@@ -288,8 +288,22 @@ Navigate to the IGV genome browser app and select the pig reference genome (Sscr
Add the ensembl gene annotation track (Sscrofa11.1_SSC18.gff3) and load the Pig1 bam file. Set the visibility window from the BAM track to 600000 (settings).
Furthermore you can select the options "View as pairs" and "Show soft clips" to visualize the read pairs that support the deletion and the clipped reads.
The deletion likely causes a loss-of-function of the BBS9 gene, look up the function of this gene?
To get further functional support of the BBS9 gene we can examine the knockout (KO) mice phenotypes in the [`MGI database`](http://www.informatics.jax.org/).
What kind of abnormal phenotypes do the KO mice develop? Do you expect this to be the same in pig?
It looks like that an impaired BBS9 gene does not lead to fetal lethality. It could be that the deletions also affects regulatory elements that are essential for normal development.
To assess the presence of regulatory elements (e.g. enhancer/promotor sites) we can use ChIP-seq data. ChIP-seq is a very powerful method to detect interaction between DNA and protein.
One of the most common applications of ChIP-seq is to detect specific histone modifications in the genome (Lecture 5). Histone modifications are one of the most important epigenetic marks in the genome for determine gene expression (or not) and a large variety of histone modifications are present in the cell.
Some histone modifications has been widely used in the ENCODE projects because they are highly informative on gene expression. Some examples:
H3K4me3 (histone H3 lysine 4 tri-methylation); found at the promoter of all expressed genes.
H3K27Ac (histone H3 lysine 27 acetylation); identifies active enhancer elements.
In this exercise you will be working with a small dataset of H3K4me3 and H3K27Ac ChIP-seq data from pig liver within the SSC18 region.
Both datasets are aligned to the pig reference genome and peaks are called to identify active enhancer and promotor sites.
Load the BAM files to IGV (). Does the deletion comprise (cis-)regulatory elements?
