Replication timing in Drosophila and its peculiarities in polytene chromosomes

Abstract

Drosophila melanogaster is one of the popular model organisms in DNA replication studies. Since the 1960s, DNA replication of polytene chromosomes has been extensively studied by cytological methods. In the recent two decades, the progress in our understanding of DNA replication was associated with new techniques. Use of fluorescent dyes increased the resolution of cytological methods significantly. High-throughput methods allowed analysis of DNA replication on a genome scale, as well as its correlation with chromatin structure and gene activi ty. Precise mapping of the cytological structures of polytene chromosomes to the genome assembly allowed comparison of replication between polytene chromosomes and chromosomes of diploid cells. New features of replication characteristic for D. melanogaster were described for both diploid and polytene chromosomes. Comparison of genomic replication profiles revealed a significant similarity between Drosophila and other well-studi ed eukaryotic species, such as human. Early replication is often confined to intensely transcribed gene-dense regions characterized by multiple replication initiation sites. Features of DNA replication in Drosophila might be explained by a compact genome. The organization of replication in polytene chromosomes has much in common with the organization of replication in chromosomes in diploid cells. The most important feature of replication in polytene chromosomes is its low rate and the dependence of S-phase duration on many factors: external and internal, local and global. The speed of replication forks in D. melanogaster polytene chromosomes is affected by SUUR and Rif1 proteins. It is not known yet how universal the mechanisms associated with these factors are, but their study is very promising.

Effects of Mutations in the Drosophila melanogaster Rif1 Gene on the Replication and Underreplication of Pericentromeric Heterochromatin in Salivary Gland Polytene Chromosomes

“…Figure 8 presents a set of successive patterns of EdU incorporation into polytene chromosomes; these patterns reflect the consequent stages of the S phase in Oregon R and mutants SuUR ES and Rif1 1 /Rif2 2 . In general, in all the three lines, replication patterns match those described for the polytene chromosomes of wild-type larvae in numerous papers published in the 60 s through 80 s (see references in [ 4 , 17 ]) and are easily categorized according to the standard classification: early discontinuous labeling (several sites in decondensed chromatin are labeled), continuous labeling (almost all structures visible in polytene chromosomes are labeled), the beginning of the stage of late discontinuous (discrete) labeling (the chromocenter and most of the bands are labeled), the late S phase (the label is detectable in the chromocenter and at discrete sites corresponding to large bands), the very late S phase (labeling exclusively in pericentromeric heterochromatin; this stage is absent in wild-type larvae, but is present in SuUR ES mutants).…”

“…An important feature of intercalary heterochromatin regions is that these are large regions almost devoid of an origin of replication. Replication forks coming from marginal regions do not have sufficient time to complete replication before the end of the S phase [ 10 , 14 , 15 , 16 , 17 ]. The underreplication points to a change in the system of DNA damage control.…”