MICHAEL R FREELING

Summary

Affiliation: University of California
Country: USA

Publications

  1. doi request reprint Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition
    Michael Freeling
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Annu Rev Plant Biol 60:433-53. 2009
  2. pmc Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
    Michael Freeling
    Department of Plant and Microbial Biology, University of California at Berkeley, California 94720, USA
    Genome Res 18:1924-37. 2008
  3. ncbi request reprint Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
    Michael Freeling
    Department of Plant and Molecular Biology, University of California Berkeley, Berkeley, California 94720, USA
    Genome Res 16:805-14. 2006
  4. pmc G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis
    Michael Freeling
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Plant Cell 19:1441-57. 2007
  5. doi request reprint Conserved noncoding sequences (CNSs) in higher plants
    Michael Freeling
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Curr Opin Plant Biol 12:126-32. 2009
  6. pmc Arabidopsis intragenomic conserved noncoding sequence
    Brian C Thomas
    College of Natural Resources and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:3348-53. 2007
  7. pmc Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
    Brian C Thomas
    College of Natural Resources, University of California Berkeley, Berkeley, California 94720, USA
    Genome Res 16:934-46. 2006
  8. pmc Conserved noncoding sequences in the grasses
    Dan Choffnes Inada
    Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
    Genome Res 13:2030-41. 2003
  9. pmc Utility and distribution of conserved noncoding sequences in the grasses
    Nicholas J Kaplinsky
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 99:6147-51. 2002
  10. pmc Initiation, establishment, and maintenance of heritable MuDR transposon silencing in maize are mediated by distinct factors
    Margaret Roth Woodhouse
    Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
    PLoS Biol 4:e339. 2006

Research Grants

  1. DEVELOPMENTAL BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 2000
  2. DEVELOPMENTAL BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 1999
  3. DEVELOPMENTAL BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 1993
  4. DEVELOPMENT BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 1992
  5. DEVELOPMENT BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 1991
  6. DEVELOPMENT BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 1990
  7. DEVELOPMENTAL BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 2001

