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Results for “Genetics”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2019

Genetic and epigenetic architectures of neurological protein biomarkers in the Lothian Birth Cohort 1936

Although plasma proteins may serve as important markers of disease risk in neurological conditions, the molecular mechanisms responsible for inter-individual variation in plasma protein levels are poorly understood. In this study, we conducted genome- and epigenome-wide association studies on the levels of 92 neurological proteins to identify genetic and epigenetic loci associated with their plasma concentrations (n = 750). We identified 62 independent genome-wide significant loci for 37 proteins (P < 5.4 x 10-10) and 68 epigenome-wide significant sites associated with the levels of 7 proteins (P < 3.9 x 10-10). Using this information, we identified biological pathways in which putative neurological biomarkers are implicated as well as molecular mechanisms through which genetic variation may perturb plasma protein levels. Additionally, we found evidence that poliovirus receptor is causally associated with Alzheimers disease. In conclusion, we identified many novel genetic and epigenetic factors that are associated with neurological protein levels which may inform disease biology and establish causal relationships between biomarkers and neurological diseases.

neuroscience↗

bioRxiv2019

Loss of function mutation of mouse Snap29 on a mixed genetic background phenocopy abnormalities found in CEDNIK and 22q11.2 Deletion Syndrome patients

Synaptosomal-associated protein 29 (SNAP29) is a member of the SNARE family of proteins involved in maintenance of various intracellular protein trafficking pathways. SNAP29 maps to the 22q11.2 region and is deleted in 90% of patients with 22q11.2 deletion syndrome (22q11.2DS). However, the contribution of hemizygosity of SNAP29 to developmental abnormalities in 22q11.2DS remains to be determined. Mutations in SNAP29 are responsible for the developmental syndrome called CEDNIK (cerebral dysgenesis, neuropathy, ichthyosis, and keratoderma). On an inbred C57Bl/6J genetic background, only the ichthyotic skin defect associated with CEDNIK was reported. In this study, we show that loss of function mutation of Snap29 on a mixed genetic background not only models skin abnormalities found in CEDNIK, but also phenocopy ophthalmological, neurological, and motor defects found in these patients and a subset of 22q11.2DS patients. Thus, our findings indicate that mouse models of human syndromes should be analyzed on a mixed genetic background. Our work also reveals an unanticipated requirement for Snap29 in male fertility, and support contribution of hemizygosity for SNAP29 to the phenotypic spectrum of abnormalities found in 22q11.2DS patients.

developmental biology↗

bioRxiv2019

Ecological strategy and genetic load in the shepherd's purse (Capsella bursa-pastoris) from the core and the limit of its natural range.

Species range expansion is a complex process whose outcome depends on the interplay of demographic, environmental and genetic factors. In plants, self-fertilizing species that do not require a mate to reproduce usually show higher invasive ability. However, this comes at a cost as both selfing and bottlenecks occurring during colonization lead to an increase in deleterious mutations accumulation (genetic load). Although they are theoretically clearly spelled out, the relationships between genomic and phenotypic characteristics of expanding populations have hitherto rarely been characterized. In the present study we analyzed how different accessions of the shepherds purse, C. bursa-pastoris, coming from the front of colonization or from the core of the natural range performed under increasing density of competitors. We first showed that, as expected, accessions from the front of colonization performed the worst for most life history traits compared with accessions from core populations. Second, competitor density had a negative impact on both vegetative growth and reproductive output in term of fruits production for all accessions. However, somewhat unexpectedly given their higher genetic load and their lower absolute performance, accessions from the front of colonization were less affected by competition than accessions from the core of the species range. This could be due to phenotypic tradeoffs and a shift in phenology that allow the accessions from the front of colonization to avoid competition. These results are discussed in terms of ecological strategies of expanding populations.

evolutionary biology↗

bioRxiv2019

In-depth genetic analysis of 6p21.3 reveals insights into associations between HLA types and complex traits and disease

