Identification of cis‐elements regulating the expression of an Arabidopsis histone H4 gene

Abstract

Protein-DNA interactions in the proximal region of an Arabidopsis H4 histone gene promoter were analyzed by DMS in vivo footprinting combined with LMPCR amplification. Interactions were identified over six particular sequence motifs, five of which were previously shown to bind proteins in maize histone H3 and H4 promoters and are commonly found in the corresponding regions of other plant histone gene promoters. These motifs are located within a 126 bp fragment which was previously shown to confer preferential expression in meristems of transgenic plants. The contribution of each cis-element to the overall expression level and specificity was investigated by testing individual or combined mutations in transgenic Arabidopsis plants. All five motifs behaved as positive cis-elements of unequal strength. The GCCAAT-like sequence GCCACT behaved as a strong positive cis-element but had no influence on the specificity. In contrast, the nonamer AGATCGACG and to a lesser extent the closely linked hexamer CCGTCG proved to be essential for meristem-specific expression. Involvement of the highly conserved histone-specific octamer CGCGGATC in specific expression was revealed at some stages of meristem development. Importance of these three cis-elements, nonamer, hexamer, and octamer, was further confirmed by the fact that combining mutations of two of them either abolished the promoter activity or completely modified the promoter specificity. Mutation of the fifth cis-element, a degenerate copy of the octamer, little perturbed the promoter function. However disruption of both octamers had a dramatic negative effect, thus suggesting that the two copies cooperate to achieve maximal function in the wild-type promoter, possibly by mobilizing the proliferation-specific factors binding to the nonamer and CCGTCG cis-elements.

Cell Cycle-regulated Gene Expression inArabidopsis

“…Known Cell Cycle-regulated Genes-Although rather few genes are known to be cell cycle-regulated in Arabidopsis, there is direct evidence for regulation of histones (53,59), mitotic cyclins (19, 60 -63), and B-type CDKs (20,22), proliferating cell nuclear antigen, and the CDC6 protein involved in initiation of DNA replication (16,64). We examined the extent to which two classes of likely co-regulated genes were identified as cell cycleregulated and whether known co-regulated genes were assigned to the same or similar clusters.…”

“…Phosphorylation of Rb in late G 1 results in activation of E2F-regulated genes including ribonucleotide reductase (100) and CDC6 (16,64). Expression of mitotic cyclins has been shown to depend on specific elements conferring mitotic-specific activation in tobacco and Arabidopsis (61), whereas histone gene expression depends on octamer (Oct) and hexamer (Hex) elements (59). We searched the regions 1 kb upstream of each open reading frame within the regulated gene set for the E2F (TTTYYC-GYY), mitotic-specific activation (YCYAACGGYY), Oct (CGCGGATC), and Hex (CCACGTCA) consensus sequences.…”

ArabidopsisPEROXIN11c-e, FISSION1b, and DYNAMIN-RELATED PROTEIN3A Cooperate in Cell Cycle–Associated Replication of Peroxisomes

“…HISTONE H4 expression, which is expressed predominately during S-phase (Chaubet et al, 1996), peaked sharply at 4 h and then remained relatively low throughout the remainder of the time course ( Figure 8A). FIS1a, FIS1b, DRP3A, PEX11c, PEX11d, and PEX11e ( Figures 8B and 8D) exhibited similar expression profiles at earlier time points with peak expression levels apparent at 2 and 12 h after amphidicolin release.…”

The regulatory code for transcriptional response diversity and its relation to genome structural properties in Arabidopsis thaliana

“…Consistent with increased intergenic upstream distances for multistimuli response genes, TATA box-containing genes were also observed to have longer upstream regions (2,370 nucleotides versus 1,737 nucleotides for TATA-less genes, p ¼ 3.4EÀ34). Motifs reported to control housekeeping genes (TELO-box promoter motif [18]; hexamer promoter motif [19]) or implicated to confer tissue-specific expression (LEAFYATAG [20]) were found to be more associated with genes with narrow range of differential expression response, i.e., their expression is constitutive or their differential expression response is very specific.…”