RT Journal Article
SR Electronic
T1 Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 067165
DO 10.1101/067165
A1 Edward S. Rice
A1 Satomi Kohno
A1 John St. John
A1 Son Pham
A1 Jonathan Howard
A1 Liana Lareau
A1 Brendan O’Connell
A1 Glenn Hickey
A1 Joel Armstrong
A1 Alden Deran
A1 Ian Fiddes
A1 Roy N. Platt II
A1 Cathy Gresham
A1 Fiona McCarthy
A1 Colin Kern
A1 David Haan
A1 Tan Phan
A1 Carl Schmidt
A1 Jeremy Sanford
A1 David A. Ray
A1 Benedict Paten
A1 Louis J. Guillette, Jr.
A1 Richard E. Green
YR 2016
UL http://biorxiv.org/content/early/2016/08/01/067165.abstract
AB The American alligator, Alligator mississippiensis, like all crocodilians, has temperature-dependent sex determination, in which the sex of an embryo is determined by the incubation temperature of the egg during a critical period of development. The lack of genetic differences between male and female alligators leaves open the question of how the genes responsible for sex determination and differentiation are regulated. One insight into this question comes from the fact that exposing an embryo incubated at male-producing temperature to estrogen causes it to develop ovaries. Because estrogen response elements are known to regulate genes over long distances, a contiguous genome assembly is crucial for predicting and understanding its impact.We present an improved assembly of the American alligator genome, scaffolded with in vitro proximity ligation (Chicago) data. We use this assembly to scaffold two other crocodilian genomes based on synteny. We perform RNA sequencing of tissues from American alligator embryos to find genes that are differentially expressed between embryos incubated at male-versus female-producing temperature. Finally, we use the improved contiguity of our assembly along with the current model of CTCF-mediated chromatin looping to predict regions of the genome likely to contain estrogen-responsive genes. We find that these regions are significantly enriched for genes with female-biased expression in developing gonads after the critical period during which sex is determined by incubation temperature. We thus conclude that estrogen signaling is a major driver of female-biased gene expression in the post-temperature sensitive period gonads.