Cluster Deletion Research Articles

Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions

Resolving functions of closely linked genes is challenging or nearly impossible with classical genetic tools. Four members of the Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) family are clustered on Arabidopsis chromosome five. To resolve the potentially redundant functions of this subclass of CrRLK1Ls named MEDOS1 to 4 (MDS1 to 4), we generated a single CRISPR/Cas9 transformation vector using a Golden Gate based cloning system to target all four genes simultaneously. We introduce single mutations within and deletions between MDS genes as well as knock-outs of the whole 11 kb gene cluster. The large MDS cluster deletion was inherited in up to 25% of plants lacking the CRISPR/Cas9 construct in the T2 generation. In contrast to described phenotypes of already characterized CrRLK1L mutants, quadruple mds knock-outs were fully fertile, developed normal root hairs and trichomes and responded to pharmacological inhibition of cellulose biosynthesis similar to wildtype. Recently, we demonstrated the role of four CrRLK1L in growth adaptation to metal ion stress. Here we show the involvement of MDS genes in response to Ni2+ during hypocotyl elongation and to Cd2+ and Zn2+ during root growth. Our finding supports the model of an organ specific network of positively and negatively acting CrRLK1Ls.

How Female Mice Attract Males: A Urinary Volatile Amine Activates a Trace Amine-Associated Receptor That Induces Male Sexual Interest.

Individuals of many species rely on odors to communicate, find breeding partners, locate resources and sense dangers. In vertebrates, odorants are detected by chemosensory receptors of the olfactory system. One class of these receptors, the trace amine-associated receptors (TAARs), was recently suggested to mediate male sexual interest and mate choice. Here we tested this hypothesis in mice by generating a cluster deletion mouse (Taar2-9−/−) lacking all TAARs expressed in the olfactory epithelium, and evaluating transduction pathways from odorants to TAARs, neural activity and behaviors reflecting sexual interest. We found that a urinary volatile amine, isobutylamine (IBA), was a potent ligand for TAAR3 (but not TAAR1, 4, 5, and 6). When males were exposed to IBA, brain regions associated with sexual behaviors were less active in Taar2-9−/− than in wild type males. Accordingly, Taar2-9−/− males spent less time sniffing both the urine of females and pure IBA than wild type males. This is the first demonstration of a comprehensive transduction pathway linking odorants to TAARs and male sexual interest. Interestingly, the concentration of IBA in female urine varied across the estrus cycle with a peak during estrus. This variation in IBA concentration may represent a simple olfactory cue for males to recognize receptive females. Our results are consistent with the hypothesis that IBA and TAARs play an important role in the recognition of breeding partners and mate choice.

Strong triadic closure in cographs and graphs of low maximum degree

The MaxSTC problem is an assignment of the edges with two types of labels, namely, strong and weak, that maximizes the number of strong edges such that any two vertices that have a common neighbor with a strong edge are adjacent. The Cluster Deletion problem seeks for the minimum number of edge removals of a given graph such that the remaining graph is a disjoint union of cliques. Both problems are known to be NP-hard and an optimal solution for the Cluster Deletion problem provides a feasible solution for the MaxSTC problem, however not necessarily an optimal one. In this work we conduct the first systematic study that reveals graph families for which the optimal solutions for MaxSTC and Cluster Deletion coincide. We first show that MaxSTC coincides with Cluster Deletion on cographs and, thus, MaxSTC is solvable in polynomial time on cographs. As a side result, we give an interesting computational characterization of the maximum independent set on the cartesian product of two cographs. Furthermore, we address the influence of the low degree bounds to the complexity of the MaxSTC problem. We show that this problem is polynomial-time solvable on graphs of maximum degree three, whereas MaxSTC becomes NP-complete on graphs of maximum degree four. The proof of the latter result implies that there is no subexponential-time algorithm for MaxSTC unless the Exponential-Time Hypothesis fails.

