| 1. |
- Guerrero Bosagna, Carlos, et al.
(författare)
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DNA methylation variation in the brain of laying hens in relation to differential behavioral patterns
- 2020
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Ingår i: Comparative Biochemistry and Physiology - Part D. - : ELSEVIER SCIENCE INC. - 1744-117X .- 1878-0407. ; 35
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Tidskriftsartikel (refereegranskat)abstract
- Domesticated animals are unique to investigate the contribution of genetic and non-genetic factors to specific phenotypes. Among non-genetic factors involved in phenotype formation are epigenetic mechanisms. Here we aimed to identify whether relative DNA methylation differences in the nidopallium between groups of individuals are among the non-genetic factors involved in the emergence of differential behavioral patterns in hens. The nidopallium was selected due to its important role in complex cognitive function (i.e., decision making) in birds. Behavioral patterns that spontaneously emerge in hens living in a highly controlled environment were identified with a unique tracking system that recorded their transitions between pen zones. Behavioral activity patterns were characterized through three classification schemes: (i) daily specific features of behavioral routines (Entropy), (ii) daily spatio-temporal activity patterns (Dynamic Time Warping), and (iii) social leading behavior (Leading Index). Unique differentially methylated regions (DMRs) were identified between behavioral patterns emerging within classification schemes, with entropy having the higher number. Functionally, DTW had double the proportion of affected promoters and half of the distal intergenic regions. Pathway enrichment analysis of DMR-associated genes revealed that Entropy relates mainly to cell cycle checkpoints, Leading Index to mitochondrial function, and DTW to gene expression regulation. Our study suggests that different biological functions within neurons (particularly in the nidopallium) could be responsible for the emergence of distinct behavior patterns and that epigenetic variation within brain tissues would be an important factor to explain behavioral variation.
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| 2. |
- Pértille, Fábio, et al.
(författare)
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Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes
- 2020
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Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Production animals are constantly subjected to early adverse environmental conditionsthat influence the adult phenotype and produce epigenetic effects. CpG dinucleotidemethylation in red blood cells (RBC) could be a useful epigenetic biomarker to identifyanimals subjected to chronic stress in the production environment. Here we compareda reduced fraction of the RBC methylome of chickens exposed to social isolation tonon-exposed. These experiments were performed in two different locations: Brazil andSweden. The aim was to identify stress-associated DNA methylation profiles in RBC across these populations, in spite of the variable conditions to which birds are exposedin each facility and their different lineages. Birds were increasingly exposed to a socialisolation treatment, combined with food and water deprivation, at random periods of theday from weeks 1–4 after hatching. We then collected the RBC DNA from individualsand compared a reduced fraction of their methylome between the experimental groupsusing two bioinformatic approaches to identify differentially methylated regions (DMRs):one using fixed-size windows and another that preselected differential peaks with MACS2. Three levels of significance were used (P ≤ 0.05, P ≤ 0.005, and P ≤ 0.0005) to identify DMRs between experimental groups, which were then used for differentanalyses. With both of the approaches more DMRs reached the defined significancethresholds in BR individuals compared to SW. However, more DMRs had higher foldchange values in SW compared to BR individuals. Interestingly, ChrZ was enrichedabove expectancy for the presence of DMRs. Additionally, when analyzing the locationsof these DMRs in relation to the transcription starting site (TSS), we found threepeaks with high DMR presence: 10 kb upstream, the TSS itself, and 20–40 kbdownstream. Interestingly, these peaks had DMRs with a high presence (>50%) ofspecific transcription factor binding sites. Three overlapping DMRs were found betweenthe BR and SW population using the most relaxed p-value (P ≤ 0.05). With the most stringent p-value (P ≤ 0.0005), we found 7 and 4 DMRs between treatmentsin the BR and SW populations, respectively. This study is the first approximation toidentify epigenetic biomarkers of long-term exposure to stress in different lineages ofproduction animals.
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| 3. |
- Rezaei, Shiva, et al.
(författare)
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GBS-MeDIP : A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals
- 2022
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Ingår i: STAR protocols. - : Cell Press. - 2666-1667. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- The GBS-MeDIP protocol combines two previously described techniques, Geno-type-by-Sequencing (GBS) and Methylated-DNA- Immunoprecipitation (MeDIP). Our method allows for parallel and cost-efficient interrogation of genetic and methylomic variants in the DNA of many reduced genomes, taking advantage of the barcoding of DNA samples performed in the GBS and the subsequent creation of DNA pools, then used as an input for the MeDIP. The GBS-MeDIP is particularly suitable to identify genetic and methylomic biomarkers when resources for whole genome interrogation are lacking.
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| 4. |
- Rezaei, Shiva, et al.
(författare)
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GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals
- 2022
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Ingår i: STAR Protocols. - : Cell Press. - 2666-1667. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Summary:The GBS-MeDIP protocol combines two previously described techniques, Genotype-by-Sequencing (GBS) and Methylated-DNA-Immunoprecipitation (MeDIP). Our method allows for parallel and cost-efficient interrogation of genetic and methylomic variants in the DNA of many reduced genomes, taking advantage of the barcoding of DNA samples performed in the GBS and the subsequent creation of DNA pools, then used as an input for the MeDIP. The GBS-MeDIP is particularly suitable to identify genetic and methylomic biomarkers when resources for whole genome interrogation are lacking.
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| 5. |
- Abbafati, Cristiana, et al.
(författare)
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- 2020
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Tidskriftsartikel (refereegranskat)
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