transcription from bidirectional promoters n.
Download
Skip this Video
Loading SlideShow in 5 Seconds..
Divergent transcription PowerPoint Presentation
Download Presentation
Divergent transcription

Loading in 2 Seconds...

play fullscreen
1 / 19

Divergent transcription - PowerPoint PPT Presentation


  • 125 Views
  • Uploaded on

Transcription from bidirectional promoters. Divergent transcription. Joern Toedling Huber group September 2007. Divergent transcription. = transcription from a bidirectional promoter region. Bidirectional promoters.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Divergent transcription' - brasen


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
divergent transcription
Divergent transcription

= transcription from a bidirectional promoter region

bidirectional promoters
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

example from zhang et al 1998
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)‏

slide6

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

slide7

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

data collection
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+)‏

actinomycin d
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

very short divergent non orf transcripts
Very short divergent non-ORF transcripts

93 bp

of these (<100 bp), we saw ~80 in the 2006 data

slide14

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

93 bp

slide15

2007 ActD- polyA-samples

2005 ActD- polyA-samples

divergent transript pairs across conditions
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
s cerevisae bidirectional promoters gc content
S. cerevisae bidirectional promoters GC content
  • far lower in yeast than reported for Human
  • not higher than in unidirectional promoter regions
to do
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