Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Science 22 December 2006:
Vol. 314. no. 5807, p. 1892
DOI: 10.1126/science.1130708
Prev | Table of Contents | Next

Brevia

Ancient Noncoding Elements Conserved in the Human Genome

Byrappa Venkatesh,1* Ewen F. Kirkness,2* Yong-Hwee Loh,1 Aaron L. Halpern,3 Alison P. Lee,1 Justin Johnson,3 Nidhi Dandona,1 Lakshmi D. Viswanathan,3 Alice Tay,1 J. Craig Venter,3 Robert L. Strausberg,3 Sydney Brenner1

Cartilaginous fishes represent the living group of jawed vertebrates that diverged from the common ancestor of human and teleost fish lineages about 530 million years ago. We generated ~1.4x genome sequence coverage for a cartilaginous fish, the elephant shark (Callorhinchus milii), and compared this genome with the human genome to identify conserved noncoding elements (CNEs). The elephant shark sequence revealed twice as many CNEs as were identified by whole-genome comparisons between teleost fishes and human. The ancient vertebrate-specific CNEs in the elephant shark and human genomes are likely to play key regulatory roles in vertebrate gene expression.

1 Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.
2 Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
3 J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA.

* To whom correspondence should be addressed. E-mail: mcbbv{at}imcb.a-star.edu.sg (B.V.); ekirknes{at}tigr.org (E.F.K.)

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Into the blue: Gene duplication and loss underlie color vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii.
W. L. Davies, L. S. Carvalho, B.-H. Tay, S. Brenner, D. M. Hunt, and B. Venkatesh (2009)
Genome Res. 19, 415-426
   Abstract »    Full Text »    PDF »
Large Number of Ultraconserved Elements Were Already Present in the Jawed Vertebrate Ancestor.
J. Wang, A. P. Lee, R. Kodzius, S. Brenner, and B. Venkatesh (2009)
Mol. Biol. Evol. 26, 487-490
   Abstract »    Full Text »    PDF »
Prediction of RNA secondary structure using generalized centroid estimators.
M. Hamada, H. Kiryu, K. Sato, T. Mituyama, and K. Asai (2009)
Bioinformatics 25, 465-473
   Abstract »    Full Text »    PDF »
The Dogfish Scyliorhinus canicula: A Reference in Jawed Vertebrates.
M. Coolen, A. Menuet, D. Chassoux, C. Compagnucci, S. Henry, L. Leveque, C. Da Silva, F. Gavory, S. Samain, P. Wincker, et al. (2008)
CSH Protocols 2008, pdb.emo111
   Abstract »    Full Text »
Cross-species de novo identification of cis-regulatory modules with GibbsModule: Application to gene regulation in embryonic stem cells.
D. Xie, J. Cai, N.-Y. Chia, H. H. Ng, and S. Zhong (2008)
Genome Res. 18, 1325-1335
   Abstract »    Full Text »    PDF »
Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: A comparative analysis of the protocadherin cluster.
W.-P. Yu, V. Rajasegaran, K. Yew, W.-l. Loh, B.-H. Tay, C. T. Amemiya, S. Brenner, and B. Venkatesh (2008)
PNAS 105, 3819-3824
   Abstract »    Full Text »    PDF »
Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b.
D. M. McGaughey, R. M. Vinton, J. Huynh, A. Al-Saif, M. A. Beer, and A. S. McCallion (2008)
Genome Res. 18, 252-260
   Abstract »    Full Text »    PDF »
Structure and Function of the Smallest Vertebrate Telomerase RNA from Teleost Fish.
M. Xie, A. Mosig, X. Qi, Y. Li, P. F. Stadler, and J. J.-L. Chen (2008)
J. Biol. Chem. 283, 2049-2059
   Abstract »    Full Text »    PDF »
Promoting transcriptome diversity.
R. L. Strausberg and S. Levy (2007)
Genome Res. 17, 965-968
   Abstract »    Full Text »    PDF »
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes.
C. B. Lowe, G. Bejerano, and D. Haussler (2007)
PNAS 104, 8005-8010
   Abstract »    Full Text »    PDF »
Osmoregulation in elephant fish Callorhinchus milii (Holocephali), with special reference to the rectal gland.
S. Hyodo, J. D. Bell, J. M. Healy, T. Kaneko, S. Hasegawa, Y. Takei, J. A. Donald, and T. Toop (2007)
J. Exp. Biol. 210, 1303-1310
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)