Abstract
Invertebrate conserved noncoding elements (CNEs) are associated with the same core set of genes as vertebrate CNEs, and may reflect the parallel evolution of enhancers in the gene regulatory networks that define alternative animal body plans.
Highlights
The human genome contains thousands of non-coding sequences that are often more conserved between vertebrate species than protein-coding exons
Identification of worm conserved non-coding elements To identify highly conserved non-coding elements in the genome of C. elegans, we searched for sequences that contain large blocks of identity with the genome of C. briggsae and show no evidence of transcription
We used MegaBlast to identify sequences that contain at least 30 to 100 consecutive nucleotides identical between the two nematode genomes, and removed any elements overlapping protein-coding exons, non-coding RNAs or repetitive sequences
Summary
The human genome contains thousands of non-coding sequences that are often more conserved between vertebrate species than protein-coding exons. These highly conserved non-coding elements (CNEs) are associated with genes that coordinate development, and have been proposed to act as transcriptional enhancers. Despite their extreme sequence conservation in vertebrates, sequences homologous to CNEs have not been identified in invertebrates. Comparisons of the human genome against the genomes of distantly related vertebrates have revealed an abundance of highly conserved non-coding elements (CNEs) that appear to have been 'frozen' throughout vertebrate evolution [1,2,3,4,5,6,7]. In support of this, where tested, the majority of assayed CNEs can act as tissue-specific enhancers for a transgene in zebrafish or mice [4,7,8,9,10]
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