The highly polymorphic major histocompatibility (MHC) region encodes the human leucocyte antigen (HLA) gene complex and is associated with many autoimmune and infectious diseases. Despite the importance of this interval, comprehensive genetic studies interrogating associations between HLA types, expression of non-HLA genes and disease, have not yet been conducted. To address this issue, we collected high-coverage whole genome sequence from 419 individuals and performed HLA typing at the highest resolution. Using RNA-seq from matched iPSC lines, we conducted an in-depth eQTL analysis using "personalized" transcripts, which significantly improved estimated expression levels of HLA genes, and showed HLA types have genetic associations independent from SNPs. We leveraged the eQTL results to examine associations between expression levels of non-HLA genes and disease. As a proof-of-principle, we investigated RNF5, whose protein product is a novel drug target in cystic fibrosis. We observed that decreased expression of RNF5 was associated with the 8.1 ancestral haplotype, which was previously found associated with protection against infection in cystic fibrosis. Overall, our study shows that genetically dissecting the MHC region provides novel insights into mechanisms underlying associations of this interval with disease.

genomics↗

bioRxiv2019

Differences in Genetic Liability for Insomnia and Hypersomnia in Bipolar Disorder Subtypes

BackgroundInsomnia and hypersomnia are common in bipolar disorder (BD) but it is unclear whether genetic factors influence this association. Stratifying by bipolar subtypes could elucidate the nature of this association and inform research on sleep and BD. We therefore aimed to determine whether polygenic risk scores (PRS) for insomnia, daytime sleepiness and sleep duration differ according to bipolar subtypes (bipolar I disorder, BD-I or bipolar II disorder, BD-II).\n\nMethodsIn this case-control study, we used multinomial regression to determine whether PRS for insomnia, daytime sleepiness, and sleep duration were associated with risk of BD-I or BD-II when compared to each other and to controls. Cases (n=4672) were recruited within the United Kingdom from the Bipolar Disorder Research Network. Controls (n=5714) were recruited from the 1958 British Birth Cohort and UK Blood Service. All participants were of European ancestry. Clinical subtypes of BD were determined by semi-structured psychiatric interview (the Schedules for Clinical Assessment in Neuropsychiatry) and case notes.\n\nResultsWithin cases, 3404 and 1268 met DSM-IV criteria for BD-I and BD-II, respectively. Insomnia PRS was associated with increased risk of BD-II (RR = 1.14, 95% CI = 1.07-1.21, P = 8.26 x 10-5) but not BD-I (RR = 0.98, 95% CI = 0.94-1.03, P = .409) relative to controls. In contrast, sleep duration PRS was associated with increased relative risk of BD-I (RR = 1.10, 95% CI = 1.06-1.15, P = 1.13 x 10-5), but not BD-II (RR = 0.99, 95% CI = 0.93-1.06, P = .818). Daytime sleepiness PRS was associated with an increased risk of BD-I (RR = 1.07, 95% CI = 1.02-1.11, P = .005) and BD-II (RR = 1.14, 95% CI = 1.07-1.22, P = 3.22 x 10-5) compared to controls, but did not distinguish subtypes from each other.\n\nConclusionsBipolar subtypes differ in genetic liability to insomnia and sleep duration. Our findings provide further evidence that the distinction between BD-I and BD-II has biological and genetic validity. This distinction will be critical in the selection of participants for future research on the role of sleep disturbance in BD.

genomics↗

bioRxiv2019

Genetic Basis of Alternative Polyadenylation is an Emerging Molecular Phenotype for Human Traits and Diseases

Genome-wide association studies have identified thousands of non-coding variants that are statistically associated with human traits and diseases. However, functional interpretation of these variants remains a major challenge. Here, we describe the first atlas of human 3-UTR alternative polyadenylation (APA) Quantitative Trait Loci (3QTLs), i.e. [~]0.4 million genetic variants associated with APA of target genes across 46 Genotype-Tissue Expression (GTEx) tissues from 467 individuals. APA occurs in approximately 70% of human genes and substantively impacts cellular proliferation, differentiation and tumorigenesis. Mechanistically, 3QTLs could alter polyA motifs and RNA-binding protein binding sites, leading to thousands of APA changes. Importantly, 3QTLs can be used to interpret [~]16.1% of trait-associated variants and are largely distinct from other QTLs such as eQTLs. The genetic basis of APA (3QTLs) thus represent a novel molecular phenotype to explain a large fraction of non-coding variants and to provide new insights into complex traits and disease etiologies.\n\nHighlightsO_LIThe first atlas of human 3QTLs: [~]0.4 million genetic variants associated with alternative polyadenylation of target genes across 46 tissues from 467 individuals\nC_LIO_LI3QTLs could alter polyA motifs and RNA-binding protein binding sites\nC_LIO_LI3QTLs can be used to interpret [~]16.1% of trait-associated variants\nC_LIO_LIMany disease-associated 3QTLs contribute to phenotype independent of gene expression\nC_LI

bioinformatics↗

bioRxiv2019

Positive genetic associations among fitness traits support evolvability of a reef-building coral under multiple stressors

