Transcriptional recording by CRISPR spacer acquisition from RNA

Systems analysis of hematopoiesis using single-cell lineage tracing

PURPOSE OF REVIEW

In the last few decades, revolutionary advances in next-generation sequencing have led to single-cell lineage tracing technologies that now enable researchers to identify and quantify hematopoietic cell behavior with unprecedented detail. Combined readouts of cell lineage and cell state from the same cell mitigate the need to prospectively isolate populations of interest, and allow a system-level understanding of dynamic developmental processes. We will discuss the advantages and shortcomings of these technologies, the intriguing discoveries that stemmed from lineage tracing hematopoiesis at the single-cell level and the directions toward which the field is moving.

RECENT FINDINGS

Single-cell lineage tracing studies unveiled extensive functional heterogeneity within discrete immunophenotypic populations. Recently, several groups merged lineage tracing with single-cell RNA sequencing to visualize clonal relationships directly on transcriptional landscapes without the requirement for prospective isolation of cell types by FACS. To study the cell dynamics of hematopoiesis, without perturbation in their native niche, researchers have developed mouse models with endogenous single-cell lineage tracing systems, which can simultaneously trace thousands of hematopoietic progenitor cells in a single mouse, without transplantation. The emerging picture is that multiple hematopoietic hierarchies coexist within a single individual, each with distinct regulatory features. These hierarchies are imprinted during development much earlier than previously predicted, persisting well into adulthood and even after injury and transplantation.

SUMMARY

Clone-tracking experiments allow stem-cell researchers to characterize lineage hierarchies during blood development and regeneration. Combined with single-cell genomics analyses, these studies are allowing system-level description of hematopoiesis in mice and humans. Early exploratory studies have unveiled features with important implications for human biology and disease. VIDEO ABSTRACT.

Context-aware synthetic biology by controller design: Engineering the mammalian cell

The rise of systems biology has ushered a new paradigm: the view of the cell as a system that processes environmental inputs to drive phenotypic outputs. Synthetic biology provides a complementary approach, allowing us to program cell behavior through the addition of synthetic genetic devices into the cellular processor. These devices, and the complex genetic circuits they compose, are engineered using a design-prototype-test cycle, allowing for predictable device performance to be achieved in a context-dependent manner. Within mammalian cells, context effects impact device performance at multiple scales, including the genetic, cellular, and extracellular levels. In order for synthetic genetic devices to achieve predictable behaviors, approaches to overcome context dependence are necessary. Here, we describe control systems approaches for achieving context-aware devices that are robust to context effects. We then consider cell fate programing as a case study to explore the potential impact of context-aware devices for regenerative medicine applications.

Novel Identification of Bacterial Epigenetic Regulations Would Benefit From a Better Exploitation of Methylomic Data

DNA methylation can be part of epigenetic mechanisms, leading to cellular subpopulations with heterogeneous phenotypes. While prokaryotic phenotypic heterogeneity is of critical importance for a successful infection by several major pathogens, the exact mechanisms involved in this phenomenon remain unknown in many cases. Powerful sequencing tools have been developed to allow the detection of the DNA methylated bases at the genome level, and they have recently been extensively applied on numerous bacterial species. Some of these tools are increasingly used for metagenomics analysis but only a limited amount of the available methylomic data is currently being exploited. Because newly developed tools now allow the detection of subpopulations differing in their genome methylation patterns, it is time to emphasize future strategies based on a more extensive use of methylomic data. This will ultimately help to discover new epigenetic gene regulations involved in bacterial phenotypic heterogeneity, including during host-pathogen interactions.

The Intestinal Epithelium - Fluid Fate and Rigid Structure From Crypt Bottom to Villus Tip

The single-layered, simple epithelium of the gastro-intestinal tract controls nutrient uptake, coordinates our metabolism and shields us from pathogens. Despite its seemingly simple architecture, the intestinal lining consists of highly distinct cell populations that are continuously renewed by the same stem cell population. The need to maintain balanced diversity of cell types in an unceasingly regenerating tissue demands intricate mechanisms of spatial or temporal cell fate control. Recent advances in single-cell sequencing, spatio-temporal profiling and organoid technology have shed new light on the intricate micro-structure of the intestinal epithelium and on the mechanisms that maintain it. This led to the discovery of unexpected plasticity, zonation along the crypt-villus axis and new mechanism of self-organization. However, not only the epithelium, but also the underlying mesenchyme is distinctly structured. Several new studies have explored the intestinal stroma with single cell resolution and unveiled important interactions with the epithelium that are crucial for intestinal function and regeneration. In this review, we will discuss these recent findings and highlight the technologies that lead to their discovery. We will examine strengths and limitations of each approach and consider the wider impact of these results on our understanding of the intestine in health and disease.

Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex

CRISPR-Cas systems provide adaptive immunity in bacteria and archaea, beginning with integration of foreign sequences into the host CRISPR genomic locus and followed by transcription and maturation of CRISPR RNAs (crRNAs). In some CRISPR systems, a reverse transcriptase (RT) fusion to the Cas1 integrase and Cas6 maturase creates a single protein that enables concerted sequence integration and crRNA production. To elucidate how the RT-integrase organizes distinct enzymatic activities, we present the cryo-EM structure of a Cas6-RT-Cas1-Cas2 CRISPR integrase complex. The structure reveals a heterohexamer in which the RT directly contacts the integrase and maturase domains, suggesting functional coordination between all three active sites. Together with biochemical experiments, our data support a model of sequential enzymatic activities that enable CRISPR sequence acquisition from RNA and DNA substrates. These findings highlight an expanded capacity of some CRISPR systems to acquire diverse sequences that direct CRISPR-mediated interference.

Robust direct digital-to-biological data storage in living cells

DNA has been the predominant information storage medium for biology and holds great promise as a next-generation high-density data medium in the digital era. Currently, the vast majority of DNA-based data storage approaches rely on in vitro DNA synthesis. As such, there are limited methods to encode digital data into the chromosomes of living cells in a single step. Here, we describe a new electrogenetic framework for direct storage of digital data in living cells. Using an engineered redox-responsive CRISPR adaptation system, we encoded binary data in 3-bit units into CRISPR arrays of bacterial cells by electrical stimulation. We demonstrate multiplex data encoding into barcoded cell populations to yield meaningful information storage and capacity up to 72 bits, which can be maintained over many generations in natural open environments. This work establishes a direct digital-to-biological data storage framework and advances our capacity for information exchange between silicon- and carbon-based entities.

Recording of elapsed time and temporal information about biological events using Cas9

DNA has not been utilized to record temporal information, although DNA has been used to record biological information and to compute mathematical problems. Here, we found that indel generation by Cas9 and guide RNA can occur at steady rates, in contrast to typical dynamic biological reactions, and the accumulated indel frequency can be a function of time. By measuring indel frequencies, we developed a method for recording and measuring absolute time periods over hours to weeks in mammalian cells. These time-recordings were conducted in several cell types, with different promoters and delivery vectors for Cas9, and in both cultured cells and cells of living mice. As applications, we recorded the duration of chemical exposure and the lengths of elapsed time since the onset of biological events (e.g., heat exposure and inflammation). We propose that our systems could serve as synthetic "DNA clocks."

Phylodynamics for cell biologists

Multicellular organisms are composed of cells connected by ancestry and descent from progenitor cells. The dynamics of cell birth, death, and inheritance within an organism give rise to the fundamental processes of development, differentiation, and cancer. Technical advances in molecular biology now allow us to study cellular composition, ancestry, and evolution at the resolution of individual cells within an organism or tissue. Here, we take a phylogenetic and phylodynamic approach to single-cell biology. We explain how "tree thinking" is important to the interpretation of the growing body of cell-level data and how ecological null models can benefit statistical hypothesis testing. Experimental progress in cell biology should be accompanied by theoretical developments if we are to exploit fully the dynamical information in single-cell data.

Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences

The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous matrices like soils, sediments, and wastewater systems, tracking cryptic element cycling in the Earth system, and establishing the dynamics of microbe-microbe, microbe-plant, and microbe-material interactions. Before these new tools can reach their potential, however, a suite of biological parts and microbial chassis appropriate for environmental conditions must be developed by the synthetic biology community. This includes diversifying sensing modules to obtain information relevant to environmental questions, creating output signals that allow dynamic reporting from hard-to-image environmental materials, and tuning these sensors so that they reliably function long enough to be useful for environmental studies. Finally, ethical questions related to the use of synthetic biosensors in environmental applications are discussed.

Novel Modalities in DNA Data Storage

The field of storing information in DNA has expanded exponentially. Most common modalities involve encoding information from bits into synthesized nucleotides, storage in liquid or dry media, and decoding via sequencing. However, limitations to this paradigm include the cost of DNA synthesis and sequencing, along with low throughput. Further unresolved questions include the appropriate media of storage and the scalability of such approaches for commercial viability. In this review, we examine various storage modalities involving the use of DNA from a systems-level perspective. We compare novel methods that draw inspiration from molecular biology techniques that have been devised to overcome the difficulties posed by standard workflows and conceptualize potential applications that can arise from these advances.

Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems

Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline for the systematic prediction of genes specifically associated with retron RTs based on a previously reported large dataset representative of the diversity of prokaryotic RTs. We found that retrons generally comprise a tripartite system composed of the ncRNA, the RT and an additional protein or RT-fused domain with diverse enzymatic functions. These retron systems are highly modular, and their components have coevolved to different extents. Based on the additional module, we classified retrons into 13 types, some of which include additional variants. Our findings provide a basis for future studies on the biological function of retrons and for expanding their biotechnological applications.

How stem cells remember their past

Somatic stem cells are required for tissue development, homeostasis, and repair. Recent data suggested that previous biographical experiences of individual stem cells influence their behavior in the context of tissue formation and govern stem cell responses to external stimuli. Here we provide a concise review how a cell's biography, for example, previous rounds of cell divisions or the age-dependent accumulation of cellular damage, is remembered in stem cells and how previous experiences affect the segregation of cellular components, thus guiding cellular behavior in vertebrate stem cells. Further, we suggest future directions of research that may help to unravel the molecular underpinnings of how past experiences guide future cellular behavior.

