Project description:Large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. We investigated 1,529 microbial metagenome-assembled genomes recovered from our site to understand carbon processing in this environment. Metabolic reconstruction, supported by metatranscriptomic and metaproteomic data, revealed key populations involved in organic matter degradation, including bacteria encoding a pathway for xylose degradation only previously identified in fungi.
Project description:In eukaryotic cells, nucleo-cytoplasmic trafficking of macromolecules across the nuclear envelope is an essential process that ensures a rapid exchange of different cellular components, including proteins and RNAs, between the nucleus and cytoplasm. The significance of the nucleo-cytoplasmic trafficking of chromatin regulators in regulating DNA methylation and gene silencing is not well understood. Here, using a genetic screen, we identified XPO1A, one of the nuclear export receptors in Arabidopsis, as an anti-silencing factor that protects transgenes from transcriptional silencing. Loss-of-function of XPO1A leads to locus-specific DNA hypermethylation at transgene promoters and some endogenous loci. We found that XPO1A directly interacts with histone deacetylase HDA6 in vivo and the xpo1a mutation causes increased nuclear retention of HDA6 protein, resulting in reduced histone acetylation and enhanced transgene silencing. Our results revealed a new mechanism of epigenetic regulation through the modulation of XPO1A-dependent nucleo-cytoplasm partitioning of a chromatin regulator.
Project description:In the recent years, RNA silencing has been studied extensively to be a conserved regulatory process in plants. In the antiviral silencing, the intermediate double-stranded RNA form during the replication of RNA viruses were recognized and processed into abundant of overlapping viral siRNA (viRNAs). Accordingly, the cloned viRNAs could be conversely assembled into some contigs of viruses, which is recently exploited for identifying new viruses and their genome sequences.To obtain rapidly the complete genome sequence of BYSMV, we carried out deep sequencing of small RNAs from healthy and BYSMV infected wheat, respectively. Thirteen contigs were assembled from the overlapping viRNAs only present in the infected wheat but not in the healthy wheat. The results of BLAST showed that ten contigs shared about 96% identity with the reported L gene of BYSMV isolate Zanjan-1. Viral assembly from the BYSMV infected wheat plants to obtain the full lengh genome and characterise the viral siRNAs
Project description:<p>Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-seq, an antibody-dependent technique with a high rate of false positives. Here, we addressed the presence of m6A in CHIKV and DENV RNAs. For this, we combined m6A-seq and the antibody-independent SELECT and nanopore direct RNA sequencing techniques with functional, molecular, and mutagenesis studies. Following this comprehensive analysis, we found no evidence of m6A modification in CHIKV or DENV transcripts. Furthermore, depletion of key components of the host m6A machinery did not affect CHIKV or DENV infection. Moreover, CHIKV or DENV infection had no effect on the m6A machinery’s localization. Our results challenge the prevailing notion that m6A modification is a general feature of cytoplasmic RNA viruses and underscore the importance of validating RNA modifications with orthogonal approaches.</p>