Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome

Singh, V. P.; Krishnamachari, Annangarachari

doi:10.1016/j.gdata.2016.07.005

Cited by 9 publications

(5 citation statements)

References 58 publications

(83 reference statements)

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“…The ACS is a loosely defined AT-rich 11–17 base pair sequence whose directionality is determined on the basis of the relative numbers of As versus Ts in the two strands ( Breier et al, 2004 ). This sequence is recognized by the Orc, a six-protein complex that loads MCM ( Bell and Stillman, 1992 ; Newlon and Theis, 1993 ; Berbenetz et al, 2010 ; Eaton et al, 2010 ; Singh and Krishnamachari, 2016 ). Although the characteristics that allow a sequence to serve as an Orc binding site remain poorly understood, with, for example, only approximately half of the origins listed in SGD reporting associated ACS signals, researchers have calculated a probability weight matrix to evaluate the fidelity of the correspondence of any 17 base pair sequence with a hypothetically ‘perfect’ ACS ( Coster and Diffley, 2017 ).…”

Section: Resultsmentioning

confidence: 99%

Identification of 1600 replication origins in S. cerevisiae

Foss

Lichauco

Gatbonton-Schwager

et al. 2024

eLife

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There are approximately 500 known origins of replication in the yeast genome, and the process by which DNA replication initiates at these locations is well understood. In particular, these sites are made competent to initiate replication by loading of the Mcm replicative helicase prior to the start of S phase; thus, “a site to which MCM is bound in G1” might be considered to provide an operational definition of a replication origin. By fusing a subunit of Mcm to micrococcal nuclease, a technique referred to as “Chromatin Endogenous Cleavage”, we previously showed that known origins are typically bound by a single Mcm double hexamer, loaded adjacent to the ARS consensus sequence (ACS). Here we extend this analysis from known origins to the entire genome, identifying candidate Mcm binding sites whose signal intensity varies over at least 3 orders of magnitude. Published data quantifying the production of ssDNA during S phase showed clear evidence of replication initiation among the most abundant 1600 of these sites, with replication activity decreasing in concert with Mcm abundance and disappearing at the limit of detection of ssDNA. Three other hallmarks of replication origins were apparent among the most abundant 5,500 sites. Specifically, these sites (1) appeared in intergenic nucleosome-free regions that were flanked on one or both sides by well-positioned nucleosomes; (2) were flanked by ACSs; and (3) exhibited a pattern of GC skew characteristic of replication initiation. Furthermore, the high resolution of this technique allowed us to demonstrate in vivo that, as is the case in vitro, the Mcm complex is loaded directionally downstream of the ACS. We conclude that DNA replication origins are at least 3-fold more abundant than previously assumed, and we suggest that replication may occasionally initiate in essentially every intergenic region. These results shed light on recent reports that as many as 15% of replication events initiate outside of known origins, and they reveal S phase in yeast to be surprisingly similar to that in humans.

show abstract

Section: Resultsmentioning

confidence: 99%

Identification of 1600 replication origins in S. cerevisiae

Foss

Lichauco

Gatbonton-Schwager

et al. 2024

eLife

View full text Add to dashboard Cite

show abstract

“…The ACS is a loosely defined AT-rich 11-17 base pair sequence whose directionality is determined on the basis of the relative numbers of As versus Ts in the two strands (Breier et al 2004 ). This sequence is recognized by the Origin Recognition Complex (Orc), a 6-protein complex that loads MCM (Bell and Stillman 1992 ;Newlon and Theis 1993 ;Eaton et al 2010 ;Singh and Krishnamachari 2016 ). Although the characteristics that allow a sequence to serve as an Orc binding site remain poorly understood, with, for example, only approximately half of the origins listed in SGD reporting associated ACS signals, researchers have calculated a probability weight matrix to evaluate the fidelity of the correspondence of any 17 base pair sequence with a hypothetically "perfect" ACS (Coster and Diffley 2017 ).…”

Section: Binding Sites Are Flanked By Acs Sequences and MCM Is Loaded...mentioning

confidence: 99%

“…1. "This sequence is recognized by the Origin Recognition Complex (Orc), a 6-protein complex that loads MCM (Broach et al, 1983;Deshpande and Newlon, 1992;Eaton et al, 2010;Kearsey, 1984;Newlon and Theis, 1993;Singh and Krishnamachari, 2016;Srienc et al, 1985)." This list should include a reference to Bell and Stillman, 1992 (PMID: 1579162), which first described ORC and showed that it recognized the ACS.…”

