Genome-wide computational and experimental anaylsis of long non-coding RNA genes in a complex human brain disorder
Leonard Lipovich, Becky Cai, Hui Jia, Fabien Dachet, Jeffrey Loeb
Center for Molecular Medicine and Genetics, School of Medicine,
Wayne State University
In the noncoding-RNA field, the biology of microRNAs, rRNAs, tRNAs, and sn/snoRNAs typically
receives much of the attention. However, transcriptome databases suggest that long non-coding RNA (lncRNA)
molecules are more prevalent than microRNAs, and as abundant as mRNAs, in mammalian transcriptional output.
Aside from select systems such as X-inactivation and telomerase, mammalian lncRNAs remain poorly understood.
To build a systems understanding of human lncRNAs, we annotated human transcript-to-genome alignments
supported by public cDNA sequences, constructed a manually curated catalog of over 6,000 lncRNAs,
and developed custom microarrays to profile the lncRNA transcriptome. With custom lncRNA, and conventional mRNA,
microarrays, we examined brain gene expression in human epilepsy patients, identifying over 300 lncRNAs differentially
expressed in surgically resected epileptic and control neocortical regions. We stratified these lncRNAs by their
cis-regulatory potential, predicted from their genomic positional relationships with known protein-coding genes. One
of the lncRNAs was BDNFOS, transcribed antisense to the BDNF (brain-derived neurotrophic factor) gene.
BDNF is a key contributor to epileptogenesis.
In human SH-SY5Y neuroblastoma cells, we observed depolarization-dependent BDNFOS suppression and BDNF activation,
paralleling microarray results from epileptic patient tissues. To test whether BDNFOS affects, and is not
merely co-regulated with, BDNF mRNA, we electroporated BDNFOS-targeting siRNAs into SH-SY5Y cells.
Upon RNAi-mediated BDNFOS suppression, BDNF mRNA levels increased, consistent with the hypothesis that the
lncRNA BDNFOS may regulate BDNF. Our studies establish a precedent for combining bioinformatics, microarrays, and
system perturbations to discern the regulatory roles of lncRNAs, but underscore a need for mechanistic
understanding of lncRNA functions.