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

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Divergent transcription

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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)‏


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


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



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


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

93 bp


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