Collaborators

Detail Information

Publications27

  1. doi request reprint Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition
    Michael Freeling
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Annu Rev Plant Biol 60:433-53. 2009
    ..Balanced gene drive is a saltation mechanism in the mutationist tradition...
  2. pmc Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
    Michael Freeling
    Department of Plant and Microbial Biology, University of California at Berkeley, California 94720, USA
    Genome Res 18:1924-37. 2008
    ..The observed differences between gene families raise important questions concerning the causes and consequences of gene transposition...
  3. ncbi request reprint Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
    Michael Freeling
    Department of Plant and Molecular Biology, University of California Berkeley, Berkeley, California 94720, USA
    Genome Res 16:805-14. 2006
    ..We argue that "balanced gene drive" is a sufficient explanation for the trend that the maximums of morphological complexity have gone up, and not down, in both plant and animal eukaryotic lineages...
  4. pmc G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis
    Michael Freeling
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Plant Cell 19:1441-57. 2007
    ..CNSs with one G-box tend to have two G-boxes. CNSs were shared with the homoeolog only and with no other gene, suggesting that binding site turnover impedes detection. Bigfoot genes may function in adaptation to environmental change...
  5. doi request reprint Conserved noncoding sequences (CNSs) in higher plants
    Michael Freeling
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Curr Opin Plant Biol 12:126-32. 2009
    ..We discuss a 'DNA-templated protein assembly' idea that might help explain Bigfoot gene CNSs...
  6. pmc Arabidopsis intragenomic conserved noncoding sequence
    Brian C Thomas
    College of Natural Resources and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:3348-53. 2007
    ..These CNSs provide a unique set of noncoding sequences enriched for function. CNS function is implied by evolutionary conservation and independently supported because CNS-richness predicts regulatory gene ontology categories...
  7. pmc Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
    Brian C Thomas
    College of Natural Resources, University of California Berkeley, Berkeley, California 94720, USA
    Genome Res 16:934-46. 2006
    ..These clusters of duplicate genes may help explain the evolutionary origin of coregulated chromosomal regions and new functional modules...
  8. pmc Conserved noncoding sequences in the grasses
    Dan Choffnes Inada
    Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
    Genome Res 13:2030-41. 2003
    ..We discuss the potential meanings of CNSs and their value as analytical tools and evolutionary characters. We advance the idea that many CNSs function to lock-in gene regulatory decisions...
  9. pmc Utility and distribution of conserved noncoding sequences in the grasses
    Nicholas J Kaplinsky
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 99:6147-51. 2002
    ..CNSs make excellent pan-grass PCR-based genetic mapping tools. They should be useful as characters in phylogenetic studies and as monitors of gene regulatory complexity...
  10. pmc Initiation, establishment, and maintenance of heritable MuDR transposon silencing in maize are mediated by distinct factors
    Margaret Roth Woodhouse
    Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
    PLoS Biol 4:e339. 2006
    ..Together, these data suggest that the establishment and maintenance of MuDR silencing have distinct requirements...
  11. pmc Horizontal transfer of a plant transposon
    Xianmin Diao
    Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
    PLoS Biol 4:e5. 2006
    ..This is the first well-documented example of horizontal transfer of any nuclear-encoded genes between higher plants...
  12. doi request reprint How to usefully compare homologous plant genes and chromosomes as DNA sequences
    Eric Lyons
    Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    Plant J 53:661-73. 2008
    ..Our tutorial encourages the reader to experiment online with the reviewed tools as a companion to the text...
  13. pmc Transposed genes in Arabidopsis are often associated with flanking repeats
    Margaret R Woodhouse
    Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
    PLoS Genet 6:e1000949. 2010
    ..We suggest that intrachromosomal recombination between tandemly duplicated sequences, and subsequent insertion of the circular product, is the predominant mechanism of gene transposition...
  14. pmc Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids
    Eric Lyons
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Plant Physiol 148:1772-81. 2008
    ..This précis of an online tutorial, CoGe with Rosids (http://tinyurl.com/4a23pk), presents sample results graphically...
  15. ncbi request reprint Biodiversity (Communications arising): maize transgene results in Mexico are artefacts
    Nick Kaplinsky
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Nature 416:601-2; discussion 600, 602. 2002
    ....
  16. ncbi request reprint Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication
    R Keith Slotkin
    Department of Plant and Microbial Biology, 111 Koshland Hall, University of California Berkeley, Berkeley, California 94720, USA
    Nat Genet 37:641-4. 2005
    ..Further, transposon-generated inverted duplications may be important for the generation of double-stranded RNAs used in gene silencing...
  17. pmc The evolution of a high copy gene array in Arabidopsis
    Joshua Kane
    Department of Plant and Microbial Biology, University of California at Berkeley, 311 Koshland Hall, Berkeley, CA 94720, USA
    J Mol Evol 70:531-44. 2010
    ..These findings hold larger implications for future research concerning gene and genome evolution...
  18. pmc Conservation and molecular dissection of ROUGH SHEATH2 and ASYMMETRIC LEAVES1 function in leaf development
    George Theodoris
    Department of Plant and Microbial Biology, University of California, Berkeley 94720, USA
    Proc Natl Acad Sci U S A 100:6837-42. 2003
    ..Homodimerization is not absolutely required for KNAT1 repression. RS2:GFP fusion protein is biologically active, localized in discrete dynamic subnuclear foci and associates with DNA during cell division...
  19. pmc Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs
    Margaret R Woodhouse
    Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
    PLoS Biol 8:e1000409. 2010
    ..Among the evolutionary benefits of this deletion/fractionation mechanism is bulk DNA removal and the generation of novel combinations of regulatory sequences and coding regions...
  20. pmc The mop1 (mediator of paramutation1) mutant progressively reactivates one of the two genes encoded by the MuDR transposon in maize
    Margaret Roth Woodhouse
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Genetics 172:579-92. 2006
    ..Conversely, mudrB expression is never restored, its TIR remains methylated, and new insertions of Mu elements are not observed. These data suggest that mudrA and mudrB silencing may be maintained via distinct mechanisms...
  21. ncbi request reprint Regulation and a conserved intron sequence of liguleless3/4 knox class-I homeobox genes in grasses
    Petra Bauer
    Department of Plant and Microbial Biology, UC Berkeley, 111 Koshland Hall, Berkeley, CA 94720 3102, USA
    Planta 219:359-68. 2004
    ..Distribution of this 14-bp sequence was examined within the public rice database. The possible function of this sequence in regulation of lg3/4 genes is discussed...
  22. pmc The extended auricle1 (eta1) gene is essential for the genetic network controlling postinitiation maize leaf development
    Karen S Osmont
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Genetics 165:1507-19. 2003
    ..We present evidence based on genetic and molecular analyses that eta1 provides a downstream link between the knox and liguleless pathways...
  23. pmc Genomic duplication, fractionation and the origin of regulatory novelty
    Richard J Langham
    Department of Plant and Microbial Biology, University of California, Berkeley 94720, USA
    Genetics 166:935-45. 2004
    ..In general, the principles of fractionation and consolidation work well in making sense of maize gene and genomic sequence data...
  24. pmc Mu killer causes the heritable inactivation of the Mutator family of transposable elements in Zea mays
    R Keith Slotkin
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Genetics 165:781-97. 2003
    ..MuDR elements silenced by Muk remain silenced even in plants that do not inherit Muk, suggesting that Muk is required for the initiation of MuDR silencing but not for its maintenance...
  25. ncbi request reprint Expression of a mutant maize gene in the ventral leaf epidermis is sufficient to signal a switch of the leaf's dorsoventral axis
    Jennifer M Nelson
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Development 129:4581-9. 2002
    ..In addition, they demonstrate the abaxial epidermis sends/receives a cell fate determining signal to/from the adaxial epidermis and controls the dorsoventral patterning of the maize leaf...
  26. ncbi request reprint Combinatorial control of meristem identity in maize inflorescences
    Nicholas J Kaplinsky
    351 Koshland Hall, University of California at Berkeley, Berkeley, CA 94720, USA
    Development 130:1149-58. 2003
    ..This pathway is combinatorially controlled by at least two genes that have overlapping functions...
  27. ncbi request reprint Mosaic analysis of extended auricle1 (eta1) suggests that a two-way signaling pathway is involved in positioning the blade/sheath boundary in Zea mays
    Karen S Osmont
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Dev Biol 295:1-12. 2006
    ..These results suggest that a two-way signaling pathway may be involved in the positioning of the blade/sheath boundary. Based on these data, we propose a model for Eta1+ function in the maize leaf...

Research Grants13

  1. DEVELOPMENTAL BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 2000
    ..We are elucidating a molecular genetic basis for heterochrony, the prevailing theory that links evolution with developmental biology. ..
  2. DEVELOPMENTAL BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 1999
    ..We are elucidating a molecular genetic basis for heterochrony, the prevailing theory that links evolution with developmental biology. ..
  3. DEVELOPMENTAL BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 1993
  4. DEVELOPMENT BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 1992
  5. DEVELOPMENT BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 1991
  6. DEVELOPMENT BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 1990
  7. DEVELOPMENTAL BIOLOGY AND GENETICS OF THE MAIZE LEAF
    Michael Freeling; Fiscal Year: 2001
    ..We are elucidating a molecular genetic basis for heterochrony, the prevailing theory that links evolution with developmental biology. ..