Title |
An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
|
---|---|
Published in |
Genome Research, January 2012
|
DOI | 10.1101/gr.132233.111 |
Pubmed ID | |
Authors |
Ignacio Maeso, Manuel Irimia, Juan J. Tena, Esther González-Pérez, David Tran, Vydianathan Ravi, Byrappa Venkatesh, Sonsoles Campuzano, José Luis Gómez-Skarmeta, Jordi Garcia-Fernàndez |
Abstract |
Developmental genes are regulated by complex, distantly located cis-regulatory modules (CRMs), often forming genomic regulatory blocks (GRBs) that are conserved among vertebrates and among insects. We have investigated GRBs associated with Iroquois homeobox genes in 39 metazoans. Despite 600 million years of independent evolution, Iroquois genes are linked to ankyrin-repeat-containing Sowah genes in nearly all studied bilaterians. We show that Iroquois-specific CRMs populate the Sowah locus, suggesting that regulatory constraints underlie the maintenance of the Iroquois-Sowah syntenic block. Surprisingly, tetrapod Sowah orthologs are intronless and not associated with Iroquois; however, teleost and elephant shark data demonstrate that this is a derived feature, and that many Iroquois-CRMs were ancestrally located within Sowah introns. Retroposition, gene, and genome duplication have allowed selective elimination of Sowah exons from the Iroquois regulatory landscape while keeping associated CRMs, resulting in large associated gene deserts. These results highlight the importance of CRMs in imposing constraints to genome architecture, even across large phylogenetic distances, and of gene duplication-mediated genetic redundancy to disentangle these constraints, increasing genomic plasticity. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 1 | 25% |
Chile | 1 | 25% |
Unknown | 2 | 50% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 3 | 75% |
Scientists | 1 | 25% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 4 | 6% |
Spain | 3 | 4% |
Japan | 2 | 3% |
Canada | 1 | 1% |
Thailand | 1 | 1% |
Singapore | 1 | 1% |
Switzerland | 1 | 1% |
Russia | 1 | 1% |
Unknown | 57 | 80% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 28 | 39% |
Student > Ph. D. Student | 15 | 21% |
Student > Bachelor | 5 | 7% |
Student > Doctoral Student | 4 | 6% |
Professor > Associate Professor | 4 | 6% |
Other | 8 | 11% |
Unknown | 7 | 10% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 42 | 59% |
Biochemistry, Genetics and Molecular Biology | 10 | 14% |
Engineering | 4 | 6% |
Computer Science | 2 | 3% |
Medicine and Dentistry | 2 | 3% |
Other | 1 | 1% |
Unknown | 10 | 14% |