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Pulakhmani: /* Origin of Replication in Eukaryotes */

2011-01-18T08:42:09Z

‎Origin of Replication in Eukaryotes

Pulakhmani at 08:41, 18 January 2011

2011-01-18T08:41:06Z

Pulakhmani at 08:38, 18 January 2011

2011-01-18T08:38:59Z

Pulakhmani at 08:17, 18 January 2011

2011-01-18T08:17:18Z

Pulakhmani at 08:14, 18 January 2011

2011-01-18T08:14:28Z

Pulakhmani at 08:09, 18 January 2011

2011-01-18T08:09:08Z

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The origin of replication is a specific DNA sequence where replication begins.[[1]] In prokaryotes, DNA replication begins at a singular AT rich origin of replication. Eukaryotes, however, can have multiple.
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== Origin of Replication in Eukaryotes ==
Analysis of the budding yeast, ''Saccharomyces cerevisiae'', genome has shed a great deal of light into the mechanisms underlying Eukaryotic DNA replication. Chromosome replication is initiated when autonomously replicating sequences (ARS) are placed in a plasmids.2 These ARSs are the site of replication initiation. The number of ARSs in the S. cervisae genome has been estimated to be around 400. Each of these ARSs contains a consensus sequence of about 11bp necessary for the recruitment of various replication proteins. 3 Furthermore, single base pair mutations in the ARS consensus sequence putatively block initiation of replication. 4, 5
However, identifying the origin of replication in other Eukaryotes has proven to be far more challenging. The ''Schizosaccharomyces pombe'' genome has much larger origins of replication which are aided by other elements that partially contribute to their activity. 6,7 In metazoans, replication origins are either localized within a few kilobases, or multiple dispersed origins appear throughout initiation zones of 10 to 50 kb.3

'''Higher Order Eukaryotes'''
For many other eukaryotic systems, almost any DNA sequence appears to be capable of initiating DNA replication. In both ''Caenorhabditis elegans'' 8 and Paramecium 9, studies demonstrate that almost any cloned plasmid DNA can replicate autonomously, indicating that replication can occur within almost any size DNA sequence in these creatures. Furthermore, systematic searches in cultured animal cells for ARSs similar to those done in budding yeast did not identify specific sequences that enhance replication when reintroduced into cells i.e. a clear origin of replication was not found in other animal cells. 3 Krysan et al. (1993) demonstrated that in human cells, DNA fragments larger than 15 kb were capable of autonomous replication, indicating that autonomous replication in human cells is stimulated by simple sequences which occur fairly often in human DNA.10 Similar results were obtained in cultured ''Drosophila'' and ''Xenopus'' cells.3

'''The Pre-RC'''
Eukaryotic origins of replication direct the formation of a number of protein complexes leading to the assembly of two bidirectional DNA replication forks. Regardless of the species, the pre-replication (pre-RC) complex forms at the origin of replication during the initiation phase of DNA replication. The pre-RC in eukaryotes is composed of the origin recognition protein complex (ORC) which recruits licensing factors such as the regulatory proteins Cdc6 and Cdt1 and various minichromosme maintenance proteins.3 The ORC and these regulatory proteins are highly conserved in numerous eukaryotes from budding yeast to humans. Regardless of the origin of initiation site in both ''Xenopus'' and ''Drosophila'' extracts, initiation of replication requires the ATP-dependent DNA binding activity of the origin of replication protein complex. 3

'''RIP Mapping'''
Recently, researchers have been able to detect start sites for DNA synthesis at the nucleotide level through the use of replication initiation point (RIP) mapping. RIP mapping in yeast and human cells indicate that the following may be true: there exists a single, defined start point at which DNA replication is initiated and the ORC tends to lie immediately adjacent to the replication start point.11

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== Chromosome Number of ''Vaccinum corymbosum'' ==
The high bush blue berry (''Vaccinum corymbosum''). It is a tetraploid with 2n=48 chromosomes. 12,13. The method behind how the chromosome number was determined is not outlined in any paper.

