Sir2 suppresses transcription-mediated displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats

Foss, Eric J.; Gatbonton-Schwager, Tonibelle; Thiesen, Adam H.; Taylor, Erin L.; Soriano, Rafael; Lao, Uyen; MacAlpine, David M.; Bedalov, Antonio

doi:10.1371/journal.pgen.1008138

Cited by 33 publications

(56 citation statements)

References 42 publications

(51 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We interpret fragment peaks in the 150-200 bp size range as reflections of cleavage by the MNase-tagged protein between flanking nucleosomes and note that such fragments have been observed for other MNase tagged proteins, including transcription factors (Foss et al, 2019). In this report, we visualize individual Mcm2-7 footprints as heat maps, with fragment size plotted according to genomic location, and read depths represented by color intensity (Foss et al, 2019). A typical example is shown in Fig.…”

Section: Mcm-chec Identifies Single MCM Double-hexamer Footprints Adjmentioning

confidence: 92%

“…Essentially identical footprints were generated by MNase-tagged Mcm4 and Mcm6 ( Fig 1B), confirming that footprints reflect Mcm2-7 binding. Furthermore, G1-specific and Cdc6-dependent footprints obtained by sequencing DNA fragments from nuclei treated with exogenous MNase (MNaseseq) coincided with these Mcm-MNase generated signals (Foss et al, 2019). The prominent…”

Section: Mcm-chec Identifies Single MCM Double-hexamer Footprints Adjmentioning

confidence: 94%

“…The Mcm2-7 complex encircles approximately 60 base pairs (bp) of DNA as a double-hexamer (DH) whose monomer components are juxtaposed head-to-head at their N-termini with Ctermini facing away from each other (Abid Ali et al, 2017). To exploit this arrangement of Mcm2-7 hexamers as a way to identify their exact loading sites in vivo, we tagged Mcm2,Mcm4 and Mcm6 subunits at their C-termini in Saccharomyces cerevisiae with micrococcal nuclease (MNase) (Schmid, Durussel, & Laemmli, 2004;Zentner, Kasinathan, Xin, Rohs, & Henikoff, 2015), permeabilized G1-arrested cells, activated the MNase by adding calcium, and prepared libraries for paired end sequencing using total extracted DNA without any size fractionation (Foss et al, 2019). Strains with tagged Mcm proteins exhibited growth rates comparable to those in wild type, indicating that the presence of the tag did not perturb protein function (Supplementary data Fig.…”

Section: Mcm-chec Identifies Single MCM Double-hexamer Footprints Adjmentioning

confidence: 99%

“…termini facing away from each other [7]. To exploit this arrangement of Mcm2-7 hexamers to identify their exact loading sites in vivo, we tagged its Mcm2, Mcm4 and Mcm6 subunits at their C-termini in Saccharomyces cerevisiae with micrococcal nuclease (MNase) [8], permeabilized G1-arrested cells, activated the MNase by addition of calcium, and prepared libraries for paired end sequencing using total extracted DNA without any size fractionation [9]. The strains with tagged MCM proteins exhibited growth rates comparable to those in wild type, indicating that the presence of the tag did not interfere with the proteins' function ( Fig.…”

mentioning

confidence: 99%

“…We have seen this phenomenon with multiple MNase-tagged DNA binding proteins (data not shown).] Individual Mcm2-7 footprints can be visualized as heat maps, with fragment size plotted according to genomic location, and read depths represented by color intensity [9]. A typical example of this is shown in Figure 1D Figure 2).…”

mentioning

confidence: 99%

See 4 more Smart Citations

Chromosomal Mcm2-7 distribution is the primary driver of the genome replication program in species from yeast to humans

