@article {RN136, title = {Reptiles and Mammals Have Differentially Retained Long Conserved Noncoding Sequences from the Amniote Ancestor}, journal = {Genome Biology and Evolution}, volume = {3}, year = {2011}, pages = {102-113}, type = {Journal Article}, abstract = {
Many noncoding regions of genomes appear to be essential to genome function. Conservation of large numbers of
noncoding sequences has been reported repeatedly among mammals but not thus far among birds and reptiles. By searching
genomes of chicken (
Gallus gallus
), zebra finch (
Taeniopygia guttata
), and green anole (
Anolis carolinensis
), we quantified
the conservation among birds and reptiles and across amniotes of long, conserved noncoding sequences (LCNS), which we
define as sequences
500 bp in length and exhibiting
95\% similarity between species. We found 4,294 LCNS shared
between chicken and zebra finch and 574 LCNS shared by the two birds and
Anolis
. The percent of genomes comprised by
LCNS in the two birds (0.0024\%) is notably higher than the percent in mammals (
,
0.0003\% to
,
0.001\%), differences that
we show may be explained in part by differences in genome-wide substitution rates. We reconstruct a large number of LCNS
for the amniote ancestor (ca. 8,630) and hypothesize differential loss and substantial turnover of these sites in descendent
lineages. By contrast, we estimated a small role for recruitment of LCNS via acquisition of novel functions over time. Across
amniotes, LCNS are significantly enriched with transcription factor binding sites for many developmental genes, and 2.9\% of
LCNS shared between the two birds show evidence of expression in brain expressed sequence tag databases. These results
show that the rate of retention of LCNS from the amniote ancestor differs between mammals and Reptilia (including birds)

and that this may reflect differing roles and constraints in gene regulation

}, issn = {1759-6653}, doi = {10.1093/gbe/evq087}, url = {http://gbe.oxfordjournals.org/content/3/102.long}, author = {Janes, D. E. and Chapus, C. and Gondo, Y. and Clayton, D. F. and Sinha, S. and Blatti, C. A. and Organ, C. L. and Fujita, M. K. and Balakrishnan, C. N. and Edwards, S. V.} }