Gu, T. | Search bioRxiv

bioRxiv2018

Expression profile analysis of circular RNAs in essential hypertension by microarray and bioinformatics.

Circular RNAs (circRNAs), widely found in human cells, are involved in disease and play an important role in progression. To determine whether circRNAs are related in essential hypertension (EH), we analyzed the expression profile of circRNAs and miRNAs in 5 EH and 5 healthy controls cases which were screened by microarray. Through microarray data and public data analysis, differently expressed transcripts were divided into modules, and circRNAs were functionally annotated by miRNAs. The expression of two circRNAs, has_circ_0037909 and has_circ_0105015, were validated in EH by qRT-PCR, which may be associated with EH. Further analysis showed that two circRNAs might through immune system by up-regulation circRNAs and down-regulation expression. These circRNAs biological functions need to be further validated.

genetics↗

bioRxiv2017

Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions

Filamentous plant pathogen genomes often display a bipartite architecture with gene sparse, repeat-rich compartments serving as a cradle for adaptive evolution. However, the extent to which this \"two-speed\" genome architecture is associated with genome-wide epigenetic modifications is unknown. Here, we show that the oomycete plant pathogens Phytophthora infestans and Phytophthora sojae possess functional adenine N6- methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome. In contrast, 5-methylcytosine (5mC) could not be detected in the two Phytophthora species. Methylated DNA IP Sequencing (MeDIP-seq) of each species revealed that 6mA is depleted around the transcriptional starting sites (TSS) and is associated with low expressed genes, particularly transposable elements. Remarkably, genes occupying the gene-sparse regions have higher levels of 6mA compared to the remainder of both genomes, possibly implicating the methylome in adaptive evolution of Phytophthora. Among three putative adenine methyltransferases, DAMT1 and DAMT3 displayed robust enzymatic activities. Surprisingly, single knockouts of each of the 6mA methyltransferases in P. sojae significantly reduced in vivo 6mA levels, indicating that the three enzymes are not fully redundant. MeDIP-seq of the damt3 mutant revealed uneven patterns of 6mA methylation across genes, suggesting that PsDAMT3 may have a preference for gene body methylation after the TSS. Our findings provide evidence that 6mA modification is an epigenetic mark of Phytophthora genomes and that complex patterns of 6mA methylation by the expanded 6mA methyltransferases may be associated with adaptive evolution in these important plant pathogens.

molecular biology↗