Incomplete replication generates somatic DNA alterations within <i>Drosophila</i> polytene salivary gland cells

Yarosh, Will; Spradling, Allan C.

doi:10.1101/gad.245811.114

Cited by 74 publications

(122 citation statements)

References 51 publications

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“…As mentioned earlier, breakpoint clustering is regional and not limited to a specific site. Similarly, late replication and under-replication are regional properties of chromosomes, extending over hundreds of kilobases (Belyaeva et al 2012;Yarosh and Spradling 2014).…”

Section: Discussionmentioning

confidence: 99%

Preferential Breakpoints in the Recovery of Broken Dicentric Chromosomes inDrosophila melanogaster

Hill¹,

Golic

2015

Genetics

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We designed a system to determine whether dicentric chromosomes in Drosophila melanogaster break at random or at preferred sites. Sister chromatid exchange in a Ring-X chromosome produced dicentric chromosomes with two bridging arms connecting segregating centromeres as cells divide. This double bridge can break in mitosis. A genetic screen recovered chromosomes that were linearized by breakage in the male germline. Because the screen required viability of males with this X chromosome, the breakpoints in each arm of the double bridge must be closely matched to produce a nearly euploid chromosome. We expected that most linear chromosomes would be broken in heterochromatin because there are no vital genes in heterochromatin, and breakpoint distribution would be relatively unconstrained. Surprisingly, approximately half the breakpoints are found in euchromatin, and the breakpoints are clustered in just a few regions of the chromosome that closely match regions identified as intercalary heterochromatin. The results support the Laird hypothesis that intercalary heterochromatin can explain fragile sites in mitotic chromosomes, including fragile X. Opened rings also were recovered after male larvae were exposed to X-rays. This method was much less efficient and produced chromosomes with a strikingly different array of breakpoints, with almost all located in heterochromatin. A series of circularly permuted linear X chromosomes was generated that may be useful for investigating aspects of chromosome behavior, such as crossover distribution and interference in meiosis, or questions of nuclear organization and function.KEYWORDS dicentric chromosome; intercalary heterochromatin; fragile X; FLP D ROSOPHILA is noted for a combination of facile genetics and high-resolution cytology that allows the recovery and characterization of a variety of chromosome rearrangements. Simple structural changes such as duplications, deficiencies, inversions, and translocations are readily produced through a variety of classical and modern techniques. More complex rearrangements such as balancers, compound chromosomes, and ring chromosomes also have been generated. Ring chromosomes historically have been of interest for a number of unique properties, such as a propensity for loss during early embryonic mitoses and dominant zygotic lethality (Leigh 1976;Ashburner et al. 2005). Despite their "instability," ring chromosome stocks can be remarkably stable, with very few reported instances of spontaneous opening into linear chromosomes.In this work, we produced a number of linearized ring chromosomes. One goal was to determine whether there are preferred sites of breakage for dicentric chromosomes. Although we have previously shown that dicentric Y, 3, and 4 chromosomes can break and heal in the male germline and be recovered in offspring, these chromosomes allowed little opportunity to determine whether there were preferred sites of breakage (Ahmad and Golic 1998; Golic 2008, 2010;Titen et al. 2014). In the case of the Y chromosome, low r...

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Section: Discussionmentioning

confidence: 99%

Preferential Breakpoints in the Recovery of Broken Dicentric Chromosomes inDrosophila melanogaster

Hill¹,

Golic

2015

Genetics

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“…Glaser et al (1992) reported evidence the forks do not build up in the transition zones between euchromatin and heterochromatin. Yarosh and Spradling (2014) analyzed whole-genome sequence from salivary glands, and found numerous deletions spanning zones of underreplication. They concluded that blocked forks break,…”

Section: Repair Of Damage Encountered During Replicationmentioning

confidence: 99%

DNA Repair inDrosophila: Mutagens, Models, and Missing Genes

2017

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The numerous processes that damage DNA are counterbalanced by a complex network of repair pathways that, collectively, can mend diverse types of damage. Insights into these pathways have come from studies in many different organisms, including Drosophila melanogaster. Indeed, the first ideas about chromosome and gene repair grew out of Drosophila research on the properties of mutations produced by ionizing radiation and mustard gas. Numerous methods have been developed to take advantage of Drosophila genetic tools to elucidate repair processes in whole animals, organs, tissues, and cells. These studies have led to the discovery of key DNA repair pathways, including synthesis-dependent strand annealing, and DNA polymerase theta-mediated end joining. Drosophila appear to utilize other major repair pathways as well, such as base excision repair, nucleotide excision repair, mismatch repair, and interstrand crosslink repair. In a surprising number of cases, however, DNA repair genes whose products play important roles in these pathways in other organisms are missing from the Drosophila genome, raising interesting questions for continued investigations.

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“…Consistent with S phase resets, polytene cells in Dipterans generally show "underreplication" of satellite-rich regions of centromeric heterochromatin, whereas Drosophila and some other higher Dipteran species also underreplicate-specific euchromatic regions that normally duplicate late in S phase (Gall et al 1971;Hammond and Laird 1985;Karpen and Spradling 1990;Spradling 1993;Moshkin et al 2001;Belyakin et al 2005;Nordman et al 2011;Yarosh and Spradling 2014). Drosophila euchromatic unfinished replication (UR) regions were originally characterized in the larval salivary gland, but most of the same major regions undergo UR in other polytene tissues examined, including larval midgut, larval fat body, and adult ovary (Nordman et al 2011;Yarosh and Spradling 2014).…”

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confidence: 91%

Polytene Chromosome Structure and Somatic Genome Instability

Spradling

2017

Cold Spring Harb Symp Quant Biol

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Polytene chromosomes have for 80 years provided the highest resolution view of interphase genome structure in an animal cell nucleus. These chromosomes represent the normal genomic state of nearly all Drosophila larval and many adult cells, and a better understanding of their striking banded structure has been sought for decades. A more recently appreciated characteristic of Drosophila polytene cells is somatic genome instability caused by unfinished replication (UR). Repair of stalled forks generates enough deletions in polytene salivary gland cells to alter 10%-90% of the DNA strands within more than 100 UR regions comprising 20% of the euchromatic genome. We accurately map UR regions and show that most approximate large polytene bands, indicating that replication forks frequently stall near band boundaries in late S phase. Chromosome conformation capture has recently identified dense topologically associated domains (TADs) in many genomes and most UR bands are similar or slightly smaller than a cognate Drosophila TAD. We argue that bands serve the evolutionarily ancient function of coordinating genome replication with local gene activity. We also discuss the relatively recent evolution of polyteny and somatic instability in Diptera and propose that these processes helped propel the amazing success of two-winged flies in becoming the most ecologically diverse insect group, with 200 times the number of species as mammals.

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Incomplete replication generates somatic DNA alterations within Drosophila polytene salivary gland cells

Cited by 74 publications

References 51 publications

Preferential Breakpoints in the Recovery of Broken Dicentric Chromosomes inDrosophila melanogaster

Preferential Breakpoints in the Recovery of Broken Dicentric Chromosomes inDrosophila melanogaster

DNA Repair inDrosophila: Mutagens, Models, and Missing Genes

Polytene Chromosome Structure and Somatic Genome Instability

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