It is unclear how important CRISPR-Cas systems are for protecting natural populations of bacteria against infections by mobile genetic elements

Articles on CRISPR commonly open with some variant of the phrase "these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements." There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical-computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.

RNA timestamps identify the age of single molecules in RNA sequencing

Current approaches to single-cell RNA sequencing (RNA-seq) provide only limited information about the dynamics of gene expression. Here we present RNA timestamps, a method for inferring the age of individual RNAs in RNA-seq data by exploiting RNA editing. To introduce timestamps, we tag RNA with a reporter motif consisting of multiple MS2 binding sites that recruit the adenosine deaminase ADAR2 fused to an MS2 capsid protein. ADAR2 binding to tagged RNA causes A-to-I edits to accumulate over time, allowing the age of the RNA to be inferred with hour-scale accuracy. By combining observations of multiple timestamped RNAs driven by the same promoter, we can determine when the promoter was active. We demonstrate that the system can infer the presence and timing of multiple past transcriptional events. Finally, we apply the method to cluster single cells according to the timing of past transcriptional activity. RNA timestamps will allow the incorporation of temporal information into RNA-seq workflows.

Long-Term Rewritable Report and Recording of Environmental Stimuli in Engineered Bacterial Populations

DNA writing (living sensing recorders) based whole-cell biosensors can capture transient signals and then convert them into readable genomic DNA changes. The primitive signals can be easily obtained by sequencing technology or analysis of protein activity (such as fluorescent protein). However, the functions of the current living sensing recorders still need to be expanded, and the difficulty of rewriting in complex biological environments has further limited their applications. In this study, we designed a long-term rewritable recording system using a CRISPR base editor-based synthetic genetic circuit, named CRISPR-istop. This system can convert stimuli into changes in the fluorescence intensity (reporter) and single-base mutations in genomic DNA (recording). Furthermore, we updated the biological circuit through the strategy of coupling the single-base mutation (record site) and the loss-of-function of the targeted protein (translation stopped by stop codon introduction), and we can remove edited bacteria from a population through selective sweeps upon applying a selective pressure. It successfully conducted the rewritable reporter and recording of the nutrient arabinose and pollutant arsenite with two rounds of continuous operation (10 passages/round, 12 h/passage). These observations indicated that the CRISPR-istop system can report and record stimuli over time; moreover, the recording can be manually erased and rewritten as needed. This method has great potential to be extended to more complicated recording systems to execute sophisticated tasks in inaccessible environments for synthetic biology and biomedical applications, such as monitoring disease-relevant physiological markers or other molecules.

The road ahead in genetics and genomics

In celebration of the 20th anniversary of Nature Reviews Genetics, we asked 12 leading researchers to reflect on the key challenges and opportunities faced by the field of genetics and genomics. Keeping their particular research area in mind, they take stock of the current state of play and emphasize the work that remains to be done over the next few years so that, ultimately, the benefits of genetic and genomic research can be felt by everyone.

To celebrate the first 20 years of Nature Reviews Genetics, we asked 12 leading scientists to reflect on the key challenges and opportunities faced by the field of genetics and genomics.

Amy L. McGuire is the Leon Jaworski Professor of Biomedical Ethics and Director of the Center for Medical Ethics and Health Policy at Baylor College of Medicine. She has received numerous teaching awards at Baylor College of Medicine, was recognized by the Texas Executive Women as a Woman on the Move in 2016 and was invited to give a TedMed talk titled “There is No Genome for the Human Spirit” in 2014. In 2020, she was elected as a Hastings Center Fellow. Her research focuses on ethical and policy issues related to emerging technologies, with a particular focus on genomic research, personalized medicine and the clinical integration of novel neurotechnologies.

Stacey Gabriel is the Senior Director of the Genomics Platform at the Broad Institute since 2012 and has led platform development, execution and operation since its founding. She is Chair of Institute Scientists and serves on the institute’s executive leadership team. She is widely recognized as a leader in genomic technology and project execution. She has led the Broad’s contributions to numerous flagship projects in human genetics, including the International HapMap Project, the 1000 Genomes Project, The Cancer Genome Atlas, the National Heart, Lung, and Blood Institute’s Exome Sequencing Project and the TOPMed programme. She is Principal Investigator of the Broad’s All of Us (AoU) Genomics Center and serves on the AoU Program Steering Committee.

Sarah A. Tishkoff is the David and Lyn Silfen University Associate Professor in Genetics and Biology at the University of Pennsylvania, Philadelphia, USA, and holds appointments in the School of Medicine and the School of Arts and Sciences. She is a member of the US National Academy of Sciences and a recipient of an NIH Pioneer Award, a David and Lucile Packard Career Award, a Burroughs/Wellcome Fund Career Award and an American Society of Human Genetics Curt Stern Award. Her work focuses on genomic variation in Africa, human evolutionary history, the genetic basis of adaptation and phenotypic variation in Africa, and the genetic basis of susceptibility to infectious disease in Africa.

