Architecture of a plant promoter: S1 nuclease hypersensitive features of maize Adh1

Genome-wide characterization of single-stranded DNA in rice

Single-stranded DNA (ssDNA) is essential for various DNA-templated processes in both eukaryotes and prokaryotes. However, comprehensive characterizations of ssDNA still lag in plants compared to nonplant systems. Here, we conducted in situ S1-sequencing, with starting gDNA ranging from 5 µg to 250 ng, followed by comprehensive characterizations of ssDNA in rice (Oryza sativa L.). We found that ssDNA loci were substantially associated with a subset of non-B DNA structures and functional genomic loci. Subtypes of ssDNA loci had distinct epigenetic features. Importantly, ssDNA may act alone or partly coordinate with non-B DNA structures, functional genomic loci, or epigenetic marks to actively or repressively modulate gene transcription, which is genomic region dependent and associated with the distinct accumulation of RNA Pol II. Moreover, distinct types of ssDNA had differential impacts on the activities and evolution of transposable elements (TEs) (especially common or conserved TEs) in the rice genome. Our study showcases an antibody-independent technique for characterizing non-B DNA structures or functional genomic loci in plants. It lays the groundwork and fills a crucial gap for further exploration of ssDNA, non-B DNA structures, or functional genomic loci, thereby advancing our understanding of their biology in plants.

Conserved noncoding sequences in the grasses

As orthologous genes from related species diverge over time, some sequences are conserved in noncoding regions. In mammals, large phylogenetic footprints, or conserved noncoding sequences (CNSs), are known to be common features of genes. Here we present the first large-scale analysis of plant genes for CNSs. We used maize and rice, maximally diverged members of the grass family of monocots. Using a local sequence alignment set to deliver only significant alignments, we found one or more CNSs in the noncoding regions of the majority of genes studied. Grass genes have dramatically fewer and much smaller CNSs than mammalian genes. Twenty-seven percent of grass gene comparisons revealed no CNSs. Genes functioning in upstream regulatory roles, such as transcription factors, are greatly enriched for CNSs relative to genes encoding enzymes or structural proteins. Further, we show that a CNS cluster in an intron of the knotted1 homeobox gene serves as a site of negative regulation. We showthat CNSs in the adh1 gene do not correlate with known cis-acting sites. 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.

Homopurine/homopyrimidine sequences as potential regulatory elements in eukaryotic cells

1. Homopurine/homopyrimidine (PuPy) repetitive duplex sequences can form intramolecular triplexes (H-DNA) or intermolecular triplexes with a third strand in a sequence-specific manner. 2. Such sequences are present in natural genomes within 5'- and 3'-flanking sequences and coding regions of genes. Triplex DNA structures have been detected in vitro and in vivo and have been immunolocalized to chromosomes by triplex-specific monoclonal antibody approaches. 3. Intermolecular triplex formation represses gene expression at the transcriptional level and is also useful in genomic mapping, gene cloning, sequence-specific drug delivery, and selective modulation of gene expression.

Isolation of matrices from maize leaf nuclei: identification of a matrix-binding site adjacent to the Adh1 gene

Nuclear matrices were isolated from maize leaves by the two conventional methods usually employed for the preparation of the corresponding structures of animal origin. It is demonstrated that functionally competent matrices, recognizing and specifically binding the MAR-containing DNA of the mouse kappa-immunoglobulin gene may be prepared by both 2 M NaCl and LIS extractions of maize nuclei. A DNA region with a high affinity for the nuclear matrix was identified at the 5' end of the maize Adh1-S gene, distal to the promoter region. The presence of sites of reported altered chromatin structure in this particular region is discussed. While the proximity and the cohabitation of MARs with different regulatory elements is a common feature of matrix association regions in animal systems, this is the first plant MAR identified in a region of known significance for gene regulation.

Osmium tetroxide footprinting of a scaffold attachment region in the maize Adh1 promoter

Osmium tetroxide (OsO4) reacts with the thymine residues of double-stranded DNA, but thymines that are unpaired or under torsional stress are hyperreactive. Although OsO4 hyperreactivity has been primarily utilized to identify Z-DNA structures in supercoiled plasmids, OsO4 will also identify other torsional perturbations of DNA. In this study, OsO4 was used to footprint an AT-rich region (between -780 and -500) of the maize Adh1 promoter. Hyperreactive sites were identified both in vitro and in vivo in an area that coincides with AT motifs similar to those found in scaffold attachment regions. Further, the region of OsO4 hyperreactivity lies within a fragment of DNA that is associated with the nuclear scaffold in histone-depleted nuclei.

DNase I hypersensitive sites in the 5'-region of the maize Shrunken gene in nuclei from different organs

The chromatin structure of the 5'-upstream region of the Shrunken (Sh) gene in Zea mays has been examined. We have identified a region of DNase I hypersensitivity extending at least from the 3'-end of exon 1 for 2 kb into the 5'-flanking region. This region is composed of a set of closely spaced hypersensitive sites separated by small regions that are less accessible to DNase I. The most sensitive sites are located within 300 bp upstream of the transcription start site. Hypersensitive sites are found essentially at the same positions in kernels, roots and leaves, although the latter display different relative intensities. No changes are found in roots within the tested region upon anaerobic induction. Testing protein-free plasmid DNA containing the 5' upstream region of the Sh gene, we found a site sensitive to the single strand specific nuclease S1 located very close to a DNase I hypersensitive site identified in chromatin. Several hypersensitive sites are flanking in vitro binding sites of nuclear proteins as determined by Werr et al. (1988; accompanying paper).