Research focus RNA interference

(in collaboration with the Buchholz lab)

Next to being an important biological mechanism of regulating expression levels of genes within cells, RNA interference has become a very powerful technique to knock down the expression of genes. Its ease of usage has revolutionized functional genomic studies and has enabled researchers to carry out genome-wide functional screens.
Long double-stranded RNA can for instance be used to knock-down genes in organisms like C. elegans and Drosophila melanogaster, while they are toxic in most mammalian cell culture systems. These unspecific, mostly apoptotic effects of long dsRNAs in mammalian cells can however be prevented when using only the small interfering RNAs (siRNAs).
Alternatively to technologies like synthetic siRNAs or shRNAs, which are made up of a single 21nt dsRNA, long dsRNA can be digested in the test tube prior to transfection. The end products, so-called dicer- or endoribonuclease-prepared small interfering RNAs (d-siRNA and esiRNAs, respectively) can then be used for RNAi-based gene knock-down.
One major research part of our lab is focused on the prediction of efficiency and specificity of esiRNAs. We have developed a web-based tool that tries to optimize esiRNAs for knock-down studies by searching the most efficient - and also most specific - region within a mRNA for subsequent processing (DEQOR). We have applied DEQOR to predict genome-wide esiRNA libraries for the genomes of human, mouse and rat, which we have made available in an esiRNA database (RiDDLE).



Research focus functional prediction of proteins

Reliable functional prediction of proteins not only helps in experimental design but also makes possible a more precise interpretation of functional screening data. The functional annotation and analysis of protein sequences is therefore the second focus of our lab. To correctly predict a protein's function based purely on sequence similarity is still a great challange in bioinformatics, especially when one looks at more distantly related protein sequences. Even if some functional information concerning the biological process of a protein is known, it is tedious and involves expert tools to correctly predict a proteins function on a molecular level.
We are currently approaching this problem from 2 sides:

1) With the web-based tool ProFAT, we have introduced a comprehensive software package that allows user to functionally annotate protein sequences based on remote sequence simlarity. By a combination of sensitive sequence search tools (PSI-BLAST) and threading techniques (Threader 3.5) and a simple text-mining algorithm, we are able to extract functional information from the wealth of literature published based on distantly related sequences.
º check out the ProFAT project or start a live ProFAT search


2) The second approach we are taking relies on a combination of sensitive domain searches (HMMer) and threading techniques (Threader 3.5), by which we can identify weakly conserved domain hits in proteins. With the HMMerThread database, we are presenting genome-wide data on remote domain family members.
º  check out the HMMerThread project or goto the HMMerThread database



Past & Future

Past Projects

In collaboration with several research groups in the MPI-CBG, we have developed an EST annotation pipeline that takes care of assembly and annotation of in-house sequenced data. The pipeline is based on Phred and TIGR-Assembler for quality control and contig assembly. Annotation is based on NCBI's Genbank data. Next to homologues, conserved domains, putative identities and Gene Ontology (GO) assignments are made. For sequence data storage, we have developed a mysql-based relational database.

  • check out the EST-database of Ambystoma mexicanum (in collaboration with the Tanaka lab)
  • check out the EST database of Xenopus laevis (in collaboration with the Hyman lab)
  • check out the EST database of Canis familiaris (in collaboration with the Simons lab)

On-going Research

Next to our research focus on the bioinformatics of RNAi in functional genomics and functional prediction of proteins, we are currently involved in two major research directions:

  • the analysis of non-coding DNA/promoter regions; together with research labs at the MPI-CBG, we are trying to decipher regulatory elements of orthologous or co-regulated genes in eukaryotic genomes.
  • identification of remote sequence orthologues; especially with research labs working in model organisms like yeast, worm or fly, it is sometimes not easy to find orthologues in higher eukaryotes. The identification of weakly conserved sequences in fungi like yeast on the other hand can help in predicting the function of vertebrate and mammalian proteins. One major research direction therefore deals with novel approaches to find remotely conserved orthologous sequences.