Karnani, N., Taylor, C., Malhotra, A. & Dutta, A. Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res. 17, 865-876

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA.
Genome Research (Impact Factor: 14.63). 07/2007; 17(6):865-76. DOI: 10.1101/gr.5427007
Source: PubMed


In eukaryotes, accurate control of replication time is required for the efficient completion of S phase and maintenance of genome stability. We present a high-resolution genome-tiling array-based profile of replication timing for approximately 1% of the human genome studied by The ENCODE Project Consortium. Twenty percent of the investigated segments replicate asynchronously (pan-S). These areas are rich in genes and CpG islands, features they share with early-replicating loci. Interphase FISH showed that pan-S replication is a consequence of interallelic variation in replication time and is not an artifact derived from a specific cell cycle synchronization method or from aneuploidy. The interallelic variation in replication time is likely due to interallelic variation in chromatin environment, because while the early- or late-replicating areas were exclusively enriched in activating or repressing histone modifications, respectively, the pan-S areas had both types of histone modification. The replication profile of the chromosomes identified contiguous chromosomal segments of hundreds of kilobases separated by smaller segments where the replication time underwent an acute transition. Close examination of one such segment demonstrated that the delay of replication time was accompanied by a decrease in level of gene expression and appearance of repressive chromatin marks, suggesting that the transition segments are boundary elements separating chromosomal domains with different chromatin environments.

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Available from: Ankit Malhotra, Apr 16, 2014
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    • "All loci analyzed showed a single 1-hr peak interval, during which the BrdU incorporation was greatest (Fig. 2B). It is known that ADH5 and the gamma-globin gene replicate in early and late S phase, respectively [30], [31]. When cumulative BrdU incorporation was correlated with specific test loci in fractions covering the S phase progression, we found that ADH5 and gamma-globin loci replicated at early and late S phase, respectively, as expected (Fig. 2C). "
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    ABSTRACT: Telomeric and subtelomeric regions of human chromosomes largely consist of highly repetitive and redundant DNA sequences, resulting in a paucity of unique DNA sequences specific to individual telomeres. Accordingly, it is difficult to analyze telomere metabolism on a single-telomere basis. To circumvent this problem, we have exploited a human artificial chromosome (HAC#21) derived from human chromosome 21 (hChr21). HAC#21 was generated through truncation of the long arm of native hChr21 by the targeted telomere seeding technique. The newly established telomere of HAC#21 lacks canonical subtelomere structures but possesses unique sequences derived from the target vector backbone and the internal region of hChr21 used for telomere targeting, which enabled us to molecularly characterize the single HAC telomere. We established HeLa and NIH-3T3 sub-lines containing a single copy of HAC#21, where it was robustly maintained. The seeded telomere is associated with telomeric proteins over a length similar to that reported in native telomeres, and is faithfully replicated in mid-S phase in HeLa cells. We found that the seeded telomere on HAC#21 is transcribed from the newly juxtaposed site. The transcript, HAC-telRNA, shares several features with TERRA (telomeric repeat-containing RNA): it is a short-lived RNA polymerase II transcript, rarely contains a poly(A) tail, and associates with chromatin. Interestingly, HAC-telRNA undergoes splicing. These results suggest that transcription into TERRA is locally influenced by the subtelomeric context. Taken together, we have established human and mouse cell lines that will be useful for analyzing the behavior of a uniquely identifiable, functional telomere.
    PLoS ONE 02/2014; 9(2):e88530. DOI:10.1371/journal.pone.0088530 · 3.23 Impact Factor
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    • "Changes in replication timing during development (see below) can strongly influence the genome-wide alignment of replication timing to isochores (Hiratani et al. 2010; Ryba et al. 2010). Moreover, homologous loci can replicate at different times in the same cells (Karnani et al. 2007; Farkash-Amar et al. 2008; Hansen et al. 2010). Isochores that exhibit the most extreme of the above-mentioned sequence compositions tend to replicate at the same time in all tissues, whereas regions with intermediate or mixed sequence features are more prone to change replication timing during development (Fig. 3, top), suggesting that sequence composition has some indirect influence on replication timing. "
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    ABSTRACT: Patterns of replication within eukaryotic genomes correlate with gene expression, chromatin structure, and genome evolution. Recent advances in genome-scale mapping of replication kinetics have allowed these correlations to be explored in many species, cell types, and growth conditions, and these large data sets have allowed quantitative and computational analyses. One striking new correlation to emerge from these analyses is between replication timing and the three-dimensional structure of chromosomes. This correlation, which is significantly stronger than with any single histone modification or chromosome-binding protein, suggests that replication timing is controlled at the level of chromosomal domains. This conclusion dovetails with parallel work on the heterogeneity of origin firing and the competition between origins for limiting activators to suggest a model in which the stochastic probability of individual origin firing is modulated by chromosomal domain structure to produce patterns of replication. Whether these patterns have inherent biological functions or simply reflect higher-order genome structure is an open question.
    Cold Spring Harbor perspectives in biology 07/2013; 5(8). DOI:10.1101/cshperspect.a010132 · 8.68 Impact Factor
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    • "Importantly, The ENCODE Pilot Project assigned function to 60% of the evolutionarily constrained bases in the 44 genomic regions and identified many additional functional elements seemingly unconstrained across mammalian evolution. Integration of the various experimental data generated by The ENCODE Pilot Project provided further insights into connections between chromatin structure (modifications and accessibility ) and gene expression (The ENCODE Project Consortium 2007; Koch et al. 2007; Thurman et al. 2007; Zhang et al. 2007) and the timing of replication (Karnani et al. 2007). "
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    ABSTRACT: Decoding the Human genome is a very up-to-date topic, raising several questions besides purely scientific, in view of the two competing teams (public and private), the ethics of using the results, and the fact that the project went apparently faster and easier than expected. The lecture series will address the following chapters: Scientific basis and challenges. Ethical and social aspects of genomics.
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