Analysing DNA methylation to study the effects of assisted reproductive technologies in cows

Principal scientist Jaana Peippo and Senior Scientist Heli Lindeberg from the Natural Resources Institute Finland (Luke) study assisted reproductive technologies in animals. Together, they worked on Luke’s Terve Tiineys (Healthy Pregnancy) -project to compare pregnancies in heifers and cows impregnated either by artificial insemination (control group), by MOET (multiple ovulation embryo transfer) or OPU (ovum pick up) embryos, and to study whether closer monitoring during pregnancy could enhance the wellbeing of the pregnant cows and their offspring. The research project involved heifers and cows on 20 different farms in Finland, and included molecular analyses of maternal and calf blood samples as well as muscle biopsies from the born calves. Genevia’s team was contracted to analyse DNA methylation data from the latter.

This 12-day-old Viking Holstein bull calf, named Misty P, was the outcome of an embryo-transfer pregnancy and provided a muscle biopsy to the Healthy Pregnancy project. Photo: Heli Lindeberg


Dr. Peippo and Dr. Lindeberg are both specialists in assisted reproductive technologies in animals. Dr. Peippo studied biology at the University of Turku, Finland, oriented towards genetics and animal physiology and, ever since, her focus has been on embryo research and laboratory work developing the technologies. Dr. Lindeberg, in turn, is a veterinarian by training, and did her PhD on reproduction and embryo technology in farmed European polecats. In addition to her research on assisted reproductive technologies she also gets to do the hands-on veterinary work at Luke’s research barn in Maaninka.

– For my whole career, I’ve studied these artificial reproductive technologies, but from a different point of view than Heli. During the pandemic, I switched organisation from Luke to Nordic Genetic Resource center (NordGen), and after working for a long time with animal breeding, I now use the same methods for the purpose of conservation of farm animal genetic resources, Dr. Peippo explains.

– That means producing embryos in the laboratory, freezing them for future transfer, and also collecting and freezing sperm. I still think this is the best job in the world, and I’ve never regretted my choice of career path, she says, and Dr. Lindeberg agrees.

Healthy Pregnancy was a project at Luke with the objective of studying variations in pregnancies among cows impregnated by different methods, and to find out whether the wellbeing of the pregnant cow and its calf benefit from closer monitoring already during the pregnancy. For humans, there are children’s health care clinics where the mother and the fetus are examined and closely followed up on throughout the pregnancy, so the idea was to see if something similar could be applied to heifers and cows in order to detect high-risk pregnancies earlier.

Three different kinds of pregnancies were studied: ones initiated by artificial insemination, which is the standard procedure, and ones in which an embryo that was produced either in a laboratory or in another cow was transferred. A total of twenty private farms in Northern Savo, Finland participated in the project, and each of them were visited 11-13 times to examine the selected heifers and cows and to collect samples, which wasn’t the easiest task during the pandemic. In the end, all the visits got done and samples collected – but new challenges were faced when analysing the collected data.

How did Genevia help?

– We were following up on the pregnancies, and aimed to monitor the health status and metabolism of both the calf and the dam during pregnancy. We took blood samples and did ultrasound scans for the pregnant dams, and once the calf was born, we examined it as well. We inspected their basic health status and weight, for example, and also took blood samples and muscle biopsies, Dr. Peippo describes.

The blood samples were used to study metabolism and gene expression in the pregnant dams and born calves. The muscle biopsies from the calves were taken to study possible differences in DNA methylation-mediated gene regulation between calves with different growth rates. To this end, bisulfite sequencing was applied to the DNA from these biopsies.

– Luke’s bioinformatician analysed the gene expression data, but the methylation data was completely new to us. With the high amount of samples and data, and analyses in which our staff was not experienced, we were falling behind our schedule. We realised we needed a different type of solution. Luckily, we were able to extend the project with the saved funding, and set out to procure the methylation analysis through competitive tendering.

After receiving offers from different service providers, it became apparent that Genevia Technologies was the best match for the project’s data analysis needs. From the very first contact, Dr. Lindeberg and Dr. Peippo were impressed by how effortless the collaboration was.

– Everything was easy. We first got in contact with Genevia with a short message describing our needs, and quickly got a meeting with the right people. Then, Dr. Joana Viana was assigned to work with us. Everything worked very well. Joana was always very well prepared for our regular meetings, says Dr. Peippo, and Dr. Lindeberg continues:

– Joana was amazing. Her delivery was extraordinarily good, and she explained everything clearly. Even after the project had ended, she still continued replying to our questions. She really fully dedicated herself to our project. I was so impressed and grateful.

Both researchers appreciated being kept up to date on the usage of contracted time, and that the remaining hours could be flexibly prioritised based on the project’s needs. They were also happy with the written project reports:

– The reports were great; they helped Luke’s bioinformatician learn about methylation analyses, and to us non-bioinformaticians, the results were explained from a biological, rather than technical, perspective, says Dr. Peippo.

– We are now writing the manuscript, and with the results we got with Genevia’s help, we may aim at a high quality journal. The idea of this project seemed challenging to us at the beginning, and we were not sure if we were going to be able to draw practical conclusions from the results. We were happy to get such novel and interesting results. In addition to a peer-reviewed paper, we are planning to publish articles in Finnish, for the general audience.

Thoughts on outsourcing bioinformatics

This was not the first time Dr. Lindeberg and Dr. Peippo have experienced a bioinformatics bottleneck, and they agree that there definitely is a lack of resources in the field. Their previous experience of data analysis services from an international sequencing service provider was challenging, and sometimes they have found it difficult to communicate with bioinformaticians without adequate knowledge in biology. Nowadays, when sequencing is so accessible, Dr. Peippo and Dr. Lindeberg think that more resources should be invested in getting more out of the huge amounts of data that almost every researcher is producing.

– We have now understood that just like with sequencing, it makes more sense to outsource the analysis. A single bioinformatician in a research group simply cannot be an expert on everything. Instead of maintaining all capacities in-house and keeping up to date with all the developments in the field, it’s easier to use the services of a specialised company and this kind of collaboration is cost-effective.

– Based on this first experience with Genevia, we simply don’t have anything negative to say. We have recommended the service to our colleagues, and we know many who are now considering this option, since extracting biological findings out of large data is the true bottleneck in most research projects, they summarise.

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