Foss

Sripathy

Gatbonton-Schwager

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

The spatio-temporal program of genome replication across eukaryotes is thought to be driven both by the uneven loading of pre-replication complexes (pre-RCs) across the genome at the onset of S-phase, and by differences in the timing of activation of these complexes during Sphase. To determine the degree to which distribution of pre-RC loading alone could account for chromosomal replication patterns, we identified the binding sites of the Mcm2-7 helicase complex, a key component of the pre-RC that is required for initiation of DNA replication, in budding yeast, fission yeast and mouse. In budding yeast, we detected Mcm2 binding in sharply focused peaks, generally with a single double hexamer bound at known origins of replication. In fission yeast, Mcm2 binding, while still concentrated at known origins, was more diffuse, often with 6 to 8 helicase complexes distributed along 0.5-1.5 kb sized origins, and with significantly more binding between origins. Finally, in mouse, we found even more diffuse Mcm2-7 distribution, with the density of Mcm2-7 binding in G1 recapitulating to a remarkable degree the replication program implemented in S-phase. Computer simulations that assign each licensed origin an equal probability of firing show that the observed Mcm2-7 density distribution in G1 across all three species largely recapitulated the DNA replication program. We conclude that the pattern of origin licensing from yeast to mammals is sufficient to explain most differences in replication timing without invoking an overarching temporal program of origin firing. ResultsInitiation of DNA replication requires activation of the MCM2-7 helicase complex (Mcm2-7) at sites at which this complex was loaded during the preceding G2/M and G1 phases [1][2][3][4].However, the order in which different regions of the genome complete replication is widely assumed to reflect not only the locations of Mcm2-7 loading but also a program of control above the level of loading, in which certain complexes are activated before others [5,6]. The distribution of Mcm2-7 is therefore expected to constrain but not fully determine the program of genome replication. Mcm2-7 encircles approximately 60 base pairs (bp) of DNA as a double hexamer whose monomer components are juxtaposed head-to-head at their N-termini with C-

show abstract

Section: Mcm-chec Identifies Single MCM Double-hexamer Footprints Adjmentioning

confidence: 92%

Section: Mcm-chec Identifies Single MCM Double-hexamer Footprints Adjmentioning

confidence: 94%

Section: Mcm-chec Identifies Single MCM Double-hexamer Footprints Adjmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Chromosomal Mcm2-7 distribution is the primary driver of the genome replication program in species from yeast to humans

Foss

Sripathy

Gatbonton-Schwager

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Concerted evolution of ribosomal DNA: Somatic peace amid germinal strife

Haig

2021

BioEssays

View full text Add to dashboard Cite

Most eukaryotes possess many copies of rDNA. Organismal selection alone cannot maintain rRNA function because the effects of mutations in one rDNA are diluted by the presence of many other rDNAs. rRNA quality is maintained by processes that increase homogeneity of rRNA within, and heterogeneity among, germ cells thereby increasing the effectiveness of cellular selection on ribosomal function. A successful rDNA repeat will possess adaptations for spreading within tandem arrays by intranuclear selection. These adaptations reside in the non-coding regions of rDNA. Singlecopy genes are predicted to manage processes of intranuclear and cellular selection in the germline to maintain the quality of rRNA expressed in somatic cells of future generations.

show abstract

Yeast autonomously replicating sequence (ARS): Identification, function, and modification

Tan

Han

et al. 2021

Engineering in Life Sciences

View full text Add to dashboard Cite

Eukaryotic DNA replication begins with multiple origins of replication (ORIs) and thus exploring and identifying ORIs is essential for further understanding of the DNA replication process. In budding yeast, certain autonomously replicating sequences (ARSs) initiate the replication as ORIs, maintaining the stability of chromosomes and plasmids during genome replication. Currently, ARS identification was further facilitated by the DNA microarray technology and bioinformatics, which is based on the previous experimental methods. The structural and functional properties of ARSs on yeast chromosomes are gradually explored in this field. In addition to the function of initiating replication, there is a growing interest for researchers in the effects of ARSs on gene silencing and expression of genes, particularly the relationship between ARSs and chromosome structure. In this review, we summarized the identification methods of ARSs, especially for the bioinformatics prediction methods over the past few years. The functions of ARSs are discussed in this research, moreover, ARS modification that combined with the high‐throughput sequencing was elaborated as well, shedding further light on the understanding of the roles of ARSs, and providing deep insights towards the optimization of ARSs.

show abstract

Sir2 suppresses transcription-mediated displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats

Cited by 33 publications

References 42 publications

Chromosomal Mcm2-7 distribution is the primary driver of the genome replication program in species from yeast to humans

Chromosomal Mcm2-7 distribution is the primary driver of the genome replication program in species from yeast to humans

Concerted evolution of ribosomal DNA: Somatic peace amid germinal strife

Yeast autonomously replicating sequence (ARS): Identification, function, and modification

Contact Info

Product

Resources

About