Mcm1 Binds Replication Origins

Chang, Victor; Fitch, Michael J.; Donato, Justin J.; Christensen, Tim W.; Merchant, Ankit Margaret; Tye, Bik Kwoon

doi:10.1074/jbc.m209827200

Cited by 29 publications

(32 citation statements)

References 59 publications

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“…It is known that replication initiation requires binding of Mcm3, Mcm4, Mcm7, and Orc1 at origins of replication across the yeast genome during G 1 (14,15) and that these replication initiation proteins are involved with transcriptional silencing at the yeast mating loci (16,17). It was suggested recently that the transcription factor Mcm1 also binds origins of replication (18). Either one of at least two mechanisms of regulation may be underlying this novel genome-scale correlation between DNA replication initiation and RNA transcription during the yeast cell cycle: The transcription of genes may reduce the binding efficiency of adjacent origins, or the binding of replication initiation proteins to origins of replication may repress, or even shut down, the transcription of adjacent genes.…”

Section: Discussionmentioning

confidence: 99%

Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription

Alter

Golub

2004

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

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We describe an integrative data-driven mathematical framework that formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the ''basis'' set. By using pseudoinverse projection, the molecular biological profiles of the data samples are least-squares-approximated as superpositions of the basis profiles. Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis and gives a global picture of the correlations and possibly also causal coordination of these two sets of states. We illustrate this framework with an integration of yeast genome-scale proteins' DNA-binding data with cell cycle mRNA expression time course data. Novel correlation between DNA replication initiation and RNA transcription during the yeast cell cycle, which might be due to a previously unknown mechanism of regulation, is predicted. singular value decomposition ͉ generalized singular value decomposition ͉ DNA microarrays ͉ yeast Saccharomyces cerevisiae cell cycle R ecent advances in high-throughput technologies enable monitoring molecular biological signals, e.g., mRNA expression levels and proteins' DNA-binding occupancy levels, that correspond to activities of cellular systems, e.g., DNA replication, RNA transcription, and proteins' DNA-binding on a genomic scale. Integrative analysis of these global signals promises to give new insights into cellular mechanisms of regulation, i.e., global causal coordination of cellular activities. Integrative analysis of different types of large-scale molecular biological data requires mathematical tools that are able to formulate any number of large-scale data sets in terms of a common frame of reference, while reducing the complexity of the data to make them comprehensible (1, 2). These tools should provide data-driven models or mathematical frameworks for the description of the data, where the variables, i.e., the patterns that they uncover in the data, and operations, i.e., data reconstruction and classification in subspaces spanned by these patterns, may represent some biological reality.Recently we showed that singular value decomposition (SVD) (3, 4) and generalized SVD (GSVD) (5) provide such data-driven frameworks for genome-scale molecular biological data. For example, the variables of SVD, ''eigengenes'' and corresponding ''eigenarrays,'' in the analyses of yeast Saccharomyces cerevisiae cell cycle time course mRNA expression data (6), and those of GSVD, ''genelets'' and corresponding ''arraylets,'' in the comparative analysis of yeast and human (7) cell cycle time course mRNA expression data, were shown to correlate with observed genome-scale effects of known cell cycle regulators and...

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Section: Discussionmentioning

confidence: 99%

Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription

Alter

Golub

2004

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

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“…SRF can mediate regenerating epithelium in an in vivo model of gastric ulceration (14), and anti-sense SRF impedes angiogenesis in the same model (15). In yeast, mutation of the minichromosome maintenance 1 (Mcm1) gene results in defective DNA replication, and there is evidence for Mcm1 binding to bonafide origins of replication in the yeast genome (18). In contrast to the above instances, much in vivo genetic evidence exists for SRF playing a critical role in processes unrelated to cell replication.…”

Section: Serum Response Factor: Toggle Switch For Disparate Programs mentioning

confidence: 99%

Serum response factor: master regulator of the actin cytoskeleton and contractile apparatus

Miano¹,

Long²,

Fujiwara³

2007

American Journal of Physiology-Cell Physiology

425

456

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“…Three elements, known as B1, B2, and B3, have been identified (44). B1 is protected by the ORC (55), whereas B3 is protected by Abf1 (41) or Mcm1 (17) in in vitro footprinting analyses. Initiation of DNA synthesis at ARS1 has been mapped to a region between the B1 and B2 elements (6).…”

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confidence: 99%

“…By itself, Mcm1 binds to the degenerate sequence CCYWWWWNGN (17,50,58,68). Like other MADS domain transcription factors (8), Mcm1 is a master regulator that specifies cell identity (33,34,51) and coordinates the expression of genes required for cell growth and proliferation (57).…”

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Mcm1 Promotes Replication Initiation by Binding Specific Elements at Replication Origins

Chang

Donato

Chan

et al. 2004

Molecular and Cellular Biology

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Replication of DNA must be inherently accurate and precisely regulated. It is therefore not surprising that the mechanism for the initiation of DNA replication is both complex and conserved. Initiation of DNA synthesis involves the assembly of a multicomponent complex at designated sites known as replication origins. While the protein components of the prereplication complex (pre-RC) used in this initiation process are conserved in all eukaryotes (5), there is little in common between the nucleotide sequences of replication origins within each eukaryote and between different eukaryotes (29).In Saccharomyces cerevisiae, replication origins (ORI) consist of defined sequences of about 200 bp that can replicate autonomously independently of their native chromosomal environment. These autonomously replicating sequences (ARSs) are modular in structure. They contain a ubiquitous 11-bp (5Ј-WTTTAYRTTTW) ARS consensus sequence (ACS) (11,22,63) where the origin recognition complex (ORC) binds (4). In certain ARSs, a 10-of-11 match of the ACS is sufficient for ORC recognition (64). The ACS is essential but not sufficient for autonomous replication. cis elements on the 5Ј (C domain) or the 3Ј (B domain) flanking sequences of the ACS are also required (12). Elements in the B domain of one particular ARS, ARS1, have been characterized in great detail. Three elements, known as B1, B2, and B3, have been identified (44). B1 is protected by the ORC (55), whereas B3 is protected by Abf1 (41) or Mcm1 (17) in in vitro footprinting analyses. Initiation of DNA synthesis at ARS1 has been mapped to a region between the B1 and B2 elements (6). Two of the three B elements in combination with the ACS are sufficient to promote autonomous replication. Although B elements of different ARSs are not conserved in nucleotide sequence, they are interchangeable between certain ARSs (31, 54, 61). The differences in size and modular composition of replication origins suggest that there are many ways to assemble a functional replication origin from a finite set of modules (60)(61)(62)65). The plasticity in the organization of replication origins is further illustrated by the dispensability of the B elements altogether in the presence of the C domain in several telomeric ARSs (13). However, because the C domain is generally larger, elements in the C domain have not been characterized.The redundant functions of the B and C domains in promoting replication initiation suggest that although the process of pre-RC assembly may be conserved, there are many ways to create an environment conducive to this assembly process. The concept of alternative pathways for creating an environment for pre-RC assembly is especially appealing in higher eukaryotes, where there appears not to be a unifying mechanism for site selection for pre-RC assembly. In Xenopus oocytes, replication initiation occurs at random sequences (38). In mammalian cells, initiation occurs at multiple sites within replication zones that are defined by their chromosomal contexts rather than nucleotide...

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Mcm1 Binds Replication Origins

Cited by 29 publications

References 59 publications

Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription

Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription

Serum response factor: master regulator of the actin cytoskeleton and contractile apparatus

Mcm1 Promotes Replication Initiation by Binding Specific Elements at Replication Origins

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