Structure of the chromosomal copy of yeast autonomously replicating sequence 1

Lohr, D.; Torchia, T

doi:10.1021/bi00411a011

Cited by 40 publications

(20 citation statements)

References 30 publications

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“…However, in the assays presented here, plasmid and genomic copies of the HSP26 gene appear to be identical in chromatin structure, consistent with other studies which compared plasmid and genomic chromatin (Bloom and Carbon, 1982;Perez-Ortin et al, 1987). In the case of the yeast TRPI gene, differences in chromatin structure between plasmid (Thoma et al, 1984) and genomic (Lohr and Torchia, 1988) Axel, 1975;Giri and Gorovsky, 1980;Bloom and Anderson, 1982;Benezra et al, 1986;DeBernardin et al, 1986;Richard-Foy and Hager, 1987;Studitsky et al, 1988;Ip et al, 1989). In other cases, however, transcribed genes have been found to undergo loss of nucleosomes or alterations in chromatin structure interpreted as an unfolding or disruption of normal chromatin structure (reviewed in Pederson et al, 1986a;Yaniv and Cereghini, 1986;Bjorkroth et al, 1988;Conconi et al, 1989).…”

Section: Introductionsupporting

confidence: 90%

Effect of transcription of yeast chromatin on DNA topology in vivo.

Pederson

Morse

1990

The EMBO Journal

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Section: Introductionsupporting

confidence: 90%

Effect of transcription of yeast chromatin on DNA topology in vivo.

Pederson

Morse

1990

The EMBO Journal

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“…For the cell cycle analysis, we used an EcoRI-RsaI fragment (Fig. 1, probe 2 (38). Deproteinized DNA also contained DNase I HS sites, but the locations of most of these sites were different from those observed in chromatin (Fig.…”

Section: Resultsmentioning

confidence: 99%

The chromatin structure of Saccharomyces cerevisiae autonomously replicating sequences changes during the cell division cycle.

1991

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The chromatin structures of two well-characterized autonomously replicating sequence (ARS) elements were examined at their chromosomal sites during the cell division cycle in Saccharomyces cerevisiae. The H4 ARS is located near one of the duplicate nonallelic histone H4 genes, while ARSI is present near the TRP1 gene. Cells blocked in G, either by a-factor arrest or by nitrogen starvation had two DNase I-hypersensitive sites of about equal intensity in the ARS element. This pattern of DNase I-hypersensitive sites was altered in synchronous cultures allowed to proceed into S phase. In addition to a general increase in DNase I sensitivity around the core consensus sequence, the DNase I-hypersensitive site closest to the core consensus became more nuclease sensitive than the distal site. This change in chromatin structure was restricted to the ARS region and depended on replication since cdc7 cells blocked near the time of replication initiation did not undergo the transition. Subsequent release of arrested cdc7 cells restored entry into S phase and was accompanied by the characteristic change in ARS chromatin structure.Autonomously replicating sequence (ARS) elements of the yeast Saccharomyces cerevisiae were first identified by their ability to enable plasmids to replicate as independent episomal minichromosomes (26,64,65). Considerable evidence has accumulated to suggest that ARS elements are origins of DNA replication (reviewed in references 42 and 71). For example, the replication of ARS plasmids take places only during S phase, is under the same genetic control as chromosomal replication, and occurs only once per division cycle (16,77,78). Electron microscopy of the 2 ,Lm plasmid (43) and the ribosomal DNA locus (50) showed that at least some of the mapped replication bubbles were coincident with known ARS elements. Recently, in vivo replication origins have been localized by two-dimensional gel mapping techniques to the 2,um plasmid ARS (6, 27), ARSI on a plasmid (6), the chromosomal ribosomal DNA ARS (35), an ARS on chromosome III called A6C (28), and ARSI on the chromosome (18).A detailed molecular examination of at least five different ARS elements has led to a consistent picture of the DNA sequence requirements for function (3,5,7,9,32,33,45,62). The ARS element is a bipartite structure composed of an 11-bp core consensus sequence and a 3' flanking domain of approximately 60 bp. Distal sequences are not required for replication activity, although they may influence efficiency depending on the particular ARS. The core consensus was first detected by comparative sequence analysis (7, 63), and its importance has since been rigorously demonstrated by point mutations, deletions, and linker-scanning mutations. The requirement for a 3' flanking domain has been established by deletion analysis; however, unlike the core consensus, the 3' flanking domain does not depend on an absolute primary DNA sequence (3,45 Chromatin structure may play an important role in the function of replication origins. Several origins h...

