Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: a technical assessment

peer-reviewedRecent advances made in “omics” technologies are contributing to a revolution in livestock selection and breeding practices. Epigenetic mechanisms, including DNA methylation are important determinants for the control of gene expression in mammals. DNA methylation research will help our understanding of how environmental factors contribute to phenotypic variation of complex production and health traits. High-throughput sequencing is a vital tool for the comprehensive analysis of DNA methylation, and bisulfite-based strategies coupled with DNA sequencing allows for quantitative, site-specific methylation analysis at the genome level or genome wide. Reduced representation bisulfite sequencing (RRBS) and more recently whole genome bisulfite sequencing (WGBS) have proven to be effective techniques for studying DNA methylation in both humans and mice. Here we report the development of RRBS and WGBS for use in sheep, the first application of this technology in livestock species. Important technical issues associated with these methodologies including fragment size selection and sequence depth are examined and discussed.AgResearch AR&C grant for funding and Teagasc for providing a short-term overseas training awar

Comparison of N. Atlantic heat storage estimates during the Argo period (1999–2010)

Ocean heat storage is an essential component of the climate system and there is considerable interest in its accurate evaluation. There are a number of heat storage products produced by many different groups. These products are derived from Argo as well as other platforms, for example XBT and CTD, in the last decade. Here we compare two heat storage estimates for the North Atlantic 0–2000 m from 10° to 70° N. One derived solely from Argo data whilst the other is derived from Argo and other platforms. It is found that there is a positive trend in heat storage over the period 1999–2010. This trend is influenced by a strong air–sea interaction event in 2009–2010, and this reduces the upward trend 1999–2008 identified previously. Both data sets are consistent with each other for the layer 0–1000 m on a timescale of beyond 1 yr. There are significant differences at sub-annual time scales and in the layer 1000–2000 m

The CD4+ T cell methylome contributes to a distinct CD4+ T cell transcriptional signature in Mycobacterium bovis-infected cattle

peer-reviewedWe hypothesised that epigenetic regulation of CD4+ T lymphocytes contributes to a shift toward a dysfunctional T cell phenotype which may impact on their ability to clear mycobacterial infection. Combined RNA-seq transcriptomic profiling and Reduced Representation Bisulfite Sequencing identified 193 significantly differentially expressed genes and 760 differentially methylated regions (DMRs), between CD4+ T cells from M. bovis infected and healthy cattle. 196 DMRs were located within 10 kb of annotated genes, including GATA3 and RORC, both of which encode transcription factors that promote TH2 and TH17 T helper cell subsets respectively. Gene-specific DNA methylation and gene expression levels for the TNFRSF4 and Interferon-γ genes were significantly negatively correlated suggesting a regulatory relationship. Pathway analysis of DMRs identified enrichment of genes involved in the anti-proliferative TGF-β signaling pathway and TGFB1 expression was significantly increased in peripheral blood leukocytes from TB-infected cattle. This first analysis of the bovine CD4+ T cell methylome suggests that DNA methylation directly contributes to a distinct gene expression signature in CD4+ T cells from cattle infected with M. bovis. Specific methylation changes proximal to key inflammatory gene loci may be critical to the emergence of a non-protective CD4+ T cell response during mycobacterial infection in cattle

De novo assembly of the cattle reference genome with single-molecule sequencing.

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species

From the editors

2014 is widely seen as marking a watershed for Afghanistan with its legacy of thirty-five years of conflict and one of the world’s largest populations in protracted displacement. International military forces are being withdrawn and the country is ‘in transition’ – politically, economically and in terms of security and its international standing. The high voter turnout in the recent presidential elections has been greeted as an encouraging sign for Afghanistan’s future but there is still considerable uncertainty about the capacity of the country to address the challenges of return, integration and reintegration, protection, access to rights, and continuing displacement

DNA methylation patterns in tissues from mid-gestation bovine foetuses produced by somatic cell nuclear transfer show subtle abnormalities in nuclear reprogramming

