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Title: An Enhancer Near ISL1 and an Ultraconserved Exon of PCBP2 areDerived from a Retroposon

Abstract

Hundreds of highly conserved distal cis-regulatory elementshave been characterized to date in vertebrate genomes1. Many thousandsmore are predicted based on comparative genomics2,3. Yet, in starkcontrast to the genes they regulate, virtually none of these regions canbe traced using sequence similarity in invertebrates, leaving theirevolutionary origin obscure. Here we show that a class of conserved,primarily non-coding regions in tetrapods originated from a novel shortinterspersed repetitive element (SINE) retroposon family that was activein Sarcopterygii (lobe-finned fishes and terrestrial vertebrates) in theSilurian at least 410 Mya4, and, remarkably, appears to be recentlyactive in the "living fossil" Indonesian coelacanth, Latimeriamenadoensis. We show that one copy is a distal enhancer, located 500kbfrom the neuro-developmental gene ISL1. Several others represent new,possibly regulatory, alternatively spliced exons in the middle ofpre-existing Sarcopterygian genes. One of these is the>200bpultraconserved region5, 100 percent identical in mammals, and 80 percentidentical to the coelacanth SINE, that contains a 31aa alternativelyspliced exon of the mRNA processing gene PCBP26. These add to a growinglist of examples7 in which relics of transposable elements have acquireda function that serves their host, a process termed "exaptation"8, andprovide an origin for at least some of the highly-conservedvertebrate-specific genomic sequences recently discovered usingcomparative genomics.

Authors:
; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
Sponsoring Org.:
USDOE Director. Office of Science. Office of Biological andEnvironmental Research; National Institutes of Health, National GenomeResearch Institute; Howard Hughes Medical Institute
OSTI Identifier:
882757
Report Number(s):
LBNL-59307
R&D Project: 626809; BnR: KP1103010
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nature; Journal Volume: 441; Journal Issue: 7089; Related Information: Journal Publication Date: 05/04/2006
Country of Publication:
United States
Language:
English
Subject:
60

Citation Formats

Bejerano, Gill, Lowe, Craig, Ahituv, Nadav, King, Bryan, Siepel,Adam, Salama, Sofie, Rubin, Edward M., Kent, W. James, and Haussler, David. An Enhancer Near ISL1 and an Ultraconserved Exon of PCBP2 areDerived from a Retroposon. United States: N. p., 2005. Web.
Bejerano, Gill, Lowe, Craig, Ahituv, Nadav, King, Bryan, Siepel,Adam, Salama, Sofie, Rubin, Edward M., Kent, W. James, & Haussler, David. An Enhancer Near ISL1 and an Ultraconserved Exon of PCBP2 areDerived from a Retroposon. United States.
Bejerano, Gill, Lowe, Craig, Ahituv, Nadav, King, Bryan, Siepel,Adam, Salama, Sofie, Rubin, Edward M., Kent, W. James, and Haussler, David. Sun . "An Enhancer Near ISL1 and an Ultraconserved Exon of PCBP2 areDerived from a Retroposon". United States. doi:. https://www.osti.gov/servlets/purl/882757.
@article{osti_882757,
title = {An Enhancer Near ISL1 and an Ultraconserved Exon of PCBP2 areDerived from a Retroposon},
author = {Bejerano, Gill and Lowe, Craig and Ahituv, Nadav and King, Bryan and Siepel,Adam and Salama, Sofie and Rubin, Edward M. and Kent, W. James and Haussler, David},
abstractNote = {Hundreds of highly conserved distal cis-regulatory elementshave been characterized to date in vertebrate genomes1. Many thousandsmore are predicted based on comparative genomics2,3. Yet, in starkcontrast to the genes they regulate, virtually none of these regions canbe traced using sequence similarity in invertebrates, leaving theirevolutionary origin obscure. Here we show that a class of conserved,primarily non-coding regions in tetrapods originated from a novel shortinterspersed repetitive element (SINE) retroposon family that was activein Sarcopterygii (lobe-finned fishes and terrestrial vertebrates) in theSilurian at least 410 Mya4, and, remarkably, appears to be recentlyactive in the "living fossil" Indonesian coelacanth, Latimeriamenadoensis. We show that one copy is a distal enhancer, located 500kbfrom the neuro-developmental gene ISL1. Several others represent new,possibly regulatory, alternatively spliced exons in the middle ofpre-existing Sarcopterygian genes. One of these is the>200bpultraconserved region5, 100 percent identical in mammals, and 80 percentidentical to the coelacanth SINE, that contains a 31aa alternativelyspliced exon of the mRNA processing gene PCBP26. These add to a growinglist of examples7 in which relics of transposable elements have acquireda function that serves their host, a process termed "exaptation"8, andprovide an origin for at least some of the highly-conservedvertebrate-specific genomic sequences recently discovered usingcomparative genomics.},
doi = {},
journal = {Nature},
number = 7089,
volume = 441,
place = {United States},
year = {Sun Nov 27 00:00:00 EST 2005},
month = {Sun Nov 27 00:00:00 EST 2005}
}