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“…Replication origins in yeast (35,36) (20,38). Two DNA-nicking reagents were used, DNase I (which can be utilized only with isolated nuclei) and DMS (a small molecule that can be used with intact cells).…”

Section: Methodsmentioning

confidence: 99%

In vivo protein-DNA interactions at human DNA replication origin.

Dimitrova

Giacca

Demarchi

et al. 1996

Proc. Natl. Acad. Sci. U.S.A.

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Protein-DNA interactions were studied in vivo at the region containing a human DNA replication origin, located at the 3' end of the lamin B2 gene and partially overlapping the promoter of another gene, located downstream. DNase I treatment of nuclei isolated from both exponentially growing and nonproliferating HL-60 cells showed that this region has an altered, highly accessible, chromatin structure. High-resolution analysis of protein-DNA interactions in a 600-bp area encompassing the origin was carried out by the in vivo footprinting technique based on the ligation-mediated polymerase chain reaction. In growing HL-60 cells, footprints at sequences homologous to binding sites for known transcription factors (members of the basichelix-loop-helix family, nuclear respiratory factor 1, transcription factor Spl, and upstream binding factor) were detected in the region corresponding to the promoter of the downstream gene. Upon conversion of cells to a nonproliferative state, a reduction in the intensity of these footprints was observed that paralleled the diminished transcriptional activity of the genomic area. In addition to these protections, in close correspondence to the replication initiation site, a prominent footprint was detected that extended over 70 nucleotides on one strand only. This footprint was absent from nonproliferating HL-60 cells, indicating that this specific protein-DNA interaction might be involved in the process of origin activation. ceding another still uncharacterized gene, provisionally named ppvl (13-15). The same origin, originally identified in HL-60 cells, was found to be active also in several other human cell types, including activated peripheral lymphocytes (S. Kumar, M.G., G.B., S.R., and A.F., unpublished results). A map of the 13.7-kb genomic fragment containing the replication origin is shown in Fig. 1A.The finding that the lamin B2 ori is located in a highly transcribed region is not surprising, since numerous reports have implicated transcriptional regulatory elements in the control of DNA replication (16)(17)(18)(19). Moreover, the domain is replicated at the very beginning of the S phase (12), consistent with the well-documented correlation between transcriptionally active genomic regions and early replication.We have now addressed the study of the specific protein-DNA interactions at the lamin B2 ori. To this purpose, we have exploited the in vivo footprinting technique based on the ligation-mediated polymerase chain reaction (LMPCR) (20).In the past few years we have extensively utilized this technique (21), which, in comparison with in vitro binding studies, is particularly suitable for the detection of the protein-DNA interactions actually occurring in the nucleus, since it is sensitive to the accessibility of sites to protein factors and possible epigenetic modification of DNA such as methylation. Furthermore, we have taken advantage of the property of HL-60 myeloid cells to undergo terminal differentiation upon chemical stimulation (22), a process which is accom...

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Structure of the chromosomal copy of yeast autonomously replicating sequence 1

Cited by 40 publications

References 30 publications

Effect of transcription of yeast chromatin on DNA topology in vivo.

Effect of transcription of yeast chromatin on DNA topology in vivo.

The chromatin structure of Saccharomyces cerevisiae autonomously replicating sequences changes during the cell division cycle.

In vivo protein-DNA interactions at human DNA replication origin.

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