iFISH:a publically available resource enabling versatile DNA FISH to study genome architecture

Crosetto, Nicola; Bienko, Magda; Gelali, Eleni; Girelli, Gabriele; Matsumoto, Masahiro; Wernersson, Erik; Custodio, Joaquín; Mota, Ana; Schweitzer, Maud; Ferenc, Katalin; Li, Xinge; Mirzazadeh, Reza; Agostini, Federico; Schell, John P.; Lanner, Fredrik

doi:10.1038/protex.2019.028

Cited by 4 publications

(3 citation statements)

References 1 publication

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“…Probes were produced as described previously (73) with slight modi cations. Brie y, oligo libraries were ampli ed by real-time PCR using PerfeCTa SYBR Green Fastmix (Quantabio, Beverly, MA, USA) in a LightCycler 480 II (Roche, Rotkreuz, Switzerland) to analyze ampli cation curves.…”

Section: Probe Synthesismentioning

confidence: 99%

“…Brie y, oligo libraries were ampli ed by real-time PCR using PerfeCTa SYBR Green Fastmix (Quantabio, Beverly, MA, USA) in a LightCycler 480 II (Roche, Rotkreuz, Switzerland) to analyze ampli cation curves. Reagents were added as described elsewhere (73). The T7 RNA polymerase recognition site was added with reverse primers (5' end)…”

Section: Probe Synthesismentioning

confidence: 99%

“…Puri ed RNA was reverse-transcribed using Maxima H Minus Reverse Transcriptase as described previously (73) with 5 µg of template RNA in 20 µL total reaction volume. Complementary DNA was puri ed using Zymo-Spin IC Columns (Cedarlane, Burlington, ON, Canada) and quanti ed using a NanoDrop One (ThermoFisher Scienti c, ON, Canada) according to the manufacturer's instructions.…”

Section: Probe Synthesismentioning

confidence: 99%

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Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights

Poisson

Prunier

Carrier

et al. 2022

Preprint

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Background:Genome assembly into chromosomes facilitates several analyses including cytogenetics, genomics and phylogenetics. Despite rapid development in bioinformatics, however, assembly beyond scaffolds remains challenging, especially in species without closely related well-assembled and available reference genomes. So far, four draft genomes of Rangifer tarandus (caribou or reindeer, a circumpolar distributed cervid species) have been published, but none with chromosome-level assembly. This emblematic northern species is of high interest in ecological studies and conservation since most populations are declining. Results:We have designed specific probes based on Oligopaint FISH technology to upgrade the latest published reindeer and caribou chromosome-level genomes. Using this oligonucleotide-based method, we found six mis-assembled scaffolds and physically mapped 68 of the largest scaffolds representing 78% of the most recent R. tarandus genome assembly. Combining physical mapping and comparative genomics, it was possible to document chromosomal evolution among Cervidaeand closely related bovids. Conclusions:Our results provide validation for the current chromosome-level genome assembly as well as resources to use chromosome banding in studies of Rangifer tarandus.

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Section: Probe Synthesismentioning

confidence: 99%

Section: Probe Synthesismentioning

confidence: 99%

Section: Probe Synthesismentioning

confidence: 99%

See 1 more Smart Citation

Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights

Poisson

Prunier

Carrier

et al. 2022

Preprint

View full text Add to dashboard Cite

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iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture

Gelali

Girelli

Matsumoto³

et al. 2019

Nat Commun

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DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. At present, there is a lack of free resources of DNA FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 DNA FISH probes targeting multiple loci on the human autosomes and chromosome X, as well as a genome-wide database of optimally designed oligonucleotides and a freely accessible web interface ( http://ifish4u.org ) that can be used to design DNA FISH probes. We individually validate 153 probes and take advantage of our probe repository to quantify the extent of intermingling between multiple heterologous chromosome pairs, showing a much higher extent of intermingling in human embryonic stem cells compared to fibroblasts. In conclusion, iFISH is a versatile and expandable resource, which can greatly facilitate the use of DNA FISH in research and diagnostics.

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Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding

et al. 2023

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Background The frequency of chromosomal rearrangements in Canadian breeding boars has been estimated at 0.91 to 1.64%. These abnormalities are widely recognized as a potential cause of subfertility in livestock production. Since artificial insemination is practiced in almost all intensive pig production systems, the use of elite boars carrying cytogenetic defects that have an impact on fertility can lead to major economic losses. To avoid keeping subfertile boars in artificial insemination centres and spreading chromosomal defects within populations, cytogenetic screening of boars is crucial. Different techniques are used for this purpose, but several issues are frequently encountered, i.e. environmental factors can influence the quality of results, the lack of genomic information outputted by these techniques, and the need for prior cytogenetic skills. The aim of this study was to develop a new pig karyotyping method based on fluorescent banding patterns. Results The use of 207,847 specific oligonucleotides generated 96 fluorescent bands that are distributed across the 18 autosomes and the sex chromosomes. Tested alongside conventional G-banding, this oligo-banding method allowed us to identify four chromosomal translocations and a rare unbalanced chromosomal rearrangement that was not detected by conventional banding. In addition, this method allowed us to investigate chromosomal imbalance in spermatozoa. Conclusions The use of oligo-banding was found to be appropriate for detecting chromosomal aberrations in a Canadian pig nucleus and its convenient design and use make it an interesting tool for livestock karyotyping and cytogenetic studies.

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iFISH:a publically available resource enabling versatile DNA FISH to study genome architecture

Cited by 4 publications

References 1 publication

Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights

Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights

iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture

Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding

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