Climate change threatens organisms in a variety of interactive ways that requires simultaneous adaptation of multiple traits. Predicting evolutionary responses requires an understanding of the potential for synergistic interactions among stressors and the genetic variance and covariance among fitness-related traits that may reinforce or constrain an adaptive response. Here we investigate the capacity of Acropora millepora, a reef-building coral, to adapt to multiple environmental stressors: rising sea surface temperature, ocean acidification, and increased prevalence of infectious diseases. We measured growth rates (weight gain), coral color (a proxy for Symbiodiniaceae density), and survival, in addition to nine physiological indicators of coral and algal health in 40 coral genets exposed to each of these three stressors singly and combined. Individual stressors resulted in predicted responses (e.g., corals developed lesions after bacterial challenge and bleached under thermal stress). However, corals did not suffer substantially more when all three stressors were combined. Nor were tradeoffs observed between tolerances to different stressors; instead, individuals performing well under one stressor also tended to perform well under every other stressor. An analysis of genetic correlations between traits revealed positive co-variances, suggesting that selection to multiple stressors will reinforce rather than constrain the simultaneous evolution of traits related to holobiont health (e.g., weight gain and algal density). These findings support the potential for rapid coral adaptation under climate change and emphasize the importance of accounting for corals adaptive capacity when predicting the future of coral reefs.

evolutionary biology↗

bioRxiv2019

Genetic variation in apolipoprotein A-I concentrations and risk of coronary artery disease

RationaleApolipoprotein A-I (apoA-I) infusions represent a potential novel therapeutic approach for the prevention of coronary artery disease (CAD) with phase III cardiovascular outcome trials currently underway. Although circulating apoA-I levels inversely associate with risk of CAD, the evidence base of this representing a causal relationship is lacking.\n\nObjectiveTo assess the causal role of apoA-I in CAD using human genetics.\n\nMethods and ResultsWe identified a variant (rs12225230) in APOA1 locus that associated with circulating apoA-I concentrations at GWAS significance (P<5x10-8) in 20,370 Finnish participants and meta-analyzed our data with a previous genome-wide association study of apoA-I. We obtained genetic estimates of CAD from UK Biobank and CARDIoGRAMplusC4D (totaling 122,733 CAD cases) and conducted a two-sample Mendelian randomization analysis. We compared our genetic findings to observational associations of apoA-I with risk of CAD in 918 incident CAD cases among 11,535 individuals from population-based prospective cohorts. We also summarized the available evidence from randomized controlled trials (RCTs) of apoA-I infusion therapies reporting CAD events. ApoA-I was associated with a lower risk of CAD in observational analyses (HR 0.81; 95%CI: 0.75, 0.88; per 1-SD higher apoA-I), with the association showing a dose-response relationship. Rs12225230 associated with apoA-I concentrations (per-C allele beta 0.076 SD; SE: 0.013; P=1.5x10-9) but not with potential confounders. In Mendelian randomization analyses, apoA-I was not related to risk of CAD (OR 1.13; 95%CI: 0.98, 1.30 per 1-SD higher apoA-I), which was different to the observational association (P-het<0.001). RCTs of apoA-I infusions did not show an effect on the risk of CAD.\n\nConclusionsGenetic evidence fails to support a cardioprotective role for apoA-I. This casts doubt on the likely benefit of apoA-I infusion therapy in the ongoing phase III cardiovascular outcome trial.

epidemiology↗

bioRxiv2019

Pathogen genetic control of transcriptome variation in the Arabidopsis thaliana - Botrytis cinerea pathosystem

