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Myb Transcription Factors

Myb Transcription Factors. Dylan Coughtrey Laboratory Methods in Genomics Spring 2011. What is Myb ?. Acronym taken from myeloblastosis First recognized as an oncogene in avian myeloblastosis virus Currently being studied to further identify genetic factors in cancer patients.

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Myb Transcription Factors

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  1. Myb Transcription Factors Dylan Coughtrey Laboratory Methods in Genomics Spring 2011

  2. What is Myb? • Acronym taken from myeloblastosis • First recognized as an oncogene in avian myeloblastosis virus • Currently being studied to further identify genetic factors in cancer patients

  3. What does it do? • Mybtranscriptionfactors regulate gene expresion by binding directly to DNA • Localizes to recently replicated DNA in mitotically cycling and endocycling cells • Absence of Myb has been shown to cause increases in: • Mitotic arrest • Abnormal chromosome number • Faulty spindle formation

  4. http://www.stanford.edu/group/lipsick/whatsmyb%20short.htm

  5. What does it do? • Myb factors regulate production of anthocyanins • Change with pH (give the fruit its blue color) • Potentially great health benefits, positive effects against: • Cancer • Aging and neurological diseases • Inflammation • Diabetes • Bacterial infection

  6. Protein Structure • Myb proteins are defined by the Myb Domain • Sequence of approximately 50 amino acids • Can be repeated up to three times • Repeat domains are imperfect, but highly conserved • The Myb Domain allow the protein to bind to DNA and regulate transcription

  7. My Progress • Blasted for known Myb nucleotide sequences from Vitisvinifera(grape) and Arabidopsis thaliana • Found nothing • Knew that there had to be Myb factors in blueberry • Found my miracle paper: • Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes • José Tomás Matus, Felipe Aquea, and Patricio Arce-Johnson

  8. M-GLKKG-WT-EED-ILV-YI-HGEG-W- LPKRAGL-RCGKSCRLRWLNYLRPDIK RGNFT-DEEDLIIRLM-LLGNRWSLIAG RLPGRTDNEIKNYWNTHL-KKL

  9. M-GLKKG-WT-EED-ILV-YI-HGEG-W- LPKRAGL-RCGKSCRLRWLNYLRPDIK RGNFT-DEEDLIIRLM-LLGNRWSLIAG RLPGRTDNEIKNYWNTHL-KKL

  10. Finally Found! • BLASTed consensus sequence using tblastn • Searches for amino acid sequences in genomic DNA • 115 hits in the 454 databast • 182 in bb_latest_assembly • 85 in Illumina • 25 in BB_EST_ALL_updated • 25 in BB_EST_cleaned • Some hits were larger than others • e-values lower than 0.001

  11. Determining the REAL Mybs • BLASTed each individual EST scaffold against Illumina and bb_latest_assembly databases • Compared EST hits to Myb hits in Illumina (9) and bb_latest_assembly (6) *Items highlighted yellow are Illumina hits, those in orange are EST hits

  12. Determining the REAL Mybs • Used the Augustus gene prediction tool • Found one Myb hit predicted in Augustus s. starts. end *Output from Augustus in bb_latest_assembly scaffold01934

  13. Further Steps • Identifying gene structure of Mybs in blueberry • Compare to Mybs of closely related plants • Examine various Myb genes in the genome to determine significant differences that could affect function

  14. Works Consulted • http://www.stanford.edu/group/lipsick/whatsmyb%20long.htm • http://pcp.oxfordjournals.org/content/early/2007/05/26/pcp.pcm066.short • http://www.stanford.edu/group/lipsick/pdf/Dubendorff%20and%20Lipsick%20Oncogene%201999.pdf • http://www.gentcare.com/EnProductShow.asp?ID=52 • http://www.eurekalert.org/pub_releases/2007-03/osu-sfn030507.php • http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2507771/?tool=pubmed

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