Diagnostic Strategies in Hemoglobinopathy Testing, the Role of a Reference Laboratory in the USA

Although commonly assessed in the context of microcytosis or sickling syndrome screening, hemoglobin mutations may not be as readily considered as a cause of other symptoms. These include macrocytosis with or without anemia, chronic or episodic hemolysis, neonatal anemia, erythrocytosis, cyanosis/hypoxia and methemoglobinemia/ sulfhemoglobinemia. Hemoglobin disorders commonly interfere with the reliability of Hb A1c measurement. Because the clinical presentation can be varied and the differential diagnosis broad, a systematic evaluation guided by signs and symptoms can be effective. A tertiary care reference laboratory is particularly challenged by the absence of pertinent clinical history and relevant laboratory findings, and appropriate use of resources in a data vacuum can be problematic. To address these issues, our laboratory has constructed testing panels with a tiered strategy utilizing screening assays that detect the most common causes and reflexing additional assays that assess less common etiologies. See Figure 1. Our testing algorithm panels include a rapid hemoglobin fraction monitoring test, a generic diagnostic hemoglobin electrophoresis profile, and more specific diagnostic evaluations for microcytic anemia, hereditary hemolytic anemia, methemoglobinemia and sufhemoglobinemia and erythrocytosis. Use of these testing strategies has facilitated the identification of rare and complex hemoglobin disorders from a wide variety of ethnic groups, including over 500 distinct named alpha, beta and gamma variants (of which 60+ were novel variants at the time of first detection), 99 beta thalassemia mutations and greater than 20 large deletional beta globin cluster deletion subtypes.

Revisiting Connected Vertex Cover: FPT Algorithms and Lossy Kernels

The CONNECTED VERTEX COVER problem asks for a vertex cover in a graph that induces a connected subgraph. The problem is known to be fixed-parameter tractable (FPT), and is unlikely to have a polynomial sized kernel (under complexity theoretic assumptions) when parameterized by the solution size. In a recent paper, Lokshtanov et al.[STOC 2017], have shown an $\alpha$-approximate kernel for the problem for every $\alpha > 1$, in the framework of approximate or lossy kernelization. In this work, we exhibit lossy kernels and FPT algorithms for CONNECTED VERTEX COVER for parameters that are more natural and functions of the input, and in some cases, smaller than the solution size. The parameters we consider are the sizes of a split deletion set, clique deletion set, clique cover, cluster deletion set and chordal deletion set.

Identification of Enzymes Involved in Sesterterpene Biosynthesis in Marine Fungi.

Diverse and bioactive terpene compounds are produced by marine fungi. The biosynthesis of sesterterpene molecules containing a C25 skeleton is catalyzed by chimeric enzymes that carry out both chain elongation and terpene cyclization reactions. These bifunctional characteristics facilitate using different chain length polyisoprenoid diphosphates as precursors to yield the geranylfarnesyl diphosphate intermediate, which is then converted to a sesterterpene in one step. In this chapter, we describe the identification of sesterterpene synthase enzymes, together with other related enzymes such as diterpene and farnesyl diphosphate synthases, in a single fungal strain. The processes are based on genome sequencing, in silico analysis of terpene synthase, in vivo gene (cluster) deletion and complementation, and in vitro protein function verification, together with the methods of detecting terpenes using high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS).

Characterization of a Large Novel α-Globin Gene Cluster Deletion Causing α0-Thalassemia in a Chinese Family

We report a large novel α-globin cluster deletion that we named – –PG (NG_000006.1: g.93628_542759del450131), in a Chinese family. This large deletion is approximately 450 kb long, spanning from upstream of the PolR3k gene at the 5′ end to the RAB11FIP3 gene at the 3′ end of chromosome 16p13.3. This deletion removes all the globin distal regulatory elements as well as the whole α-globin gene cluster. Patients with heterozygous – –PG/αα had red blood cell (RBC) indices consistent with α-thalassemia (α-thal) trait, but no apparent increase in a cancer tendency or mental disability, microcephaly, relative hypertelorism, unusual facies or genital anomalies.

Widening the spectrum of deletions and molecular mechanisms underlying alpha-thalassemia.

