Replication timing of 10 developmentally regulated genes in<i>Physarum polycephalum</i>

Pierron, Gérard; Bénard, Marianne; Puvion, Edmond; Flanagan, Ronald; Sauer, Helmut W.; Pallotta, Dominick

doi:10.1093/nar/17.2.553

Cited by 26 publications

(27 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, we also found that the highly expressed php gene is late replicated in plasmodia (21,22). Here, we used neutral bidimensional agarose gel electrophoresis (2D-gel) method (23) to determine whether php gene late replication comes from its association to a late firing origin or from its long distance from an early firing origin.…”

Section: Introductionmentioning

confidence: 56%

Low rate of replication fork progression lengthens the replication timing of a locus containing an early firing origin

Bénard¹,

Maric²,

Pierron³

2007

Nucleic Acids Research

View full text Add to dashboard Cite

Invariance of temporal order of genome replication in eukaryotic cells and its correlation with gene activity has been well-documented. However, recent data suggest a relax control of replication timing. To evaluate replication schedule accuracy, we detailed the replicational organization of the developmentally regulated php locus that we previously found to be lately replicated, even though php gene is highly transcribed in naturally synchronous plasmodia of Physarum. Unexpectedly, bi-dimensional agarose gel electrophoreses of DNA samples prepared at specific time points of S phase showed that replication of the locus actually begins at the onset of S phase but it proceeds through the first half of S phase, so that complete replication of php-containing DNA fragments occurs in late S phase. Origin mapping located replication initiation upstream php coding region. This proximity and rapid fork progression through the coding region result in an early replication of php gene. We demonstrated that afterwards an unusually low fork rate and unidirectional fork pausing prolong complete replication of php locus, and we excluded random replication timing. Importantly, we evidenced that the origin linked to php gene in plasmodium is not fired in amoebae when php expression dramatically reduced, further illustrating replication-transcription coupling in Physarum.

show abstract

Section: Introductionmentioning

confidence: 56%

Low rate of replication fork progression lengthens the replication timing of a locus containing an early firing origin

Bénard¹,

Maric²,

Pierron³

2007

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Under our stringent hybridization conditions, these two cDNAs do not cross-hybridize (Pallotta et al, 1986a;Pierron et al, 1989). Therefore, we could use the LAV3-1 and LAV 1-5 cDNAs to detect specifically the profilin A and profilin P mRNAs.…”

Section: Northern Hybridizationsmentioning

confidence: 88%

Cell-Specific Expression of a Profilin Gene Family

Binette

Bénard²,

Laroche³

et al. 1990

DNA and Cell Biology

Self Cite

View full text Add to dashboard Cite

Profilin is a ubiquitous eukaryotic protein that inhibits actin polymerization. We cloned and sequenced the two profilin genes from the acellular slime mold Physarum polycephalum. The genes, proA and proP, each contain two introns. Primer extension experiments showed two possible transcription start sites in the profilin A gene and one start site in the profilin P gene. The profilin A mRNA has two polyadenylation sites, which yield mRNAs of about 600 and 500 nucleotides. The profilin P mRNA has a single polyadenylation site. The protein sequences were deduced from cDNA nucleotide sequencing. The profilin A and profilin P proteins contain 125 amino acids and are 66% identical in sequence. They show sequence similarity to Acanthamoeba (approximately 54%), yeast (approximately 46%), mouse (approximately 22%), calf (approximately 21%), and human (approximately 21%) profilins. The presence of the profilin A and profilin P mRNAs was studied throughout the life cycle. Profilin A mRNA was found in amebas, encysted amebas, and mature spores. The profilin P mRNA was present in plasmodia and spherulating plasmodia. Most cell types of P. polycephalum contain either the amebal or the plasmodial profilin mRNA, and no cell contains both mRNAs. This is the first evidence for developmental regulation of profilin isoforms.

show abstract

“…Given that incorporation of different amounts of exogenous histones led to distinct distributions of the tagged histones in the incorporated and free nuclear histone pools, we first monitored histones associated with specific DNA sequences by ChIP, using the ‘low’ amount of exogenous histone, as in these conditions the exogenous histones were almost entirely assembled into chromatin at the beginning of G 2 -phase (Figure 2A). To carry out these analyses, loci were chosen for their different representative chromatin structures and transcription regulation during the cell cycle (22,35,36) (Supplementary Figure S2A and B). The amount of tagged protein associated with the 5′-region, coding region and 3′-region of each locus at three time points during G 2 -phase was determined by ChIP and qPCR analyses (Figure 2B and Supplementary Figure S3A).…”

Section: Resultsmentioning

confidence: 99%

Replication-independent nucleosome exchange is enhanced by local and specific acetylation of histone H4

Elliott

Murphy

Hayes

et al. 2013

Nucleic Acids Research

View full text Add to dashboard Cite

We used a novel single-cell strategy to examine the fate of histones during G2-phase. Consistent with previous results, we find that in G2-phase, the majority of nuclear histones are assembled into chromatin, whereas a small fraction comprises an unassembled pool. Small increases in the amount of histones within the free pool affect the extent of exchange, suggesting that the free pool is in dynamic equilibrium with chromatin proteins. Unexpectedly, acetylated H4 is preferentially partitioned to the unassembled pool. Although an increase in global histone acetylation did not affect overall nucleosome dynamics, an H4 containing lysine to glutamine substitutions as mimics of acetylation significantly increased the rate of exchange, but did not affect the acetylation state of neighbouring nucleosomes. Interestingly, transcribed regions are particularly predisposed to exchange on incorporation of H4 acetylation mimics compared with surrounding regions. Our results support a model whereby histone acetylation on K8 and K16 specifically marks nucleosomes for eviction, with histones being rapidly deacetylated on reassembly.

show abstract

Replication timing of 10 developmentally regulated genes inPhysarum polycephalum

Cited by 26 publications

References 38 publications

Low rate of replication fork progression lengthens the replication timing of a locus containing an early firing origin

Low rate of replication fork progression lengthens the replication timing of a locus containing an early firing origin

Cell-Specific Expression of a Profilin Gene Family

Replication-independent nucleosome exchange is enhanced by local and specific acetylation of histone H4

Contact Info

Product

Resources

About