<p>Abstract</p> <p>Background</p> <p>Cloning of cattle by somatic cell nuclear transfer (SCNT) is associated with a high incidence of pregnancy failure characterized by abnormal placental and foetal development. These abnormalities are thought to be due, in part, to incomplete re-setting of the epigenetic state of DNA in the donor somatic cell nucleus to a state that is capable of driving embryonic and foetal development to completion. Here, we tested the hypothesis that DNA methylation patterns were not appropriately established during nuclear reprogramming following SCNT. A panel of imprinted, non-imprinted genes and satellite repeat sequences was examined in tissues collected from viable and failing mid-gestation SCNT foetuses and compared with similar tissues from gestation-matched normal foetuses generated by artificial insemination (AI).</p> <p>Results</p> <p>Most of the genomic regions examined in tissues from viable and failing SCNT foetuses had DNA methylation patterns similar to those in comparable tissues from AI controls. However, statistically significant differences were found between SCNT and AI at specific CpG sites in some regions of the genome, particularly those associated with SNRPN and KCNQ1OT1, which tended to be hypomethylated in SCNT tissues. There was a high degree of variation between individuals in methylation levels at almost every CpG site in these two regions, even in AI controls. In other genomic regions, methylation levels at specific CpG sites were tightly controlled with little variation between individuals. Only one site (HAND1) showed a tissue-specific pattern of DNA methylation. Overall, DNA methylation patterns in tissues of failing foetuses were similar to apparently viable SCNT foetuses, although there were individuals showing extreme deviant patterns.</p> <p>Conclusion</p> <p>These results show that SCNT foetuses that had developed to mid-gestation had largely undergone nuclear reprogramming and that the epigenetic signature at this stage was not a good predictor of whether the foetus would develop to term or not.</p

On which timescales do gas transfer velocities control North Atlantic CO2 flux variability?

The North Atlantic is an important basin for the global ocean's uptake of anthropogenic and natural carbon dioxide (CO2), but the mechanisms controlling this carbon flux are not fully understood. The air-sea flux of CO2, F, is the product of a gas transfer velocity, k, the air-sea CO2 concentration gradient, ΔpCO2, and the temperature and salinity-dependent solubility coefficient, α. k is difficult to constrain, representing the dominant uncertainty in F on short (instantaneous to interannual) timescales. Previous work shows that in the North Atlantic, ΔpCO2 and k both contribute significantly to interannual F variability, but that k is unimportant for multidecadal variability. On some timescale between interannual and multidecadal, gas transfer velocity variability and its associated uncertainty become negligible. Here, we quantify this critical timescale for the first time. Using an ocean model, we determine the importance of k, ΔpCO2 and α on a range of timescales. On interannual and shorter timescales, both ΔpCO2 and k are important controls on F. In contrast, pentadal to multidecadal North Atlantic flux variability is driven almost entirely by ΔpCO2; k contributes less than 25%. Finally, we explore how accurately one can estimate North Atlantic F without a knowledge of non-seasonal k variability, finding it possible for interannual and longer timescales. These findings suggest that continued efforts to better constrain gas transfer velocities are necessary to quantify interannual variability in the North Atlantic carbon sink. However, uncertainty in k variability is unlikely to limit the accuracy of estimates of longer term flux variability

On which timescales do gas transfer velocities control North Atlantic CO2 flux variability?

This is the final version of the article. Available from AGU via the DOI in this record.The North Atlantic is an important basin for the global ocean's uptake of anthropogenic and natural carbon dioxide (CO 2 ), but the mechanisms controlling this carbon flux are not fully understood. The air-sea flux of CO 2 , F, is the product of a gas transfer velocity, k, the air-sea CO 2 concentration gradient, ΔpCO 2 , and the temperature- and salinity-dependent solubility coefficient, α. k is difficult to constrain, representing the dominant uncertainty in F on short (instantaneous to interannual) timescales. Previous work shows that in the North Atlantic, ΔpCO 2 and k both contribute significantly to interannual F variability but that k is unimportant for multidecadal variability. On some timescale between interannual and multidecadal, gas transfer velocity variability and its associated uncertainty become negligible. Here we quantify this critical timescale for the first time. Using an ocean model, we determine the importance of k, ΔpCO 2 , and α on a range of timescales. On interannual and shorter timescales, both ΔpCO 2 and k are important controls on F. In contrast, pentadal to multidecadal North Atlantic flux variability is driven almost entirely by ΔpCO 2 ; k contributes less than 25%. Finally, we explore how accurately one can estimate North Atlantic F without a knowledge of nonseasonal k variability, finding it possible for interannual and longer timescales. These findings suggest that continued efforts to better constrain gas transfer velocities are necessary to quantify interannual variability in the North Atlantic carbon sink. However, uncertainty in k variability is unlikely to limit the accuracy of estimates of longer-term flux variability.This work was supported the RAGNARoCC NERC directed research program (NE/K002546/1, NE/K00249X/1, and NE/K002473/1)