Identification of conserved Drosophila-specific euchromatin-restricted non-coding sequence motifs

Jung, Chol-Hee, Makunin, Igor V. and Mattick, John S. (2010) Identification of conserved Drosophila-specific euchromatin-restricted non-coding sequence motifs. Genomics, 96 3: 154-166. doi:10.1016/j.ygeno.2010.05.006


Author Jung, Chol-Hee
Makunin, Igor V.
Mattick, John S.
Title Identification of conserved Drosophila-specific euchromatin-restricted non-coding sequence motifs
Formatted title
Identification of conserved Drosophila-specific euchromatin-restricted non-coding sequence motifs
Journal name Genomics   Check publisher's open access policy
ISSN 0888-7543
1089-8646
Publication date 2010-09
Sub-type Article (original research)
DOI 10.1016/j.ygeno.2010.05.006
Volume 96
Issue 3
Start page 154
End page 166
Total pages 13
Editor J. Quackenbush
Place of publication San Diego, CA, U.S.A.
Publisher Academic Press
Collection year 2011
Language eng
Formatted abstract
Non-protein-coding DNA comprises the majority of animal genomes but its functions are largely unknown. We identified over 17,000 different tetranucleotide pairs in the Drosophila melanogaster genome that are over-represented at distances up to 100 nt in conserved non-exonic sequences. Those exhibiting the highest information content in surrounding nucleotides were classified into five groups: tRNAs, motifs associated with histone genes, Suppressor-of-Hairy-wing binding sites, and two sets of previously unrecognized motifs (DLM3 and DLM4). There are hundreds to thousands of copies of DLM3 and DLM4, respectively, in the genome, located almost exclusively in non-coding regions. They have similar copy numbers among drosophilids, but are largely absent in other insects. DLM3 is likely a cis-regulatory element, whereas DLM4 sequences are capable of forming a short hairpin structure and are expressed as ∼ 80 nt RNAs. This work reports the existence of Drosophila genus-specific sequence motifs, and suggests that many more novel functional elements may be discovered in genomes using the general approach outlined herein.
© 2010 Elsevier Inc.
Keyword tRNA
Exaptation
Regulatory elements
Non-coding RNA
Predicting regulatory regions
Factor-binding sites
Human genome
Morphological evolution
Ultraconserved elements
Statistical properties
Transposable elements
Systematic discovery
DNA-sequences
RNA
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2011 Collection
Institute for Molecular Bioscience - Publications
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 3 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 3 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Sun, 12 Sep 2010, 00:04:17 EST