Research

The Genomics unit runs various types of research projects.

On the one hand the group performs comprehensive genomic approaches in a number of collaborations. These collaborative projects cover a broad spectrum of biological, medical and bioinformatic questions (see Publications).

On the other hand the group uses its state of the art techniques in own research projects, e.g.:

Fine mapping of genome activation in bovine embryos by RNA sequencing                                          

In this project we used next generation sequencing of cDNA (RNA-Seq) to obtain insights into the onset of bovine embryonic genome activation. This activation is accompanied by the degradation of maternal RNAs and proteins stored in the oocytes. This process is known as maternal-to-embryonic transition (MET).  Sequencing libraries were derived from the transcriptomes of germinal vesicle and metaphase II oocytes, embryos at the four-cell, eight-cell, 16-cell and blastocyst stages were sequenced on the Illumina Genome Analyser IIx sequencing system. Embryos were produced by in vitro fertilization of German Simmental oocytes with sperm from a single bull (Bos indicus) to facilitate parent-specific transcriptome analysis. For every developmental stage 10 oocytes/embryos were pooled for sequencing. The embryonic genome activation was analyzed with different strategies starting from the four-cell to the blastocyst stage: i) detection of embryonic transcripts, which are not present in oocytes; ii) detection of transcripts from the paternal allele; and iii) detection of primary transcripts with intronic sequences. Most of the activated genes were found at the eight-cell stage, indicating major genome activation at this stage. This activation is prepared at the four-cell stage as shown by gene ontology analysis. In summary, using these three approaches we were able to map the onset of embryonic transcription for almost 7,400 genes, providing a new layer of information for detecting disturbances of early development due to genetic, epigenetic, and environmental factors.