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LETTER: Comparison of Human Chromosome 21 Conserved Nongenic Sequences (CNGs) With the Mouse and Dog Genomes Shows That Their Selective Constraint Is Independent of Their Genic Environment
- Emmanouil T. Dermitzakis,
- Ewen Kirkness,
- Scott Schwarz,
- Ewan Birney,
- Alexandre Reymond,
- and Stylianos E. Antonarakis
Genome Res. May 2004 14: 852-859; Published in Advance April 12, 2004, doi:10.1101/gr.1934904
...Comparison of Human Chromosome 21 Conserved Nongenic Sequences (CNGs) With the Mouse and Dog Genomes Shows That Their Selective Constraint Is Independent of Their Genic Environment Emmanouil T. Dermitzakis 1 , 5 , Ewen Kirkness 2 , Scott Schwarz 3 , Ewan...
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LETTER: Noncoding Sequences Conserved in a Limited Number of Mammals in the SIM2 Interval are Frequently Functional
- Kelly A. Frazer,
- Heng Tao,
- Kazutoyo Osoegawa,
- Pieter J. de Jong,
- Xiyin Chen,
- Mark F. Doherty,
- and David R. Cox
Genome Res. March 2004 14: 367-372; Published in Advance February 12, 2004, doi:10.1101/gr.1961204
...Noncoding Sequences Conserved in a Limited Number of Mammals in the SIM2 Interval are Frequently Functional Kelly A. Frazer 1 , 3 , Heng Tao 1 , Kazutoyo Osoegawa 2 , Pieter J. de Jong 2 , Xiyin Chen 1 , Mark F. Doherty 1...
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LETTER: Evolutionarily Conserved Sequences on Human Chromosome 21
- Kelly A. Frazer,
- John B. Sheehan,
- Renee P. Stokowski,
- Xiyin Chen,
- Roya Hosseini,
- Jan-Fang Cheng,
- Stephen P.A. Fodor,
- David R. Cox,
- and Nila Patil
Genome Res. October 1, 2001 11: 1651-1659; doi:10.1101/gr.198201
...of evolutionarily conserved sequences across gene-rich and gene-poor intervals is not known. Conserved sequences between humans and mice can be present either as a result of active conservation due to functional constraints or as a result of shared ancestry due to insufficient divergence time. Long human...
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Chicken Special/Letters: Comparison of splice sites in mammals and chicken
- Josep F. Abril,
- Robert Castelo,
- and Roderic Guigó
Genome Res. January 2005 15: 111-119; Published in Advance December 8, 2004, doi:10.1101/gr.3108805
...be found upstream of the acceptor site. With the exception of these two cases, the branchpoint sequence was extremely conserved between mammals and chicken, showing no more than two mismatches, but often being identical. The position of the branch point has also been conserved; with only one exception...
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LETTER: Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes
- Gregory M. Cooper,
- Michael Brudno,
- Eric A. Stone,
- Inna Dubchak,
- Serafim Batzoglou,
- and Arend Sidow
Genome Res. April 2004 14: 539-548; doi:10.1101/gr.2034704
...be exons that have not been annotated, but we suggest that this is relatively rare given that the gene annotations used included nearly 40,000 genes from multiple annotation sources. Additionally, the relatively high abundance of “nongenic” conserved sequences in mammalian s has been previously documented...
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LETTER: Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
- Daniel L. Halligan and
- Peter D. Keightley
Genome Res. July 2006 16: 875-884; Published in Advance June 2, 2006, doi:10.1101/gr.5022906
...evidence for strong constraints in intergenic DNA by inferring that there are similar numbers of conserved bases in intergenic sequences as in introns (22%–26%). Halligan et al. (2004) showed that this fraction may be as high as ∼44% in an analysis of 119 intergenic DNA fragments flanking known genes...
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LETTER: Functional noncoding sequences derived from SINEs in the mammalian genome
- Hidenori Nishihara,
- Arian F.A. Smit,
- and Norihiro Okada
Genome Res. July 2006 16: 864-874; Published in Advance May 22, 2006, doi:10.1101/gr.5255506
...identified many interspersed conserved sequences. For example, Bejerano et al. (2004b) listed ∼5000 kinds of sequence categories, each of which is conserved among mammals and is present in more than one copy in the human . The detailed functions of most of these regions have not been elucidated. Eukaryotic s...
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ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- Adam Siepel,
- Gill Bejerano,
- Jakob S. Pedersen,
- Angie S. Hinrichs,
- Minmei Hou,
- Kate Rosenbloom,
- Hiram Clawson,
- John Spieth,
- LaDeana W. Hillier,
- Stephen Richards,
- George M. Weinstock,
- Richard K. Wilson,
- Richard A. Gibbs,
- W. James Kent,
- Webb Miller,
- and David Haussler
Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
...-HMM). PhastCons works by fitting a phylo-HMM to the data by maximum likelihood, subject to constraints designed to calibrate the model across species groups, and then predicting conserved elements based on this model. The predicted elements cover roughly 3%–8% of the human genome (depending on the details...
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ARTICLE: Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis
- Gayle K. McEwen,
- Adam Woolfe,
- Debbie Goode,
- Tanya Vavouri,
- Heather Callaway,
- and Greg Elgar
Genome Res. April 2006 16: 451-465; Published in Advance March 13, 2006, doi:10.1101/gr.4143406
...( Kleinjan and van Heyningen 2005 ). Identifying putative CRMs computationally relies on phylogenetic footprinting (for overview, see Ureta-Vidal et al. 2003 ) with sequence conservation implying functional constraint, although the confidence of such predictions depends on the evolutionary distance between...
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Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
- Zhengcao Li,
- Xiaohong Liu,
- Chen Wang,
- Zhenyang Li,
- Bo Jiang,
- Ruifeng Zhang,
- Lu Tong,
- Youping Qu,
- Sheng He,
- Haifan Chen,
- Yafei Mao,
- Qingnan Li,
- Torsten Pook,
- Yu Wu,
- Yanjun Zan,
- Hui Zhang,
- Lu Li,
- Keying Wen,
- and Yaosheng Chen
Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
.... 2010; Duan et al. 2019), with myriad dispensable genes responsible for agronomic traits and human diseases uncovered (Yu et al. 2022). In contrast to microorganisms, mammals typically have larger size and less flexibility, where genes in the usual sense constitute a minor fraction of total sequences...
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