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ModM has six target recognition domain alleles (<jats:italic>modM1\u20136<\/jats:italic>), and we have previously shown that <jats:italic>modM2<\/jats:italic> is the predominant allele, while <jats:italic>modM3<\/jats:italic> is associated with OM. Phase-variable DNA methyltransferases mediate epigenetic regulation and modulate pathogenesis in several bacteria. ModM2 of <jats:italic>M. catarrhalis<\/jats:italic> regulates the expression of a phasevarion containing genes important for colonization and infection. Here we describe the phase-variable expression of <jats:italic>modM3<\/jats:italic>, the ModM3 methylation site and the suite of genes regulated within the ModM3 phasevarion.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Phase-variable expression of <jats:italic>modM3<\/jats:italic>, mediated by variation in length of a 5\u2032-(CAAC)<jats:sub>n<\/jats:sub>-3\u2032 tetranucleotide repeat tract in the open reading frame was demonstrated in <jats:italic>M. catarrhalis<\/jats:italic> strain CCRI-195ME with GeneScan fragment length analysis and western immunoblot. We determined that ModM3 is an active N6-adenine methyltransferase that methylates the sequence 5\u2032-AC<jats:sup>m6<\/jats:sup>ATC-3\u2032. Methylation was detected at all 4446 5\u2032-ACATC-3\u2032 sites in the genome when ModM3 is expressed. RNASeq analysis identified 31 genes that are differentially expressed between <jats:italic>modM3<\/jats:italic> ON and OFF variants, including five genes that are involved in the response to oxidative and nitrosative stress, with potential roles in biofilm formation and survival in anaerobic environments. An in vivo chinchilla (<jats:italic>Chinchilla lanigera)<\/jats:italic> model of otitis media demonstrated that transbullar challenge with the <jats:italic>modM3<\/jats:italic> OFF variant resulted in an increased middle ear bacterial load compared to a <jats:italic>modM3<\/jats:italic> ON variant. In addition, co-infection experiments with NTHi and <jats:italic>M. catarrhalis modM3<\/jats:italic> ON or <jats:italic>modM3<\/jats:italic> OFF variants revealed that phase variation of <jats:italic>modM3<\/jats:italic> altered survival of NTHi in the middle ear during early and late stage infection.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Phase variation of ModM3 epigenetically regulates the expression of a phasevarion containing multiple genes that are potentially important in the progression of otitis media.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12866-019-1660-y","type":"journal-article","created":{"date-parts":[[2019,12,9]],"date-time":"2019-12-09T17:03:31Z","timestamp":1575911011000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["The Moraxella catarrhalis phase-variable DNA methyltransferase ModM3 is an epigenetic regulator that affects bacterial survival in an in vivo model of otitis media"],"prefix":"10.1186","volume":"19","author":[{"given":"Luke V.","family":"Blakeway","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aimee","family":"Tan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph A.","family":"Jurcisek","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lauren O.","family":"Bakaletz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John M.","family":"Atack","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian R.","family":"Peak","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7094-3528","authenticated-orcid":false,"given":"Kate L.","family":"Seib","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,12,9]]},"reference":[{"issue":"12","key":"1660_CR1","doi-asserted-by":"crossref","first-page":"2674","DOI":"10.1128\/JCM.28.12.2674-2680.1990","volume":"28","author":"M Vaneechoutte","year":"1990","unstructured":"Vaneechoutte M, Verschraegen G, Claeys G, Weise B, Van den Abeele AM. 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Animal care and all procedures were performed under a protocol approved by the Nationwide Children\u2019s Hospital Research Institute Animal Care and Use Committee (Protocol #01304AR) and in compliance with the U.S. Department of Health and Human Services Guide for the Care and Use of Laboratory Animals. Strain CCRI-195ME was recovered from a patient undergoing surgery for tympanostomy tube insertion, after obtaining written Informed Consent from patient\u2019s guardian. Consent forms and study protocols were approved by the Nationwide Children\u2019s Hospital Institutional Review Board (protocol #0312HS196).","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"KLS is a member of the editorial board (Associate Editor) of BMC Microbiology. The authors declare that they have no other competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"276"}}