Disease symptoms arise from the interaction of the host and pathogen genomes. However, little is known about how genetic variation in the interaction modulates both organisms transcriptomes, especially in complex interactions like those between generalist pathogens and their plant hosts. To begin mapping how polygenic pathogen variation influences both organisms transcriptomes, we used the Botrytis cinerea - Arabidopsis thaliana pathosystem. We measured the co-transcriptome across a genetically diverse collection of 96 B. cinerea isolates infected on the Arabidopsis wildtype, Col-0. Using the B. cinerea genomic variation, we performed genome-wide association (GWA) for each of 23,947 measurable transcripts in the host, and 9,267 measurable transcripts in the pathogen. Unlike other eGWA studies, there was a relative absence of cis-eQTL that is likely explained by structural variants and allelic heterogeneity within the pathogens genome. This analysis identified mostly trans-eQTL in the pathogen with eQTL hotspots dispersed across the pathogen genome that altered the pathogens transcripts, the hosts transcripts, or both the pathogen and the host. Gene membership in the trans-eQTL hotspots suggests links to several known and many novel virulence mechanisms in the plant-pathogen interaction. Genes annotated to these hotspots provide potential targets for blocking manipulation of the host response by this ubiquitous generalist pathogen. This shows that genetic control over the co-transcriptome is polygenic, similar to the virulence outcome in the interaction of Botrytis cinerea on Arabidopsis thaliana.

plant biology↗

bioRxiv2019

An open resource of structural variation for medical and population genetics

Structural variants (SVs) rearrange large segments of the genome and can have profound consequences for evolution and human diseases. As national biobanks, disease association studies, and clinical genetic testing grow increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD) have become integral for interpreting genetic variation. To date, no large-scale reference maps of SVs exist from high-coverage sequencing comparable to those available for point mutations in protein-coding genes. Here, we constructed a reference atlas of SVs across 14,891 genomes from diverse global populations (54% non-European) as a component of gnomAD. We discovered a rich landscape of 433,371 distinct SVs, including 5,295 multi-breakpoint complex SVs across 11 mutational subclasses, and examples of localized chromosome shattering, as in chromothripsis. The average individual harbored 7,439 SVs, which accounted for 25-29% of all rare protein-truncating events per genome. We found strong correlations between constraint against damaging point mutations and rare SVs that both disrupt and duplicate protein-coding sequence, suggesting intolerance to reciprocal dosage alterations for a subset of tightly regulated genes. We also uncovered modest selection against noncoding SVs in cis-regulatory elements, although selection against protein-truncating SVs was stronger than any effect on noncoding SVs. Finally, we benchmarked carrier rates for medically relevant SVs, finding very large ([≥]1Mb) rare SVs in 3.8% of genomes (~1:26 individuals) and clinically reportable incidental SVs in 0.18% of genomes (~1:556 individuals). These data have been integrated directly into the gnomAD browser (https://gnomad.broadinstitute.org) and will have broad utility for population genetics, disease association, and diagnostic screening.

genomics↗

bioRxiv2019

Combined morphological and transcriptomic analyses reveal genetic regulation underlying the species-specific bulbil outgrowth in Dioscorea alata L

In yam (Dioscorea spp) species, bulbil at leaf axils is the most striking species-specific axillary structure and exhibits important ecological niches as well as crop yields. Genetic regulation underlying bulbil outgrowth remain largely unclear. We here first characterized the development of bulbil from Dioscorea alata L. using histological analysis and further performed full transcriptional profiling on its key developmental stages. Comprehensive mRNA analyses suggested that long-distance phytohormone signals including auxin, CK and ABA, play critical roles in controlling the initiation of bulbil through coordinately altering expression levels of genes involved in localized hormone metabolism and transport. Sucrose functioned as a novel signal and was required strongly at the early stage of bulbil formation, thus promoting its outgrowth through up-regulating trehalose-6-phophate pathway. GO pathway analysis demonstrated that genes are enriched in biological processes related to light stimuli, cell division, cell wall modification and carbohydrate metabolism. Particularly, some novel genes including dioscorin A/B, starch synthetic enzymes and chitinases showed remarkably high expression levels and strengthened the outgrowth of bulbil. Our data set demonstrated that the initiation of bulbil was highly regulated by a large number of transcriptional regulators. RNA in situ hybridization with MYB, WRKY and NAC transcription factors confirmed their key roles in triggering bulbil initiation. Together, our findings provide a crucial angle for genetic regulation of controlling the unique reproductive development of bulbils. Transcriptome data set can serve as a valuable genomic resource for yam research community or further genetic manipulation to improve bulbil yields.\n\nHighlightTranscriptomic data identified multiple functional genes and regulators; long-distance signals (auxin, CK, ABA), and sucrose as a novel signal play critical roles in controlling bulbil outgrowth.

plant biology↗

bioRxiv2019

A multi-omics digital research object for the genetics of sleep regulation.

