Gene density profile reveals the marking of late replicated domains in the Drosophila melanogaster genome

Belyakin, Stepan N.; Babenko, Vladimir N.; Maksimov, Daniil A.; Shloma, Victor V.; Kvon, Evgeny Z.; Belyaeva, E. S.; Жимулев, И. Ф.

doi:10.1007/s00412-010-0280-y

Cited by 26 publications

(41 citation statements)

References 27 publications

(55 reference statements)

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“…We found few differences in the distribution of replication timing ratios across each of the chromosomes with the exception of 2R and the X chromosome. Chromosome 2R replicated slightly earlier in all three cell lines, likely due to the higher gene density on this chromosome, a characteristic that has been previously linked to earlier replication timing (Belyakin et al 2010). The X chromosome replicated significantly earlier than the autosomes (Fig.…”

Section: Male-specific Early Replication Of the X Chromosomementioning

confidence: 76%

DNA replication and transcription programs respond to the same chromatin cues

et al. 2014

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DNA replication is a dynamic process that occurs in a temporal order along each of the chromosomes. A consequence of the temporally coordinated activation of replication origins is the establishment of broad domains (>100 kb) that replicate either early or late in S phase. This partitioning of the genome into early and late replication domains is important for maintaining genome stability, gene dosage, and epigenetic inheritance; however, the molecular mechanisms that define and establish these domains are poorly understood. The modENCODE Project provided an opportunity to investigate the chromatin features that define the Drosophila replication timing program in multiple cell lines. The majority of early and late replicating domains in the Drosophila genome were static across all cell lines; however, a small subset of domains was dynamic and exhibited differences in replication timing between the cell lines. Both origin selection and activation contribute to defining the DNA replication program. Our results suggest that static early and late replicating domains were defined at the level of origin selection (ORC binding) and likely mediated by chromatin accessibility. In contrast, dynamic domains exhibited low ORC densities in both cell types, suggesting that origin activation and not origin selection governs the plasticity of the DNA replication program. Finally, we show that the male-specific early replication of the X chromosome is dependent on the dosage compensation complex (DCC), suggesting that the transcription and replication programs respond to the same chromatin cues. Specifically, MOF-mediated hyperacetylation of H4K16 on the X chromosome promotes both the up-regulation of male-specific transcription and origin activation.

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Section: Male-specific Early Replication Of the X Chromosomementioning

confidence: 76%

DNA replication and transcription programs respond to the same chromatin cues

et al. 2014

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“…The UR(B) regions have low gene density (Belyakin et al 2010). Although the gene order in these regions is maintained in drosophilids (Andreyenkova et al 2013), few UR(B) genes have homologs in distant species such as mosquito and human.…”

Section: Discussionmentioning

confidence: 99%

“…Domains can be characterized by specific proteins such as LAM (Shevelyov et al 2009), groups of proteins (Filion et al 2010; Kharchenko et al 2011), or replication timing (Schwaiger et al 2009). These features are interdependant, for example, early and late replication domains correlate with chromatin architecture (Eaton et al 2011) or gene density (Hiratani and Gilbert 2009; Belyakin et al 2010). Although localization of early and late replication domains is not identical in different cell types (Hiratani et al 2008; Schwaiger et al 2009), the replication timing is remarkably conserved between distant species such as human and mouse (Yaffe et al 2010).…”

Section: Introductionmentioning

confidence: 99%

Underreplicated Regions in Drosophila melanogaster Are Enriched with Fast-Evolving Genes and Highly Conserved Noncoding Sequences

Makunin

Колесникова

Andreyenkova

2014

Genome Biology and Evolution

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Many late replicating regions are underreplicated in polytene chromosomes of Drosophila melanogaster. These regions contain silenced chromatin and overlap long syntenic blocks of conserved gene order in drosophilids. In this report we show that in D. melanogaster the underreplicated regions are enriched with fast-evolving genes lacking homologs in distant species such as mosquito or human, indicating that the phylogenetic conservation of genes correlates with replication timing and chromatin status. Drosophila genes without human homologs located in the underreplicated regions have higher nonsynonymous substitution rate and tend to encode shorter proteins when compared with those in the adjacent regions. At the same time, the underreplicated regions are enriched with ultraconserved elements and highly conserved noncoding sequences, especially in introns of very long genes indicating the presence of an extensive regulatory network that may be responsible for the conservation of gene order in these regions. The regions have a modest preference for long noncoding RNAs but are depleted for small nucleolar RNAs, microRNAs, and transfer RNAs. Our results demonstrate that the underreplicated regions have a specific genic composition and distinct pattern of evolution.

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“…Extensive overlap between IH regions and Lamin-associated DNA sequences suggests their role in the maintenance of spatial organization of a nucleus (Belyaeva et al 2012). Furthermore, IH is characterized by low gene density, and IH-resident genes typically have narrow tissue-and stage-specific expression patterns, being particularly active in the male germ line (MacAlpine et al 2004;Belyakin et al 2010). Additionally, in different Drosophila species, the gene order in the latereplicating and SUUR-containing regions is well conserved throughout evolution (Ranz et al 2012).…”

Section: Introductionmentioning

confidence: 95%

Induced transcription results in local changes in chromatin structure, replication timing, and DNA polytenization in a site of intercalary heterochromatin

et al. 2012

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In salivary gland polytene chromosomes of Drosophila melanogaster, the regions of intercalary heterochromatin are characterized by late replication, under-replication, and genetic silencing. Using Gal4/UAS system, we induced transcription of sequences adjacent to transgene insertions in the band 11A6-9. This activation resulted in a loss of "silent" and appearance of "active" epigenetic marks, recruitment of RNA polymerase II, and formation of a puff. The activated region is now early replicating and shows increased level of DNA polytenization. Notably, all these changes are restricted to the area around the inserts, whereas the rest of the band remains inactive and late replicating. Although only a short area near the insertion site is transcribed, it results in an "open" chromatin conformation in a much broader region. We conclude that regions of intercalary heterochromatin do not form stand-alone units of late replication and under-replication. Every part of such regions can be activated and polytenized independently of other parts.

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Gene density profile reveals the marking of late replicated domains in the Drosophila melanogaster genome

Cited by 26 publications

References 27 publications

DNA replication and transcription programs respond to the same chromatin cues

DNA replication and transcription programs respond to the same chromatin cues

Underreplicated Regions in Drosophila melanogaster Are Enriched with Fast-Evolving Genes and Highly Conserved Noncoding Sequences

Induced transcription results in local changes in chromatin structure, replication timing, and DNA polytenization in a site of intercalary heterochromatin

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