, November 1, 2004; 150(11): 3783 - 3795.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
W. Thompson, M. J. Palumbo, W. W. Wasserman, J. S. Liu, and C. E. Lawrence
Decoding Human Regulatory Circuits
Genome Res., October 1, 2004; 14(10a): 1967 - 1974.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
W. B.L. Alkema, B. Lenhard, and W. W. Wasserman
Regulog Analysis: Detection of Conserved Regulatory Networks Across Bacteria: Application to Staphylococcus aureus
Genome Res., July 1, 2004; 14(7): 1362 - 1373.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
C. T. Brown and C. G. Callan Jr.
Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli
PNAS, February 24, 2004; 101(8): 2404 - 2409.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
M. Pritsker, Y.-C. Liu, M. A. Beer, and S. Tavazoie
Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation
Genome Res., January 1, 2004; 14(1): 99 - 108.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
P. Cliften, P. Sudarsanam, A. Desikan, L. Fulton, B. Fulton, J. Majors, R. Waterston, B. A. Cohen, and M. Johnston
Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting
Science, July 4, 2003; 301(5629): 71 - 76.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Madan Babu and S. A. Teichmann
Evolution of transcription factors and the gene regulatory network in Escherichia coli
Nucleic Acids Res., February 15, 2003; 31(4): 1234 - 1244.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
L. A. McCue, W. Thompson, C. S. Carmack, and C. E. Lawrence
Factors Influencing the Identification of Transcription Factor Binding Sites by Cross-Species Comparison
Genome Res., October 1, 2002; 12(10): 1523 - 1532.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
H. Li, V. Rhodius, C. Gross, and E. D. Siggia
Identification of the binding sites of regulatory proteins in bacterial genomes
PNAS, September 3, 2002; 99(18): 11772 - 11777.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
E. van Nimwegen, M. Zavolan, N. Rajewsky, and E. D. Siggia
Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics
PNAS, May 28, 2002; 99(11): 7323 - 7328.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.