← Older revision		Revision as of 08:42, 18 January 2011
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	'''RIP Mapping'''		'''RIP Mapping'''

−	Recently, researchers have been able to detect start sites for DNA synthesis at the nucleotide level through the use of replication initiation point (RIP) mapping. RIP mapping in yeast and human cells indicate that the following may be true: there exists a single, defined start point at which DNA replication is initiated and the ORC tends to lie immediately adjacent to the replication start point.[http://www.qb.fcen.uba.ar/biomol/2002/replicacion_eucariota_2.pdf]	+	Recently, researchers have been able to detect start sites for DNA synthesis at the nucleotide level through the use of replication initiation point (RIP) mapping. RIP mapping in yeast and human cells indicate that the following may be true: there exists a single, defined start point at which DNA replication is initiated and the ORC binding site tends to lie immediately adjacent to the replication start point.[http://www.qb.fcen.uba.ar/biomol/2002/replicacion_eucariota_2.pdf]

@@ Line 5: / Line 5: @@
 Analysis of the budding yeast, ''Saccharomyces cerevisiae'', genome has shed a great deal of light into the mechanisms underlying Eukaryotic DNA replication. Chromosome replication is initiated when autonomously replicating sequences (ARS) are placed in a plasmids.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138988/pdf/gb-2001-2-12-reports4030.pdf/?tool=pmcentrez] These ARSs are the site of replication initiation.  The number of ARSs in the S. cervisae genome has been estimated to be around 400. Each of these ARSs contains a consensus sequence of about 11bp necessary for the recruitment of various replication proteins. [http://www.ncbi.nlm.nih.gov/pubmed/11588251] Furthermore, single base pair mutations in the ARS consensus sequence putatively block initiation of replication. [http://www.ncbi.nlm.nih.gov/pubmed/1536007],[http://www.ncbi.nlm.nih.gov/pubmed/2196439]
-However, identifying the origin of replication in other Eukaryotes has proven to be far more challenging. The ''Schizosaccharomyces pombe'' genome has much larger origins of replication which are aided by other elements that partially contribute to their activity. [http://www.ncbi.nlm.nih.gov/pubmed/10966477],[http://www.ncbi.nlm.nih.gov/pubmed/10490609]  In metazoans, replication origins are either localized within a few kilobases, or multiple dispersed origins appear throughout initiation zones of 10 to 50 kb.[[3]]
+However, identifying the origin of replication in other Eukaryotes has proven to be far more challenging. The ''Schizosaccharomyces pombe'' genome has much larger origins of replication which are aided by other elements that partially contribute to their activity. [http://www.ncbi.nlm.nih.gov/pubmed/10966477],[http://www.ncbi.nlm.nih.gov/pubmed/10490609]  In metazoans, replication origins are either localized within a few kilobases, or multiple dispersed origins appear throughout initiation zones of 10 to 50 kb.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138988/pdf/gb-2001-2-12-reports4030.pdf/?tool=pmcentrez]
 '''Higher Order Eukaryotes'''
-For many other eukaryotic systems, almost any DNA sequence appears to be capable of initiating DNA replication. In both ''Caenorhabditis elegans'' [http://www.ncbi.nlm.nih.gov/pubmed/1935914] and Paramecium ,[http://www.ncbi.nlm.nih.gov/pubmed/1386793], studies demonstrate that almost any cloned plasmid DNA can replicate autonomously, indicating that replication can occur within almost any size DNA sequence in these creatures. Furthermore, systematic searches in cultured animal cells for ARSs similar to those done in budding yeast did not identify specific sequences that enhance replication when reintroduced into cells i.e. a clear origin of replication was not found in other animal cells. [[3]] Krysan et al. (1993) demonstrated that in human cells, DNA fragments larger than 15 kb were capable of autonomous replication, indicating that autonomous replication in human cells is stimulated by simple sequences which occur fairly often in human DNA.[http://www.ncbi.nlm.nih.gov/pubmed/8386315]  Similar results were obtained in cultured ''Drosophila'' and ''Xenopus'' cells.[[3]]
