Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination

Abstract

Long non-coding RNAs (lncRNAs) (> 200 bp) play crucial roles in transcriptional regulation during numerous biological processes. However, it is challenging to comprehensively identify lncRNAs, because they are often expressed at low levels and with more cell-type specificity than are protein-coding genes. In the present study, we performed ab initio transcriptome reconstruction using eight purified cell populations from mouse cortex and detected more than 5000 lncRNAs. Predicting the functions of lncRNAs using cell-type specific data revealed their potential functional roles in Central Nervous System (CNS) development. We performed motif searches in ENCODE DNase I digital footprint data and Mouse ENCODE promoters to infer transcription factor (TF) occupancy. By integrating TF binding and cell-type specific transcriptomic data, we constructed a novel framework that is useful for systematically identifying lncRNAs that are potentially essential for brain cell fate determination. Based on this integrative analysis, we identified lncRNAs that are regulated during Oligodendrocyte Precursor Cell (OPC) differentiation from Neural Stem Cells (NSCs) and that are likely to be involved in oligodendrogenesis. The top candidate, lnc-OPC, shows highly specific expression in OPCs and remarkable sequence conservation among placental mammals. Interestingly, lnc-OPC is significantly up-regulated in glial progenitors from experimental autoimmune encephalomyelitis (EAE) mouse models compared to wild-type mice. OLIG2-binding sites in the upstream regulatory region of lnc-OPC were identified by ChIP (chromatin immunoprecipitation)-Sequencing and validated by luciferase assays. Loss-of-function experiments confirmed that lnc-OPC plays a functional role in OPC genesis. Overall, our results substantiated the role of lncRNA in OPC fate determination and provided an unprecedented data source for future functional investigations in CNS cell types. We present our datasets and analysis results via the interactive genome browser at our laboratory website that is freely accessible to the research community. This is the first lncRNA expression database of collective populations of glia, vascular cells, and neurons. We anticipate that these studies will advance the knowledge of this major class of non-coding genes and their potential roles in neurological development and diseases.

Abnormalities in A-to-I RNA editing patterns in CNS injuries correlate with dynamic changes in cell type composition

“…To this collection, we added RNA sequencing data from purchased primary neural stem cells (NSCs), that were isolated from embryonic mouse cortex (E14.5) (GEO accession number GSE74643)42. The SCI data was reported by Chen et al 44.…”

lncRNA Functional Networks in Oligodendrocytes Reveal Stage-Specific Myelination Control by an lncOL1 /Suz12 Complex in the CNS

“…Although studies have shown expression of lncRNAs during CNS development (Mercer et al, 2010; Ramos et al, 2013) and in OPCs (Dong et al, 2015), a mechanistic understanding of the functions of lncRNAs in myelinogenesis in the CNS remains elusive. Identification and characterization of lncRNAs during OL lineage progression are vital to our full understanding of the mechanisms of myelinogenesis and myelin repair in the CNS.…”

Cocaine alters Homer1 natural antisense transcript in the nucleus accumbens

“…The stringency of the Benjamini and Hochberg false discovery rate test likely accounts for why only one of the NATs examined met statistical significance. Although only a portion of lncRNAs that were significantly altered by drugs of abuse were NATs in the above studies, it is important to note that many NATs are expressed at low levels and in a cell type-specific manner (Cabili et al , 2011; Derrien et al , 2012; Li et al , 2013; Dong et al , 2015). Thus, small changes in expression that are observed in tissue homogenate may have functional importance in specific cell types.…”