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Divergent transcription

Divergent transcription

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Divergent transcription

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  1. Transcription from bidirectional promoters Divergent transcription Joern Toedling Huber group September 2007

  2. Divergent transcription = transcription from a bidirectional promoter region

  3. Bidirectional promoters have been described, mainly for H.sapiens, with the following characteristics: quite short (< 1000 bp, majority < 300 bp)‏ very GC-rich; median 66% vs. 53% for uni-directional promoters certain transcription factor binding motives are over-represented (e.g. GAPB1 in H.sapiens), while others are under-represented

  4. Example from Zhang et al. 1998 ORFs of PRP16 and MRPL2D are co-transcribed in our poly-A RNA data (yeast strain S96 on YPD medium in exponentional growth phase)‏

  5. and we saw them co-expressed along the cell cycle...

  6. but others did not found them to be co-expressed along the cell cycle (Kruglyak and Tang, 2000)‏

  7. Genechip S. cerevisae tiling array 4 bp tiling path over complete genome (12 M basepairs, 16 chromosomes)‏ Sense and Antisense strands 6.5 M oligonucleotides manufactured by Affymetrix

  8. Data Collection Poly-A-RNA and Total-RNA from David et al. (2006), S96 strain, grown on YPD (glucose) medium S90 samples, some treated with Actinomycin D (ActD+); grown on YPD YP+Galactose YPE: YP+Ethanol (S96 cell cycle ActD+)‏

  9. Actinomycin D antibiotic polypetide from Streptomyces bacteria selectively inhibits DNA-dependent DNA-Polymerase but not RNA-dependent one; thereby prevents second-strand cDNA synthesis during reverse transcription step

  10. Example 1 from Kruglyak and Tang, 2000

  11. Example 2 from Kruglyak and Tang, 2000

  12. Categories of divergent transcript pairs

  13. Very short divergent non-ORF transcripts 93 bp of these (<100 bp), we saw ~80 in the 2006 data

  14. maybe artifact of old data, only 30 found in new non-Actinomycin-D (ActD-) treated samples, only 15 in new ActD+ samples 93 bp

  15. 2007 ActD- polyA-samples 2005 ActD- polyA-samples

  16. Divergent transcript pairs are consistent across conditions

  17. Divergent transript pairs across conditions • 70% of divergent-transcript pairs seen in YPD are transcribed in YPGal as well • 76% of YPGal ones in YPD as well

  18. S. cerevisae bidirectional promoters GC content • far lower in yeast than reported for Human • not higher than in unidirectional promoter regions

  19. To do... investigate more conditions and ActD+ cell-cycle data TF binding motif enrichment in found bidirectional promoters investigate importance of GC content for bidirectional promoters in yeast functional characterization of bidirectional promoters observed under two or more conditions or for which transcripts' expression correlate along cell cycle describe functional bidirectional promoters in yeast describe filtered novel transcripts from bidirectional promoters