Meiotic analyses show adaptations to maintenance of fertility in X1Y1X2Y2X3Y3X4Y4X5Y5 system of amazon frog Leptodactylus pentadactylus (Laurenti, 1768)

Abstract Heterozygous chromosomal rearrangements can result in failures during the meiotic cycle and the apoptosis of germline, making carrier individuals infertile. The Amazon frog Leptodactylus pentadactylus has a meiotic multivalent, composed of 12 sex chromosomes. The mechanisms by which this multi-chromosome system maintains fertility in males of this species remain undetermined. In this study we investigated the meiotic behavior of this multivalent to understand how synapse, recombination and epigenetic modifications contribute to maintaining fertility and chromosomal sexual determination in this species. Our sample had 2n = 22, with a ring formed by ten chromosomes in meiosis, indicating a new system of sex determination for this species (X1Y1X2Y2X3Y3X4Y4X5Y5). Synapsis occurs in the homologous terminal portion of the chromosomes, while part of the heterologous interstitial regions performed synaptic adjustment. The multivalent center remains asynaptic until the end of pachytene, with interlocks, gaps and rich-chromatin in histone H2A phosphorylation at serine 139 (γH2AX), suggesting transcriptional silence. In late pachytene, paired regions show repair of double strand-breaks (DSBs) with RAD51 homolog 1 (Rad51). These findings suggest that Rad51 persistence creates positive feedback at the pachytene checkpoint, allowing meiosis I to progress normally. Additionally, histone H3 trimethylation at lysine 27 in the pericentromeric heterochromatin of this anuran can suppress recombination in this region, preventing failed chromosomal segregation. Taken together, these results indicate that these meiotic adaptations are required for maintenance of fertility in L. pentadactylus.

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Dynamics of RecA-mediated repair of replication-dependent DNA breaks

The Journal of Cell Biology ◽

10.1083/jcb.201803020 ◽

2018 ◽

Vol 217 (7) ◽

pp. 2299-2307 ◽

Cited By ~ 12

Author(s):

Vincent Amarh ◽

Martin A. White ◽

David R.F. Leach

Keyword(s):

Temporal Dynamics ◽

Chromosomal Rearrangements ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Dna Breaks ◽

Chromosomal Locus ◽

Chromosomal Replication ◽

Strand Breaks ◽

Sister Chromosome ◽

Temporal Efficiency

Chromosomal replication is the major source of spontaneous DNA double-strand breaks (DSBs) in living cells. Repair of these DSBs is essential for cell viability, and accuracy of repair is critical to avoid chromosomal rearrangements. Repair of replication-dependent DSBs occurs primarily by homologous recombination with a sister chromosome. However, this reaction has never been visualized at a defined chromosomal locus, so little is known about its spatial or temporal dynamics. Repair of a replication-independent DSB generated in Escherichia coli by a rare-cutting endonuclease leads to the formation of a bundle of RecA filaments. In this study, we show that in contrast, repair of a replication-dependent DSB involves a transient RecA focus localized in the central region of the cell in which the DNA is replicated. The recombining loci remain centrally located with restricted movement before segregating with little extension to the period of postreplicative sister-chromosome cohesion. The spatial and temporal efficiency of this reaction is remarkable.

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COMMD4 Functions with the Histone H2A-H2B Dimer for the Timely Repair of DNA Double Strand Breaks

SSRN Electronic Journal ◽

10.2139/ssrn.3516893 ◽

2020 ◽

Cited By ~ 1

Author(s):

Amila Suraweera ◽

Neha Gandhi ◽

Sam Beard ◽

Joshua Burgess ◽

Ali Naqi ◽

...

Keyword(s):

Double Strand Breaks ◽

Histone H2a ◽

Dna Double Strand Breaks ◽

Strand Breaks

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Genome-Wide Amplifications Caused by Chromosomal Rearrangements Play a Major Role in the Adaptive Evolution of Natural Yeast

Genetics ◽

10.1093/genetics/165.4.1745 ◽

2003 ◽

Vol 165 (4) ◽

pp. 1745-1759 ◽

Cited By ~ 1

Author(s):

Juan J Infante ◽

Kenneth M Dombek ◽

Laureana Rebordinos ◽

Jesús M Cantoral ◽

Elton T Young

Keyword(s):

Adaptive Evolution ◽

Chromosomal Rearrangements ◽

Sexual Isolation ◽

Chromosomal Evolution ◽

Double Strand Breaks ◽

Chromosomal Dna ◽

Strand Breaks ◽

Yeast Strains ◽

Gross Chromosomal Rearrangements ◽

Flor Yeast

Abstract The relative importance of gross chromosomal rearrangements to adaptive evolution has not been precisely defined. The Saccharomyces cerevisiae flor yeast strains offer significant advantages for the study of molecular evolution since they have recently evolved to a high degree of specialization in a very restrictive environment. Using DNA microarray technology, we have compared the genomes of two prominent variants of S. cerevisiae flor yeast strains. The strains differ from one another in the DNA copy number of 116 genomic regions that comprise 38% of the genome. In most cases, these regions are amplicons flanked by repeated sequences or other recombination hotspots previously described as regions where double-strand breaks occur. The presence of genes that confer specific characteristics to the flor yeast within the amplicons supports the role of chromosomal rearrangements as a major mechanism of adaptive evolution in S. cerevisiae. We propose that nonallelic interactions are enhanced by ethanol- and acetaldehyde-induced double-strand breaks in the chromosomal DNA, which are repaired by pathways that yield gross chromosomal rearrangements. This mechanism of chromosomal evolution could also account for the sexual isolation shown among the flor yeast.

