Open Access Research

Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns

Joachim Weischenfeldt123, Johannes Waage124, Geng Tian5, Jing Zhao5, Inge Damgaard123, Janus Schou Jakobsen12, Karsten Kristiansen6, Anders Krogh246, Jun Wang56 and Bo T Porse123*

Author Affiliations

1 The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, DK2200 Copenhagen, Denmark

2 Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen, Denmark

3 Section for Gene Therapy Research, Rigshospitalet, University of Copenhagen, DK-2100 Copenhagen, Denmark

4 The Bioinformatics Centre, University of Copenhagen, DK-2200, Copenhagen, Denmark

5 BGI-Shenzhen, Shenzhen 518083, China

6 Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark

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Genome Biology 2012, 13:R35  doi:10.1186/gb-2012-13-5-r35

Published: 24 May 2012

Additional files

Additional file 1:

Supplementary Information and Supplementary Tables S1, S2 and S5. Supplementary Materials, Methods and References. Supplementary Table S1: number of mapped junctions contributed uniquely by the combinatorial database (Comb DB only) or TopHat (TopHat only) and the number of mapped junctions detected by both the combinatorial database and TopHat (Both). Supplementary Table S2: the contribution of TopHat to the number of junctions predicted to generate a PTC versus all junctions (minimum of three reads per junction). Supplementary Table S5: deregulation of core splice factors. Gene FC indicates the change in mRNA levels for all the isoforms for the particular gene between KO and WT.

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Additional file 2:

Supplementary Figure S1. UCSC Genome browser output of Pion gene and schematic of the RAINMAN pipeline with steps for mapping and processing of reads.

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Additional file 3:

Supplementary Figure S2. Histogram showing distance from normal stop codon to the 3' end of RefSeq genes with stops in final exon, and distances to nearest downstream exon-exon junction for genes with stop codons in the second to last exon.

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Additional file 4:

Supplementary Table S3. Reads per unique junction statistics for all samples, split into junctions discovered by mapping to the combinatorial database versus junctions discovered by TopHat.

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Additional file 5:

Supplementary Table S4. Table with Gene Ontology terms associated with genes containing upregulated PTC+ junctions that are unique for Upf2 KO liver or BMM.

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Additional file 6:

Supplementary Table S6. Results from validation by manual inspection of output from isoform class inference.

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Additional file 7:

Supplementary Figure S3. Validation of expression change inference and isoform inference.

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Additional file 8:

Supplementary Table S7. PTC upon inclusion isoforms (SES) upregulated in both Upf2 KO liver and BMM (ΔPSI > 20%).

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Additional file 9:

Supplementary Table S8. PTC upon exclusion isoforms (SES) upregulated in both Upf2 KO liver and BMM (ΔPSI < -20%).

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Additional file 10:

Supplementary Figure S4. Mean per position phastCon conservation score around single exon skipping events for BMMs. Numbers on x-axis indicate nucleotide intervals - 25 and 75 nucleotides for exons and flanking introns, respectively.

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Additional file 11:

Supplementary Figure S5. Conservation around upregulated PTCs, with mean per-position phastCon scores centered on the PTC for upregulated junctions in liver and BMMs.

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Additional file 12:

Supplementary Table S9. List of primers used in RT-PCR validation of splicing events.

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