Ambroise Wonkam is Professor of Medical Genetics, Director of GeneMAP (Genetic Medicine of African Populations Research Centre) and Deputy Dean Research in the Faculty of Health Sciences, University of Cape Town, South Africa. He has successfully led numerous NIH- and Wellcome Trust-funded projects over the past decade to investigate clinical variability in sickle cell disease, hearing impairment genetics and the return of individual findings in genetic research in Africa. He won the competitive Clinical Genetics Society International Award for 2014 from the British Society of Genetic Medicine. He is president of the African Society of Human Genetics.

Aravinda Chakravarti is Director of the Center for Human Genetics and Genomics, the Muriel G. and George W. Singer Professor of Neuroscience and Physiology, and Professor of Medicine at New York University School of Medicine. He is an elected member of the US National Academy of Sciences, the US National Academy of Medicine and the Indian National Science Academy. He has been a key participant in the Human Genome Project, the International HapMap Project and the 1000 Genomes Project. His research attempts to understand the molecular basis of multifactorial disease. He was awarded the 2013 William Allan Award by the American Society of Human Genetics and the 2018 Chen Award by the Human Genome Organization.

Eileen E. M. Furlong is Head of the Genome Biology Department at the European Molecular Biology Laboratory (EMBL) and a member of the EMBL Directorate. She is an elected member of the European Molecular Biology Organization (EMBO) and the Academia Europaea, and a European Research Council (ERC) advanced investigator. Her group dissects fundamental principles of how the genome is regulated and how it drives cell fate decisions during embryonic development, including how developmental enhancers are organized and function within the 3D nucleus. Her work combines genetics, (single-cell) genomics, imaging and computational approaches to understand these processes. Her research has advanced the development of genomic methods for use in complex multicellular organisms.

Barbara Treutlein is Associate Professor of Quantitative Developmental Biology in the Department of Biosystems Science and Engineering of ETH Zurich in Basel, Switzerland. Her group uses and develops single-cell genomics approaches in combination with stem cell-based 2D and 3D culture systems to study how human organs develop and regenerate and how cell fate is regulated. For her work, Barbara has received multiple awards, including the Friedmund Neumann Prize of the Schering Foundation, the Dr. Susan Lim Award for Outstanding Young Investigator of the International Society of Stem Cell Research and the EMBO Young Investigator Award.

Alexander Meissner is a scientific member of the Max Planck Society and currently Managing Director of the Max Planck Institute (MPI) for Molecular Genetics in Berlin, Germany. He heads the Department of Genome Regulation and is a visiting scientist in the Department of Stem Cell and Regenerative Biology at Harvard University. Before his move to the MPI, he was a tenured professor at Harvard University and a senior associate member of the Broad Institute, where he co-directed the epigenomics programme. In 2018, he was elected as an EMBO member. His laboratory uses genomic tools to study developmental and disease biology with a particular focus on epigenetic regulation.

Howard Y. Chang is the Virginia and D. K. Ludwig Professor of Cancer Genomics at Stanford University and an investigator at the Howard Hughes Medical Institute. He is a physician–scientist who has focused on deciphering the hidden information in the non-coding genome. His laboratory is best known for studies of long non-coding RNAs in gene regulation and development of new epigenomic technologies. He is an elected member of the US National Academy of Sciences, the US National Academy of Medicine, and the American Academy of Arts and Sciences.

Núria López-Bigas is ICREA research Professor at the Institute for Research in Biomedicine and Associate Professor at the University Pompeu Fabra. She obtained an ERC Consolidator Grant in 2015 and was elected as an EMBO member in 2016. Her work has been recognized with the prestigious Banc de Sabadell Award for Research in Biomedicine, the Catalan National Award for Young Research Talent and the Career Development Award from the Human Frontier Science Program. Her research focuses on the identification of cancer driver mutations, genes and pathways across tumour types and in understanding the mutational processes that lead to the accumulation of mutations in cancer cells.

Eran Segal is Professor in the Department of Computer Science and Applied Mathematics at the Weizmann Institute of Science, heading a multidisciplinary laboratory with extensive experience in machine learning, computational biology and analysis of heterogeneous high-throughput genomic data. His research focuses on the microbiome, nutrition and genetics, and their effect on health and disease and aims to develop personalized medicine based on big data from human cohorts. He has published more than 150 publications and received several awards and honours for his work, including the Overton and the Michael Bruno awards. He was recently elected as an EMBO member and as a member of the Israel Young Academy.

Jin-Soo Kim is Director of the Center for Genome Engineering in the Institute for Basic Science in Daejon, South Korea. He has received numerous awards, including the 2017 Asan Award in Medicine, the 2017 Yumin Award in Science and the 2019 Research Excellence Award (Federation of Asian and Oceanian Biochemists and Molecular Biologists). He was featured as one of ten Science Stars of East Asia in Nature (558, 502–510 (2018)) and has been recognized as a highly cited researcher by Clarivate Analytics since 2018. His work focuses on developing tools for genome editing in biomedical research.

