We used previously published microarray data from E. histoly tica HM 1 IMSS trophozoites. The analysis was conducted for the three groups of protein coding genes with distinct small RNA mapping patterns. For group I genes, there were 226 protein coding genes that selleck products met the criteria. of these, 116 genes are represented on the microarray. We plotted the number of mapped small RNA reads for each gene as a function of normalized mi croarray expression data and identified that most genes in this category are not expressed. For group II genes there Inhibitors,Modulators,Libraries are 45 genes that met our criteria and 26 are represented on the microarray and most of these genes are also not expressed. In order to determine whether these 112 genes are expressed under other condi tions, we compared the expression profiles of these genes across all other conditions tested.
Of these 112 genes, 30 were expressed in a strain specific manner, 35 were regulated under various culture conditions, and 55 were regulated during stage conversion. Overall, a total of 270 protein coding genes are not expressed in E. histolytica HM 1 IMSS trophozoites under standard in vitro growth conditions. Based on our sequencing data we esti mated Inhibitors,Modulators,Libraries that small RNAs target about 41% of these protein coding genes. Of these 112 genes, a large proportion change in expression profile under one or more conditions examined indicating that they are not permanently silenced and may be regulated by small RNAs. For the genes in group III, 87 genes met our criteria with 64 represented on the microarray.
Plotting the number Inhibitors,Modulators,Libraries of mapped reads for each gene as a function of its normalized microarray gene expression value showed no direct link between numbers of sense small RNAs to a gene and the expres sion level of that gene. We rea soned that for genes with high expression value, the sense small RNAs may represent degradation products. However, for genes with very low mRNA expression, we have no good ex planation on how these sense small RNAs were gener ated. Whether this represents an artifact of errors in genome assembly or some other factor is not clear at present. Interestingly, none of these genes are regulated under other conditions tested. In summary, the strongest correlation between Inhibitors,Modulators,Libraries gene expression and small RNA abundance was for genes Inhibitors,Modulators,Libraries that had either abundant antisense small RNAs or abundant sense and antisense small RNAs.
Although simply selleck Cabozantinib correla tive at present, the inverse correlation between antisense small RNA abundance and gene expression suggests that antisense small RNAs mediate target gene silencing in E. histolytica and are potentially involved in gene regulation under various conditions. Small RNA sequencing from the nonvirulent E. histolytica Rahman strain It has been observed that pathogenicity varies greatly among different E. histolytica strains. E.