Neural Differentiation Modulates the Vertebrate Brain Specific Splicing Program

Abstract

Alternative splicing patterns are known to vary between tissues but these patterns have been found to be predominantly peculiar to one species or another, implying only a limited function in fundamental neural biology. Here we used high-throughput RT-PCR to monitor the expression pattern of all the annotated simple alternative splicing events (ASEs) in the Reference Sequence Database, in different mouse tissues and identified 93 brain-specific events that shift from one isoform to another (switch-like) between brain and other tissues. Consistent with an important function, regulation of a core set of 9 conserved switch-like ASEs is highly conserved, as they have the same pattern of tissue-specific splicing in all vertebrates tested: human, mouse and zebrafish. Several of these ASEs are embedded within genes that encode proteins associated with the neuronal microtubule network, and show a dramatic and concerted shift within a short time window of human neural stem cell differentiation. Similarly these exons are dynamically regulated in zebrafish development. These data demonstrate that although alternative splicing patterns often vary between species, there is nonetheless a core set of vertebrate brain-specific ASEs that are conserved between species and associated with neural differentiation.

Telomerase Activity is Downregulated Early During Human Brain Development

“…The hNPSC line N1997 was isolated from forebrain of a fetus at 6 pcw with the approval from the National Research Ethics System (15/NE/0090). Cells were grown as neurospheres and differentiated, as described in Madgwick et al , 2015 [ 35 ]. Briefly, hNPSCs were grown on Geltrex-coated 6-well plates in proliferation medium for 4 days, then growth medium was replaced with differentiation medium, which was changed every other day.…”

An alternatively spliced zebrafishjnk1atranscript has an essential and non-redundant role in development of the first heart field derived proximal ventricular chamber

“…The importance of alternative splicing for regulating specific developmental processes remains underexplored. Whilst it has been shown to be important for regulating embryonic aspects of stem cell pluripotency and differentiation [49, 50] and has been shown to be common in the early mouse embryo [51] and in the zebrafish [52], there are few, if any, reports where specific splice variants have been shown to play a discrete mechanistic role during embryogenesis that is unique to that transcript and not shared with other related transcripts. There is tantalising circumstantial evidence in the literature to support the idea that individual transcripts may be specifically activated by different gene networks, for example the phosphatase DUSP8 preferentially inactivates exon 6a-containing (equivalent of Ex7 in zebrafish) JNK1 peptides [53].…”

Impacts of Alternative Splicing Events on the Differentiation of Adipocytes

“…Experimental results of RT-PCR have confident percent spliced-in (PSI, the ratio of transcripts including alternatively spliced exons) values, which should be highly relevant to RNA-Seq data [ 112 ]. However, design of RT-PCR analyses for AS events is a time-consuming process that should be manually conducted.…”