Engineered bacteria to report gut function: technologies and implementation

Advances in synthetic biology and microbiology have enabled the creation of engineered bacteria which can sense and report on intracellular and extracellular signals. When deployed in vivo these whole-cell bacterial biosensors can act as sentinels to monitor biomolecules of interest in human health and disease settings. This is particularly interesting in the context of the gut microbiota, which interacts extensively with the human host throughout time and transit of the gut and can be accessed from feces without requiring invasive collection. Leveraging rational engineering approaches for genetic circuits as well as an expanding catalog of disease-associated biomarkers, bacterial biosensors can act as non-invasive and easy-to-monitor reporters of the gut. Here, we summarize recent engineering approaches applied in vivo in animal models and then highlight promising technologies for designing the next generation of bacterial biosensors.

CRISPR type II-A subgroups exhibit phylogenetically distinct mechanisms for prespacer insertion

CRISPR-Cas is an adaptive immune system that protects prokaryotes against foreign nucleic acids. Prokaryotes gain immunity by acquiring short pieces of the invading nucleic acid termed prespacers and inserting them into their CRISPR array. In type II-A systems, Cas1 and Cas2 proteins insert prespacers always at the leader-repeat junction of the CRISPR array. Among type II-A CRISPR systems, three distinct groups (G1, G2, and G3) exist according to the extent of DNA sequence conservation at the 3' end of the leader. However, the mechanisms by which these conserved motifs interact with their cognate Cas1 and Cas2 proteins remain unclear. Here, we performed in vitro integration assays, finding that for G1 and G2, the insertion site is recognized through defined mechanisms, at least in members examined to date, whereas G3 exhibits no sequence-specific insertion. G1 first recognized a 12-bp sequence at the leader-repeat junction and performed leader-side insertion before proceeding to spacer-side insertion. G2 recognized the full repeat sequence and could perform independent leader-side or spacer-side insertions, although the leader-side insertion was faster than spacer-side. The prespacer morphology requirements for Cas1-Cas2 varied, with G1 stringently requiring a 5-nucleotide 3' overhang and G2 being able to insert many forms of prespacers with variable efficiencies. These results highlight the intricacy of protein-DNA sequence interactions within the seemingly similar type II-A integration complexes and provide mechanistic insights into prespacer insertion. These interactions can be fine-tuned to expand the Cas1-Cas2 toolset for inserting small DNAs into diverse DNA targets.

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla.

Metagenomic analysis of a single RNA virome from the Yangshan Deep-Water Harbour in China enabled the recovery of more than 4,500 distinct RNA viruses, doubling the known set of RNA viruses to date, and provided insights into their biology.

Detection of CRISPR adaptation

Prokaryotic adaptive immunity is built when short DNA fragments called spacers are acquired into CRISPR (clustered regularly interspaced short palindromic repeats) arrays. CRISPR adaptation is a multistep process which comprises selection, generation, and incorporation of prespacers into arrays. Once adapted, spacers provide immunity through the recognition of complementary nucleic acid sequences, channeling them for destruction. To prevent deleterious autoimmunity, CRISPR adaptation must therefore be a highly regulated and infrequent process, at least in the absence of genetic invaders. Over the years, ingenious methods to study CRISPR adaptation have been developed. In this paper, we discuss and compare methods that detect CRISPR adaptation and its intermediates in vivo and propose suppressing PCR as a simple modification of a popular assay to monitor spacer acquisition with increased sensitivity.

Mapping human cell phenotypes to genotypes with single-cell genomics

The cumulative activity of all of the body's cells, with their myriad interactions, life histories, and environmental experiences, gives rise to a condition that is distinctly human and specific to each individual. It is an enduring goal to catalog our human cell types, to understand how they develop, how they vary between individuals, and how they fail in disease. Single-cell genomics has revolutionized this endeavor because sequencing-based methods provide a means to quantitatively annotate cell states on the basis of high-information content and high-throughput measurements. Together with advances in stem cell biology and gene editing, we are in the midst of a fascinating journey to understand the cellular phenotypes that compose human bodies and how the human genome is used to build and maintain each cell. Here, we will review recent advances into how single-cell genomics is being used to develop personalized phenotyping strategies that cross subcellular, cellular, and tissue scales to link our genome to our cumulative cellular phenotypes.

Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity

Genome-wide CRISPR screens enable systematic interrogation of gene function. However, guide RNA libraries are costly to synthesize, and their limited diversity compromises the sensitivity of CRISPR screens. Using the Streptococcus pyogenes CRISPR-Cas adaptation machinery, we developed CRISPR adaptation-mediated library manufacturing (CALM), which turns bacterial cells into "factories" for generating hundreds of thousands of crRNAs covering 95% of all targetable genomic sites. With an average gene targeted by more than 100 distinct crRNAs, these highly comprehensive CRISPRi libraries produced varying degrees of transcriptional repression critical for uncovering novel antibiotic resistance determinants. Furthermore, by iterating CRISPR adaptation, we rapidly generated dual-crRNA libraries representing more than 100,000 dual-gene perturbations. The polarized nature of spacer adaptation revealed the historical contingency in the stepwise acquisition of genetic perturbations leading to increasing antibiotic resistance. CALM circumvents the expense, labor, and time required for synthesis and cloning of gRNAs, allowing generation of CRISPRi libraries in wild-type bacteria refractory to routine genetic manipulation.

CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers

CRISPR-Cas immune systems in bacteria and archaea record prior infections as spacers within each system’s CRISPR arrays. Spacers are normally derived from invasive genetic material and direct the immune system to complementary targets as part of future infections. However, not all spacers appear to be derived from foreign genetic material and instead can originate from the host genome. Their presence poses a paradox, as self-targeting spacers would be expected to induce an autoimmune response and cell death. In this review, we discuss the known frequency of self-targeting spacers in natural CRISPR-Cas systems, how these spacers can be incorporated into CRISPR arrays, and how the host can evade lethal attack. We also discuss how self-targeting spacers can become the basis for alternative functions performed by CRISPR-Cas systems that extend beyond adaptive immunity. Overall, the acquisition of genome-targeting spacers poses a substantial risk but can aid in the host’s evolution and potentially lead to or support new functionalities.

Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform

The flow of genetic material between bacteria is central to the adaptation and evolution of bacterial genomes. However, our knowledge about DNA transfer within complex microbiomes is lacking, with most studies of horizontal gene transfer (HGT) relying on bioinformatic analyses of genetic elements maintained on evolutionary timescales or experimental measurements of phenotypically trackable markers. Here, we utilize the CRISPR-Cas spacer acquisition process to detect DNA acquisition events from complex microbiota in real-time and at nucleotide resolution. In this system, an E. coli recording strain is exposed to a microbial sample and spacers are acquired from transferred plasmids and permanently stored in genomic CRISPR arrays. Sequencing and analysis of acquired spacers enables identification of the transferred plasmids. This approach allowed us to identify individual mobile elements without relying on phenotypic markers or post-transfer replication. We found that HGT into the recording strain in human clinical fecal samples can be extensive and is driven by different plasmid types, with the IncX type being the most actively transferred.

Spacer acquisition from RNA mediated by a natural reverse transcriptase-Cas1 fusion protein associated with a type III-D CRISPR-Cas system in Vibrio vulnificus

The association of reverse transcriptases (RTs) with CRISPR–Cas system has recently attracted interest because the RT activity appears to facilitate the RT-dependent acquisition of spacers from RNA molecules. However, our understanding of this spacer acquisition process remains limited. We characterized the in vivo acquisition of spacers mediated by an RT-Cas1 fusion protein linked to a type III-D system from Vibrio vulnificus strain YJ016, and showed that the adaptation module, consisting of the RT-Cas1 fusion, two different Cas2 proteins (A and B) and one of the two CRISPR arrays, was completely functional in a heterologous host. We found that mutations of the active site of the RT domain significantly decreased the acquisition of new spacers and showed that this RT-Cas1-associated adaptation module was able to incorporate spacers from RNA molecules into the CRISPR array. We demonstrated that the two Cas2 proteins of the adaptation module were required for spacer acquisition. Furthermore, we found that several sequence-specific features were required for the acquisition and integration of spacers derived from any region of the genome, with no bias along the 5′and 3′ends of coding sequences. This study provides new insight into the RT-Cas1 fusion protein-mediated acquisition of spacers from RNA molecules.

Spacer acquisition from RNA mediated by a natural reverse transcriptase-Cas1 fusion protein associated with a type III-D CRISPR-Cas system in Vibrio vulnificus

The association of reverse transcriptases (RTs) with CRISPR-Cas system has recently attracted interest because the RT activity appears to facilitate the RT-dependent acquisition of spacers from RNA molecules. However, our understanding of this spacer acquisition process remains limited. We characterized the in vivo acquisition of spacers mediated by an RT-Cas1 fusion protein linked to a type III-D system from Vibrio vulnificus strain YJ016, and showed that the adaptation module, consisting of the RT-Cas1 fusion, two different Cas2 proteins (A and B) and one of the two CRISPR arrays, was completely functional in a heterologous host. We found that mutations of the active site of the RT domain significantly decreased the acquisition of new spacers and showed that this RT-Cas1-associated adaptation module was able to incorporate spacers from RNA molecules into the CRISPR array. We demonstrated that the two Cas2 proteins of the adaptation module were required for spacer acquisition. Furthermore, we found that several sequence-specific features were required for the acquisition and integration of spacers derived from any region of the genome, with no bias along the 5'and 3'ends of coding sequences. This study provides new insight into the RT-Cas1 fusion protein-mediated acquisition of spacers from RNA molecules.

