Highlights d Exposure to the psychedelic drug DOI results in enduring molecular adaptations d Post-acute DOI unveils phenotypes akin to antidepressant adaptations d Concurrent occurrence of synaptic plasticity mediated via 5-HT

Epigenetic mechanisms such as histone modifications play critical roles in adaptive tuning of chromatin structures. Profiling various histone modifications at the genome scale using tissues from animal and human samples is an important step for functional studies of epigenomes and epigenomics-based precision medicine. Because the profile of a histone mark is highly specific to a cell type, cell isolation from tissues is often necessary to generate a homogeneous cell population and such operation tends to yield a low number of cells. In addition, high-throughput processing is often desirable due to the multiplexity of histone marks of interest and the large quantity of samples in a hospital setting. In this protocol, we describe detailed instructions on device fabrication, setup, and operation of microfluidic oscillatory washing-based chromatin immunoprecipitation followed by sequencing (MOWChIP-seq) for profiling histone modifications using as few as 100 cells per assay with a throughput as high as 8 assays in a run. MOWChIP-seq operation involves flowing of chromatin fragments through a packed bed of antibody-coated beads followed by vigorous microfluidic oscillatory washing. Our process is semi-automated for reduced labor and improved reproducibility. Using one 8-unit device, it takes 2 d to produce 8 sequencing libraries from chromatin samples. The technology is scalable. We used the protocol to study a number of histone modifications in various types of mouse and human tissues. The protocol can be conducted by a user who is familiar with molecular biology procedures and has basic engineering skills.

The velvet regulator VosA plays a pivotal role in asexual sporulation in the model filamentous fungus Aspergillus nidulans. In the present study, we characterize the roles of VosA in sexual spores (ascospores) in A. nidulans. During ascospore maturation, the deletion of vosA causes a rapid decrease in spore viability. The absence of vosA also results in a lack of trehalose biogenesis and decreased tolerance of ascospores to thermal and oxidative stresses. RNA-seq-based genome-wide expression analysis demonstrated that the loss of vosA leads to elevated expression of sterigmatocystin (ST) biosynthetic genes and a slight increase in ST production in ascospores. Moreover, the deletion of vosA causes upregulation of additional gene clusters associated with the biosynthesis of other secondary metabolites, including asperthecin, microperfuranone, and monodictyphenone. On the other hand, the lack of vosA results in the downregulation of various genes involved in primary metabolism. In addition, vosA deletion alters mRNA levels of genes associated with the cell wall integrity and trehalose biosynthesis. Overall, these results demonstrate that the velvet regulator VosA plays a key role in the maturation and the cellular and metabolic integrity of sexual spores in A. nidulans.

Advances in Next Generation Sequencing (NGS) have made available a wealth of information that had previously been inaccessible to researchers and clinicians. NGS has been applied to understand genomic, transcriptomic, and epigenomic changes and gained traction as a significant tool capable of accelerating diagnosis, prognosis, and biomarker discovery. However, these NGS assays have yet to be practical methods for patient stratification or diagnosis because of the gap between the tiny quantities of biomaterials provided by a clinical sample and the large DNA input required by most of these assays. Current library preparation methodologies typically require large input amounts of DNA and a long and complicated manual process. Here, we present a microfluidic droplet-based system for NGS library preparation, capable of reducing the number of pipetting steps significantly, reducing reagent consumption by 10x, automating much of the process, while supporting extremely low DNA input requirement (10 pg per library). This semiautomated technology will allow for low-input preparations of 8 libraries simultaneously while reducing batch-to-batch variation and operator hands-on time.

Aspergillus parasiticus is a notorious filamentous fungus, which can produce aflatoxin B and G. Here, we reported the complete mitochondrial genome sequence of Aspergillus parasiticus isolated from air in South Korea. Its mitochondrial genome was successfully assembled from raw reads sequenced using MiSeq by Velvet and GapCloser. Total length of the mitochondrial genome is 29,141 bp and encoded 45 genes (17 protein-coding genes, 2 rRNAs, and 26 tRNAs). Nucleotide sequence of coding region takes over 25.4% and overall GC content is 26.2%. Phylogenetic tree presents that A. parasiticus is clustered with Aspergillus oryzae, which is same section Flavi in Aspergillus genus. It will be a useful molecular resource to understand section Flavi in Aspergillus genus. ARTICLE HISTORY

Aspergillus luchuensis is a filamentous fungus used for food and alcohol fermentation in many Asian countries. Here, we reported the complete mitochondrial genome sequence of A. luchuensis isolated from fermented soybean brick, called as Meju, in Korea. Its mitochondrial genome was successfully assembled from raw reads sequenced using MiSeq by Velvet and GapCloser. Total length of the mitochondrial genome is 31,228 bp and encoded 44 genes (16 protein-coding genes, two rRNAs, and 26 tRNAs). Nucleotide sequence of coding region takes over 25.6%, and overall GC content is 26.4%. Phylogenetic tree of mitochondrial genomes presented A. luchuensis and Aspergillus kawachii are clustered in one clade. This mitochondrial genome can be used for further analyses of Aspergillus mitochondrial comparative genomics to improve understanding of diverse Aspergillus species. ARTICLE HISTORY

Genome wide association studies have revealed >150 loci associated with schizophrenia risk, yet these genetic factors do not seem to be sufficient to fully explain the molecular determinants behind this psychiatric condition. Epigenetic marks such as post-translational histone modifications remain largely plastic during development and adulthood, allowing a dynamic impact of environmental factors, including antipsychotic medications, on access to genes and regulatory elements. However, no study so far has profiled cell-specific genome-wide histone modifications in postmortem brain samples from schizophrenia subjects or the effect of antipsychotic treatment on such epigenetic marks. Here we show the first comprehensive epigenomic characterization of the frontal cortex of 29 individuals with schizophrenia and 29 matched controls, including histone modifications associated with active promoters and enhancers H3K4me3 and H3K27ac along with RNA expression in neuronal and glial nuclei. Schizophrenia subjects exhibited thousands of cell type-specific epigenetic differences at regions that included several susceptibility genetic loci, such as NRG1, RGS4 and HTR2A. Comparing untreated and treated schizophrenia subjects with controls, our findings provide entirely new insights into differentially modified genes associated with unexpected pathways that are potential markers of antipsychotic treatment. Additionally, we show that the effect of age on the epigenomic landscape is more pronounced in frontal cortex samples of antipsychotic-treated schizophrenia subjects. Together, our data provide important evidence of epigenetic alterations in the frontal cortex of individuals with schizophrenia, and remark the impact of age and antipsychotic treatment on chromatin organization.

The genome-wide DNA methylation profile, or DNA methylome, is a critical component of the overall epigenomic landscape that modulates gene activities and cell fate. Single-cell DNA methylomic studies offer unprecedented resolution for detecting and profiling cell subsets based on methylomic features. However, existing single-cell methylomic technologies are based on use of tubes or well plates and these platforms are not easily scalable for handling a large number of single cells. Here we demonstrate a droplet-based microfluidic technology, Drop-BS, to construct single-cell bisulfite sequencing libraries for DNA methylome profiling. Drop-BS takes advantage of the ultrahigh throughput offered by droplet microfluidics to prepare bisulfite sequencing libraries of up to 10,000 single cells within 2 days. We apply the technology to profile mixed cell lines, mouse and human brain tissues to reveal cell type heterogeneity. Drop-BS offers a promising solution for single-cell methylomic studies requiring examination of a large cell population.