+For many other eukaryotic systems, almost any DNA sequence appears to be capable of initiating DNA replication. In both ''Caenorhabditis elegans'' [http://www.ncbi.nlm.nih.gov/pubmed/1935914] and Paramecium ,[http://www.ncbi.nlm.nih.gov/pubmed/1386793], studies demonstrate that almost any cloned plasmid DNA can replicate autonomously, indicating that replication can occur within almost any size DNA sequence in these creatures. Furthermore, systematic searches in cultured animal cells for ARSs similar to those done in budding yeast did not identify specific sequences that enhance replication when reintroduced into cells i.e. a clear origin of replication was not found in other animal cells. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138988/pdf/gb-2001-2-12-reports4030.pdf/?tool=pmcentrez]Krysan et al. (1993) demonstrated that in human cells, DNA fragments larger than 15 kb were capable of autonomous replication, indicating that autonomous replication in human cells is stimulated by simple sequences which occur fairly often in human DNA.[http://www.ncbi.nlm.nih.gov/pubmed/8386315]  Similar results were obtained in cultured ''Drosophila'' and ''Xenopus'' cells.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138988/pdf/gb-2001-2-12-reports4030.pdf/?tool=pmcentrez]
 '''The Pre-RC'''
-Eukaryotic origins of replication direct the formation of a number of protein complexes leading to the assembly of two bidirectional DNA replication forks. Regardless of the species, the pre-replication (pre-RC) complex forms at the origin of replication during the initiation phase of DNA replication. The pre-RC in eukaryotes is composed of the origin recognition protein complex (ORC) which recruits licensing factors such as the regulatory proteins Cdc6 and Cdt1 and various minichromosme maintenance proteins.[[3]] The ORC and these regulatory proteins are highly conserved in numerous eukaryotes from budding yeast to humans.  Regardless of the origin of initiation site in both ''Xenopus'' and ''Drosophila'' extracts, initiation of replication requires the ATP-dependent DNA binding activity of the origin of replication protein complex. [[3]]
+Eukaryotic origins of replication direct the formation of a number of protein complexes leading to the assembly of two bidirectional DNA replication forks. Regardless of the species, the pre-replication (pre-RC) complex forms at the origin of replication during the initiation phase of DNA replication. The pre-RC in eukaryotes is composed of the origin recognition protein complex (ORC) which recruits licensing factors such as the regulatory proteins Cdc6 and Cdt1 and various minichromosme maintenance proteins.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138988/pdf/gb-2001-2-12-reports4030.pdf/?tool=pmcentrez] The ORC and these regulatory proteins are highly conserved in numerous eukaryotes from budding yeast to humans.  Regardless of the origin of initiation site in both ''Xenopus'' and ''Drosophila'' extracts, initiation of replication requires the ATP-dependent DNA binding activity of the origin of replication protein complex. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138988/pdf/gb-2001-2-12-reports4030.pdf/?tool=pmcentrez]
 '''RIP Mapping'''
@@ Line 23: / Line 23: @@
 == Chromosome Number of ''Vaccinum corymbosum'' ==
-The high bush blue berry (''Vaccinum corymbosum''). It is a tetraploid with 2n=48 chromosomes. [http://www.jstor.org/stable/2481242],[http://www.jstor.org/stable/2446540]The method behind how the chromosome number was determined is not outlined in any paper.
+The high bush blue berry (''Vaccinum corymbosum'') is a tetraploid with 2n=48 chromosomes. [http://www.jstor.org/stable/2481242],[http://www.jstor.org/stable/2446540]The method behind how the chromosome number was determined is not outlined in any paper that I could find.

