Identification of group II intron binding sites along the bacterial genome

Sinorhizobium meliloti RmInt1 intron is a group II intron which encode a protein that lacks the C-terminal DNA binding and endonuclease domains. Nevertheless, RmInt1 is an efficient mobile retroelement that predominantly reverse splices into the transient single-stranded DNA at the template for lagging strand DNA synthesis during host replication. In fact, RmInt1 IEP interacts with DnaN using a conserved structural binding motif, facilitating the access to single-stranded DNA at the replication fork. However, some authors proposed that the DNA binding occurs nonspecifically, and then ribonucleoprotein particles scan for the correct target site. In this work, we investigate RmInt1 binding sites along Sinorhizobium meliloti genome using chromatin-immunoprecipitation coupled with next-generation sequencing. The RmInt1 binding sites were mainly detected around the replication origin and they did not always correspond with potential recognition sites for intron insertion. Our results support the nonspecific binding of RmInt1 ribonucleoprotein particles to the bacterial genome, besides they accumulate at regions with high replication yields.