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An Efficient Method to Generate Chromosomal Rearrangements by Targeted DNA Double-Strand Breaks in Drosophila melanogaster

Genome Research ◽

10.1101/gr.2279804 ◽

2004 ◽

Vol 14 (7) ◽

pp. 1382-1393 ◽

Cited By ~ 22

Author(s):

D. Egli

Keyword(s):

Drosophila Melanogaster ◽

Efficient Method ◽

Chromosomal Rearrangements ◽

Double Strand Breaks ◽

Dna Double Strand Breaks ◽

Strand Breaks

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Reciprocal Translocations in Saccharomyces cerevisiae Formed by Nonhomologous End Joining

Genetics ◽

10.1093/genetics/166.2.741 ◽

2004 ◽

Vol 166 (2) ◽

pp. 741-751 ◽

Cited By ~ 1

Author(s):

Xin Yu ◽

Abram Gabriel

Keyword(s):

Saccharomyces Cerevisiae ◽

Chromosomal Rearrangements ◽

Double Strand Breaks ◽

Open Reading Frames ◽

Nonhomologous End Joining ◽

Wild Type ◽

End Joining ◽

Reciprocal Translocations ◽

Strand Breaks ◽

Reading Frames

Abstract Reciprocal translocations are common in cancer cells, but their creation is poorly understood. We have developed an assay system in Saccharomyces cerevisiae to study reciprocal translocation formation in the absence of homology. We induce two specific double-strand breaks (DSBs) simultaneously on separate chromosomes with HO endonuclease and analyze the subsequent chromosomal rearrangements among surviving cells. Under these conditions, reciprocal translocations via nonhomologous end joining (NHEJ) occur at frequencies of ∼2-7 × 10-5/cell exposed to the DSBs. Yku80p is a component of the cell’s NHEJ machinery. In its absence, reciprocal translocations still occur, but the junctions are associated with deletions and extended overlapping sequences. After induction of a single DSB, translocations and inversions are recovered in wild-type and rad52 strains. In these rearrangements, a nonrandom assortment of sites have fused to the DSB, and their junctions show typical signs of NHEJ. The sites tend to be between open reading frames or within Ty1 LTRs. In some cases the translocation partner is formed by a break at a cryptic HO recognition site. Our results demonstrate that NHEJ-mediated reciprocal translocations can form in S. cerevisiae as a consequence of DSB repair.

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A Phosphorylated Histone H2A Variant Displays Properties of Chromatin Insulator Proteins in Drosophila

10.1101/2021.02.23.432395 ◽

2021 ◽

Author(s):

James R. Simmons ◽

Ran An ◽

Bright Amankwaa ◽

Shannon Zayac ◽

Justin Kemp ◽

...

Keyword(s):

Genome Stability ◽

Double Strand Breaks ◽

Histone H2a ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Chromatin Insulator ◽

Long Range Interactions ◽

Insulator Proteins ◽

Tight Association ◽

Insulator Body

AbstractChromatin insulators are responsible for mediating long-range interactions between enhancers and promoters throughout the genome and align with the boundaries of topologically associating domains (TADs). Here, we demonstrate an interaction between proteins that associate with the gypsy insulator and the phosphorylated histone variant H2Av (γH2Av), a marker of DNA double strand breaks. Gypsy insulator components colocalize with γH2Av throughout the genome. Mutation of insulator components prevents stable H2Av phosphorylation in polytene chromatin. Phosphatase inhibition strengthens the association between insulator components and γH2Av and rescues γH2Av localization in insulator mutants. We also show that γH2Av is a component of insulator bodies, and that phosphatase activity is required for insulator body dissolution after recovery from osmotic stress. We further demonstrate a tight association between γH2Av and TAD boundaries. Together, our results indicate a novel mechanism linking insulator function with a histone H2A variant and with genome stability.

