Research Overview

What are replication conflicts?
Accurate, timely, and faithful duplication of the genome is essential for production of viable progeny. Impediments to replication lead to conflicts that disrupt this process, reduce fitness, and cause genomic instability. Some known impediments to replication include DNA lesions, breaks, tightly bound proteins, as well as the transcription machinery. We are currently working on identifying and understanding the consequences of these obstacles to DNA replication and genome integrity. Using Bacillus subtilis as a model organism, we are taking advantage of cutting edge tools such as in vivo single molecule microscopy, deep sequencing, whole genome bioinformatics analyses, as well as standard genetics and molecular biology techniques to study the nature and consequences of these impediments. Currently, we are particularly interested in collisions between replication and transcription.
                                         
How are replication-transcription conflicts resolved?
In bacteria, replication and transcription are not temporally separated leading to collisions between these two complexes as they move along the DNA. Because transcription can occur on either the Watson or the Crick strand, these collisions occur in both head-on and co-directional orientations. Although head-on conflicts appear to have much more significant consequences for the replisome, both types of collisions can promote breakage of the DNA strands. In addition, even co-directional replication-transcription conflicts can be detrimental to the cell, causing the replisome to collapse, and requiring the action of replisome restart proteins. To maximize fitness and protect the genome from unwanted instability caused by these inevitable encounters, cells have developed mechanisms to resolve conflicts. We are currently working on identifying and characterizing these mechanisms in vivo. Many of the resolution mechanisms we are focused on are essential and highly conserved across all domains of life, shedding light on the significance of these problems and their resolution.

How do replication-transcription conflicts influence genome organization?
Replication-transcription conflicts are especially detrimental to fitness when the two machineries meet head-on – i.e. on the lagging strand. Presumably, to avoid these encounters that can destabilize the genome and are also detrimental for the rate of replication, bacteria have co-oriented the majority of their genes with replication such that they are on the leading strand. However, a significant number of genes, including some highly conserved and essential genes, remain on the lagging strand, head-on to replication. We are interested in identifying the biological reason behind the head-on orientation of these genes, as well as determining, in general, the reasons behind how bacterial genomes are organized.

What are the evolutionary consequences of replication-transcription conflicts?
We recently discovered that head-on genes are evolving faster than their co-directional counterparts on the leading strand. We have proposed that this accelerated evolution mechanism is at least partly due to the head-on collisions between the replication and transcription machineries. Our lab is currently working on characterizing the underlying conflict-dependent mechanisms that influence the mutagenesis of lagging strand genes and drive evolution of bacteria.


The Merrikh Lab - Summer 2013
from left: Christopher Merrikh, Ariana Samadpour, Sam Million-Weaver, Houra Merrikh (PI), Daniela Moreno, Mark Ragheb, Patrick Nugent
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