@@ Line 1: / Line 1: @@
-The origin of replication is a specific DNA sequence where replication begins.1 In prokaryotes, DNA replication begins at a singular AT rich origin of replication. Eukaryotes, however, can have multiple.
+The origin of replication is a specific DNA sequence where replication begins.[[1]] In prokaryotes, DNA replication begins at a singular AT rich origin of replication. Eukaryotes, however, can have multiple.
 ----
 == Origin of Replication in Eukaryotes ==
@@ Line 6: / Line 6: @@
 '''Higher Order Eukaryotes'''
 For many other eukaryotic systems, almost any DNA sequence appears to be capable of initiating DNA replication. In both ''Caenorhabditis elegans'' 8 and Paramecium 9, studies demonstrate that almost any cloned plasmid DNA can replicate autonomously, indicating that replication can occur within almost any size DNA sequence in these creatures. Furthermore, systematic searches in cultured animal cells for ARSs similar to those done in budding yeast did not identify specific sequences that enhance replication when reintroduced into cells i.e. a clear origin of replication was not found in other animal cells. 3 Krysan et al. (1993) demonstrated that in human cells, DNA fragments larger than 15 kb were capable of autonomous replication, indicating that autonomous replication in human cells is stimulated by simple sequences which occur fairly often in human DNA.10  Similar results were obtained in cultured ''Drosophila'' and ''Xenopus'' cells.3
 '''The Pre-RC'''
 Eukaryotic origins of replication direct the formation of a number of protein complexes leading to the assembly of two bidirectional DNA replication forks. Regardless of the species, the pre-replication (pre-RC) complex forms at the origin of replication during the initiation phase of DNA replication. The pre-RC in eukaryotes is composed of the origin recognition protein complex (ORC) which recruits licensing factors such as the regulatory proteins Cdc6 and Cdt1 and various minichromosme maintenance proteins.3 The ORC and these regulatory proteins are highly conserved in numerous eukaryotes from budding yeast to humans.  Regardless of the origin of initiation site in both ''Xenopus'' and ''Drosophila'' extracts, initiation of replication requires the ATP-dependent DNA binding activity of the origin of replication protein complex. 3
 '''RIP Mapping'''
 Recently, researchers have been able to detect start sites for DNA synthesis at the nucleotide level through the use of replication initiation point (RIP) mapping. RIP mapping in yeast and human cells indicate that the following may be true: there exists a single, defined start point at which DNA replication is initiated and the ORC tends to lie immediately adjacent to the replication start point.11
@@ Line 22: / Line 25: @@
 .Technical Glossary Edward K. Wagner, Martinez Hewlett, David Bloom and David Camerini Basic Virology Third Edition, Blackwell publishing, 2007 ISBN 1-4051-4715-6
 . The Autonomously Replicating Sequence (ARS) of the Yeast Saccharomyces exiguus. Taisuke Hisatomi, Kenji Kubota and Michio Tsuboi. Volume 38, Number 2, 122-125, DOI: 10.1007/s002849900414
 . Making sense of eukaryotic DNA replication origins. Gilbert DM. Science. 2001 Oct 5;294(5540):96-100. [http://www.ncbi.nlm.nih.gov/pubmed/11588251]
 .  A yeast chromosomal origin of DNA replication defined by multiple functional elements. Marahrens Y, Stillman B. Science. 1992;255:817. [http://www.ncbi.nlm.nih.gov/pubmed/1536007]
 Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III. Van Houten J, Newlon CS. Mol Cell Biol. 1990;10:3917. [http://www.ncbi.nlm.nih.gov/pubmed/2196439].
 . Regulation of chromosome replication. Kelly TJ, Brown GW. Annu Rev Biochem. 2000;69:829.[http://www.ncbi.nlm.nih.gov/pubmed/10966477]
 . Clustered adenine/thymine stretches are essential for function of a fission yeast replication origin. Okuno Y, Satoh H, Sekiguchi M, Masukata H. Mol Cell Biol. 1999;19:6699. [http://www.ncbi.nlm.nih.gov/pubmed/10490609]
 . Efficient gene transfer in C.elegans: extrachromosomal maintenance and integration of transforming sequences. Mello CC, Kramer JM, Stinchcomb D, Ambros V. EMBO J. 1991;10:3959.[http://www.ncbi.nlm.nih.gov/pubmed/1935914]
 . Bacteriophage lambda DNA fragments replicate in the Paramecium macronucleus: absence of active copy number control. Kim CS, Preer JR, Polisky B. Dev Genet. 1992;13:97.[http://www.ncbi.nlm.nih.gov/pubmed/1386793]
 .  Autonomous replication in human cells of multimers of specific human and bacterial DNA sequences.Krysan PJ, Smith JG, Calos MP. Mol Cell Biol. 1993;13:2688. [http://www.ncbi.nlm.nih.gov/pubmed/8386315]
 . Where it all starts: eukaryotic origins of DNA replication. Bielinsky, A and Gerb, S. Journal of Cell Science 114, 643-651. [http://www.qb.fcen.uba.ar/biomol/2002/replicacion_eucariota_2.pdf]
 . Chromosome Numbers in Vaccinium and Related Groups. George M. Darrow, W. H. Camp, H. E. Fischer and Haig Dermen. Bulletin of the Torrey Botanical Club Vol. 71, No. 5, Sep., 1944. [http://www.jstor.org/stable/2481242].
 . Evolution in an Autopolyploid Group Displaying Predominantly Bivalent Pairing at Meiosis: Genomic Similarity of Diploid Vaccinium darrowi and Autotetraploid V. Corymbosum (Ericaceae). Luping Qu, James F. Hancock and J. H. Whallon. American Journal of Botany. Vol. 85, No. 5, May, 1998. [http://www.jstor.org/stable/2446540]