Zhan, Z. | Search bioRxiv

bioRxiv2021

The REF6-dependent H3K27 demethylation establishes transcriptional competence to promote germination in Arabidopsis

Seed germination is a critical developmental switch from a dormant state to active growth, which involves extensive changes in metabolism, gene expression and cellular identity. However, our understanding of epigenetic and transcriptional reprogramming during this process is limited. The histone H3 lysine 27 trimethylation (H3K27me3) plays a key role in regulating gene repression and cell fate specification. Here, we profile H3K27me3 dynamics and dissect the function of H3K27 demethylation during germination. Our temporal genome-wide profiling of H3K27me3 and transcription reveal delayed H3K27me3 reprogramming compared with transcriptomic changes during germination, with H3K27me3 changes mainly occurring when the embryo is entering into vegetative development. REF6-mediated H3K27 demethylation promotes germination but does not significantly contribute to H3K27me3 dynamics during germination, but rather stably establishes an H3K27me3-depleted state permissive to transcription. By analyzing REF6 genomic binding, we show that it is absent from mature embryo chromatin and gradually establishes occupancy during the course of germination to counteract increased PRC2 activity. Our study provides key insights into the dynamics of gene expression and H3K27me3 during seed germination and suggests the function of H3K27me3 in facilitating cell fate switch. Furthermore, we reveal the importance of H3K27 demethylation-established transcriptional competence in germination and likely other developmental processes.

plant biology↗

bioRxiv2021

Population genomics of Salmonella enterica serovar Weltevreden ST365, an emerging predominant causative agent of diarrheal disease

Salmonella enterica serovar Weltevreden is a recently emerged pathogen, and as such we lack a comprehensive knowledge of its microbiology, genomics, epidemiology and biogeography. In this study, we analyzed 174 novel S. Weltevreden isolates including 111 isolates recovered from diarrheal patients in China between 2006 and 2017. Our results demonstrate that the ST365 clone was the predominant causative agent of the diarrhea-outbreak during this period, as vast majority of the isolates recovered from diarrheal patients belonged to this sequence type (97.37%, 74/76). We also determined the ST365 clone as the predominant sequence type of S. Weltevreden from diarrheal patients globally from previously published sequences (97.51%, 196/201). In order to determine the possible antimicrobial genes and virulence factors associated with S. Weltevreden, we performed whole genome sequencing on our novel isolates. We were able to identify a range of key virulence factors associated with S. Weltevreden that are likely to be beneficial to their fitness and pathogenesis. Furthermore, we were able to isolate a novel 100.03-kb IncFII(S) type virulence plasmid that used the same replicon as pSPCV virulence plasmid. Importantly, we demonstrated through plasmid elimination a functional role for this plasmid in bacterial virulence. These findings are critical to further our knowledge of this high consequence pathogen. ImportanceSalmonella Weltevreden is a newly emerged foodborne pathogen and has caused several outbreaks of diarrheal diseases in some regions in the world. However, comprehensive knowledge of microbiology, genomics, epidemiology and biogeography of this newly emerged pathogen is still lack. In this study, we made an unexpected discovery that S. Weltevreden sequence type (ST) 365 is the causative agent in the diarrhea-outbreak in China and many other regions of the world. We also shown that this sequence type was widely recovered from animal, food, and environmental samples collected in different regions in the world. Importantly, we discovered a novel IncFII(S) type virulence plasmid commonly carried by S. Weltevreden strains of both human, animal, and food origins. These data facilitate future studies investigating the emergence of S. Weltevreden involved in diarrheal outbreaks and the global spread of S. Weltevreden strains.

microbiology↗