This Article Full Text Full Text (PDF) Supplemental Research Data The Chicken Genome All Versions of this Article: gr.3015505v1 15/1/137    most recent Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Ovcharenko, I. Articles by Stubbs, L. Search for Related Content PubMed PubMed Citation Articles by Ovcharenko, I. Articles by Stubbs, L. Pubmed/NCBI databases Medline Plus Health Information Genes and Gene Therapy Social Bookmarking                   What's this?

Chicken Special/Letter

Evolution and functional classification of vertebrate gene deserts

¹ Energy, Environment, Biology, and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA ² Genome Biology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA ³ Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA ⁴ Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA ⁵ Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA ⁶ Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA

Large tracts of the human genome, known as gene deserts, are devoid of protein-coding genes. Dichotomy in their level of conservation with chicken separates these regions into two distinct categories, stable and variable. The separation is not caused by differences in rates of neutral evolution but instead appears to be related to different biological functions of stable and variable gene deserts in the human genome. Gene Ontology categories of the adjacent genes are strongly biased toward transcriptional regulation and development for the stable gene deserts, and toward distinctively different functions for the variable gene deserts. Stable gene deserts resist chromosomal rearrangements and appear to harbor multiple distant regulatory elements physically linked to their neighboring genes, with the linearity of conservation invariant throughout vertebrate evolution.

⁷ Corresponding author
E-mail ovcharenko1{at}llnl.gov; fax (925) 422-2099.

[Supplemental material is available online at www.genome.org.]

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				S. Stephen, M. Pheasant, I. V. Makunin, and J. S. Mattick Large-Scale Appearance of Ultraconserved Elements in Tetrapod Genomes and Slowdown of the Molecular Clock Mol. Biol. Evol., February 1, 2008; 25(2): 402 - 408. [Abstract] [Full Text] [PDF]

				P. G. Engstrom, S. J. Ho Sui, O. Drivenes, T. S. Becker, and B. Lenhard Genomic regulatory blocks underlie extensive microsynteny conservation in insects Genome Res., December 1, 2007; 17(12): 1898 - 1908. [Abstract] [Full Text] [PDF]

				L. Gordon, S. Yang, M. Tran-Gyamfi, D. Baggott, M. Christensen, A. Hamilton, R. Crooijmans, M. Groenen, S. Lucas, I. Ovcharenko, et al. Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions Genome Res., November 1, 2007; 17(11): 1603 - 1613. [Abstract] [Full Text] [PDF]

				M. Huvet, S. Nicolay, M. Touchon, B. Audit, Y. d'Aubenton-Carafa, A. Arneodo, and C. Thermes Human gene organization driven by the coordination of replication and transcription Genome Res., September 1, 2007; 17(9): 1278 - 1285. [Abstract] [Full Text] [PDF]

				M. Pheasant and J. S. Mattick Raising the estimate of functional human sequences Genome Res., September 1, 2007; 17(9): 1245 - 1253. [Abstract] [Full Text] [PDF]

				J. S. Mattick A new paradigm for developmental biology J. Exp. Biol., May 1, 2007; 210(9): 1526 - 1547. [Abstract] [Full Text] [PDF]

				H. Kikuta, M. Laplante, P. Navratilova, A. Z. Komisarczuk, P. G. Engstrom, D. Fredman, A. Akalin, M. Caccamo, I. Sealy, K. Howe, et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates Genome Res., May 1, 2007; 17(5): 545 - 555. [Abstract] [Full Text] [PDF]

				M. Freeling, L. Rapaka, E. Lyons, B. Pedersen, and B. C. Thomas G-Boxes, Bigfoot Genes, and Environmental Response: Characterization of Intragenomic Conserved Noncoding Sequences in Arabidopsis PLANT CELL, May 1, 2007; 19(5): 1441 - 1457. [Abstract] [Full Text] [PDF]

				R. L. Chandler, K. J. Chandler, K. A. McFarland, and D. P. Mortlock Bmp2 Transcription in Osteoblast Progenitors Is Regulated by a Distant 3' Enhancer Located 156.3 Kilobases from the Promoter Mol. Cell. Biol., April 15, 2007; 27(8): 2934 - 2951. [Abstract] [Full Text] [PDF]

