An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803.
There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and because of their potential for the production of biofuels. However, the exploitation of cyanobacteria for bioengineering requires knowledge of their transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map of 3,527 transcriptional start sites (TSS) of the model organism Synechocystis sp. PCC6803. One-third of all TSS were located upstream of an annotated gene; another third were on the reverse complementary strand of 866 genes, suggesting massive antisense transcription. Orphan TSS located in intergenic regions led us to predict 314 noncoding RNAs (ncRNAs). Complementary microarray-based RNA profiling verified a high number of noncoding transcripts and identified strong ncRNA regulations. Thus, ∼64% of all TSS give rise to antisense or ncRNAs in a genome that is to 87% protein coding. Our data enhance the information on promoters by a factor of 40, suggest the existence of additional small peptide-encoding mRNAs, and provide corrected 5' annotations for many genes of this cyanobacterium. The global TSS map will facilitate the use of Synechocystis sp. PCC6803 as a model organism for further research on photosynthesis and energy research.
Faculty of Biology and Freiburg Initiative in Systems Biology, University of Freiburg, D-79104 Freiburg, Germany.
Jan
J
Mitschke
Jens
J
Georg
Ingeborg
I
Scholz
Cynthia M
CM
Sharma
Dennis
D
Dienst
Jens
J
Bantscheff
Björn
B
Voss
Claudia
C
Steglich
Annegret
A
Wilde
Jörg
J
Vogel
Wolfgang R
WR
Hess
D001483:Base Sequence; D005798:Genes, Bacterial; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D010788:Photosynthesis; D022661:RNA, Untranslated / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D046939:Synechocystis / Q000235:genetics* / Q000502:physiology; D014158:Transcription, Genetic
D022661:RNA, Untranslated
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