Iboro Umana
Computational Analysis of Heterochromatin-Associated Proteins
Mentors:  Dr. Nicole Riddle and Dr. Sarah Elgin, Biology Department, Washington University in St. Louis 

While there are thousands of genes in a genome, not all are expressed.  Gene silencing occurs for a variety of reasons.  One particular explanation is the formation of a specialized chromatin structure called heterochromatin.  Heterochromatin packages DNA in an inactive form.  Thus, it serves to regulate gene expression and as a defense mechanism by silencing transposons and other harmful repetitious sequences.  The process leading to heterochromatin formation is unknown.  However, researchers have discovered several proteins such as HP1, Su(var) 3-7, and HP2 that are associated with heterochromatin and are important for its assembly.

My project’s main objective was to learn more about these heterochromatin-associated proteins and their function by studying their evolution across twelve Drosophila fruit fly species.  We used Drosophila melanogaster as a starting point and studied protein evolution by comparison.  The BLAST program was used to identify the most likely location of the gene under study in a species’ genomic sequence.  After that, I annotated the gene that coded for the heterochromatin-associated protein, determining its intron/exon structure.  Once I had compiled protein sequences for all twelve fly species, I constructed a phylogenetic tree to look at some of the evolutionary relationships.

We were initially surprised to see that HP1, the most conserved protein that I am studying, produced a low-quality phylogenetic tree.  This could be due to multiple amino acid changes at the same site, which is possible, but normally unlikely. As a result, this can detract from the integrity of the tree.  The phylogenetic tree for HP2 also did not correspond well with the known species' tree based on ribosomal sequences, possibly due to HP2’s size, which rapidly changed as we moved from species to species.  Su(var) 3-7 sequences produced a very good phylogenetic tree with high values at the nodes, which showed how confident the program was in the phylogenetic tree.

An interesting observation that merits further research is the apparent insertion of an intron in a coding exon of the HP2 gene in D. ananassae. This potentially new intron was also seen in several other fly species that have diverged further than D. ananassae.  The fact that RT-PCR yielded a cDNA of the same size as the original DNA is very interesting, as we are not sure why the intron was not excised out.  I hope to continue to study this as well as expand our protein evolution study to other heterochromatin-associated proteins.