Table I.

Predicted Arabidopsis subunit isovariant diversity for three chromatin-remodeling complexes

Yeast Complex-Protein SubunitsaGenes in Arabidopsis Encoding IsovariantsbcAccession Nos. of Arabidopsis Genes
SWI/SNF
    Arp7 (YPR034W)1 (ARP7d)At3g60830b
    Arp9 (YMR033W)N.D.e
    Snf2 (YOR290C)4At5g19310, At3g06010, At2g28290, At3g06400, At5g18620b
    Snf5 (YBR289W)1At3g17590b
    Snf12 (YNR023W)2At5g14170, At3g01890b
    Swi1 (YPL016W)2At1g79000, At1g16710b
    Swi3 (YJL176C)4At2g33610, At1g21700, At4g34430, At2g47620b
    Taf14 (YPL129W)2At2g18000, At5g45600c
    Rtt102 (YGR275W), Snf11 (YDR073W), Snf6 (YHL025W),N.D.e
SWR1/SWR-C
    Arp4 (YJL081C)1 (ARP4)At1g18450
    Arp6 (YLR085C)1 (ARP6)At3g33520
    Actin ACT1 (YFL039C)8f
    Swr1 (YDR334W) Snf2 homolog4At3g12810, At3g57300, At3g06400, At5g19310b
    Swc3 (YAL011W)5At4g23800, At1g15340, At3g16000, At4g11080, At1g65470b
    Swc5 (YBR231C)3At3g28730, At1g08600, At1g58025b
    Vps72 (YDR485C)5At4g23800, At5g22650, At2g06210, At4g11080, At5g18620b
    Rvb1 (YDR190C)1At5g22330c
    Rvb2 (YPL235W)2At5g67630, At3g49830c
    Swc4 (YGR002C)1At2g47210c
    Vps71 (YML041C)1At5g37055c
    Yaf9 (YNL107W)2At5g45600, At2g18000c
    Swc7 (YLR385C)N.D.e
INO80
    Arp4 (YJL081C)1 (ARP4)At1g18450b
    Arp5 (YNL059C)1 (ARP5)At3g12380b
    Arp8 (YOR141C)1 (ARP9)At5g43500b
    Actin ACT1 (YFL039C)8f
    Ino80 (YGL150C) snf2 homolog3At3g57300, At3g12810, At5g66750b
    Nhp10 (YDL002C)7At4g23800, At4g11080, At1g20693, At3g51880, At1g20696, At3g28730, At5g23420b
    Rvb1 (YDR190C)1At5g22330c
    Rvb2 (YPL235W)2At5g67630, At3g49830c
    Taf14 (YPL129W)2At2g18000, At5g45600c
    Ies1 (YFL013C), Ies3 (YLR052W)N.D.e
  • a Systematic yeast gene name (dp.yeastgenome.org).

  • b The Plant Chromatin Database (www.chromdb.org) and cThe Arabidopsis Information Resource were searched for various protein homologs of the yeast proteins. The phylogeny of related gene sequences was examined to make an estimate of the number of hits in the databases with scores equal to or less than (more significant than) E = 0.001 (the expectation of finding two sequences with a given amount of similarity by chance). An E value of 0.001 is considered statistically significant in large databases (Gerstein, 1998; Pearson, 2000).

  • d Arabidopsis has no unambiguous homolog of yeast ARP7, but the orphaned plant ARP7 could be its immediate ortholog (Kandasamy et al., 2005b). In animals, ARP4 homologs have been found in most SWI/SNF complexes and the same could be true in plants.

  • e None detected based on a homology score of less than 0.001.

  • f The Arabidopsis genome encodes eight isovariants of conventional actin that were not included in calculations of isoform diversity.