Overreplication of short DNA regions during S phase in human cells

Gómez, Marı́a; Antequera, Francisco

doi:10.1101/gad.445608

Cited by 33 publications

(39 citation statements)

References 45 publications

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“…We found a link between CGI and Oris in all cell types analyzed, as reported for a subset of human and mouse Oris (Delgado et al 1998;Cadoret et al 2008;Gomez and Antequera 2008;SequeiraMendes et al 2009). CGI are essential elements for transcriptional control and imprinting in mammals and are regulated by DNA methylation.…”

Section: Metazoan Origins Exhibit Common Sequences Featuressupporting

confidence: 86%

Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features

Cayrou¹,

Coulombe²,

Vigneron³

et al. 2011

Genome Res.

306

373

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In metazoans, thousands of DNA replication origins (Oris) are activated at each cell cycle. Their genomic organization and their genetic nature remain elusive. Here, we characterized Oris by nascent strand (NS) purification and a genome-wide analysis in Drosophila and mouse cells. We show that in both species most CpG islands (CGI) contain Oris, although methylation is nearly absent in Drosophila, indicating that this epigenetic mark is not crucial for defining the activated origin. Initiation of DNA synthesis starts at the borders of CGI, resulting in a striking bimodal distribution of NS, suggestive of a dual initiation event. Oris contain a unique nucleotide skew around NS peaks, characterized by G/T and C/A overrepresentation at the 59 and 39 of Ori sites, respectively. Repeated GC-rich elements were detected, which are good predictors of Oris, suggesting that common sequence features are part of metazoan Oris. In the heterochromatic chromosome 4 of Drosophila, Oris correlated with HP1 binding sites. At the chromosome level, regions rich in Oris are early replicating, whereas Ori-poor regions are late replicating. The genome-wide analysis was coupled with a DNA combing analysis to unravel the organization of Oris. The results indicate that Oris are in a large excess, but their activation does not occur at random. They are organized in groups of site-specific but flexible origins that define replicons, where a single origin is activated in each replicon. This organization provides both site specificity and Ori firing flexibility in each replicon, allowing possible adaptation to environmental cues and cell fates.

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Section: Metazoan Origins Exhibit Common Sequences Featuressupporting

confidence: 86%

Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features

Cayrou¹,

Coulombe²,

Vigneron³

et al. 2011

Genome Res.

306

373

View full text Add to dashboard Cite

show abstract

“…The observation of increased buds at the nuclear envelope in Dnase2a-deficient cells may thus indicate a higher rate of damaged DNA generation than removal. Nevertheless, other studies have detected DNA fragments arising from replication in budding yeast (Sogo et al, 2002) and fly (Blumenthal and Clark, 1977), over represented dsDNA fragments from chromosomes as free dsDNA molecules in human cells during S phase (Gomez and Antequera, 2008), and release of short DNA fragments into the cytosol prompted by physical (Kawashima et al, 2011) or radiation-induced injury (Pang et al, 2011). Interestingly, unrepaired or irreparable DNA has been found to re-localize to the nuclear periphery (Nagai et al, 2008; Oza et al, 2009), suggesting that it may be segregated from replicating DNA for clearance.…”

Section: Discussionmentioning

confidence: 99%

“…A more detailed analysis of the excess DNA in Dnase2 −/− cells, will be informative for tracing the chromosomal origin of the observed damaged DNA fragments (e.g. to mutation-prone common fragile sites (Ozeri-Galai et al, 2012), or early replication fragile sites (Barlow et al, 2013), regions of increased synthesis at re-replication sites (Green et al, 2010) or nucleosome-free gaps (Gomez and Antequera, 2008)).…”

Section: Discussionmentioning

confidence: 99%

Dnase2a Deficiency Uncovers Lysosomal Clearance of Damaged Nuclear DNA via Autophagy

et al. 2014

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Summary Deficiencies in DNA degrading nucleases lead to accumulation of self DNA and induction of autoimmunity in mice and in monogenic and polygenic human diseases. However, the sources of DNA and the mechanisms that trigger immunity remain unclear. We analyzed mice deficient for the lysosomal nuclease, Dnase2a, and observed elevated levels of undegraded DNA in both phagocytic and non-phagocytic cells. In non-phagocytic cells, the excess DNA originated from damaged DNA in the nucleus based on co-localization studies, live cell imaging and exacerbation by DNA-damaging agents. Removal of damaged DNA by Dnase2a required nuclear export and autophagy-mediated delivery of the DNA to lysosomes. Finally, DNA was found to accumulate in Dnase2a−/− or autophagy-deficient cells and induce inflammation via the Sting cytosolic DNA-sensing pathway. Our results reveal a cell-autonomous process for removal of damaged nuclear DNA with implications for conditions with elevated DNA damage, such as inflammation, cancer and chemotherapy.

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“…1F). 59 This phenomenon appears analogous to the short bidirectional transcripts initiating from CpG island promoters and could result from non-productive initiation of ORIs in the absence of factors needed for processive replication. More work is clearly required to understand what features of CpG islands make these preferential targets for initiating DNA replication.…”

Section: O N O T D I S T R I B U T Ementioning

confidence: 99%