scholarly journals Genome-wide mapping of 8-oxo-7,8-dihydro-2′-deoxyguanosine reveals accumulation of oxidatively-generated damage at DNA replication origins within transcribed long genes of mammalian cells

2018 ◽  
Vol 47 (1) ◽  
pp. 221-236 ◽  
Author(s):  
Stefano Amente ◽  
Giacomo Di Palo ◽  
Giovanni Scala ◽  
Tiziana Castrignanò ◽  
Francesca Gorini ◽  
...  
Keyword(s):  
Dna Replication ◽  
Mammalian Cells ◽  
Replication Origins ◽  
Genome Wide ◽  
Dna Replication Origins ◽  
Long Genes

scholarly journals Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

2012 ◽  
Vol 23 (1) ◽  
pp. 1-11 ◽  
Author(s):  
G. I. Dellino ◽  
D. Cittaro ◽  
R. Piccioni ◽  
L. Luzi ◽  
S. Banfi ◽  
...  
Keyword(s):  
Dna Replication ◽  
Replication Timing ◽  
Replication Origins ◽  
Human Dna ◽  
Genome Wide ◽  
Dna Replication Origins

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.

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