Although ribonuclease H activity has long been implicated as a molecular mechanism by which DNA-like oligonucleotides induce degradation of target RNAs, definitive proof that one or more RNase H is responsible is lacking. To date, two RNase H enzymes (H1 and H2) have been cloned and shown to be expressed in human cells and tissues. To determine the role of RNase H1 in the mechanism of action of DNA-like antisense drugs, we varied the levels of the enzyme in human cells and mouse liver and determined the correlation of those levels with the effects of a number of DNA-like antisense drugs. Our results demonstrate that in human cells RNase H1 is responsible for most of the activity of DNAlike antisense drugs. Further, we show that there are several additional previously undescribed RNases H in human cells that may participate in the effects of DNAlike antisense oligonucleotides.

The interaction between a pathogen and a host is a highly dynamic process in which both agents activate complex programs. Here, we introduce a single-cell RNA-sequencing method, scDual-Seq, that simultaneously captures both host and pathogen transcriptomes. We use it to study the process of infection of individual mouse macrophages with the intracellular pathogen Salmonella typhimurium. Among the infected macrophages, we find three subpopulations and we show evidence for a linear progression through these subpopulations, supporting a model in which these three states correspond to consecutive stages of infection.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1340-x) contains supplementary material, which is available to authorized users.

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EDITORIAL SUMMARY:This protocol enables simultaneous analysis of host and bacterial transcripts by RNA-Seq. Including procedures for efficient host and bacterial cell lysis, barcoding of samples, and analysis of both mammalian and microbial reads from mixed host-pathogen RNA-Seq data.TWEET: Simultaneous analysis of host and pathogen transcriptomes by RNA-Seq. Abstract The ability to simultaneously characterize the bacterial and host expression programs during infection would facilitate a comprehensive understanding of pathogen-host interactions. While RNA-Seq has greatly advanced our ability to study the transcriptomes of prokaryote and eukaryotes separately, limitations in existing protocols for generating and analyzing RNA-Seq data have hindered simultaneous profiling of host and bacterial pathogen transcripts from the same sample. Here we provide a detailed protocol for simultaneous analysis of host and bacterial transcripts by RNA-Seq. Importantly, this protocol details the steps required for efficient host and bacteria lysis, barcoding of samples, technical advances in sample preparation for low yield sample inputs and a computational pipeline to analyze both mammalian and microbial reads from mixed hostpathogen RNA-Seq data. Sample preparation takes 3 d from cultured cells to pooled libraries. Data analysis takes an additional day. Compared with previous methods, the protocol detailed here provides a sensitive, facile and generalizable approach, suitable for large-scale studies, which will enable the field to obtain in-depth analysis of hostpathogen interactions in infection models. Introduction Intracellular bacterial pathogens, such as Mycobacterium tuberculosis, Salmonella enterica, Legionella pneumophilia, and Neisseria gonorrhea, spend a significant portion of their life-cycle surviving and replicating within host cells. The cellular interaction entails both a complex virulence program executed by the bacterial pathogen during infection 1 and activation of an orchestrated defense response by the host to counter the pathogen 2 . Genomic approaches have been employed in recent years to uncover substantial molecular details of this rich host-pathogen biology 3, 4 . However, technical constraints limit these studies to profiling either the host or the pathogen -while a comprehensive understanding of host-pathogen interactions requires simultaneous analysis of the associated gene expression changes in both the pathogen and the host 5 . The limitations of conventional protocols for simultaneous analysis of host and pathogen transcripts include 1) the inability to obtain high quality RNA with efficient lysis of both bacterial and mammalian host cells; 2) inefficient depletion of both microbial and mammalian ribosomal RNA species; 3) inability to simultaneously process polyadenylated and non-polyadenylated transcripts from low yield samples (>10ng of RNA); and 4) a lack of robust computational approaches for analyzing the often small subset of bacterial transcripts in infected cells or tissue. Recently, sever...

are coinventors on a patent application for a CD93-CAR. C.L.M. is a cofounder and consultant for Lyell Immunopharma, and Syncopation Life Sciences, which are developing CAR-based therapies, and serves as an advisor and consultant for Roche, NeoImmune Tech, Immatics, Apricity and Nektar. R.G.M. is a cofounder of Syncopation. E.S. is a consultant for Lyell Immunopharma. R.G.M. is a consultant for Lyell Immunopharma, Gamma Delta Therapeutics, Zai Lab, and Aptorum Group. R.M. is on the Board of Directors of BeyondSpring Inc, on the Scientific Advisory Boards of Kodikaz Therapeutic Solutions Inc., Coherus Biosciences, and Zenshine Pharmaceuticals, and is an inventor on a number of patents related to CD47 cancer immunotherapy licensed to Gilead Sciences, Inc. K.R.P., A.T.S., and HYC are cofounders of Cartography Biosciences. A.T.S is a scientific founder of Immunai and receives research funding from Arsenal Biosciences. H.Y.C is a cofounder of Accent Therapeutics and Boundless Bio, and an advisor to 10X Genomics, Arsenal Biosciences, and Spring Discovery. The remaining authors declare no competing financial interests.