Molecular Epigenetics Biol 456/656 Molecular Epigenetics Lecture #3 Aug 28, 2015

Videos explaining Illumina Hi-Seq https://www.youtube.com/watch?v=d2AxXv_6UTQ Reversible terminator chemistry https://www.youtube.com/watch?v=HMyCqWhwB8E

See Brown_Celniker_Nature_2014.pdf http://www.nature.com/nature/journal/v512/n7515/full/nature12962.html

Figure 1 90% of genes express at least 10 transcripts and 5 protein isoforms. 1% of genes have complex patterns of alternative splicing, promoter usage and polyadenylation, and can be processed into 100s of transcrtips.

Figure 1 What is CAGE?

Figure 1 Dystrophin 3’ end

Figure 1 Go to: chrX:4,892,228-4,981,117 ChrX:4850000-4950000 http://genome.ucsc.edu/cgi-bin/hgTracks?db=dm3&position=chrX%3A4892228-4981117&hgsid=388211723_0698XNSkXMdUaPylRi1AqNjbx1bx Go to: chrX:4,892,228-4,981,117

Figure 2

Figure 2 chrX:15,753,078-15,761,360

Figure 2 Per cent spliced in index

Figure 3

Figure 3

Figure 4

Figure 5

Figure 6

Homework: Read “Diversity and dynamics of the Drosophila transcriptome” 1. Draw or explain in words “gene models” illustrating: A. First exon variant alternative splicing B. Convergent transcription C. Antisense transcription 2. Use the UCSC genome browser to find examples of the above events (1A, 1B, 1C) and take screenshots of these. Use arrows and text boxes to point out relevant information. 3. Identify 3 aspects of the paper (a figure, technique, approach or statement made) that you completely do not understand. 4. Explain, briefly, how you attempted to read the paper. 5. What would you score this paper out of 10? Email me your answers prior to Monday’s class in a word, pages or powerpoint file.