Small RNA and Cyanobacteria

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Small RNA and Cyanobacteria
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Characteristics of Cyanobacteria

• Aquatic
• Photosynthetic
• Usually unicellular

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Importance of Cyanobacteria

• Atmosphere

• Chloroplast

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What is sRNA?

• Encoded in the intergenic regions

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Why do we want to learn about sRNAs?

• To predict them in any genome of an organism
• To experimentally analyze their function
• To control gene expression

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Why have few sRNAs been found?

• Very small (usually 40-300 nt)
• Less sensitive to point mutations
• Function at the 2º structure level
• Do not encode protein sequence
• No coding signals (start/stop codon)

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How Biolingua can search for sRNAs in
cyanobacteria?

• Compare the sequences of intergenic regions by
  BLAST
• These results will include both an e-value and a
  percent identical score
• Run the similar sequences from multiple organisms
  thru RNAz, which predicts if an RNA exists by its
  2º structure

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To further verify an sRNA

• M-Fold takes a potential RNA sequence and
  incorporates its structure
• Experiments test by northern blot analysis

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Acknowledgements

• Jeff Elhai and
• Dr. You Chen