The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells

Abstract

While thousands of long noncoding RNAs (lncRNAs) have been identified, few lncRNAs that control neural stem cell (NSC) behavior are known. Here, we identify Pinky (Pnky) as a neural-specific lncRNA that regulates neurogenesis from NSCs in the embryonic and postnatal brain. In postnatal NSCs, Pnky knockdown potentiates neuronal lineage commitment and expands the transit-amplifying cell population, increasing neuron production several-fold. Pnky is evolutionarily conserved and expressed in NSCs of the developing human brain. In the embryonic mouse cortex, Pnky knockdown increases neuronal differentiation and depletes the NSC population. Pnky interacts with the splicing regulator PTBP1, and PTBP1 knockdown also enhances neurogenesis. In NSCs, Pnky and PTBP1 regulate the expression and alternative splicing of a core set of transcripts that relates to the cellular phenotype. These data thus unveil Pnky as a conserved lncRNA that interacts with a key RNA processing factor and regulates neurogenesis from embryonic and postnatal NSC populations.

Figure 1. The lncRNA Pinky is expressed in SVZ-NSCs and regulates neuronal differentiation

A) UCSC genome browser view of the Pnky locus. Also shown are ChIP-seq tracks for H3K4me3 and H3K27me3 in ESCs and V-SVZ NSCs. B) Fragments per kilobase per million mapped reads (FPKM) values for Pnky in indicated tissues. C) Subcellular fractionation followed by RT-qPCR for indicated lncRNAs and mRNAs. Error bars are propagated standard deviation (S.D.) from technical triplicate wells. D) Branched-DNA ISH for Pnky in V-SVZ NSC cultures. Nuclei are counter-stained with 4',6-diamidino-2-phenylindole (DAPI). Scale bar = 10 μm. E) Branched-DNA ISH for Pnky (brown) in adult mouse coronal brain section. Nuclei are counter-stained with hematoxylin. V = ventricle, CC = corpus collosum, STR = striatum. Scale bar = 50 μm. F) Microarray expression analysis from FACS-isolated neural stem cells (NSC), transit-amplifying cells (TA), and neuroblasts (NB). Value in NSCs set to 0. G) Schematic of V-SVZ NSC culture system. H) Quantification of EdU labeling counted from GFP+ cultures of V-SVZ NSCs infected with control or Pnky-KD constructs. I) ICC for TUJ1 (red) after 7d of differentiation in control or Pnky-KD GFP+ cultures. Nuclei are counter-stained with DAPI (blue). Scale bar = 50 μm. J) Quantification of TUJ1+ NBs produced after 7d differentiation. K) Quantification of the number of TA cells after 2d of differentiation. Error bars for H, J, and K are S.D. from triplicate wells, * p < 0.05, **p < 0.01, Student's t-test. See also Figure S1.

Figure 2. Pinky knockdown leads to an expansion of neurogenic transit-amplifying progenitors

A) Schematic of experimental design. B) Representative images of isolated colonies after 4d of differentiation. ICC for TUJ1 (red) and GFP (green). Nuclei are DAPI counterstained (blue). Scale bar = 50 μm. C) Quantification of the fate of isolated GFP+ colonies. Error bars = S.D. of triplicate experiments. D) Quantification of TUJ1+ neuroblasts found in individual neurogenic colonies. E) Representative frames from time-lapse video of control (top) or Pnky-KD (bottom) single cells. Time of differentiation is indicated. Yellow arrows indicate daughter cells resulting from a recent division, red arrows indicate cell death. Scale bar = 25 μm. F) Bar graph representing the percentage of initial tracked progenitors that gave rise to neuroblasts. N= 531 GFP+ shCtrl NSCs and 316 GFP+ shPnky NSCs. G) Violin plots overlaying box-and-whisker plots of total number of divisions undergone by a single initial neurogenic progenitor and all of its daughter cells. N = 44 shCtrl and 33 shPnky progenitors. H) Violin plots overlaying box-and-whisker plots of the number of generations per initial neurogenic progenitor for shCtrl and shPnky. N = 44 shCtrl and 33 shPnky progenitors. I) Violin plots overlaying box-and-whisker plots of % of progeny per single neurogenic progenitor that underwent cell death. N = 44 shCtrl and 33 shPnky progenitors. J) Tree diagram for the frames shown in E and corresponding time-lapse movies. X indicates cell underwent cell death. *p < 0.05 ***p<0.001, Student's t-test. See also Figure S2.

Figure 3. Pinky is expressed in the developing mouse and human cortex and regulates the differentiation of mouse cortical progenitors in vivo

A) ISH for Pnky in embryonic day 16.5 (E16.5) mouse brain. B) Genome browser track showing two regions of high conservation, determined by PhyloP score (yellow boxes). Human PNKY genomic region is shown below with conservation indicated. For clarity, the mouse – strand is shown left to right. C) ISH for PNKY in gestational week 14.5 (GW14.5) human brain. D) Schematic of in utero.electroporation of mouse embryonic brain. E) Cortical sections at E15.5, 2d after electroporation with shCtrl (left) or shPnky (right). IHC for GFP (top) and with DAPI counterstain (bottom). VZ = ventricular zone, SVZ/IZ = subventricular zone/intermediate zone, CP = cortical plate. F) Quantification of GFP+ cell distribution in indicated zones as a percentage of total GFP+ cells. G) Left: Cortical sections at E15.5, 2d after electroporation with shCtrl or shPnky. IHC for GFP (green) and SOX2 (red), with DAPI nuclear counterstain (blue). Yellow box indicates region enlarged in the adjacent panels. Arrowheads indicate co-labeled cells. Right: quantification of SOX2+, GFP+ cells as a percentage of total GFP+ cells. H) Left: Cortical sections immunostained for GFP (green) and SATB2 (red), with DAPI nuclear counterstain (blue). Yellow box indicates region enlarged in the adjacent panels. Right: Quantification of SATB2+, GFP+ cells as a percentage of total GFP+ cells. All error bars are S.D., n=4 brains of each condition from 3 separate surgeries. *p<0.05, **p<0.01. All scale bars = 50 μm. See also Figure S3.

Figure 4. Pinky interacts with PTBP1 and regulates transcript expression and differential splicing

A) Immunoblot for PTBP1 or HNRNPK following RNA-pulldown with biotin-labeled sense (S) or anti-sense (AS) Pnky RNA incubated with V-SVZ NSC nuclear extract. IN = input V-SVZ nuclear extract. B) RT-qPCR detection for indicated RNA recovered by PTBP1-specific antibody normalized to control FLAG antibody. Error bars are propagated S.D. from technical triplicates. C) Quantification of number of TUJ1+ neuroblasts found in individual neurogenic colonies with Ptbp1-knockdown or control. D) Venn Diagram demonstrating the overlap between genes differentially expressed (FDR < 0.05) upon Ptbp1 or Pnky knockdown. Heatmap representation of the differential expression of the overlapping gene set in shCtrl, shPnky, and shPtbp1 biological duplicate cultures. E) Venn Diagram demonstrating the overlap between exons showing differential usage (FDR < 0.01) upon Ptbp1 or Pnky knockdown. Heatmap representation of the differential usage of the overlapping gene set in shPnky and shPtbp1 cultures compared to control. F-H) RT-qPCR detection of expression of indicated genes normalized to Gapdh. Expression in each condition is shown relative to control (shCtrl-GFP, shCtrl-mCherry). Error bars are 95% confidence intervals from 3 separate cultures. See also Figure S4 and Tables S1-S3.