Chromosome complement, C-banding, Ag-NOR and replication banding in the zebrafishDanio reio

Daga, Rafael R.; Thode, G.; Amores, Angel

doi:10.1007/bf02254941

Cited by 56 publications

(51 citation statements)

References 13 publications

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“…S2). The long arm of Chromosome 4 was late replicating in 28 hpf embryos, which is consistent with previously published cytological data (Daga et al 1996;Sola and Gornung 2001;Anderson et al 2012). To further validate our results, an independent experimental replicate of 28 hpf embryos was generated.…”

Section: Resultssupporting

confidence: 91%

DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation

et al. 2017

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In dividing cells, DNA replication occurs in a precise order, but many questions remain regarding the mechanisms of replication timing establishment and regulation. We now have generated genome-wide, high-resolution replication timing maps throughout zebrafish development. Unexpectedly, in the rapid cell cycles preceding the midblastula transition, a defined timing program was present that predicted the initial wave of zygotic transcription. Replication timing was thereafter progressively and continuously remodeled across the majority of the genome, and epigenetic changes involved in enhancer activation frequently paralleled developmental changes in replication timing. The long arm of Chromosome 4 underwent a dramatic developmentally regulated switch to late replication during gastrulation, reminiscent of mammalian X Chromosome inactivation. This study reveals that replication timing is dynamic and tightly linked to epigenetic and transcriptional changes throughout early zebrafish development. These data provide insight into the regulation and functions of replication timing and will enable further mechanistic studies.

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Section: Resultssupporting

confidence: 91%

DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation

et al. 2017

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“…Cytogeneticists numbered zebrafish chromosomes based on physical length (Pijnacker and Ferwerda 1995;Daga et al 1996;Gornung et al 1997Gornung et al , 2000Amores and Postlethwait 1999;Sola and Gornung 2001), so zebrafish genetic linkage group number and cytogenetic chromosome number are generally not the same. We assigned genetic linkage groups to physical chromosomes by fluorescent in situ hybridization (Phillips et al 2006), which showed that, for example, cytogenetic chromosome 3 is linkage group 4, called chromosome 4 in the reference genome and Chr4 in this work.…”

Section: Rad-tag Genotypingmentioning

confidence: 99%

“…Zebrafish does not, however, have a typical environmental sex-determination (ESD) mechanism like some sauropsids for which temperature is a cue (Charnier 1966;Lang and Andrews 1994;Merchant-Larios and Diaz-Hernandez 2013;Mork et al 2014). It is more probable that zebrafish is like medaka (Oryzias latipes) in having a genetic sex-determination mechanism that is sensitive to environmental conditions (Hattori et al 2007; Sato et al 2005;Selim et al 2009;Hayashi et al 2010).Zebrafish not only lacks classic ESD, but most stocks investigated do not have cytogenetically detectable chromosomal sex determination (Schreeb et al 1993;Pijnacker and Ferwerda 1995;Daga et al 1996;Gornung et al 1997;Amores and Postlethwait 1999;Gornung et al 2000;Sola and Gornung 2001;Traut and Winking 2001;Phillips et al 2006). In contrast, the only investigation of zebrafish taken directly from nature in India concluded that zebrafish females are the heterogametic sex (Sharma et al 1998).…”

mentioning

confidence: 99%

“…Zebrafish linkage group numbers assigned based on genetic length (Postlethwait et al 1994;Johnson et al 1996) are given the name "chromosome" in the Zv9 version of the zebrafish reference genome; here we abbreviate "linkage group" as Chr according to zebrafish nomenclature conventions (https:// wiki.zfin.org/display/general/zfin+zebrafish+nomenclature+ guidelines). Cytogeneticists numbered zebrafish chromosomes based on physical length (Pijnacker and Ferwerda 1995;Daga et al 1996;Gornung et al 1997Gornung et al , 2000Amores and Postlethwait 1999;Sola and Gornung 2001), so zebrafish genetic linkage group number and cytogenetic chromosome number are generally not the same. We assigned genetic linkage groups to physical chromosomes by fluorescent in situ hybridization (Phillips et al 2006), which showed that, for example, cytogenetic chromosome 3 is linkage group 4, called chromosome 4 in the reference genome and Chr4 in this work.…”

mentioning

confidence: 99%

“…Zebrafish not only lacks classic ESD, but most stocks investigated do not have cytogenetically detectable chromosomal sex determination (Schreeb et al 1993;Pijnacker and Ferwerda 1995;Daga et al 1996;Gornung et al 1997;Amores and Postlethwait 1999;Gornung et al 2000;Sola and Gornung 2001;Traut and Winking 2001;Phillips et al 2006). In contrast, the only investigation of zebrafish taken directly from nature in India concluded that zebrafish females are the heterogametic sex (Sharma et al 1998).…”

mentioning

confidence: 99%

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Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains

et al. 2014

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Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RADtag population genomics to identify sex-linked polymorphisms. After verifying this "RAD-sex" method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, "male genotypes" became males and some "female genotypes" also became males, suggesting that the environment or genetic background can cause female-to-male sex reversal. Surprisingly, TU and AB lacked detectable sex-linked loci. Phylogenomics rooted on D. nigrofasciatus verified that all strains are monophyletic. Because AB and TU branched as a monophyletic clade, we could not rule out shared loss of the wild sex locus in a common ancestor despite their independent domestication. Mitochondrial DNA sequences showed that investigated strains represent only one of the three identified zebrafish haplogroups. Results suggest that zebrafish in nature possess a WZ/ZZ sex-determination mechanism with a major determinant lying near the right telomere of chromosome 4 that was modified during domestication. Strains providing the zebrafish reference genome lack key components of the natural sex-determination system but may have evolved variant sex-determining mechanisms during two decades in laboratory culture.. . .researchers using standard lines of zebrafish that have long been maintained in laboratories are often plagued by severe sex ratio distortions. . .. C. Lawrence, J. P. Ebersole, and R. V. Kesseli (2008) C ONSIDERING the fundamental importance of sex for species propagation, it is surprising that primary sexdetermining mechanisms are not strongly conserved among animal taxa (Bull 1983;Charlesworth 1996;Ming et al. 2011;Bachtrog et al. 2014). Closely related species or even populations of the same species can have different sexdetermining mechanisms (Takehana et al. 2007;Ross et al. 2009;Kobayashi et al. 2013;Heule et al. 2014;Larney et al. 2014). Zebrafish (Danio rerio) is a popular model for studies of vertebrate development, behavior, physiology, evolution, disease, and human health (Mills et al. 2007;Seth et al. 2013;Braasch et al. 2014;Ota and Kawahara 2014;Wilkinson et al. 2014), but researchers struggle with highly variable and distorted sex ratios, and investigations into the genetic nature of zebrafish sex determination are conflicting. To help understand these issues, we conducted a population genomic study of sex determination in multiple zebrafish strains. Zebrafish exhibit...

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Zebrafish Models for Human Diseases and Drug Discovery

Zhong

Liu

Lin

2008

Drug Efficacy, Safety, and Biologics Discovery

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Chromosome complement, C-banding, Ag-NOR and replication banding in the zebrafishDanio reio

Cited by 56 publications

References 13 publications

DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation

DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation

Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains

Zebrafish Models for Human Diseases and Drug Discovery

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