DNase-sensitive chromatin structure near a chromosomal origin of bidirectional replication of the avian alpha-globin locus

Specific signals at the 3' end of the DHFR gene define one boundary of the downstream origin of replication

The Chinese hamster dihydrofolate reductase (DHFR) origin of replication consists of a 55-kb zone of potential initiation sites lying between the convergently transcribed DHFR and 2BE2121 genes. Two subregions within this zone (ori-beta/ori-beta' and ori-gamma) are preferred. In the DHFR-deficient variant, DR8, which has deleted a 14-kb sequence straddling the 3' end of the DHFR gene, early-firing origin activity in the downstream ori-beta/ori-beta' and ori-gamma regions is completely suppressed. We show that the critical deleted sequences reside within a 168-bp segment encompassing the intron 5/exon 6 boundary, exon 6, 54 bp of the 3' untranslated region (UTR), but not the three natural polyA sites. In wild-type cells, this sequence efficiently arrests transcription in a region a few kilobases downstream, which coincides with the 5' boundary of the replication initiation zone. In DR8, DHFR-specific transcripts efficiently use an alternative sixth exon (6c) and polyA signals near the middle of the former intergenic region to process primary transcripts. However, transcription proceeds to a position almost 35 kb downstream from these signals, and replication initiation can only be detected beyond this point. When the wild-type 168-bp 3' element is inserted into DR8 at the same position as alternative exon 6c, transcription is arrested efficiently and initiations occur almost immediately downstream. Thus, the normal 3' end of the DHFR gene constitutes a boundary element not only for the gene but also for the local origin of replication.

Analysis of the chicken DNA fragments that contain structural sites of attachment to the nuclear matrix: DNA-matrix interactions and replication

Ten short DNA fragments have been selected from a library of the nuclear matrix-attached DNA (nmDNA) from chicken erythrocytes by their ability to hybridize with the fraction of chicken replication origins isolated by nascent DNA strand extrusion. The primary structure of these fragments has been determined. Five of the sequences contained a topoisomerase II recognition site. Most of the studied DNA fragments also have a common eight-nucleotide motif, GCAGACCG/A. A sequence-specific DNA-binding protein with a MW of 55 kDa that interacted with this motif has been identified. Some of the cloned DNA fragments promoted an increased level of transient plasmid replication in transfected chicken cells. The ability of plasmid bearing nmDNA fragments to replicate correlated directly with their ability to target plasmids to the nuclear matrix compartment.

Mapping of replication initiation sites in the mouse ribosomal gene cluster

We have used nascent strand determination analysis to map start sites of DNA replication in the mouse ribosomal gene cluster in which individual copies of the ribosomal genes are separated by intergenic spacer regions. One origin of bidirectional replication (OBR) was localized within a 3 kb region centered about 1.6 kb upstream of the rDNA transcription start site. At least one additional initiation site is situated near the 3' end of the transcription unit. Adjacent to the OBR at the transcription start site are located two amplification-promoting sequences, i.e., APS1 and APS2. Nuclease-hypersensitive sites were identified in both of the two APSs as well as in the OBR region, thus indicating that these sequences have an altered chromatin structure. In the OBR an intrinsically bent region, a purine-rich element and other prospective initiation zone components are found.

Mapping of replication initiation sites in human ribosomal DNA by nascent-strand abundance analysis

New techniques for mapping mammalian DNA replication origins are needed. We have modified the existing nascent-strand size analysis technique (L. Vassilev and E.M. Johnson, Nucleic Acids Res. 17:7693-7705, 1989) to provide an independent means of studying replication initiation sites. We call the new method nascent-strand abundance analysis. We confirmed the validity of this method with replicating simian virus 40 DNA as a model. We then applied nascent-strand abundance and nascent-strand size analyses to mapping of initiation sites in human (HeLa) ribosomal DNA (rDNA), a region previously examined exclusively by two-dimensional gel electrophoresis methods (R.D. Little, T.H.K. Platt, and C.L. Schildkraut, Mol. Cell. Biol. 13:6600-6613, 1993). Our results partly confirm those obtained by two-dimensional gel electrophoresis techniques. Both studies suggest that replication initiates at relatively high frequency a few kilobase pairs upstream of the transcribed region and that many additional low-frequency initiation sites are distributed through most of the remainder of the ribosomal DNA repeat unit.

Developmental alteration of the chromatin state at promoter/replication origin region of the aldolase B locus precedes transcriptional activation in the liver

Liver-specific expression of the rat aldolase B (AldB) gene is conferred by proximal promoter region (-200 bp to + 1 bp), which is centered on an origin region of DNA replication. Transcriptional activation of the gene in the liver occurs during the late one-third of fetal stage. To know the mechanism involved in such activation, we studied developmental changes in chromatin structure and in the extent of CpG methylation in the promoter/origin region of the gene. At an early fetal stage, when the AldB gene in the liver is not yet activated, the gene chromatin had two DNase 1-hypersensitive sites in the promoter region. One corresponded to that typical of AldB-expressing cells in the adult. The other, located approximately 200 bp upstream of the above site, disappeared as the activation of transcription started. A CpG dinucleotide in the promoter/origin region was heavily methylated at an early stage of gestation, but progressively demethylated as the liver develops. This CpG site is located at the center of an important binding site for a transcription factor. These changes occurred early in the fetal stage, prior to the gene activation, and were thus thought to be associated with differentiation of the liver cell or with cessation of cell proliferation.

Nuclear matrix-associated DNA fragments enhance autonomous replication of plasmids in chicken cells

Most cells of higher eukaryotes may maintain several rounds of replication of circular DNA. Efficiency of replication is usually low, and depends on the length of the circular DNA rather than on the sequence context. We have isolated and characterized several short DNA fragments that form structural sites of attachment to the nuclear matrix (nmDNA) in chicken cells, and tested whether they would enhance autonomous replication of DNA in chicken cells as compared to the vector DNA. Indeed, a several-fold increase in a short-term replication efficiency was detected using a semi-conservative replication and a DpnI-resistance assay. Most of the cloned matrix-associated fragments were recovered in the nuclear matrix fraction when introduced into cultured chicken cells as a circular DNA. The data obtained suggest that the observed enhancement in the replication efficiency of the circular DNA may be due to their recruitment to the nuclear matrix by the nmDNA.