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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
.... The results showed that both sequences showed strong enhancer activity, with the aUCE showing significantly higher activity than the mUCE (P-value < 0.0001) (Fig. 6E). SEdb and SEA support that mUCE.1304 served as an enhancer involved in a superenhancer, one of which putative target genes encode an important...
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Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
- Ignacio Maeso,
- Manuel Irimia,
- Juan J. Tena,
- Esther González-Pérez,
- David Tran,
- Vydianathan Ravi,
- Byrappa Venkatesh,
- Sonsoles Campuzano,
- José Luis Gómez-Skarmeta,
- and Jordi Garcia-Fernàndez
Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
...in this species (Jime´nez-Delgado et al. 2006; Irimia et al. 2008). We had previously identified several highly conserved noncoding sequences by crossed VISTA alignments between the regions surrounding the three Irx genes in the amphioxus cluster (Irimia et al. 2008). Here, we have expanded these analyses...
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LETTER: Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b
- David M. McGaughey,
- Ryan M. Vinton,
- Jimmy Huynh,
- Amr Al-Saif,
- Michael A. Beer,
- and Andrew S. McCallion
Genome Res. February 2008 18: 252-260; Published in Advance December 10, 2007, doi:10.1101/gr.6929408
.... Science 311 : 796 – 800 . ↵ de la Calle-Mustienes, E. , Feijoo, C.G. , Manzanares, M. , Tena, J.J. , Rodriguez-Seguel, E. , Letizia, A. , Allende, M.L. , Gomez-Skarmeta, J.L. ( 2005 ) A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene...
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ARTICLE: Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
- Hiroshi Kikuta,
- Mary Laplante,
- Pavla Navratilova,
- Anna Z. Komisarczuk,
- Pär G. Engström,
- David Fredman,
- Altuna Akalin,
- Mario Caccamo,
- Ian Sealy,
- Kerstin Howe,
- Julien Ghislain,
- Guillaume Pezeron,
- Philippe Mourrain,
- Staale Ellingsen,
- Andrew C. Oates,
- Christine Thisse,
- Bernard Thisse,
- Isabelle Foucher,
- Birgit Adolf,
- Andrea Geling,
- Boris Lenhard,
- and Thomas S. Becker
Genome Res. May 2007 17: 545-555; Published in Advance March 26, 2007, doi:10.1101/gr.6086307
...by regulatory sequences: hox clusters are conserved throughout most metazoan s, as are other gene clusters, such as irx , as well as certain loci that consist of tandem duplications of regulatory genes, for example, myf5/mrf4 and dlx genes ( Zerucha and Ekker 2000 ; Carvajal et al. 2001 ; Spitz et al. 2003 ; de...
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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
..., or in other invertebrate s, despite the fact that these elements can exhibit a higher level of conservation than other functional sequences such as coding exons and noncoding RNAs. CNEs, and other similar highly conserved noncoding sequences, are found to cluster in the vicinity of genes implicated...
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Methods: Genome-wide discovery of human heart enhancers
- Leelavati Narlikar,
- Noboru J. Sakabe,
- Alexander A. Blanski,
- Fabio E. Arimura,
- John M. Westlund,
- Marcelo A. Nobrega,
- and Ivan Ovcharenko
Genome Res. March 2010 20: 381-392; Published in Advance January 14, 2010, doi:10.1101/gr.098657.109
..., deliberately picking sequences that flank genes with well-established expression in the heart, thus enriching our set of negative controls with elements with a higher likelihood of containing heart enhancer properties. All elements tested are evolutionarily conserved at least among mammals. We used a zebrafish...
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LETTER: Close sequence comparisons are sufficient to identify human cis-regulatory elements
- Shyam Prabhakar,
- Francis Poulin,
- Malak Shoukry,
- Veena Afzal,
- Edward M. Rubin,
- Olivier Couronne,
- and Len A. Pennacchio
Genome Res. July 2006 16: 855-863; Published in Advance June 12, 2006, doi:10.1101/gr.4717506
...the mainstay of searches for enhancers of key developmental genes, whereas mammalian sequence comparisons have been considered insufficiently specific, especially in large, highly conserved intergenic regions harboring hundreds of human–rodent CNSs. This dichotomy disappears in light of the funnel principle...
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Methods: Predicting tissue-specific enhancers in the human genome
- Len A. Pennacchio,
- Gabriela G. Loots,
- Marcelo A. Nobrega,
- and Ivan Ovcharenko
Genome Res. February 2007 17: 201-211; Published in Advance January 8, 2007, doi:10.1101/gr.5972507
...of enhancer activity assigned to promoters versus more distant-acting sequences. This measurement was possible since the EI approach utilizes the three most highly conserved human–mouse elements neighboring the gene under investigation and thus goes beyond promoter only exploration of cis -regulatory features...
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12 Drosophila Genomes/Letter: Genomic regulatory blocks underlie extensive microsynteny conservation in insects
- Pär G. Engström,
- Shannan J. Ho Sui,
- Øyvind Drivenes,
- Thomas S. Becker,
- and Boris Lenhard
Genome Res. December 2007 17: 1898-1908; Published in Advance November 7, 2007, doi:10.1101/gr.6669607
...their clusters has resulted in microsynteny conservation, which is detectable because protein-coding sequences align between Drosophila and Anopheles . To quantitatively assess whether genes regulated by HCNE arrays are more likely to be in large regions of microsynteny between Dmel and Agam , we constructed...
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Resource: Multiple whole-genome alignments without a reference organism
- Inna Dubchak,
- Alexander Poliakov,
- Andrey Kislyuk,
- and Michael Brudno
Genome Res. April 2009 19: 682-689; Published in Advance January 28, 2009, doi:10.1101/gr.081778.108
...of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. Genome Res. 15: 1061–1072. Dewey, C.N. 2007. Aligning multiple whole s with Mercator and MAVID. Methods Mol. Biol. 395: 221–236. Dewey, C., Wu, J.Q., Cawley, S., Alexandersson, M., Gibbs, R., and Pachter, L...

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