Identification of long non-coding RNAs involved in neuronal development and intellectual disability.
Recently, exome sequencing led to the identification of causal mutations in 16-31% of patients with intellectual disability (ID), leaving the underlying cause for many patients unidentified. In this context, the noncoding part of the human genome remains largely unexplored. For many long non-coding RNAs (lncRNAs) a crucial role in neurodevelopment and hence the human brain is anticipated. Here we aimed at identifying lncRNAs associated with neuronal development and ID. Therefore, we applied an integrated genomics approach, harnessing several public epigenetic datasets. We found that the presence of neuron-specific H3K4me3 confers the highest specificity for genes involved in neurodevelopment and ID. Based on the presence of this feature and GWAS hits for CNS disorders, we identified 53 candidate lncRNA genes. Extensive expression profiling on human brain samples and other tissues, followed by Gene Set Enrichment Analysis indicates that at least 24 of these lncRNAs are indeed implicated in processes such as synaptic transmission, nervous system development and neurogenesis. The bidirectional or antisense overlapping orientation relative to multiple coding genes involved in neuronal processes supports these results. In conclusion, we identified several lncRNA genes putatively involved in neurodevelopment and CNS disorders, providing a resource for functional studies.
Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.|Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
Eva
E
D'haene
Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.
Eva Z
EZ
Jacobs
Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.|Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
Pieter-Jan
PJ
Volders
Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.|Dept. of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium.
Tim
T
De Meyer
Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.|Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
Björn
B
Menten
Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.|Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
Sarah
S
Vergult
D001921:Brain / Q000196:embryology / Q000378:metabolism; D002490:Central Nervous System / Q000254:growth & development*; D002493:Central Nervous System Diseases / Q000473:pathology; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D015894:Genome, Human; D055106:Genome-Wide Association Study; D023281:Genomics; D006657:Histones / Q000737:chemistry; D006801:Humans; D008607:Intellectual Disability / Q000235:genetics*; D055495:Neurogenesis; D009474:Neurons / Q000378:metabolism; D016376:Oligonucleotides, Antisense; D020641:Polymorphism, Single Nucleotide; D062085:RNA, Long Noncoding / Q000235:genetics*; D014018:Tissue Distribution; D059467:Transcriptome
D006657:Histones; D016376:Oligonucleotides, Antisense; D062085:RNA, Long Noncoding