Rapid and inexpensive preparation of genome-wide nucleosome footprints from model and non-model organisms

Abstract Background 2-Oxoglutarate and Fe(II)-dependent dioxygenases (2ODDs) belong to the 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily and are involved in various vital metabolic pathways of plants at different developmental stages. These proteins have been extensively investigated in multiple model organisms. However, these enzymes have not been systematically analyzed in tomato. In addition, type I flavone synthase (FNSI) belongs to the 2ODD family and contributes to the biosynthesis of flavones, but this protein has not been characterized in tomato. Results A total of 131 2ODDs from tomato were identified and divided into seven clades by phylogenetic classification. The Sl2ODDs in the same clade showed similar intron/exon distributions and conserved motifs. The Sl2ODDs were unevenly distributed across the 12 chromosomes, with different expression patterns among major tissues and at different developmental stages of the tomato growth cycle. We characterized several Sl2ODDs and their expression patterns involved in various metabolic pathways, such as gibberellin biosynthesis and catabolism, ethylene biosynthesis, steroidal glycoalkaloid biosynthesis, and flavonoid metabolism. We found that the Sl2ODD expression patterns were consistent with their functions during the tomato growth cycle. These results indicated the significance of Sl2ODDs in tomato growth and metabolism. Based on this genome-wide analysis of Sl2ODDs, we screened six potential FNSI genes using a phylogenetic tree and coexpression analysis. However, none of them exhibited FNSI activity. Conclusions Our study provided a comprehensive understanding of the tomato 2ODD family and demonstrated the significant roles of these family members in plant metabolism. We also suggest that no FNSI genes in tomato contribute to the biosynthesis of flavones.

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Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

Genes ◽

10.3390/genes12071074 ◽

2021 ◽

Vol 12 (7) ◽

pp. 1074

Author(s):

Joanna Grzegorczyk ◽

Artur Gurgul ◽

Maria Oczkowicz ◽

Tomasz Szmatoła ◽

Agnieszka Fornal ◽

...

Keyword(s):

Genotyping By Sequencing ◽

Read Depth ◽

Model Organisms ◽

Single Nucleotide Polymorphism Discovery ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Polymorphism Discovery ◽

Genome Wide ◽

Plumage Development ◽

Edar Gene

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.

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Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments

Nature Communications ◽

10.1038/s41467-021-25411-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Puneet Sharma ◽

Jie Wu ◽

Benedikt S. Nilges ◽

Sebastian A. Leidel

Keyword(s):

Human Cells ◽

Ribosome Profiling ◽

Model Organisms ◽

Treatment Conditions ◽

Genome Wide ◽

Optimized Protocol ◽

Gene Level ◽

Translation Inhibitor ◽

Species Specific ◽

Conformational Restrictions

AbstractRibosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments.

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On the Diversification of the Translation Apparatus across Eukaryotes

Comparative and Functional Genomics ◽

10.1155/2012/256848 ◽

2012 ◽

Vol 2012 ◽

pp. 1-14 ◽

Cited By ~ 5

Author(s):

Greco Hernández ◽

Christopher G. Proud ◽

Thomas Preiss ◽

Armen Parsyan

Keyword(s):

Model Organisms ◽

Ecological Niches ◽

Translational Machinery ◽

Functional Differences ◽

Profound Knowledge ◽

Genome Wide ◽

Translation Apparatus ◽

Fundamental Process ◽

Organismal Complexity ◽

Living Organisms

Diversity is one of the most remarkable features of living organisms. Current assessments of eukaryote biodiversity reaches 1.5 million species, but the true figure could be several times that number. Diversity is ingrained in all stages and echelons of life, namely, the occupancy of ecological niches, behavioral patterns, body plans and organismal complexity, as well as metabolic needs and genetics. In this review, we will discuss that diversity also exists in a key biochemical process, translation, across eukaryotes. Translation is a fundamental process for all forms of life, and the basic components and mechanisms of translation in eukaryotes have been largely established upon the study of traditional, so-called model organisms. By using modern genome-wide, high-throughput technologies, recent studies of many nonmodel eukaryotes have unveiled a surprising diversity in the configuration of the translation apparatus across eukaryotes, showing that this apparatus is far from being evolutionarily static. For some of the components of this machinery, functional differences between different species have also been found. The recent research reviewed in this article highlights the molecular and functional diversification the translational machinery has undergone during eukaryotic evolution. A better understanding of all aspects of organismal diversity is key to a more profound knowledge of life.

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Analysis of genetic dominance in the UK Biobank

10.1101/2021.08.15.456387 ◽

2021 ◽

Author(s):

Duncan S Palmer ◽

Wei Zhou ◽

Liam Abbott ◽

Nik Baya ◽

Claire Churchhouse ◽

...

