MICHAEL AXTELL

Summary

Affiliation: Pennsylvania State University
Country: USA

Publications

  1. pmc ShortStack: comprehensive annotation and quantification of small RNA genes
    Michael J Axtell
    Department of Biology, and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA
    RNA 19:740-51. 2013
  2. doi request reprint Classification and comparison of small RNAs from plants
    Michael J Axtell
    Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
    Annu Rev Plant Biol 64:137-59. 2013
  3. pmc Vive la différence: biogenesis and evolution of microRNAs in plants and animals
    Michael J Axtell
    Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA
    Genome Biol 12:221. 2011
  4. pmc Common functions for diverse small RNAs of land plants
    Michael J Axtell
    Department of Biology and Huck Institutes of the Life Sciences, Pensylvania State University, University Park, PA 16802, USA
    Plant Cell 19:1750-69. 2007
  5. doi request reprint Evolution of microRNAs and their targets: are all microRNAs biologically relevant?
    Michael J Axtell
    Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Biochim Biophys Acta 1779:725-34. 2008
  6. ncbi request reprint A two-hit trigger for siRNA biogenesis in plants
    Michael J Axtell
    Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
    Cell 127:565-77. 2006
  7. pmc Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus
    Zhaorong Ma
    Integrative Biosciences PhD Program in Bioinformatics and Genomics, Huck Institutes of the Life Sciences, Pensylvania State University, University Park, Pensylvania 16802, USA
    Plant Cell 22:1090-103. 2010
  8. pmc Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development
    Sung Hyun Cho
    Department of Biology, Pennsylvania State University, University Park, PA, USA
    PLoS Genet 4:e1000314. 2008
  9. pmc Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
    Charles Addo-Quaye
    Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA
    Curr Biol 18:758-62. 2008
  10. doi request reprint Evolution of plant microRNAs and their targets
    Michael J Axtell
    Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
    Trends Plant Sci 13:343-9. 2008