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The Deubiquitylating Enzyme USP44 Counteracts the DNA Double-strand Break Response Mediated by the RNF8 and RNF168 Ubiquitin Ligases

Journal of Biological Chemistry ◽

10.1074/jbc.m113.459917 ◽

2013 ◽

Vol 288 (23) ◽

pp. 16579-16587 ◽

Cited By ~ 78

Author(s):

Anna Mosbech ◽

Claudia Lukas ◽

Simon Bekker-Jensen ◽

Niels Mailand

Keyword(s):

Ring Finger ◽

Ubiquitin Ligases ◽

Strand Break ◽

Double Strand Breaks ◽

Histone H2a ◽

Dna Double Strand Breaks ◽

Strand Breaks ◽

Dna Double Strand Break ◽

Dependent Protein ◽

Protein Recruitment

Protein recruitment to DNA double-strand breaks (DSBs) relies on ubiquitylation of the surrounding chromatin by the RING finger ubiquitin ligases RNF8 and RNF168. Flux through this pathway is opposed by several deubiquitylating enzymes (DUBs), including OTUB1 and USP3. By analyzing the effect of individually overexpressing the majority of human DUBs on RNF8/RNF168-mediated 53BP1 retention at DSB sites, we found that USP44 and USP29 powerfully inhibited this response at the level of RNF168 accrual. Both USP44 and USP29 promoted efficient deubiquitylation of histone H2A, but unlike USP44, USP29 displayed nonspecific reactivity toward ubiquitylated substrates. Moreover, USP44 but not other H2A DUBs was recruited to RNF168-generated ubiquitylation products at DSB sites. Individual depletion of these DUBs only mildly enhanced accumulation of ubiquitin conjugates and 53BP1 at DSBs, suggesting considerable functional redundancy among cellular DUBs that restrict ubiquitin-dependent protein assembly at DSBs. Our findings implicate USP44 in negative regulation of the RNF8/RNF168 pathway and illustrate the usefulness of DUB overexpression screens for identification of antagonizers of ubiquitin-dependent cellular responses.

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Frequency of DNA end joining in trans is not determined by the predamage spatial proximity of double-strand breaks in yeast

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1818595116 ◽

2019 ◽

Vol 116 (19) ◽

pp. 9481-9490 ◽

Cited By ~ 3

Author(s):

Sham Sunder ◽

Thomas E. Wilson

Keyword(s):

Chromosomal Rearrangements ◽

Double Strand Breaks ◽

Yeast Cells ◽

Spatial Distance ◽

Spatial Proximity ◽

Dna Double Strand Breaks ◽

End Joining ◽

Strand Breaks ◽

Repair Efficiency ◽

In Trans

DNA double-strand breaks (DSBs) are serious genomic insults that can lead to chromosomal rearrangements if repaired incorrectly. To gain insight into the nuclear mechanisms contributing to these rearrangements, we developed an assay in yeast to measure cis (same site) vs. trans (different site) repair for the majority process of precise nonhomologous end joining (NHEJ). In the assay, the HO endonuclease gene is placed between two HO cut sites such that HO expression is self-terminated upon induction. We further placed an additional cut site in various genomic loci such that NHEJ in trans led to expression of a LEU2 reporter gene. Consistent with prior reports, cis NHEJ was more efficient than trans NHEJ. However, unlike homologous recombination, where spatial distance between a single DSB and donor locus was previously shown to correlate with repair efficiency, trans NHEJ frequency remained essentially constant regardless of the position of the two DSB loci, even when they were on the same chromosome or when two trans repair events were put in competition. Repair of similar DSBs via single-strand annealing of short terminal direct repeats showed substantially higher repair efficiency and trans repair frequency, but still without a strong correlation of trans repair to genomic position. Our results support a model in which yeast cells mobilize, and perhaps compartmentalize, multiple DSBs in a manner that no longer reflects the predamage position of two broken loci.

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COMMD4 functions with the histone H2A-H2B dimer for the timely repair of DNA double-strand breaks

Communications Biology ◽

10.1038/s42003-021-01998-2 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Amila Suraweera ◽

Neha S. Gandhi ◽

Sam Beard ◽

Joshua T. Burgess ◽

Laura V. Croft ◽

...

Keyword(s):

Molecular Mechanisms ◽

Peptide Mapping ◽

Genomic Stability ◽

Double Strand Breaks ◽

Histone H2a ◽

Dna Double Strand Breaks ◽

Critical Function ◽

Strand Breaks ◽

Break Site ◽

Non Homologous End Joining

AbstractGenomic stability is critical for normal cellular function and its deregulation is a universal hallmark of cancer. Here we outline a previously undescribed role of COMMD4 in maintaining genomic stability, by regulation of chromatin remodelling at sites of DNA double-strand breaks. At break-sites, COMMD4 binds to and protects histone H2B from monoubiquitination by RNF20/RNF40. DNA damage-induced phosphorylation of the H2A-H2B heterodimer disrupts the dimer allowing COMMD4 to preferentially bind H2A. Displacement of COMMD4 from H2B allows RNF20/40 to monoubiquitinate H2B and for remodelling of the break-site. Consistent with this critical function, COMMD4-deficient cells show excessive elongation of remodelled chromatin and failure of both non-homologous-end-joining and homologous recombination. We present peptide-mapping and mutagenesis data for the potential molecular mechanisms governing COMMD4-mediated chromatin regulation at DNA double-strand breaks.

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