Germ cell-specific DNA methylation and genome diploidization in primitive vertebrates

Zhang

et al. 2018

BMC Genomics

Self Cite

BackgroundIn somatic cells, homologous recombination (HR) is a rare event caused by eventual DNA double-strand breaks (DSBs). In contrast, germ cells show high frequency of HR caused by programmed DSBs. Microsatellites are prone to DSBs during genome replication and, thereby, capable of promoting HR. It remains unclear whether HR occurs frequently at microsatellites both in normal somatic cells and germ cells in a similar manner.ResultsBy examining the linkage pattern of multiple paternal and maternal markers flanking innate GT microsatellites, we measured HR at the GT microsatellites in various somatic cells and germ cells in a goldfish intraspecific heterozygote. During embryogenesis, the HR products accumulate gradually with the increase of the number of cell divisions. The frequency of HR at the GT microsatellites in advanced embryos, adult tissues and germ cells is surprisingly high. The type of exchanges between the homologous chromosomes is similar in normal advanced embryos and germ cells. Furthermore, a long GT microsatellite is more active than a short one in promoting HR in both somatic and germ cells.ConclusionsHR occurs frequently at innate GT microsatellites in normal somatic cells and germ cells in a similar manner.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4758-y) contains supplementary material, which is available to authorized users.

Section: Methodsmentioning

confidence: 99%

Homologous recombination occurs frequently at innate GT microsatellites in normal somatic and germ cells in vivo

Zhang

et al. 2018

BMC Genomics

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“…Bisexual diploid goldfish ( C. auratus ) and unisexual polyploid goldfish ( C. auratus pengze) were purchased from nearby farms and maintained in our laboratory in the breeding season. Artificial spawning and fertilization were performed as previously reported [20]. This study was approved by the Ethics Committee of Laboratory Animal Center of Zhejiang University (Zju201306-1-11-060).…”

Section: Methodsmentioning

confidence: 99%

“…The survival rate was accounted at 1 day post fertilization (dpf). Genomic DNA from single 4 dpf embryos was extracted following our previously reported procedure [20]. A ∼470bp DNA fragment (in wild type) encompassing the TALEN target site and the TR region was amplified by PCR using the primers as follows: 5'-TCCTGTTCAATGTGTTTTATCAGTATGC-3' (forward) and 5'-CTTAATTTCTTCATGTTGTTCTAATGCAA-3' (reverse).…”

Section: Methodsmentioning

confidence: 99%

Tandem Repeat Modification during Double-Strand Break Repair Induced by an Engineered TAL Effector Nuclease in Zebrafish Genome

Huang

et al. 2013

PLoS ONE

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Tandem repeats (TRs) are abundant and widely distributed in eukaryotic genomes. TRs are thought to have various functions in gene transcription, DNA methylation, nucleosome position and chromatin organization. Variation of repeat units in the genome is observed in association with a number of diseases, such as Fragile X Syndrome, Huntington's disease and Friedreich's ataxia. However, the underlying mechanisms involved are poorly understood, largely owing to the technical limitations in modification of TRs at definite sites in the genome in vivo. Transcription activator-like effector nucleases (TALENs) are widely used in recent years in gene targeting for their specific binding to target sequences when engineered in vitro. Here, we show that the repair of a double-strand break (DSB) induced by TALENs adjacent to a TR can produce serial types of mutations in the TR region. Sequencing analysis revealed that there are three types of mutations induced by the DSB repair, including indels only within the TR region or within the flanking TALEN target region or simutaneously within both regions. Therefore, desired TR mutant types can be conveniently obtained by using engineered TALENs. These results demonstrate that TALENs can serve as a convenient tool for modifying TRs in the genome in studying the functions of TRs.

“…In the promoter of no tail ( ntl ), there is a CpG island close to the transcription start site and a conserved GT microsatellite at the upstream region in both zebrafish and goldfish a key developmental regulatory gene. Previous study has observed that this CpG island is highly methylated in the eggs of zebrafish and a bisexual diploid goldfish strain, C. auratus auratus , but unmethylated in the eggs of a unisexual polyploid goldfish strain, C. auratus pengze [28]. During embryogenesis, goldfish and zebrafish maternally methylated ntl CpG islands undergo demethylation first, followed by de novo methylation of both maternal and paternal alleles [28,29], indicating that ntl is a non-imprinted locus.…”

Section: Introductionmentioning

confidence: 99%

A Long Polymorphic GT Microsatellite within a Gene Promoter Mediates Non-Imprinted Allele-Specific DNA Methylation of a CpG Island in a Goldfish Inter-Strain Hybrid

Cao

2019

IJMS

It is now widely accepted that allele-specific DNA methylation (ASM) commonly occurs at non-imprinted loci. Most of the non-imprinted ASM regions observed both within and outside of the CpG island show a strong correlation with DNA polymorphisms. However, what polymorphic cis-acting elements mediate non-imprinted ASM of the CpG island remains unclear. In this study, we investigated the impact of polymorphic GT microsatellites within the gene promoter on non-imprinted ASM of the local CpG island in goldfish. We generated various goldfish heterozygotes, in which the length of GT microsatellites or some non-repetitive sequences in the promoter of no tail alleles was different. By examining the methylation status of the downstream CpG island in these heterozygotes, we found that polymorphisms of a long GT microsatellite can lead to the ASM of the downstream CpG island during oogenesis and embryogenesis, polymorphisms of short GT microsatellites and non-repetitive sequences in the promoter exhibited no significant effect on the methylation of the CpG island. We also observed that the ASM of the CpG island was associated with allele-specific expression in heterozygous embryos. These results suggest that a long polymorphic GT microsatellite within a gene promoter mediates non-imprinted ASM of the local CpG island in a goldfish inter-strain hybrid.