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. 2014 Aug 7;95(2):143–161. doi: 10.1016/j.ajhg.2014.06.014

Figure 5.

Figure 5

SPAST CNVs Extending into 3′ Genes Create Chimeric Genes, and Deletions Involving the Final Exon of SPAST Might Create SPAST:SLC30A6 Fusion Transcripts or Alter SLC30A6 Expression

(A–C) Deletions extending into 3′ genes.

(A) Fourteen CNVs (black bars) extend into genes 3′ of SPAST (13 deletions, 1 duplication). Three of the downstream genes (SLC30A6, BIRC6, TTC27) are in direct orientation with SPAST; thus, SPAST deletions intersecting these 3′ genes potentially yield chimeric genes.

(B) Potential fusion transcripts resulting from the deletions shown in (A) for which the 3′ intersected gene is directly oriented with SPAST. Potential fusion transcripts are based only on known splice isoforms of the 3′ genes and include all SPAST exons present, although other splice variants are possible. Predicted in-frame splicing is shown in black, out-of-frame in red. The deletion intersecting NLRC4 (Spain 6) is not shown, because this gene is oriented oppositely to SPAST.

(C) Potential fusion transcript resulting from the duplication in subject SPAST_3. This tandem, directly oriented duplication results in duplication of three genes (SLC30A6, NLRC4, YIPF4) and a potential in-frame transcript joining exons 1–46 of BIRC6 with exons 2–17 of SPAST; the normal, diploid copy number of full-length SPAST and BIRC6 are left intact.

(D and E) Deletions involving the final exon of SPAST.

(D) Deletions with 3′ breakpoints in the intergenic space between SPAST and SLC30A6 (top, “span exon 17”) or within the final exon of SPAST (exon 17) (bottom, “interrupt exon 17”). The former group of deletions may alter SLC30A6 expression by eliminating upstream SLC30A6 regulatory sequence (potential regulatory sequences shown by H3K27Ac track from UCSC), and both groups of CNVs may result in fusion transcripts with SLC30A6 by eliminating splicing to SPAST exon 17.

(E) Potential fusion transcripts resulting from the deletions shown in (D). Potential fusion transcripts are based only on known splice isoforms of SLC30A6 and include all SPAST exons present. Black, predicted in-frame; red, predicted out of frame.