Section: Data Availabilitymentioning

confidence: 99%

Identification of 1600 replication origins in S. cerevisiae

Foss,

Lichauco,

Gatbonton-Schwager

et al. 2023

Preprint

View full text Add to dashboard Cite

There are approximately 500 known origins of replication in the yeast genome, and the process by which DNA replication initiates at these locations is well understood. In particular, these sites are made competent to initiate replication by loading of the Mcm replicative helicase prior to the start of S phase; thus, “a site to which MCM is bound in G1” might be considered to provide an operational definition of a replication origin. By fusing a subunit of Mcm to micrococcal nuclease, a technique referred to as “Chromatin Endogenous Cleavage”, we previously showed that known origins are typically bound by a single Mcm double hexamer, loaded adjacent to the ARS consensus sequence (ACS). Here we extend this analysis from known origins to the entire genome, identifying candidate Mcm binding sites whose signal intensity varies over at least 3 orders of magnitude. Published data quantifying the production of ssDNA during S phase showed clear evidence of replication initiation among the most abundant 1600 of these sites, with replication activity decreasing in concert with Mcm abundance and disappearing at the limit of detection of ssDNA. Three other hallmarks of replication origins were apparent among the most abundant 5,500 sites. Specifically, these sites (1) appeared in intergenic nucleosome-free regions that were flanked on one or both sides by well-positioned nucleosomes; (2) were flanked by ACSs; and (3) exhibited a pattern of GC skew characteristic of replication initiation. Furthermore, the high resolution of this technique allowed us to demonstrate a strong bias for detecting Mcm double-hexamers downstream rather than upstream of the ACS, which is consistent with the directionality of Mcm loading by Orc that has been observed in vitro. We conclude that, if sites at which Mcm double-hexamers are loaded can function as replication origins, then DNA replication origins are at least 3-fold more abundant than previously assumed, and we suggest that replication may occasionally initiate in essentially every intergenic region. These results shed light on recent reports that as many as 15% of replication events initiate outside of known origins, and this broader distribution of replication origins suggest that S phase in yeast may be less distinct from that in humans than is widely assumed.

show abstract

“…The ACS is a loosely defined AT-rich 11-17 base pair sequence whose directionality is determined on the basis of the relative numbers of As versus Ts in the two strands (Breier et al, 2004). This sequence is recognized by the Origin Recognition Complex (Orc), a 6-protein complex that loads MCM (Broach et al, 1983;Deshpande and Newlon, 1992;Eaton et al, 2010;Kearsey, 1984;Newlon and Theis, 1993;Singh and Krishnamachari, 2016;Srienc et al, 1985). Although the characteristics that allow a sequence to serve as an Orc binding site remain poorly understood, with, for example, only approximately half of the origins listed in SGD reporting associated ACS signals, researchers have calculated a probability weight matrix to evaluate the fidelity of the correspondence of any 17 base pair sequence with a hypothetically "perfect" ACS (Coster and Diffley, 2017).…”

Section: Acssmentioning

confidence: 99%

Section: Acssmentioning

confidence: 99%

Identification of 1600 replication origins inS. cerevisiae

Foss

Lichauco

Gatbonton-Schwager

et al. 2023

Preprint

View full text Add to dashboard Cite

There are approximately 500 known origins of replication in the yeast genome, and the process by which DNA replication initiates at these locations is well understood. In particular, these sites are made competent to initiate replication by loading of the Mcm replicative helicase prior to the start of S phase; thus, "a site to which MCM is bound in G1" might be considered to provide an operational definition of a replication origin. By fusing a subunit of Mcm to micrococcal nuclease, a technique referred to as "Chromatin Endogenous Cleavage", we previously showed that known origins are typically bound by a single Mcm double hexamer, loaded adjacent to the ARS consensus sequence (ACS). Here we extend this analysis from known origins to the entire genome, identifying candidate Mcm binding sites whose signal intensity varies over at least 3 orders of magnitude. Published data quantifying the production of ssDNA during S phase showed clear evidence of replication initiation among the most abundant 1600 of these sites, with replication activity decreasing in concert with Mcm abundance and disappearing at the limit of detection of ssDNA. Three other hallmarks of replication origins were apparent among the most abundant 5,500 sites. Specifically, these sites (1) appeared in intergenic nucleosome-free regions that were flanked on one or both sides by well-positioned nucleosomes; (2) were flanked by ACSs; and (3) exhibited a pattern of GC skew characteristic of replication initiation. Furthermore, the high resolution of this technique allowed us to demonstratein vivothat, as is the casein vitro, the Mcm complex is loaded directionally downstream of the ACS. We conclude that DNA replication origins are at least 3-fold more abundant than previously assumed, and we suggest that replication may occasionally initiate in essentially every intergenic region. These results shed light on recent reports that as many as 15% of replication events initiate outside of known origins, and they reveal S phase in yeast to be surprisingly similar to that in humans.

show abstract

Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome

Cited by 9 publications

References 58 publications

Identification of 1600 replication origins in S. cerevisiae

Identification of 1600 replication origins in S. cerevisiae

Identification of 1600 replication origins in S. cerevisiae

Identification of 1600 replication origins inS. cerevisiae

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