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. Author manuscript; available in PMC: 2014 May 2.
Published in final edited form as: Cell Stem Cell. 2013 Apr 11;12(5):616–628. doi: 10.1016/j.stem.2013.03.003

Figure 4. RNA CaptureSeq validates SVZ lncRNA expression and reveals multiple isoforms and complex locus structures, see also Figure S4.

Figure 4

(A) Schematic of RNA-Capture seq procedure. We used Cufflinlks’ lncRNA assembly to define putative lncRNA loci and designed tiled probe libraries against these loci. The cDNA library was then hybridized to this biotin-labeled probe library, and after purification by streptavidin, the enriched population of lncRNAs was sequenced by 454 (Roche) long-read chemistry. (B) Isotigs assembled at the Pou3f3 locus revealed a distal transcriptional start site for a transcript that can be spliced into known noncoding RNA 2610017I09Rik. (C) CaptureSeq-derived reads correctly assembled known protein-coding gene Nr2f1 and identified 4 distinct TSS’s for a lncRNA transcribed divergently from the Nr2f1 promoter. The syntentic region in human reveals a similar organization of CpG islands and divergent transcriptional start sites for non-coding transcripts. Genes derived from RefSeq are colored purple, genes from Ensembl are red.