A WWW supplement to:
Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA
transcription motifs in S. cerevisiae
Genome Research (in press)
Priya Sudarsanam*
Yitzhak (Tzachi) Pilpel*
George M. Church
*These authors made equal contributions to this work
Department of Genetics, Harvard Medical School, and
Lipper Center for Computational
Genetics
Abstract
Combinatorial regulation is an important feature of eukaryotic transcription. However, only a
limited number of studies have characterized this aspect on a whole-genome level. We have
conducted a genome-wide computational survey to identify cis-regulatory motif pairs that
co-occur in a significantly high number of promoters in the S. cerevisiae genome. A pair of
novel motifs, mRRPE and PAC, co-occur most highly in the genome, primarily in the promoters of
genes involved in rRNA transcription and processing. The two motifs show significant
positional and orientational bias with mRRPE being closer to the ATG than PAC in most
promoters. Two additional rRNA-related motifs, mRRSE3 and mRRSE10, also co-occur with mRRPE
and PAC. mRRPE and PAC are the primary determinants of expression profiles while mRRSE3 and
mRRSE10 modulate these patterns. We describe a new computational approach for studying the
functional significance of the physical locations of promoter elements that uses combined
analyses of genome sequence and microarray data. Applying this methodology to the regulatory
cassette containing the four rRNA motifs demonstrates that the relative promoter locations of
these elements have a profound effect on the expression patterns of the downstream genes.
These findings provide a function for these novel motifs and insight into the mechanism by
which they regulate gene expression. The methodology introduced here should prove particularly
useful for analyzing transcriptional regulation in more complex genomes.
Figures
Positional Combinograms
Positional Combinogram for sporulation
Combinograms of rRNA transcription genes
rRNA transcription genes in DNA-damage
rRNA transcription genes in DNA-damage
Tables
1) Our full collection of
356 known and putative promoter element motifs
2) The MIPS rRNA synthesis set of ORFs (used to derived
motifs m_RRSE3
and m_rRSE10
)
3) The MIPS rRNA processing set of ORFs (used to
derived
motifs PAC and
mRRPE)
4) Also, please view here a Fasta formatted file
with the up-stream
regions of all ORFs in the genome
(provided by Jason Hughes, and used by AlignACE to derive
motifs from the respective MIPS categories)
Data & Resources
All expression data were
taken from ExpressDB
Motifs were derived using AlignACE
and matched to promoters in the genome using ScanACE
Contacts
Correspondence may be addressed to George M. Church at:
Department of Genetics,
Harvard Medical School
200 Longwood Avenue,
Boston, MA 02115 USA
fax (617) 432-7266
Or Email to:
Tzachi Pilpel
Priya Sudarsanam
George Church