A meta-analysis of the genomic and transcriptomic composition of complex life

Liu, Ganqiang, Mattick, John S. and Taft, Ryan (2013) A meta-analysis of the genomic and transcriptomic composition of complex life. Cell Cycle, 12 13: 2061-2072. doi:10.4161/cc.25134

Author Liu, Ganqiang
Mattick, John S.
Taft, Ryan
Title A meta-analysis of the genomic and transcriptomic composition of complex life
Journal name Cell Cycle   Check publisher's open access policy
ISSN 1538-4101
Publication date 2013-07-01
Year available 2013
Sub-type Article (original research)
DOI 10.4161/cc.25134
Volume 12
Issue 13
Start page 2061
End page 2072
Total pages 12
Place of publication Austin, TX, United States
Publisher Landes Bioscience
Language eng
Abstract It is now clear that animal genomes are predominantly non-protein-coding, and that these sequences encode a wide array of RNA transcripts and other regulatory elements that are fundamental to the development of complex life. We have previously argued that the proportion of an animal genome that is non-protein-coding DNA (ncDNA) correlates well with its apparent biological complexity. Here we extend on that work and, using data from a total of 1,627 prokaryotic and 153 eukaryotic complete and annotated genomes, show that the proportion of ncDNA per haploid genome is significantly positively correlated with a previously published proxy of biological complexity, the number of distinct cell types. This is in contrast to the amount of the genome that encodes proteins, which we show is essentially unchanged across Metazoa. Furthermore, using a total of 179 RNA-seq data sets from nematode (47), fruit fly (72), zebrafish (20) and human (42), we show, consistent with other recent reports, that the vast majority of ncDNA in animals is transcribed. This includes more than 60 human loci previously considered "gene deserts," many of which are expressed tissue-specifically and associated with previously reported GWAS SNPs. These results suggest that ncDNA, and the ncRNAs encoded within it, may be intimately involved in the evolution, maintenance and development of complex life.
Keyword Complexity
Non-coding DNA
Noncoding RNA
Small RNA
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
Institute for Molecular Bioscience - Publications
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 46 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 46 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Wed, 24 Jul 2013, 19:49:04 EST by Susan Allen on behalf of Institute for Molecular Bioscience