More and more researchers make use of multi-omics approaches to tackle complex cellular and organismal systems. It has become apparent that the potential for re-use and integrate data generated by different labs can enhance knowledge. However, a meaningful and efficient re-use of data generated by others is difficult to achieve without in depth understanding of how these datasets were assembled. We therefore designed and describe in detail a digital research object embedding data, documentation and analytics on mouse sleep regulation. The aim of this study was to bring together electrophysiological recordings, sleep-wake behavior, metabolomics, genetics, and gene regulatory data in a systems genetics model to investigate sleep regulation in the BXD panel of recombinant inbred lines. We here showcase both the advantages and limitations of providing such multi-modal data and analytics. The reproducibility of the results was tested by a bioinformatician not implicated in the original project and the robustness of results was assessed by re-annotating genetic and transcriptome data from the mm9 to the mm10 mouse genome assembly.

bioinformatics↗

bioRxiv2019

The role of genetic constraints and social environment in explaining female extra-pair mating

Why females of socially monogamous species copulate with males other than their partner has been a long-standing, unresolved puzzle. We previously reported that female promiscuity appears to be a genetic corollary of male promiscuity (intersexual pleiotropy hypothesis). Here we put this earlier finding to a critical test using the same population of zebra finches Taeniopygia guttata. After three generations of artificial selection on male courtship rate, a correlate of extra-pair mating, we assess whether female promiscuity changed by indirect selection and we re-examine the crucial genetic correlations. Our new analyses with substantially increased statistical power clearly reject the hypothesis that male and female promiscuity are genetically homologous traits. Our study highlights that individual females show low repeatability in extra-pair mating behavior across different social environments. This emphasizes the potential importance of pair bond strength and the availability of favored extra-pair males as factors explaining variation in patterns of female promiscuity.

evolutionary biology↗

bioRxiv2019

Strong spatial genetic structure in a Baltic Sea herbivore due to recent range expansion, multiple bottlenecks and low connectivity

In the Baltic Sea, recent range expansions following the opening of the Danish straits have resulted in a low-diversity ecosystem, both among and within species. However, relatively little is known about population genetic patterns within the basin, except for in a few commercially caught species and some primary producers thought to be ecosystem engineers. Here, we investigate the population genetic structure of the ecologically important crustacean Idotea balthica throughout the Baltic Sea using an array of 33,774 genome-wide SNP markers derived from 2b-RAD sequencing. We also generate a biophysical connectivity matrix, with which we compare the genomic data. We find strong population structure on small scales across the Baltic Sea, and that genomic patterns in most cases closely match biophysical connectivity, suggesting that current patterns are important for dispersal of this species. We also find a strong signal of multiple bottlenecks during the initial range expansion, in the form of reduced heterozygosity along the historical expansion front. The lack of gene flow among sampling sites in the Baltic Sea environmental gradient potentiates local adaptation, while at the same time also increasing genetic drift in low-diversity areas.

evolutionary biology↗

bioRxiv2019

Genetic contributions to health literacy

Higher health literacy is associated with higher cognitive function and better health. Despite its wide use in medical research, no study has investigated the genetic contributions to health literacy. Using 5,783 English Longitudinal Study of Ageing (ELSA) participants (mean age=65.49, SD=9.55) who had genotyping data and had completed a health literacy test at wave 2 (2004-2005), we carried out a genome-wide association study (GWAS) of health literacy. We estimated the proportion of variance in health literacy explained by all common single nucleotide polymorphisms (SNPs). Polygenic profile scores were calculated using summary statistics from GWAS of 21 cognitive and health measures. Logistic regression was used to test whether polygenic scores for cognitive and health-related traits were associated with having adequate, compared to limited, health literacy. No SNPs achieved genome-wide significance for association with health literacy. The proportion of variance in health literacy accounted for by common SNPs was 8.5% (SE=7.2%). Greater odds of having adequate health literacy were associated with a 1SD higher polygenic score for general cognitive ability (OR=1.34, 95% CI 1.26-1.42), verbal-numerical reasoning (OR=1.30, 1.23-1.39), and years of schooling (OR=1.29, 1.21-1.36). Reduced odds of having adequate health literacy were associated with higher polygenic profiles for poorer self-rated health (OR=0.92, 0.87-0.98) and schizophrenia (OR=0.91, 0.85-0.96). The well-documented associations between health literacy, cognitive function and health may partly be due to shared genetic aetiology. Larger studies are required to obtain accurate estimates of SNP-based heritability, and to discover specific health literacy-associated genetic variants.

