These authors contributed equally to this work.
Genome-Wide Analysis of Human SNPs at Long Intergenic Noncoding RNAs
Article first published online: 27 NOV 2012
© 2012 Wiley Periodicals, Inc.
Volume 34, Issue 2, pages 338–344, February 2013
How to Cite
Chen, G., Qiu, C., Zhang, Q., Liu, B. and Cui, Q. (2013), Genome-Wide Analysis of Human SNPs at Long Intergenic Noncoding RNAs. Hum. Mutat., 34: 338–344. doi: 10.1002/humu.22239
Communicated by Michael Dean
Contract grant sponsors: National Basic Research program of China (2012CB517500); Natural Science Foundation of China (31000585, 81000582).
- Issue published online: 29 JAN 2013
- Article first published online: 27 NOV 2012
- Accepted manuscript online: 15 OCT 2012 04:35AM EST
- Manuscript Accepted: 2 OCT 2012
- Manuscript Received: 3 JUL 2012
- National Basic Research program of China. Grant Number: 2012CB517500
- Natural Science Foundation of China. Grant Numbers: 31000585, 81000582
- long intergenic noncoding RNA;
- Alzheimer disease;
Long intergenic noncoding RNAs (lincRNAs) represent a large portion of the noncoding genes in mammals and other eukaryotes but remains among the least well-understood of genetic factors to date. Here, we systematically analyzed the human SNPs of lincRNAs at a genome level. We found a significantly lower SNP density in lincRNA regions than both their upstream and downstream flanking regions. Functional regions show lower SNP density than other regions in lincRNAs. We revealed that lincRNAs with higher expression levels and broader expression spectrum have significantly lower SNP density. Moreover, we identified lincRNAs that are under recent positive selection and revealed that these lincRNAs show distinct SNP density, expression level, and tissue specificity. Importantly, we identified a genetic variant (rs7990916:T>C) under recent positive selection at a brain-specific lincRNA that significantly affects the structure of normal brain. Analysis of brain magnetic resonance images showed that individuals with CC genotype have significant bigger regional gray matter volume than individuals with TT genotype. Moreover, the genotype of this SNP shows different distribution in normal elders, mild cognitive impairment, and Alzheimer disease subjects, suggesting that this lincRNA may have a role in physiology and pathophysiology of human brain.