2013
DOI: 10.1371/journal.pcbi.1003017
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Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

Abstract: Several recent studies have examined different aspects of mammalian higher order chromatin structure – replication timing, lamina association and Hi-C inter-locus interactions — and have suggested that most of these features of genome organisation are conserved over evolution. However, the extent of evolutionary divergence in higher order structure has not been rigorously measured across the mammalian genome, and until now little has been known about the characteristics of any divergent loci present. Here, we … Show more

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Cited by 36 publications
(29 citation statements)
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“…The novel human epigenetic marks at the chromosome 2 fusion point might also reflect its ancestral subtelomeric location. Of note, increased epigenetic diversity at subtelomeric regions was observed in two recent comparisons: the 5-hydroxymethylcytosine epigenetic mark between induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs) in human (Wang et al 2013) and higher order chromatin structure between human and mouse (Chambers et al 2013). Moreover, an example of the emergence of novel promoters and expression modules through segmental duplications was described for the human core duplicon LRRC37 (Bekpen et al 2012;Giannuzzi et al 2013).…”
Section: Discussionmentioning
confidence: 93%
“…The novel human epigenetic marks at the chromosome 2 fusion point might also reflect its ancestral subtelomeric location. Of note, increased epigenetic diversity at subtelomeric regions was observed in two recent comparisons: the 5-hydroxymethylcytosine epigenetic mark between induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs) in human (Wang et al 2013) and higher order chromatin structure between human and mouse (Chambers et al 2013). Moreover, an example of the emergence of novel promoters and expression modules through segmental duplications was described for the human core duplicon LRRC37 (Bekpen et al 2012;Giannuzzi et al 2013).…”
Section: Discussionmentioning
confidence: 93%
“…Changes in higher-order chromatin structure have been noted at developmental loci in mammalian cells (Chambers et al 2013), linked to gene functions that impact phenotype (Chen et al 2015), respond to hormonal alterations (Le Dily et al 2014), and can be associated with divergent histone marks (Lan et al 2012;Huang et al 2015). The implementation of a novel visualization tool has allowed us to explore the Hi-C interaction in relation to the transcription and epigenetic changes between normal and prostate cancer cells.…”
Section: Discussionmentioning
confidence: 99%
“…We generated a primary adult zebrafish tailfin fibroblast cell line (ZTF cells) and performed replication timing analysis as described above. We first assessed the distribution of timing values throughout the genome, as replication timing in mammals is bimodal, with most DNA replication occurring either in early or late S-phase (Goldman et al 1984;Chambers et al 2013). Unexpectedly, the distribution of replication timing throughout the zebrafish genome in 28 hpf embryos and ZTF cells was unimodal, indicating DNA replication is not biased toward early or late S-phase ( Fig.…”
Section: Characteristics Of the Zebrafish Replication Timing Programmentioning
confidence: 99%