Keyword(s):

Complex Traits ◽

Multiple Testing ◽

Model Organisms ◽

Systematic Evaluation ◽

Hair Color ◽

Phenotypic Variance ◽

Additive Effects ◽

Uk Biobank ◽

Genome Wide ◽

The Uk

In classical statistical genetic theory, a dominance effect is defined as the deviation from a purely additive genetic effect for a biallelic variant. Dominance effects are well documented in model organisms. However, evidence in humans is limited to a handful of traits, particularly those with strong single locus effects such as hair color. We carried out the largest systematic evaluation of dominance effects on phenotypic variance in the UK Biobank. We curated and tested over 1,000 phenotypes for dominance effects through GWAS scans, identifying 175 loci at genome-wide significance correcting for multiple testing (P < 4.7 × 10-11). Power to detect non-additive loci is much lower than power to detect additive effects for complex traits: based on the relative effect sizes at genome-wide significant additive loci, we estimate a factor of 20-30 increase in sample size will be necessary to capture clear evidence of dominance similar to those currently observed for additive effects. However, these localised dominance hits do not extend to a significant aggregate contribution to phenotypic variance genome-wide. By deriving a version of LD-score regression to detect dominance effects tagged by common variation genome-wide (minor allele frequency > 0.05), we found no strong evidence of a contribution to phenotypic variance when accounting for multiple testing. Across the 267 continuous and 793 binary traits the median contribution was 5.73 × 10-4, with unbiased point estimates ranging from -0.261 to 0.131. Finally, we introduce dominance fine-mapping to explore whether the more rapid decay of dominance LD can be leveraged to find causal variants. These results provide the most comprehensive assessment of dominance trait variation in humans to date.

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Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows

10.1101/2020.07.24.220582 ◽

2020 ◽

Cited By ~ 1

Author(s):

Dan Sun ◽

Thomas S. Layman ◽

Hyeonsoo Jeong ◽

Paramita Chatterjee ◽

Kathleen Grogan ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Chromosome Pair ◽

Dna Methyltransferases ◽

Model Organisms ◽

Phenotypic Traits ◽

Zonotrichia Albicollis ◽

Single Nucleotide ◽

Genome Wide ◽

Nucleotide Resolution

ABSTRACTDNA methylation is known to play critical roles in key biological processes. Most of our knowledge on regulatory impacts of DNA methylation has come from laboratory-bred model organisms, which may not exhibit the full extent of variation found in wild populations. Here, we investigated naturally-occurring variation in DNA methylation in a wild avian species, the white-throated sparrow (Zonotrichia albicollis). This species offers exceptional opportunities for studying the link between genetic differentiation and phenotypic traits because of a non-recombining chromosome pair linked to both plumage and behavioral phenotypes. Using novel single-nucleotide resolution methylation maps and gene expression data, we show that DNA methylation and the expression of DNA methyltransferases are significantly higher in adults than in nestlings. Genes for which DNA methylation varied between nestlings and adults were implicated in development and cell differentiation and were located throughout the genome. In contrast, differential methylation between plumage morphs was localized to the non-recombining chromosome pair. One subset of CpGs on the non-recombining chromosome was extremely hypomethylated and localized to transposable elements. Changes in methylation predicted changes in gene expression for both chromosomes. In summary, we demonstrate changes in genome-wide DNA methylation that are associated with development and with specific functional categories of genes in white-throated sparrows. Moreover, we observe substantial DNA methylation reprogramming associated with the suppression of recombination, with implications for genome integrity and gene expression divergence. These results offer an unprecedented view of ongoing epigenetic reprogramming in a wild population.

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Efficient CRISPR/Cas9 genome editing in a salmonid fish cell line using a lentivirus delivery system

10.1101/734442 ◽

2019 ◽

Cited By ~ 2

Author(s):

Remi L. Gratacap ◽

Tim Regan ◽

Carola E. Dehler ◽

Samuel A.M. Martin ◽

Pierre Boudinot ◽

...

Keyword(s):

Disease Resistance ◽

Cell Line ◽

Genome Editing ◽

Target Genes ◽

High Efficiency ◽

Genetic Resistance ◽

Model Organisms ◽

Fish Cell ◽

Genome Wide ◽

Lentivirus Transduction

1AbstractGenome editing is transforming bioscience research, but its application to non-model organisms, such as farmed animal species, requires optimisation. Salmonids are the most important aquaculture species by value, and improving genetic resistance to infectious disease is a major goal. However, use of genome editing to evaluate putative disease resistance genes in cell lines, and the use of genome-wide CRISPR screens is currently limited by a lack of available tools and techniques. In the current study, an optimised protocol using lentivirus transduction for efficient integration of constructs into the genome of a Chinook salmon (Oncorhynchus tshwaytcha) cell line (CHSE-214) was developed. As proof-of-principle, two target genes were edited with high efficiency in an EGFP-Cas9 stable CHSE cell line; specifically, the exogenous, integrated EGFP and the endogenous RIG-I locus. Finally, the effective use of antibiotic selection to enrich the successfully edited targeted population was demonstrated. The optimised lentiviral-mediated CRISPR method reported here increases possibilities for efficient genome editing in salmonid cells, in particular for future applications of genome-wide CRISPR screens for disease resistance.