Recruitment of Reverse Transcriptase-Cas1 Fusion Proteins by Type VI-A CRISPR-Cas Systems

Type VI CRISPR-Cas systems contain a single effector nuclease (Cas13) that exclusively targets single-stranded RNA. It remains unknown how these systems acquire spacers. It has been suggested that type VI systems with adaptation modules can acquire spacers from RNA bacteriophages, but sequence similarities suggest that spacers may provide immunity to DNA phages. We searched databases for Cas13 proteins with linked RTs. We identified two different type VI-A systems with adaptation modules including an RT-Cas1 fusion and Cas2 proteins. Phylogenetic reconstruction analyses revealed that these adaptation modules were recruited by different effector Cas13a proteins, possibly from RT-associated type III-D systems within the bacterial classes Alphaproteobacteria and Clostridia. These type VI-A systems are predicted to acquire spacers from RNA molecules, paving the way for future studies investigating their role in bacterial adaptive immunity and biotechnological applications.

Multiple origins of reverse transcriptases linked to CRISPR-Cas systems

Prokaryotic genomes harbour a plethora of uncharacterized reverse transcriptases (RTs). RTs phylogenetically related to those encoded by group-II introns have been found associated with type III CRISPR-Cas systems, adjacent or fused at the C-terminus to Cas1. It is thought that these RTs may have a relevant function in the CRISPR immune response mediating spacer acquisition from RNA molecules. The origin and relationships of these RTs and the ways in which the various protein domains evolved remain matters of debate. We carried out a large survey of annotated RTs in databases (198,760 sequences) and constructed a large dataset of unique representative sequences (9,141). The combined phylogenetic reconstruction and identification of the RTs and their various protein domains in the vicinity of CRISPR adaptation and effector modules revealed three different origins for these RTs, consistent with their emergence on multiple occasions: a larger group that have evolved from group-II intron RTs, and two minor lineages that may have arisen more recently from Retron/retron-like sequences and Abi-P2 RTs, the latter associated with type I-C systems. We also identified a particular group of RTs associated with CRISPR-cas loci in clade 12, fused C-terminally to an archaeo-eukaryotic primase (AEP), a protein domain (AE-Prim_S_like) forming a particular family within the AEP proper clade. Together, these data provide new insight into the evolution of CRISPR-Cas/RT systems.

Adaptation processes that build CRISPR immunity: creative destruction, updated

Prokaryotes can defend themselves against invading mobile genetic elements (MGEs) by acquiring immune memory against them. The memory is a DNA database located at specific chromosomal sites called CRISPRs (clustered regularly interspaced short palindromic repeats) that store fragments of MGE DNA. These are utilised to target and destroy returning MGEs, preventing re-infection. The effectiveness of CRISPR-based immune defence depends on 'adaptation' reactions that capture and integrate MGE DNA fragments into CRISPRs. This provides the means for immunity to be delivered against MGEs in 'interference' reactions. Adaptation and interference are catalysed by Cas (CRISPR-associated) proteins, aided by enzymes well known for other roles in cells. We survey the molecular biology of CRISPR adaptation, highlighting entirely new developments that may help us to understand how MGE DNA is captured. We focus on processes in Escherichia coli, punctuated with reference to other prokaryotes that illustrate how common requirements for adaptation, DNA capture and integration, can be achieved in different ways. We also comment on how CRISPR adaptation enzymes, and their antecedents, can be utilised for biotechnology.

Transposon-encoded CRISPR-Cas systems direct RNA-guided DNA integration

Conventional CRISPR-Cas systems maintain genomic integrity by leveraging guide RNAs for the nuclease-dependent degradation of mobile genetic elements, including plasmids and viruses. Here we describe a notable inversion of this paradigm, in which bacterial Tn7-like transposons have co-opted nuclease-deficient CRISPR-Cas systems to catalyse RNA-guided integration of mobile genetic elements into the genome. Programmable transposition of Vibrio cholerae Tn6677 in Escherichia coli requires CRISPR- and transposon-associated molecular machineries, including a co-complex between the DNA-targeting complex Cascade and the transposition protein TniQ. Integration of donor DNA occurs in one of two possible orientations at a fixed distance downstream of target DNA sequences, and can accommodate variable length genetic payloads. Deep-sequencing experiments reveal highly specific, genome-wide DNA insertion across dozens of unique target sites. This discovery of a fully programmable, RNA-guided integrase lays the foundation for genomic manipulations that obviate the requirements for double-strand breaks and homology-directed repair.

Recording development with single cell dynamic lineage tracing

Every animal grows from a single fertilized egg into an intricate network of cell types and organ systems. This process is captured in a lineage tree: a diagram of every cell's ancestry back to the founding zygote. Biologists have long sought to trace this cell lineage tree in individual organisms and have developed a variety of technologies to map the progeny of specific cells. However, there are billions to trillions of cells in complex organisms, and conventional approaches can only map a limited number of clonal populations per experiment. A new generation of tools that use molecular recording methods integrated with single cell profiling technologies may provide a solution. Here, we summarize recent breakthroughs in these technologies, outline experimental and computational challenges, and discuss biological questions that can be addressed using single cell dynamic lineage tracing.

