Genome-Wide Characterization of the HD-ZIP IV Transcription Factor Family in Maize: Preferential Expression in the Epidermis    

Abstract

Transcription factors of the plant-specific homeodomain leucine zipper IV (HD-ZIP IV) family have been found from moss to higher plants, and several family members have been associated with epidermis-related expression and/or function. In maize (Zea mays), four of the five characterized HD-ZIP IV family members are expressed specifically in the epidermis, one contributes to trichome development, and target genes of another one are involved in cuticle biosynthesis. Assessing the phylogeny, synteny, gene structure, expression, and regulation of the entire family in maize, 12 novel ZmHDZIV genes were identified in the recently sequenced maize genome. Among the 17 genes, eight form homeologous pairs duplicated after the split of maize and sorghum (Sorghum bicolor), whereas a fifth duplication is shared with sorghum. All 17 ZmHDZIV genes appear to be derived from a basic module containing seven introns in the coding region. With one possible exception, all 17 ZmHDZIV genes are expressed and show preferential expression in immature reproductive organs. Fourteen of 15 ZmHDZIV genes with detectable expression in laser-dissected tissues exhibit a moderate to very strong expression preference for the epidermis, suggesting that at least in maize, the majority of HD-ZIP IV family members may have epidermis-related functions. Thirteen ZmHDZIV genes carry conserved motifs of 19 and 21 nucleotides in their 3′ untranslated region. The strong evolutionary conservation and the size of the conserved motifs in the 3′ untranslated region suggest that the expression of HD-ZIP IV genes may be regulated by small RNAs.

Nascent Transcription Affected by RNA Polymerase IV inZea mays

“…The candidate showing the second greatest increased transcription is ocl2 ( Figure 4C), a member of the plant-specific homeodomain leucine zipper IV (HD-ZIP IV) family of transcription factors predicted to have leaf epidermisrelated functions in maize (Javelle et al 2011). Mature rpd1-2 mutant plants often exhibit problems maintaining proper leaf polarity (adaxialized leaf sectors) (Parkinson et al 2007).…”

“…Mature rpd1-2 mutant plants often exhibit problems maintaining proper leaf polarity (adaxialized leaf sectors) (Parkinson et al 2007). Interestingly, ocl2 is not normally expressed in epidermal or mesophyll cells (Javelle et al 2011), which comprise the majority of cells used for GRO-seq library generation, indicating that this gene is transcribed outside its normal expression domain in rpd1 mutants.Genome browser visualization of GRO-seq reads uniquely mapping to the genomic region containing ocl2 ( Figure 4C) highlights coincident transcription profiles of a proximate TE and this RPD1-regulated gene. A fragment of an LTR retrotransposon of the Gypsy class (RLG) assigned to the ubid family located 1.3 kb upstream of the ocl2 gene is also transcribed in rpd1 mutants, but in antisense orientation with respect to the ocl2-coding region ( Figure 4C).…”

Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica)

“…In Arabidopsis, HD-ZIP IV constitutes a large subfamily of genes that is composed of 16 members: GLABRA2 (GL2)/ATHB10, ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1), ANTHOCYANINLESS2 (ANL2), PROTODERMAL FACTOR2 (PDF2), HOME-ODOMAIN GLABROUS 1-5 (HDG1-5), HDG6/FWA, and HDG7-12 (Nakamura et al, 2006). Genetic analysis shows that HD-ZIP IV proteins function in epidermal processes, trichome formation, root development, and anthocyanin accumulation (Javelle et al, 2011).…”

Arabidopsishomeodomain-leucine zipper IV proteins promote stomatal development and ectopically induce stomata beyond the epidermis

“…In Arabidopsis, two closely related genes, A. thaliana MERISTEM LAYER1 (AtML1) and PROTODERMAL FACTOR2 (PDF2), redundantly specify epidermal identity; their double loss of function results in an embryo that is lethally devoid of a protoderm (Abe et al, 2003). AtML1 and PDF2 belong to a family of plant-specific homeodomain leucine zipper class IV (HD-ZIP IV) transcription factors (Mukherjee et al, 2009), many showing preferential expression in the epidermis (Ingram et al, 2000;Javelle et al, 2011a;Nakamura et al, 2006). The Arabidopsis genome contains 16 HD-ZIP IV (AtHD-ZIP IV) genes, of which at least nine exhibit expression in leaf epidermal cells (Nakamura et al, 2006;supplementary material Fig.…”