RNA-seq of Moraxella catarrhalis CCRI-195ME ModM3 ON and ModM3 OFF phase variants

Moraxella catarrhalis contains an N6-adenine DNA-methyltransferase (ModM3), that is subject to phase variable expression (random ON/OFF switching). Phase-variable switching of DNA methyltransferase activity results in the presence or absence of methylation at a specific target sequence, leading to co-ordinated, epigenetically-regulated switching of expression of multiple genes across the genome. The suite of genes thus regulated are known as a phasevarion (phase-variable regulon). Phase variation of modM is mediated at the translational level by a 5′-(CAAC)n-3′ tetranucleotide repeat tract present within its open reading frame (ORF). Analysis of the genomes of 51 M. catarrhalis strains identified six modM alleles (modM1-6) that vary in their target recognition domains. The modM3 allele is also overrepresented in middle ear isolates of M. catarrhalis from children with OM. Here we characterise the genes regulated in the ModM3 phasevarion and show that phase variation of the M.catarrhalis CCRI-195ME ModM3 epigenetically regulates the expression of a phasevarion containing multiple genes that are potentially important in the progression of otitis media. Direct comparison of biological triplicates of modM3 ON and modM3 OFF variants

卡他莫拉菌（Moraxella catarrhalis）携带一种N6-腺嘌呤DNA甲基转移酶（N6-adenine DNA-methyltransferase，ModM3），该酶的表达存在相变量调控现象，即随机通断切换。DNA甲基转移酶活性的相变量切换会导致特异性靶序列发生甲基化或去甲基化，进而引发全基因组范围内多基因表达的协同表观遗传调控切换。此类被调控的基因集合被称为相可变调节子（phasevarion，即phase-variable regulon）。modM基因的相变现象由其开放阅读框（open reading frame, ORF）内存在的5′-(CAAC)n-3′四核苷酸重复序列区域在翻译水平介导。对51株卡他莫拉菌的基因组分析共鉴定出6种modM等位基因（modM1-6），各等位基因的靶识别结构域存在序列差异。modM3等位基因在儿童中耳炎（otitis media, OM）患者的卡他莫拉菌中耳分离株中同样过度富集。本研究对ModM3相可变调节子中的调控基因进行了表征，并证实卡他莫拉菌CCRI-195ME菌株的ModM3相变量变化可表观遗传调控一个包含多个与中耳炎进展潜在相关基因的相可变调节子的表达。对modM3通态（ON）与关断态（OFF）变体的生物学重复样本进行直接比较