scholarly journals Spatiotemporal coupling and decoupling of gene transcription with DNA replication origins during embryogenesis in C. elegans

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Ehsan Pourkarimi ◽  
James M Bellush ◽  
Iestyn Whitehouse
Keyword(s):  
Dna Replication ◽  
Developmental Stages ◽  
Embryonic Cell ◽  
Genome Replication ◽  
Replication Origins ◽  
C Elegans ◽  
Cellular Changes ◽  
Zygotic Transcription ◽  
Close Proximity ◽  
Dna Replication Origins

The primary task of developing embryos is genome replication, yet how DNA replication is integrated with the profound cellular changes that occur through development is largely unknown. Using an approach to map DNA replication at high resolution in C. elegans, we show that replication origins are marked with specific histone modifications that define gene enhancers. We demonstrate that the level of enhancer associated modifications scale with the efficiency at which the origin is utilized. By mapping replication origins at different developmental stages, we show that the positions and activity of origins is largely invariant through embryogenesis. Contrary to expectation, we find that replication origins are specified prior to the broad onset of zygotic transcription, yet when transcription initiates it does so in close proximity to the pre-defined replication origins. Transcription and DNA replication origins are correlated, but the association breaks down when embryonic cell division ceases. Collectively, our data indicate that replication origins are fundamental organizers and regulators of gene activity through embryonic development.

scholarly journals Mapping vaccinia virus DNA replication origins at nucleotide level by deep sequencing

2015 ◽  
Vol 112 (35) ◽  
pp. 10908-10913 ◽  
Author(s):  
Tatiana G. Senkevich ◽  
Daniel Bruno ◽  
Craig Martens ◽  
Stephen F. Porcella ◽  
Yuri I. Wolf ◽  
...  
Keyword(s):  
Dna Replication ◽  
Vaccinia Virus ◽  
Deep Sequencing ◽  
Genome Replication ◽  
Replication Origins ◽  
Electron Microscopic ◽  
Initiation Point ◽  
Host Cytoplasm ◽  
Poxvirus Genome ◽  
Dna Replication Origins

Poxviruses reproduce in the host cytoplasm and encode most or all of the enzymes and factors needed for expression and synthesis of their double-stranded DNA genomes. Nevertheless, the mode of poxvirus DNA replication and the nature and location of the replication origins remain unknown. A current but unsubstantiated model posits only leading strand synthesis starting at a nick near one covalently closed end of the genome and continuing around the other end to generate a concatemer that is subsequently resolved into unit genomes. The existence of specific origins has been questioned because any plasmid can replicate in cells infected by vaccinia virus (VACV), the prototype poxvirus. We applied directional deep sequencing of short single-stranded DNA fragments enriched for RNA-primed nascent strands isolated from the cytoplasm of VACV-infected cells to pinpoint replication origins. The origins were identified as the switching points of the fragment directions, which correspond to the transition from continuous to discontinuous DNA synthesis. Origins containing a prominent initiation point mapped to a sequence within the hairpin loop at one end of the VACV genome and to the same sequence within the concatemeric junction of replication intermediates. These findings support a model for poxvirus genome replication that involves leading and lagging strand synthesis and is consistent with the requirements for primase and ligase activities as well as earlier electron microscopic and biochemical studies implicating a replication origin at the end of the VACV genome.

scholarly journals Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin

2016 ◽  
Author(s):  
Zaida Vergara ◽  
Joana Sequeira-Mendes ◽  
Jordi Morata ◽  
Elizabeth Hénaff ◽  
Ramón Peiró ◽  
...  
Keyword(s):  
Dna Replication ◽  
Gc Content ◽  
Genomic Stability ◽  
Genome Replication ◽  
Replication Origins ◽  
Entire Genome ◽  
Genome Wide ◽  
Concerted Activity ◽  
Dna Replication Origins ◽  
Multicellular Organisms

AbstractGenomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands of DNA replication origins (ORIs) scattered throughout the genome. In spite of multiple efforts, the DNA and chromatin features that determine ORI specification are not presently known. We have generated a high-resolution genome-wide map of ORIs in cultured Arabidopsis thaliana cells that rendered a collection of 3230 ORIs. In this study we focused on defining the features associated with ORIs in heterochromatin. We found that while ORIs tend to colocalize with genes in euchromatic gene-rich regions, they frequently colocalize with transposable elements (TEs) in pericentromeric gene-poor domains. Interestingly, ORIs in TEs associate almost exclusively with retrotransposons, in particular, of the Gypsy family. ORI activity in retrotransposons occurs independently of TE expression and while maintaining high levels of H3K9me2 and H3K27me1, typical marks of repressed heterochromatin. ORI-TEs largely colocalize with chromatin signatures defining GC-rich heterochromatin. Importantly, TEs with active ORIs contain a local GC content higher than the TEs lacking them. Our results lead us to conclude that ORI colocalization with TEs is largely limited to retrotransposons, which are defined by their transposition mechanisms based on transcription, and they occur in a specific chromatin landscape. Our detailed analysis of ORIs responsible for heterochromatin replication has also implications on the mechanisms of ORI specification in other multicellular organisms in which retrotransposons are major components of heterochromatin as well as of the entire genome.

scholarly journals Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans

2019 ◽  
Author(s):  
Maude Strobino ◽  
Joanna M. Wenda ◽  
Florian A. Steiner
Keyword(s):  
Cell Cycle ◽  
Dna Replication ◽  
Replication Fork ◽  
Replication Timing ◽  
Embryonic Cell ◽  
Stress Conditions ◽  
Replication Origins ◽  
C Elegans ◽  
Replication Fork Progression ◽  
Histone H3.3

AbstractHistone H3.3 is a replication-independent variant of histone H3 with important roles in development, differentiation and fertility. Here we show that loss of H3.3 results in replication defects in Caenorhabditis elegans embryos. To characterize these defects, we adapt methods to determine replication timing, map replication origins, and examine replication fork progression. Our analysis of the spatiotemporal regulation of DNA replication shows that despite the very rapid embryonic cell cycle, the genome is replicated from early and late firing origins and is partitioned into domains of early and late replication. We find that under temperature stress conditions, additional replication origins become activated. Moreover, loss of H3.3 results in impaired replication fork progression around origins, which is particularly evident at stress-activated origins. These replication defects are accompanied by replication checkpoint activation, a prolonged cell cycle, and increased lethality in checkpoint-compromised embryos. Our comprehensive analysis of DNA replication in C. elegans reveals the genomic location of replication origins and the dynamics of their firing, and uncovers a role of H3.3 in the regulation of replication origins under stress conditions.

Sign in / Sign up

Export Citation Format

Share Document