Fig. 2
C9orf72 locus. a Represents the three coding transcripts for the C9orf72 gene located on the reverse strand of chromosome 9: NM_145005 (transcript 1), NM_18325 (transcript 2) and NM_1256054 (transcript 3). The HRE is located either in intron 1 considering transcripts 1 and 3, or at the promoter region considering transcript 2. The region captured in the figure encompasses the 41 kb identified by the hg19 coordinates chr9:27539713-27580694. b Zooming in of the 1,6 kb region identified by the hg19 coordinates chr9:27572455-27574064 (grey box in a) and depicting the 5′ end of the C9orf72 locus as represented by the ZENBU Genome Browser. As indicated by the labels in the left side of each track, the following features are depicted from top to bottom: Entrez gene; refGene transcripts; C9orf72 TSSs (the details about their definition is available in material and methods); the CAGEseq expression profile obtained combining myeloid, lymphoid and CNS samples available in the FANTOM5 tissue collection; the expression profile restricted to myeloid-high samples and the expression profile restricted to CNS samples. The height of the expression profiles is scaled to the maximum value for the corresponding set of samples and it clearly highlights the differences between TSS usage in CNS and myeloid-high samples. The actual expression levels are represented as tpm in Additional file 1: Figure S3. c Schematic representation of the C9orf72 locus showing the three AS transcripts C9orf72-AS1, C9orf72-AS2 and C9orf72-AS3, C9orf72 annotated transcripts 1, 2 and 3 and the newly identified C9orf72 transcripts 4 and 5. The dash-arrow in C9orf72-AS1 indicates the transcript might be longer than what detected in our experimental set-up. C9orf72-AS is located at chr9: 27573532-27574512 (hg19) immediately adjacent to the C9orf72-HRE. C9orf72-AS3 chr9: 27573906-27575066 (hg19) starts 40 bp downstream exon 1a of C9orf72 presents a conserved poly-adenylation (poly-A) 692 bp from the 5′end and an alternative poly-A site 1029 bp from the 5′ end