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Regulated process or chance observation?. Divergent transcription. Joern Toedling Huber group November 2007. Divergent transcription. Transcript orientation. Data Collection. S90 samples, treated with Actinomycin D (ActD+); grown on 3 * YPD 3 * YP+Galactose 3 * YPE: YP+Ethanol

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Regulated process or chance observation

Regulated process or chance observation?

Divergent transcription

Joern Toedling

Huber group

November 2007


Divergent transcription

Divergent transcription


Transcript orientation

Transcript orientation


Data collection

Data Collection

S90 samples, treated with Actinomycin D (ActD+); grown on

3 * YPD

3 * YP+Galactose

3 * YPE: YP+Ethanol

S96 cell cycle ActD+: 45 samples, one taken each 5 min for 220 min (~ 2 iterations of cell cycle)‏


Post processing segmentation revisited

Post-processing: segmentation revisited


Exponential growth data

Exponential growth data

9 samples, normalized by use of a genomic DNA sample, grown under 3 different growth conditions, one common segmentation and post-processing, results in 5510 transcripts:

1360 pairs of divergent transcripts

672 pairs of convergent transcripts

781 pairs of tandem transcripts


Divergent transcripts in exponential growth data

Divergent transcripts in exponential growth data


Divergent transcript pairs are consistent across conditions

Divergent transcript pairs are consistent across conditions


Cell cycle data

Cell-cycle data

45 samples, normalized by use of a genomic DNA sample, one common segmentation and post-processing, results in 5596 transcripts:

1266 pairs of divergent transcripts

829 pairs of convergent transcripts

847 pairs of tandem transcripts


Divergent transcripts in cell cycle data

Divergent transcripts in cell-cycle data


Divergent transcription

are divergent transcripts' levels correlated across cell cycle and is this correlation dependant on the closeness of the transcript boundaries


Divergent transcription

Which correlation coefficient?

Pearson CC

cov(X,Y)‏

ρX,Y =

sd(X) * sd(Y)‏

Spearman CC is based on ranks(X) and ranks(Y) instead of X and Y


Divergent transcription

Interlude: Interpreting Pearson CC = 0.8

Anscombe, Francis J. (1973) Graphs in statistical analysis. American Statistician, 27, 17–21.


Spearman correlation of divergent transcripts levels during cell cycle

Spearman correlation of divergent transcripts' levels during cell cycle


Spearman correlation of divergent transcripts levels across 3 conditions w 3 samples each

Spearman correlation of divergent transcripts' levels across 3 conditions w/ 3 samples each


Does transcript orientation have a meaning according to gene ontology

Does transcript orientation have a meaning according to Gene Ontology?

  • Only 18% of divergently transcribed ORFs share common GO Terms (22% for convergently transcribed ORFs)‏

  • mostly very common ones (nucleus, cytoplasm)‏

  • divergently transcribed ORFs share “nucleus” a bit less often than convergently transcribed ones


Interlude go evidence codes

Interlude: GO evidence codes

  • IMP: inferred from mutant phenotype

  • IGI: inferred from genetic interaction

  • IPI: inferred from physical interaction

  • ISS: inferred from sequence similarity

  • IDA: inferred from direct assay

  • IEP: inferred from expression pattern

  • IEA: inferred from electronic annotation

  • TAS: traceable author statement

  • NAS: non-traceable author statement

  • ND: no biological data available

  • IC: inferred by curator


Is transcript closeness meaningful

Is transcript “closeness” meaningful?

  • 12,162,996 bp total size of yeast strain S288c genome

  • 9,043,789 bp summed up length of transcribed regions

  • 558 bp average space between transcripts

  • yeast genome is very compact !

  • maybe restrict to very close divergent transcripts (< 300bp ?)‏


To do

To do...

investigate ActD+ Cdc28 cell-cycle data

TF binding motif enrichment in found bidirectional promoters

binding of known motifs (annotated in Transfac and SCPD data bases)‏

discovery of new motifs, using tools such as MEME

consider restriction to those pairs of divergent transcripts whose expression is correlated across the cell-cycle to distinguish functional divergent pairs from those that just appear to be divergent due to compactness of yeast genome

describe functional bidirectional promoters in yeast

describe filtered novel transcripts from bidirectional promoters


Leisure activities

Leisure activities...

look for new and known TF binding motifs upstream of periodic anti-sense transcripts:


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