Additional file 7.

Malat1 and neat1 are examples of poly(A)- and bimorphic long non-coding RNAs. (a) Malat1 exists in both poly(A)+ and poly(A)- isoforms and the poly(A)- isoform is more abundant than the poly(A)+ isoform. Fewer reads from the 5' end in the poly(A)- fraction are aligned to the genome in both cell lines. Malat1 is also more abundantly expressed in HeLa cells than in H9 cells. (b) Semi-quantitative RT-PCR with two sets of primers confirmed that malat1 is more abundant in poly(A)- samples. (c) Deep sequencing reveals that both isoforms of neat1 are undetectable in H9 cells. In HeLa cells, while the shorter isoform of neat1 is entirely poly(A)+ (pink color), the longer isoform is more enriched in the poly(A)- fraction (red), also seen in (d) for its relative abundance with the same y-axis in HeLa cells.

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Yang et al. Genome Biology 2011 12:R16   doi:10.1186/gb-2011-12-2-r16