The Populus ARBORKNOX1 homeodomain transcription factor regulates woody growth through binding to evolutionarily conserved target genes of diverse function.
The class I KNOX homeodomain transcription factor ARBORKNOX1 (ARK1) is a key regulator of vascular cambium maintenance and cell differentiation in Populus. Currently, basic information is lacking concerning the distribution, functional characteristics, and evolution of ARK1 binding in the Populus genome. Here, we used chromatin immunoprecipitation sequencing (ChIP-seq) technology to identify ARK1 binding loci genome-wide in Populus. Computational analyses evaluated the distribution of ARK1 binding loci, the function of genes associated with bound loci, the effect of ARK1 binding on transcript levels, and evolutionary conservation of ARK1 binding loci. ARK1 binds to thousands of loci which are highly enriched proximal to the transcriptional start sites of genes of diverse functions. ARK1 target genes are significantly enriched in paralogs derived from the whole-genome salicoid duplication event. Both ARK1 and a maize (Zea mays) homolog, KNOTTED1, preferentially target evolutionarily conserved genes. However, only a small portion of ARK1 target genes are significantly differentially expressed in an ARK1 over-expression mutant. This study describes the functional characteristics and evolution of DNA binding by a transcription factor in an undomesticated tree, revealing complexities similar to those shown for transcription factors in model animal species.
Pacific Southwest Research Station, USDA Forest Service, Davis, CA, 95618, USA.
Lijun
L
Liu
Matthew
M
Zinkgraf
H Earl
HE
Petzold
Eric P
EP
Beers
Vladimir
V
Filkov
Andrew
A
Groover
D000595:Amino Acid Sequence; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D055106:Genome-Wide Association Study; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D032107:Populus / Q000235:genetics / Q000254:growth & development*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014934:Wood / Q000235:genetics / Q000254:growth & development; D003313:Zea mays / Q000235:genetics / Q000378:metabolism
D018398:Homeodomain Proteins; D010940:Plant Proteins; D014157:Transcription Factors
Populus; chromatin immunoprecipitation sequencing (ChIP-seq); forest tree; transcriptional regulation; wood formation