The missing lnc: long noncoding RNAs in neuroblast migration

Thesis

The Ventricular Subventricular Zone (V-SVZ) is the largest postnatal stem cell niche in the mammalian brain, it continuously generates Olfactory Bulb (OB) interneurons, but can also act as a source of glioblastomas. While there is a wealth of information regarding V-SVZ neural stem cell (NSC) proliferation, there is a relative dearth regarding how V-SVZ derived precursors migrate to their final destination. The site of maturation of V-SVZ derived progenitors is in the OB, therefore newly generated cells cannot function if they cannot migrate.

Long noncoding RNAs (lncRNAs) are RNA molecules that are greater than 200nt in length with minimal protein coding capacity. A large number of lncRNAs are specifically expressed in the V-SVZ. By comparing V-SVZ scRNAseq I found striking inconsistencies in methodology and reporting between studies. Despite these differences, trends in lncRNA expression in the V-SVZ were observed, which I analysed in a semi-quantitative manner and found several candidate lncRNAs for regulation of V-SVZ neurogenesis.

The lncRNA 2610307P16Rik (also known as Cancer susceptibility 15, Casc15), is unusually well-conserved and is highly expressed in migratory V-SVZ neuroblasts. Through a combination of in vitro and in vivo studies I found that Casc15 is a powerful regulator of neuroblast migration. However, OB interneurons that were depleted of Casc15 exhibited defects in polarity, location, and structure. Unexpectedly, our transcriptomics revealed significant changes in a swathe of genes regulating cholesterol biogenesis.

In order to interrogate potential molecular mechanisms of Casc15 on migration I focused on genes associated with cholesterol biosynthesis, as well as the upstream mevalonate pathway. I found an inverse relationship between Casc15 expression and the expression of Srebp2, the master regulator of cholesterol biosynthesis. RNA-immunoprecipitation (RIP) and chromatin immunoprecipitation (ChIP) revealed that Casc15 physically interacts with the Polycomb Repressive Complex 2 (PRC2) and that PRC2 repressive activity at the Srebp2 promoter is lost upon Casc15 depletion. These data lead to the development of a novel circular mechanism in which Casc15 regulates mevalonate and cholesterol pathway genes, and is in turn regulated by the product of the mevalonate pathway. lncRNAs are frequently dismissed as transcriptional noise or even genomic “junk”, but the profound migratory and metabolic changes observed upon loss of Casc15 suggest that this is far from the truth.

Authors: Becker, J

• DOI: 10.5287/ora-14y8g9krg
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: metabolism; neurogenesis; stem cells; lncRNA; epigenetics
• Subjects: Non-coding RNA; Cell migration; Stem cells; Neurobiology