News archives


OCTOBER - DECEMBER 17

JULY - SEPTEMBER 17

APRIL - JUNE 17

JANUARY - MARCH 17

OCTOBER - DECEMBER 16

JULY - SEPTEMBER 16

APRIL - JUNE 16

JANUARY - MARCH 16

OCTOBER - DECEMBER 15

JULY - SEPTEMBER 15

APRIL - JUNE 15

JANUARY - MARCH 15

OCTOBER - DECEMBER 14

JULY - SEPTEMBER 14

APRIL - JUNE 14

JANUARY - MARCH 14

OCTOBER - DECEMBER 13

JULY - SEPTEMBER 13

APRIL - JUNE 13

JANUARY - MARCH 13

OCTOBER - DECEMBER 12

JULY - SEPTEMBER 12

APRIL - JUNE 12

JANUARY - MARCH 12

OCTOBER - DECEMBER 11

JULY - SEPTEMBER 11

APRIL - JUNE 11

JANUARY - MARCH 11

OCTOBER - DECEMBER 10

JULY - SEPTEMBER 10

APRIL - JUNE 10

JANUARY - MARCH 10

OCTOBER - DECEMBER 09

JULY - SEPTEMBER 09

APRIL - JUNE 09

JANUARY - MARCH 09

OCTOBER - DECEMBER 08

JULY - SEPTEMBER 08

APRIL - JUNE 08

JANUARY - MARCH 08

OCTOBER - DECEMBER 07

JULY - SEPTEMBER 07

APRIL - JUNE 07

JANUARY - MARCH 07

 
  current news   Press   selected story    
     
  15th December 2010  
 

Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes

 
 




Authors
Alison P. Lee, Sze Yen Kerk, Yue Ying Tan, Sydney Brenner and B. Venkatesh.

Comparative Genomics Lab, Institute of Molecular and Cell Biology, Biopolis, Singapore.

Published in Molecular Biology and Evolution on 15 Nov 2010 [Epub ahead of print].

Abstract
Vertebrate genomes contain thousands of conserved noncoding elements (CNEs) that often function as tissue-specific enhancers. In this study, we have identified CNEs in human, dog, chicken, Xenopus, and four teleost fishes (zebrafish, stickleback, medaka and fugu) using elephant shark, a cartilaginous vertebrate, as the base genome and investigated the evolution of these ancient vertebrate CNEs (aCNEs) in bony vertebrate lineages. Our analysis shows that aCNEs have been evolving at different rates in different bony vertebrate lineages. While 78-83% of CNEs have diverged beyond recognition (“lost”) in different teleost fishes, only 24% and 40% have been lost in the chicken and mammalian lineages, respectively. Relative rate tests of substitution rates in CNEs revealed that the teleost fish CNEs have been evolving at a significantly higher rate than those in other bony vertebrates. In the ray-finned fish lineage, 68% of aCNEs were lost before the divergence of the four teleosts. This implicates the ‘fish-specific’ whole-genome duplication in the accelerated evolution and the loss of a large number of both copies of duplicated CNEs in teleost fishes. The aCNEs are rich in tissue-specific enhancers and thus many of them are likely to be evolutionarily constrained cis-regulatory elements. The rapid evolution of aCNEs might have affected the expression patterns driven by them. Transgenic zebrafish assay of some human CNE enhancers that have been lost in teleosts has indicated instances of conservation or changes in trans-acting factors between mammals and fishes.

 
 

 
 


Figure 1: Distribution of ancient conserved noncoding elements (CNEs) in different vertebrate lineages. The numbers at the nodes are the ancient CNEs retained in at least one of the descendant taxa. Teleost fishes have lost nearly 70% of all ancient CNEs.

 
 

 
 


Figure 2: Expression driven by two ancient CNEs (HE27233 and HE20676) in transgenic mouse (11.5 dpc) and zebrafish (72 hpf). The trans-factors in zebrafish are able to recognize and interpret these ancient CNEs even though they have been lost from teleost fish genomes, indicating the conservation of trans-factors in spite of changes in cis-regulatory elements of mammals and teleost fish. Mouse pictures courtesy of Axel Visel and Len Pennacchio.

For more information on Prof. B.VENKATESH’s Lab, please click here.