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Bring It to an End: Does Telomeres Size Matter?

Cells ◽

10.3390/cells8010030 ◽

2019 ◽

Vol 8 (1) ◽

pp. 30 ◽

Cited By ~ 15

Author(s):

Camille Laberthonnière ◽

Frédérique Magdinier ◽

Jérôme D. Robin

Keyword(s):

Position Effect ◽

Critical Length ◽

Model Organisms ◽

Human Biology ◽

Cell Divisions ◽

Genome Wide ◽

Mitotic Clock ◽

Size Matter ◽

Dna Ends ◽

Telomere Dynamics

Telomeres are unique nucleoprotein structures. Found at the edge of each chromosome, their main purpose is to mask DNA ends from the DNA-repair machinery by formation of protective loops. Through life and cell divisions, telomeres shorten and bring cells closer to either cell proliferation crisis or senescence. Beyond this mitotic clock role attributed to the need for telomere to be maintained over a critical length, the very tip of our DNA has been shown to impact transcription by position effect. TPE and a long-reach counterpart, TPE-OLD, are mechanisms recently described in human biology. Still in infancy, the mechanism of action of these processes and their respective genome wide impact remain to be resolved. In this review, we will discuss recent findings on telomere dynamics, TPE, TPE-OLD, and lessons learnt from model organisms.

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Transcriptome Analysis in Domesticated Species: Challenges and Strategies

Bioinformatics and Biology Insights ◽

10.4137/bbi.s29334 ◽

2015 ◽

Vol 9S4 ◽

pp. BBI.S29334 ◽

Cited By ~ 4

Author(s):

Jessica P. Hekman ◽

Jennifer L Johnson ◽

Anna V. Kukekova

Keyword(s):

Complex Traits ◽

Gene Networks ◽

Association Studies ◽

Cultural Value ◽

Genomic Research ◽

Model Organisms ◽

Genome Wide Association Studies ◽

Rna Seq ◽

Genome Wide ◽

Genome Assemblies

Domesticated species occupy a special place in the human world due to their economic and cultural value. In the era of genomic research, domesticated species provide unique advantages for investigation of diseases and complex phenotypes. RNA sequencing, or RNA-seq, has recently emerged as a new approach for studying transcriptional activity of the whole genome, changing the focus from individual genes to gene networks. RNA-seq analysis in domesticated species may complement genome-wide association studies of complex traits with economic importance or direct relevance to biomedical research. However, RNA-seq studies are more challenging in domesticated species than in model organisms. These challenges are at least in part associated with the lack of quality genome assemblies for some domesticated species and the absence of genome assemblies for others. In this review, we discuss strategies for analyzing RNA-seq data, focusing particularly on questions and examples relevant to domesticated species.

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Genome-wide association studies on endometriosis and endometriosis-related infertility

10.1101/401448 ◽

2018 ◽

Cited By ~ 1

Author(s):

Geneviève Galarneau ◽

Pierre Fontanillas ◽

Caterina Clementi ◽

Tina Hu-Seliger ◽

David-Emlyn Parfitt ◽

...

Keyword(s):

Genome Wide Association Study ◽

Association Studies ◽

Reproductive Age ◽

Genome Wide Association ◽

European Ancestry ◽

Model Organisms ◽

Genome Wide Association Studies ◽

Gwas Study ◽

Genome Wide ◽

Genome Wide Significance

AbstractEndometriosis affects ∼10% of women of reproductive age. It is characterized by the growth of endometrial-like tissue outside the uterus and is frequently associated with severe pain and infertility. We performed the largest endometriosis genome-wide association study (GWAS) to date, with 37,183 cases and 251,258 controls. All women were of European ancestry. We also performed the first GWAS of endometriosis-related infertility, including 2,969 cases and 3,770 controls. Our endometriosis GWAS study replicated, at genome-wide significance, seven loci identified in previous endometriosis GWASs (CELA3A-CDC42, SYNE1, KDR, FSHB-ARL14EP, GREB1, ID4, and CEP112) and identified seven new candidate loci with genome-wide significance (NGF, ATP1B1-F5, CD109, HEY2, OSR2-VPS13B, WT1, and TEX11-SLC7A3). No loci demonstrated genome-wide significance for endometriosis-related infertility, however, the three most strongly associated loci (MCTP1, EPS8L3-CSF1, and LPIN1) were in or near genes associated with female fertility or embryonic lethality in model organisms. These results reveal new candidate genes with potential involvement in the pathophysiology of endometriosis and endometriosis-related infertility.

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