New Bioinformatics Tool – MHcut By Kyoto & Montreal Scientists

lign: center;">New Bioinformatics Tool MHcut

A new bioinformatics tool, MHcut, invented by researchers in Kyoto, Japan, and Montreal, Canada, reveals that a natural repair system for DNA damage, microhomology-mediated end joining, is probably far more common in humans than initially assumed.

Using the new bioinformatics tool MHcut and commercial genome-editing technology, the scientists created mutations in iPS cells with extraordinary precision to model diseases without the need for patient samples.

The microhomology-mediated end-joining [MMEJ] repairs double-stranded breaks that are flanked by short identical sequences called microhomologies. It is a less appreciated repair system, and the laboratory of CiRA Associate Professor Knut Woltjen has been studying this method to develop new gene-editing technology.

New Bioinformatics Tool MHcut- The Use Of The New Tool

Using the new bioinformatics tool MHcut, Ph.D. student Janin Grajcarek discovered that 57 percent of all deletion mutations in the human genome is flanked by microhomologous sequences that are at least three base pairs long, a percentage much larger than expected by chance alone.

Grajcarek believes that these deletions will enable new insights on the function of the genome. Popular gene-editing technologies like CRISPR-Cas9 gene-editing technology operate by exploiting natural DNA repair systems such as non-homologous end joining, homology-directed repair, and MMEJ.

Woltjen’s team of researchers has shown in earlier work that MMEJ offers higher precision than these other gene-editing systems. Now with MHcut, the new study shows scientists how to identify deletion mutations in the human genome that can be recreated with microhomology-mediated end-joining in the research laboratory.

New Bioinformatics Tool MHcut- The Research Methodology

To demonstrate this point, the lab modified three genes in human iPS cells.

ALAS2 and FECH code enzymes for the heme synthesis pathway. Mutations in ALAS2 and FECH code cause photosensitivity of the skin and some cases, liver damage. DYSF regulates muscle repair, and its mutations are associated with muscular dystrophy.

After the mutations, the Woltjen group joined efforts with CiRA colleagues who are experts in generating muscle cells (for the DYSF mutation) and red blood cells (for the ALAS2 and FECH mutations) from iPS cells. The edited cells demonstrated characteristics consistent with the disease in patients.

According to Grajcarek, the success of the project was coincidental. Using fundamental software, she had discovered that microhomologies were surprisingly common in gene variants of the X chromosome, but to confirm this feature in all chromosomes required more sophisticated analysis.

The New Bioinformatics Tool MHcut is expected to make it easier to study diseases even when patients are rare or unavailable.