Quy Nguyen Manpreet Singh D145 – 13 February 2014

1. Quy Nguyen Manpreet Singh D145 – 13 February 2014

2. Previous knowledge of transcriptome • Both the mouse and human genomes contain about 3.1 billion base pairs • Only about 5 percent of the sequence consist of protein-coding regions (genes). • 22,000 coding genes in the mouse genome

3. Genome tiling arrays

4. Methods • Combined full length cDNA isolation and 5’ and 3’ end sequencing of cloned cDNAs Analysis: • CAGE -new cap analysis gene expression • GIS –gene identification signature • GSC – gene signature cloning • Identify transcriptional start sites and termination sites.

5. CAGE Shiraki et al. 2003.

6. GIS/GSC Ng et al. 2005

7. Results

8. Results

9. Results

10. Results

11. Results • Identified for 181,047 independent transcripts • One order of magnitude greater than the estimated number of genes in the mouse genome, 22,000 genes • Alternative promoters and polyadenylation sites are associated with most transcriptional units. 65% of transcriptional units contain several splice variants.

12. Results • More than a third of the cDNAs in the FANTOM3 data set represent non-coding RNA • Non-coding RNAs are less conserved than 5' and 3' UTRs • Promoters are more conserved than those of protein-coding RNAs • 72% of transcriptional units overlap • Sense–antisense co-expression show complex and tissue-specific regulation • Transcription from the antisense promoter may generate the regulatory interaction

13. Conclusion • Created database for cDNA annotation, expression, and promoter analysis. • The complexity found in the genome would indicate the limitations in microarray interpretation and genome manipulation in mice • Data indicating the existence of very long transcripts shows that there is a need new cloning and isolation techniques • Many more transcripts have yet to be discovered • Gives a better understanding on transcriptional control