				C. W. Hay and K. Docherty Comparative Analysis of Insulin Gene Promoters: Implications for Diabetes Research Diabetes, December 1, 2006; 55(12): 3201 - 3213. [Abstract] [Full Text] [PDF]

				P. B. Siegel, J. B. Dodgson, and L. Andersson Progress from Chicken Genetics to the Chicken Genome Poult. Sci., December 1, 2006; 85(12): 2050 - 2060. [Abstract] [Full Text] [PDF]

				L. S. Shopland, C. R. Lynch, K. A. Peterson, K. Thornton, N. Kepper, J. v. Hase, S. Stein, S. Vincent, K. R. Molloy, G. Kreth, et al. Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence J. Cell Biol., July 3, 2006; 174(1): 27 - 38. [Abstract] [Full Text] [PDF]

				L. Feuk, C. R. Marshall, R. F. Wintle, and S. W. Scherer Structural variants: changing the landscape of chromosomes and design of disease studies. Hum. Mol. Genet., April 15, 2006; 15(suppl_1): R57 - R66. [Abstract] [Full Text] [PDF]

				G. K. McEwen, A. Woolfe, D. Goode, T. Vavouri, H. Callaway, and G. Elgar Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis Genome Res., April 1, 2006; 16(4): 451 - 465. [Abstract] [Full Text] [PDF]

				V. Boeva, M. Regnier, D. Papatsenko, and V. Makeev Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression Bioinformatics, March 15, 2006; 22(6): 676 - 684. [Abstract] [Full Text] [PDF]

				I. M. Smyth, L. Wilming, A. W. Lee, M. S. Taylor, P. Gautier, K. Barlow, J. Wallis, S. Martin, R. Glithero, B. Phillimore, et al. Genomic anatomy of the Tyrp1 (brown) deletion complex PNAS, March 7, 2006; 103(10): 3704 - 3709. [Abstract] [Full Text] [PDF]

				F.-C. Chen, S.-S. Wang, C.-J. Chen, W.-H. Li, and T.-J. Chuang Alternatively and Constitutively Spliced Exons Are Subject to Different Evolutionary Forces Mol. Biol. Evol., March 1, 2006; 23(3): 675 - 682. [Abstract] [Full Text] [PDF]

				C. Simons, M. Pheasant, I. V. Makunin, and J. S. Mattick Transposon-free regions in mammalian genomes Genome Res., February 1, 2006; 16(2): 164 - 172. [Abstract] [Full Text] [PDF]

				D. W. Burt Chicken genome: Current status and future opportunities Genome Res., December 1, 2005; 15(12): 1692 - 1698. [Abstract] [Full Text] [PDF]

				P. F.R. Little Structure and function of the human genome Genome Res., December 1, 2005; 15(12): 1759 - 1766. [Abstract] [Full Text] [PDF]

				N. Ahituv, S. Prabhakar, F. Poulin, E. M. Rubin, and O. Couronne Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny Hum. Mol. Genet., October 15, 2005; 14(20): 3057 - 3063. [Abstract] [Full Text] [PDF]

				J. T. Shin, J. R. Priest, I. Ovcharenko, A. Ronco, R. K. Moore, C. G. Burns, and C. A. MacRae Human-zebrafish non-coding conserved elements act in vivo to regulate transcription Nucleic Acids Res., September 22, 2005; 33(17): 5437 - 5445. [Abstract] [Full Text] [PDF]

				M. Sironi, G. Menozzi, G. P. Comi, R. Cagliani, N. Bresolin, and U. Pozzoli Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences Hum. Mol. Genet., September 1, 2005; 14(17): 2533 - 2546. [Abstract] [Full Text] [PDF]

				A. Siepel, G. Bejerano, J. S. Pedersen, A. S. Hinrichs, M. Hou, K. Rosenbloom, H. Clawson, J. Spieth, L. W. Hillier, S. Richards, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes Genome Res., August 1, 2005; 15(8): 1034 - 1050. [Abstract] [Full Text] [PDF]

				E. de la Calle-Mustienes, C. G. Feijoo, M. Manzanares, J. J. Tena, E. Rodriguez-Seguel, A. Letizia, M. L. Allende, and J. L. Gomez-Skarmeta A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts Genome Res., August 1, 2005; 15(8): 1061 - 1072. [Abstract] [Full Text] [PDF]