Liu Siyuan John, Nowakowski Tomasz J, Pollen Alex A, Lui Jan H, Horlbeck Max A, Attenello Frank J, He Daniel, Weissman Jonathan S, Kriegstein Arnold R, Diaz Aaron A, Lim Daniel A
Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA.
Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, 94143, USA.
Genome Biol. 2016 Apr 14;17:67. doi: 10.1186/s13059-016-0932-1.
Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that can regulate molecular and cellular processes in brain development and disease. LncRNAs exhibit cell type- and tissue-specific expression, but little is known about the expression and function of lncRNAs in the developing human brain. Furthermore, it has been unclear whether lncRNAs are highly expressed in subsets of cells within tissues, despite appearing lowly expressed in bulk populations.
We use strand-specific RNA-seq to deeply profile lncRNAs from polyadenylated and total RNA obtained from human neocortex at different stages of development, and we apply this reference to analyze the transcriptomes of single cells. While lncRNAs are generally detected at low levels in bulk tissues, single-cell transcriptomics of hundreds of neocortex cells reveal that many lncRNAs are abundantly expressed in individual cells and are cell type-specific. Notably, LOC646329 is a lncRNA enriched in single radial glia cells but is detected at low abundance in tissues. CRISPRi knockdown of LOC646329 indicates that this lncRNA regulates cell proliferation.
The discrete and abundant expression of lncRNAs among individual cells has important implications for both their biological function and utility for distinguishing neural cell types.
长链非编码RNA（lncRNA）构成了一类多样的转录本，可调节大脑发育和疾病中的分子与细胞过程。lncRNA表现出细胞类型和组织特异性表达，但对于发育中的人类大脑中lncRNA的表达和功能了解甚少。此外，尽管lncRNA在总体细胞群中表达水平较低，但它们是否在组织内的细胞亚群中高表达尚不清楚。
我们使用链特异性RNA测序对来自人类不同发育阶段新皮质的聚腺苷酸化RNA和总RNA中的lncRNA进行深度分析，并将此参考用于分析单细胞转录组。虽然lncRNA在总体组织中通常检测到的水平较低，但对数百个新皮质细胞的单细胞转录组学分析表明，许多lncRNA在单个细胞中大量表达且具有细胞类型特异性。值得注意的是，LOC646329是一种在单个放射状胶质细胞中富集但在组织中检测到的丰度较低的lncRNA。对LOC646329进行CRISPRi敲低表明该lncRNA调节细胞增殖。
lncRNA在单个细胞中的离散且丰富的表达对其生物学功能以及区分神经细胞类型的实用性都具有重要意义。