Development of CRISPR-Cas systems for genome editing and beyond

The development of clustered regularly interspaced short-palindromic repeat (CRISPR)-Cas systems for genome editing has transformed the way life science research is conducted and holds enormous potential for the treatment of disease as well as for many aspects of biotechnology. Here, I provide a personal perspective on the development of CRISPR-Cas9 for genome editing within the broader context of the field and discuss our work to discover novel Cas effectors and develop them into additional molecular tools. The initial demonstration of Cas9-mediated genome editing launched the development of many other technologies, enabled new lines of biological inquiry, and motivated a deeper examination of natural CRISPR-Cas systems, including the discovery of new types of CRISPR-Cas systems. These new discoveries in turn spurred further technological developments. I review these exciting discoveries and technologies as well as provide an overview of the broad array of applications of these technologies in basic research and in the improvement of human health. It is clear that we are only just beginning to unravel the potential within microbial diversity, and it is quite likely that we will continue to discover other exciting phenomena, some of which it may be possible to repurpose as molecular technologies. The transformation of mysterious natural phenomena to powerful tools, however, takes a collective effort to discover, characterize, and engineer them, and it has been a privilege to join the numerous researchers who have contributed to this transformation of CRISPR-Cas systems.

DNA event recorders send past information of cells to the time of observation

While current omics and single cell technologies have enabled measurements of high-resolution molecular snapshots of cells at a large scale, these technologies all require destruction of samples and prevent us from analyzing dynamic changes in molecular profiles, phenotypes, and behaviors of individual cells in a complex system. One possible direction to overcome this issue is the development of a cell-embedded 'event recorder' system, whereby molecular and phenotypic information of a cell(s) can be obtained at the time of observation with their past event information stored in 'heritable polymers' of the same cell. This concept has been demonstrated by many synthetic cellular circuits that monitor and transmit a certain set of environmental and intracellular signals into DNA, and have now been further accelerated by recent CRISPR-related technologies. Notably, the discovery of the RT-Cas1-Cas2 system, which acquires sequences of cellular transcripts into a specific host genomic region, has enabled recording of a broader range of molecular profile histories in the DNA tapes of cells, to understand the dynamics of complex biological processes that cannot be addressed by current technologies.

Using CAPTURE to detect spacer acquisition in native CRISPR arrays

CRISPR-Cas systems are able to acquire immunological memories (spacers) from bacteriophages and plasmids in order to survive infection; however, this often occurs at low frequency within a population, which can make it difficult to detect. Here we describe CAPTURE (CRISPR adaptation PCR technique using reamplification and electrophoresis), a versatile and adaptable protocol to detect spacer-acquisition events by electrophoresis imaging with high-enough sensitivity to identify spacer acquisition in 1 in 105 cells. Our method harnesses two simple PCR steps, separated by automated electrophoresis and extraction of size-selected DNA amplicons, thus allowing the removal of unexpanded arrays from the sample pool and enabling 1,000-times more sensitive detection of new spacers than alternative PCR protocols. CAPTURE is a straightforward method that requires only 1 d to enable the detection of spacer acquisition in all native CRISPR systems and facilitate studies aimed both at unraveling the mechanism of spacer integration and more sensitive tracing of integration events in natural ecosystems.

CRISPR/Cas Systems towards Next-Generation Biosensing

Beyond its remarkable genome editing ability, the CRISPR/Cas9 effector has also been utilized in biosensing applications. The recent discovery of the collateral RNA cleavage activity of the Cas13a effector has sparked even greater interest in developing novel biosensing technologies for nucleic acid detection and promised significant advances in CRISPR diagnostics. Now, along with the discovery of Cas12 collateral cleavage activities on single-stranded DNA (ssDNA), several CRISPR/Cas systems have been established for detecting various targets, including bacteria, viruses, cancer mutations, and others. Based on key Cas effectors, we provide a detailed classification of CRISPR/Cas biosensing systems and propose their future utility. As the field continues to mature, CRISPR/Cas systems have the potential to become promising candidates for next-generation diagnostic biosensing platforms.

Applications of CRISPR-Cas in Bioengineering, Biotechnology, and Translational Research

CRISPR technology is rapidly evolving, and the scope of CRISPR applications is constantly expanding. CRISPR was originally employed for genome editing. Its application was then extended to epigenome editing, karyotype engineering, chromatin imaging, transcriptome, and metabolic pathway engineering. Now, CRISPR technology is being harnessed for genetic circuits engineering, cell signaling sensing, cellular events recording, lineage information reconstruction, gene drive, DNA genotyping, miRNA quantification, in vivo cloning, site-directed mutagenesis, genomic diversification, and proteomic analysis in situ. It has also been implemented in the translational research of human diseases such as cancer immunotherapy, antiviral therapy, bacteriophage therapy, cancer diagnosis, pathogen screening, microbiota remodeling, stem-cell reprogramming, immunogenomic engineering, vaccine development, and antibody production. This review aims to summarize the key concepts of these CRISPR applications in order to capture the current state of play in this fast-moving field. The key mechanisms, strategies, and design principles for each technological advance are also highlighted.