epidemiology↗

bioRxiv2019

A distinct cardiopharyngeal mesoderm genetic hierarchy establishes antero-posterior patterning of esophagus striated muscle

In most vertebrates, the upper digestive tract is composed of muscularised jaws linked to the esophagus that permit food uptake and swallowing. Masticatory and esophagus striated muscles (ESM) share a common cardiopharyngeal mesoderm (CPM) origin, however ESM are unusual among striated muscles as they are established in the absence of a primary skeletal muscle scaffold. Using mouse chimeras, we show that the transcription factors Tbx1 and Isl1 are required cell-autonomously for myogenic specification of ESM progenitors. Further, genetic loss-of-function and pharmacological studies point to Met/HGF signalling for antero-posterior migration of esophagus muscle progenitors, where HGF ligand is expressed in adjacent smooth muscle cells. These observations highlight the functional relevance of a smooth and striated muscle progenitor dialogue for ESM patterning. Our findings establish a Tbx1-Isl1-Met genetic hierarchy that uniquely regulate esophagus myogenesis and identify distinct genetic signatures that can be used as a framework to interpret pathologies arising within CPM derivatives.

developmental biology↗

bioRxiv2019

Role of host genetic diversity for susceptibility-to-infection in the evolution of virulence of a plant virus

Predicting viral emergence is difficult due to the stochastic nature of the underlying processes and the many factors that govern pathogen evolution. Environmental factors affecting the host, the pathogen and the interaction between both are key in emergence. In particular, infectious disease dynamics are affected by spatiotemporal heterogeneity in their environments. A broad knowledge of these factors will allow better estimating where and when viral emergence is more likely to occur. Here we investigate how the population structure for susceptibility-to-infection genes of the plant Arabidopsis thaliana shapes the evolution of Turnip mosaic virus (TuMV). For doing so we have evolved TuMV lineages in two radically different host population structures: (i) multiple genetically homogeneous A. thaliana subpopulations and (ii) a single maximally genetically heterogeneous population. We found faster adaptation of TuMV to homogeneous than to heterogeneous host populations. However, viruses evolved in heterogeneous host populations were more pathogenic and infectious than viruses evolved in the homogeneous population. Furthermore, the viruses evolved in homogeneous populations showed stronger signatures of local specialization than viruses evolved in heterogeneous populations. These results illustrate how the genetic diversity of hosts in an experimental ecosystem favors the evolution of virulence of a pathogen.

evolutionary biology↗

bioRxiv2019

CRISPR-Cas9-assisted native end-joining editing offers a simple strategy for efficient genetic engineering in Escherichia coli

Unlike eukaryotes, bacteria are less proficient in homologous recombination (HR) and non-homologous end joining (NHEJ). All existing genomic editing methods for Escherichia coli rely on exogenous HR or NHEJ systems to repair DNA double-strand breaks (DSBs). Although an E. coli native end-joining (ENEJ) system has been reported, its potential in chromosomal engineering has not yet been explored. Here, we present a CRISPR-Cas9-assisted native end-joining editing and show that ENEJ-dependent DNA repair can be used to conduct rapid and efficient knocking-out of E. coli genomic sequence of up to 83 kb. Moreover, the positive rate and editing efficiency is independent of high-efficiency competent cells. The method requires neither exogenous DNA repair systems nor introduced editing template. The Cas9 complex is the only foreign element in this method. This study is the first successful engineering effort to utilize ENEJ mechanism in genomic editing and provides an effective strategy for genetic engineering in bacteria that are inefficient in HR and NHEJ.\n\nSignificanceThe application in prokaryotes is difficult because of the weak homologous recombination and non-homologous end joining systems. E. coli, as the most-used prokaryote in metabolic engineering, has no NHEJ system. All existing genomic editing methods for E. coli rely on exogenous HR or NHEJ systems to repair double-strand breaks introduced by CRISPR/Cas9. In this report, we firstly demonstrate that the weak and previously ignored end-joining mechanism in E. coli can be used for efficient large-scale genetic engineering assisted by CRISPR/Cas9. Our efforts greatly simplify the genomic editing procedure of E. coli and provide an effective strategy for genetic engineering in bacteria that are inefficient in HR and NHEJ.

bioengineering↗