Research Grants

Collaborators

Detail Information

Publications19

  1. pmc ShortStack: comprehensive annotation and quantification of small RNA genes
    Michael J Axtell
    Department of Biology, and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA
    RNA 19:740-51. 2013
    ..Annotation of MIRNA loci by ShortStack is highly specific in both plants and animals. ShortStack is freely available under a GNU General Public License...
  2. doi request reprint Classification and comparison of small RNAs from plants
    Michael J Axtell
    Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
    Annu Rev Plant Biol 64:137-59. 2013
    ..Tertiary subdivisions can be identified within many of the secondary classifications as well. Comparisons between the different classes of plant small RNAs help to illuminate key goals for future research...
  3. pmc Vive la différence: biogenesis and evolution of microRNAs in plants and animals
    Michael J Axtell
    Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA
    Genome Biol 12:221. 2011
    ..MicroRNAs are pervasive in both plants and animals, but many aspects of their biogenesis, function and evolution differ. We reveal how these differences contribute to characteristic features of microRNA evolution in the two kingdoms...
  4. pmc Common functions for diverse small RNAs of land plants
    Michael J Axtell
    Department of Biology and Huck Institutes of the Life Sciences, Pensylvania State University, University Park, PA 16802, USA
    Plant Cell 19:1750-69. 2007
    ..Diverse, lineage-specific, small RNAs can therefore perform common biological functions in plants...
  5. doi request reprint Evolution of microRNAs and their targets: are all microRNAs biologically relevant?
    Michael J Axtell
    Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Biochim Biophys Acta 1779:725-34. 2008
    ..However, this ever-changing cast of transient miRNAs could provide a reservoir of potentially useful miRNAs from which new regulatory interactions sometimes are selected...
  6. ncbi request reprint A two-hit trigger for siRNA biogenesis in plants
    Michael J Axtell
    Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
    Cell 127:565-77. 2006
    ..Therefore, two "hits,"--often, but not always, two cleavage events--constitute a conserved trigger for siRNA biogenesis, a finding with implications for recognition and silencing of aberrant RNA...
  7. pmc Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus
    Zhaorong Ma
    Integrative Biosciences PhD Program in Bioinformatics and Genomics, Huck Institutes of the Life Sciences, Pensylvania State University, University Park, Pensylvania 16802, USA
    Plant Cell 22:1090-103. 2010
    ..thaliana. Altogether, our findings indicate that many MIRNAs and most p4-siRNA hot spots are rapidly changing and evolutionarily transient within the Arabidopsis genus...
  8. pmc Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development
    Sung Hyun Cho
    Department of Biology, Pennsylvania State University, University Park, PA, USA
    PLoS Genet 4:e1000314. 2008
    ..patens. We conclude that intergenic/repeat-derived siRNAs are indeed a broadly conserved, distinct class of small regulatory RNAs within land plants...
  9. pmc Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
    Charles Addo-Quaye
    Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA
    Curr Biol 18:758-62. 2008
    ..This empirical method is broadly applicable to the discovery and quantification of cleaved targets of small RNAs without a priori predictions...
  10. doi request reprint Evolution of plant microRNAs and their targets
    Michael J Axtell
    Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
    Trends Plant Sci 13:343-9. 2008
    ..These data have provided a coherent set of hypotheses explaining the birth, selection and death of miRNAs in land plants...
  11. pmc Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome
    Charles Addo-Quaye
    Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    RNA 15:2112-21. 2009
    ..MIR319 is thus a conserved exception to the general rule of loop-last processing of MIRNA hairpins. Loop-first MIR319 processing may contribute to the high efficacy of a widely used MIR319-based strategy for aMIRNA production in plants...
  12. doi request reprint RNA secondary structural determinants of miRNA precursor processing in Arabidopsis
    Liang Song
    The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
    Curr Biol 20:37-41. 2010
    ....
  13. pmc CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets
    Charles Addo-Quaye
    Department of Computer Science and Engineering and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
    Bioinformatics 25:130-1. 2009
    ..CleaveLand can thus be applied to degradome data from any species provided a set of mRNA transcripts and a set of query miRNAs or other small RNAs are available...
  14. doi request reprint A method to discover phased siRNA loci
    Michael J Axtell
    Department of Biology, Pennsylvania State University, University Park, PA, USA
    Methods Mol Biol 592:59-70. 2010
    ..Top ranked loci are candidates for further computational and biological analyses...
  15. ncbi request reprint Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans
    J Graham Ruby
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 127:1193-207. 2006
    ..The motif is conserved in other nematodes, presumably because of its importance for producing these diverse, autonomously expressed, small RNAs (dasRNAs)...
  16. pmc Antiquity of microRNAs and their targets in land plants
    Michael J Axtell
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Plant Cell 17:1658-73. 2005
    ..Therefore, several individual miRNA regulatory circuits have ancient origins and have remained intact throughout the evolution and diversification of plants...
  17. ncbi request reprint Initiation of RPS2-specified disease resistance in Arabidopsis is coupled to the AvrRpt2-directed elimination of RIN4
    Michael J Axtell
    Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Cell 112:369-77. 2003
    ..Therefore, we suggest that RPS2 initiates signaling based upon perception of RIN4 disappearance rather than direct recognition of AvrRpt2...
  18. ncbi request reprint Genetic and molecular evidence that the Pseudomonas syringae type III effector protein AvrRpt2 is a cysteine protease
    Michael J Axtell
    University of California, Berkeley, Department of Plant and Microbial Biology, 111 Koshland Hall, Berkeley, CA 94720, USA
    Mol Microbiol 49:1537-46. 2003
    ..These data indicate that AvrRpt2 is most likely a sequence divergent cysteine protease whose activity is required for elimination of RIN4 during infection...
  19. ncbi request reprint NPK1, an MEKK1-like mitogen-activated protein kinase kinase kinase, regulates innate immunity and development in plants
    Hailing Jin
    Department of Plant and Microbial Biology, University of California, Berkeley, 94720, USA
    Dev Cell 3:291-7. 2002
    ..Our results provide evidence that NPK1 functions in the regulation of N-, Bs2-, and Rx-mediated resistance responses and may play a role in one or more MAPK cascades, regulating multiple cellular processes...

Research Grants2

  1. Functional and Evolutionary Genomics of Ancient Small RNAs
    Michael J Axtell; Fiscal Year: 2010
    ..This project will reveal basic mechanisms of microRNA-mediated gene control by defining the roles of ancient microRNAs in readily studied model organisms. ..
  2. Functional and Evolutionary Genomics of Ancient Small RNAs
    MICHAEL AXTELL; Fiscal Year: 2009
    ..This project will reveal basic mechanisms of microRNA-mediated gene control by defining the roles of ancient microRNAs in readily studied model organisms. ..