Bioinformatics approach to unearthing bimolecular hammerhead ribozymes

Abstract

Background. Motif finding in large genomic datasets is one of the most powerful bioinformatics techniques in research. It acts as an important gateway to answering a wide variety of biological questions. However, it also remains one of bioinformatics' most challenging and computationally-expensive aspects.

Motivation. In this work, we focus on small catalytic RNA molecules, i.e. hammerhead ribozymes, that over the past decades have been found to be present among the entire tree of life. Hammerhead ribozymes have been observed in many different forms and unusualities across biological samples and organisms of different origins. Nonetheless, bioinformatics searches have only concentrated on hammerhead ribozymes that are contiguous and wholly found on a single chromosome. In this work, we concentrate on hammerheads that are composed of two split RNA molecules each found on a different chromosome. Such hammerheads have been widely the focus of laboratory design and experiments due to their importance in medicine and therapeutics, and as of yet have not been reported as naturally-occurring motifs.

Objective. Development and design of a bioinformatics tool that has the capability of locating bimolecular motifs that span two chromosomes; using hammerhead ribozymes and their consensus sequence structure to evaluate the tool on a certain model organism; discovering whether there is a theoretical probability that such motifs could occur in nature or they are truly restricted to laboratory design.

Results. We have developed a hybrid pipeline in R, Perl, and Bash languages that utilizes regular expressions and BLAST for exact pattern matching of small motifs. We evaluated our tool on five chromosomes of Drosophila melanogaster and obtained thousands of results that match the structural requirements of a bimolecular discontiguous hammerhead ribozyme. These results showcase a high chance of occurrence for such motifs in nature. Moreover, many of the hits show characteristics of trans-acting and multiple-turnover hammerheads.