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Rodolfo Aramayo

Rodolfo Aramayo

Associate Professor

Department of Biology

Room 412A Biological Sciences Building West
3258 TAMU

College Station , TX 77843-3258
Office Phone: (979) 862-4354


Genetics, Epigenetics and Meiotic RNA Silencing

In my laboratory, we use the filamentous fungus Neurospora crassa, as a model organism to understand the molecular basis of some of the most amazing genetic phenomena observed in eukaryotic cells. For example, we would like to understand how the pairing of specific DNA regions during meiosis controls gene expression and how the presence of unpaired DNA triggers meiotic RNA silencing at this particular developmental stage. RNA silencing pathways are thought to be derived from ancestral natural defense systems directed against invading nucleic acids. Consistent with this, all known PTGS mechanisms share similar components including RNA-dependent RNA polymerases (RdRPs), Argonautes (related to translation initiation factors), Dicers (double stranded-specific endonucleases), as well as many other ATP-dependent DNA and ATP-dependent RNA helicases and dsRNA-binding proteins.

To further our understanding, we are isolating and dissecting the players involved in this pathway. To our surprise, we find that mutations in genes coding for RdRP, Argonaute-like and Dicer-like proteins block meiosis. How could this be? We hypothesize that the gene product of these genes (i.e., the RdRP, the Argonaute-like, and the Dicer-like proteins) play a fundamental role in the regulation of meiotic gene expression via RNA (either double-stranded-RNAs, small-interfering-RNAs, or micro-RNAs). Understanding the role of meiotic RNA silencing during meiosis is important given that PTGS mechanisms like meiotic RNA silencing are being increasingly recognized as fundamental players in the control of eukaryotic gene expression. PTGS phenomena have broad implications for microbial, plant and animal biology. Neurospora is a powerful model organism and an excellent system where to study the molecular basis of these mechanisms. The availability of its genomic sequence plus the increasing repertoire of molecular tools designed for this organism have both simplified and speed up research.

Selected References

  1.  Lee DW, Freitag M, Selker EU & Aramayo R (2008) A cytosine methyltransferase homologue is essential for sexual development in Aspergillus nidulans. PLoS One 3: e2531
  2. Hu JC, Aramayo R, Bolser D, Conway T, Elsik CG, Gribskov M, Kelder T, Kihara D, Knight TF Jr, Pico AR, Siegele DA, Wanner BL & Welch RD (2008) The emerging world of wikis. Science 320: 1289-90
  3. Vestergaard G, Aramayo R, Basta T, Häring M, Peng X, Brügger K, Chen L, Rachel R, Boisset N, Garrett RA & Prangishvili D (2008) Structure of the acidianus filamentous virus 3 and comparative genomics of related archaeal lipothrixviruses. J Virol 82: 371-81
  4. Kelly WG & Aramayo R (2007) Meiotic silencing and the epigenetics of sex. Chromosome Res 15: 633-51
  5. Ng DW, Wang T, Chandrasekharan MB, Aramayo R, Kertbundit S & Hall TC (2007) Plant SET domain-containing proteins: structure, function and regulation. Biochim Biophys Acta 1769: 316-29
  6. Pratt RJ, Lee DW & Aramayo R (2004) DNA methylation affects meiotic trans-sensing, not meiotic silencing, in Neurospora. Genetics 168: 1925-35
  7. Bogomolnaya LM, Pathak R, Guo J, Cham R, Aramayo R & Polymenis M (2004) Hym1p affects cell cycle progression in Saccharomyces cerevisiae. Curr Genet 46: 183-92
  8. Freitag M, Lee DW, Kothe GO, Pratt RJ, Aramayo R & Selker EU (2004) DNA methylation is independent of RNA interference in Neurospora. Science 304: 1939
  9. Lee DW, Seong KY, Pratt RJ, Baker K & Aramayo R (2004) Properties of unpaired DNA required for efficient silencing in Neurospora crassa. Genetics 167: 131-50
  10. Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W & Pratt R (2004) Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev 68: 1-108
  11. Han BK, Aramayo R & Polymenis M (2003) The G1 cyclin Cln3p controls vacuolar biogenesis in Saccharomyces cerevisiae. Genetics 165: 467-76
  12. Lee DW, Pratt RJ, McLaughlin M & Aramayo R (2003) An argonaute-like protein is required for meiotic silencing. Genetics 164: 821-8Kutil BL, Seong KY & Aramayo R (2003) Unpaired genes do not silence their paired neighbors. Curr Genet 43: 425-32
  13. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C & Birren B (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-68
  14. Lee DW, Haag JR & Aramayo R (2003) Construction of strains for rapid homokaryon purification after integration of constructs at the histidine-3 ( his-3) locus of Neurospora crassa. Curr Genet 43: 17-23
  15. Pratt RJ & Aramayo R (2002) Improving the efficiency of gene replacements in Neurospora crassa: a first step towards a large-scale functional genomics project.Fungal Genet Biol 37: 56-71
  16. Bruno KS, Aramayo R, Minke PF, Metzenberg RL & Plamann M (1996) Loss of growth polarity and mislocalization of septa in a Neurospora mutant altered in the regulatory subunit of cAMP-dependent protein kinase. EMBO J 15: 5772-82
  17. Aramayo R, Peleg Y, Addison R & Metzenberg R (1996) Asm-1+, a Neurospora crassa gene related to transcriptional regulators of fungal development. Genetics144: 991-1003
  18. Poleg Y, Aramayo R, Kang S, Hall JG & Metzenberg RL (1996) NUC-2, a component of the phosphate-regulated signal transduction pathway in Neurospora crassa, is an ankyrin repeat protein. Mol Gen Genet 252: 709-16
  19. Peleg Y, Addison R, Aramayo R & Metzenberg RL (1996) Translocation of Neurospora crassa transcription factor NUC-1 into the nucleus is induced by phosphorus limitation. Fungal Genet Biol 20: 185-91

Current Genetics Students:

Ryan Millimaki