Inherited deletions of α-globin genes and/or their upstream regulatory elements (MCSs) give rise to α-thalassemia, an autosomal recessive microcytic hypochromic anemia. In this study, multiplex ligation-dependent probe amplification performed with commercial and synthetic engineered probes, Gap-PCR, and DNA sequencing were used to characterize lesions in the sub-telomeric region of the short arm of chromosome 16, possibly explaining the α-thalassemia/HbH disease phenotype in ten patients. We have found six different deletions, in heterozygosity, ranging from approximately 3.3 to 323kb, two of them not previously described. The deletions fall into two categories: one includes deletions which totally remove the α-globin gene cluster, whereas the other includes deletions removing only the distal regulatory elements and keeping the α-globin genes structurally intact. An indel was observed in one patient involving the loss of the MCS-R2 and the insertion of 39bp originated from a complex rearrangement spanning the deletion breakpoints. Finally, in another case, no α-globin gene cluster deletion was found and the patient revealed to be a very unusual case of acquired α-thalassemia-myelodysplastic syndrome. This study further illustrates the diversity of genomic lesions and underlying molecular mechanisms leading to α-thalassemia.

Evolution of Anabaenopeptin Peptide Structural Variability in the Cyanobacterium Planktothrix.

Cyanobacteria are frequently involved in the formation of harmful algal blooms wherein, apart from the toxic microcystins, other groups of bioactive peptides are abundant as well, such as anabaenopeptins (APs). The APs are synthesized nonribosomally as cyclic hexapeptides with various amino acids at the exocyclic position. We investigated the presence and recombination of the AP synthesis gene cluster (apnA-E) through comparing 125 strains of the bloom-forming cyanobacterium Planktothrix spp., which were isolated from numerous shallow and deep water habitats in the temperate and tropical climatic zone. Ten ecologically divergent strains were purified and genome sequenced to compare their entire apnA-E gene cluster. In order to quantify apn gene distribution patterns, all the strains were investigated by PCR amplification of 2 kbp portions of the entire apn gene cluster without interruption. Within the 11 strains assigned to P. pseudagardhii, P. mougeotii, or P. tepida (Lineage 3), neither apnA-E genes nor remnants were observed. Within the P. agardhii/P. rubescens strains from shallow waters (Lineage 1, 52 strains), strains both carrying and lacking apn genes occurred, while among the strains lacking the apnA-E genes, the presence of the 5′end flanking region indicated a gene cluster deletion. Among the strains of the more derived deep water ecotype (Lineage 2, 62 strains), apnA-E genes were always present. A high similarity of apn genes of the genus Planktothrix when compared with strains of the genus Microcystis suggested its horizontal gene transfer during the speciation of P. agardhii/P. rubescens. Genetic analysis of the first (A1-) domain of the apnA gene, encoding synthesis of the exocyclic position of the AP molecule, revealed four genotype groups that corresponded with substrate activation. Groups of genotypes were either related to Arginine only, the coproduction of Arginine and Tyrosine or Arginine and Lysine, or even the coproduction of Arginine, Tyrosine, and Lysine in the exocyclic position of the AP-molecule. The increased structural diversity resulted from the evolution of apnA A1 genotypes through a small number of positively selected point mutations that occurred repeatedly and independently from phylogenetic association.

Deficiency of Functional Iron-Sulfur Domains in ABCE1 Inhibits the Proliferation and Migration of Lung Adenocarcinomas By Regulating the Biogenesis of Beta-Actin In Vitro

Background/Aims: ATP-binding cassette transporter E1 (ABCE1), a unique ABC superfamily member that bears two Fe-S clusters, is essential for metastatic progression in lung cancer. Fe-S clusters within ABCE1 are crucial for ribosome dissociation and translation reinitiation; however, whether these clusters promote tumor proliferation and migration is unclear. Methods: The interaction between ABCE1 and β-actin was confirmed using GST pull-down. The lung adenocarcinoma (LUAD) cell line A549 was transduced with lentiviral packaging vectors overexpressing either wild-type ABCE1 or ABCE1 with Fe-S cluster deletions (ΔABCE1). The role of Fe-S clusters in the viability and migration of cancer cells was evaluated using clonogenic, MTT, Transwell and wound healing assays. Cytoskeletal rearrangement was determined using immunofluorescent techniques. Results: Fe-S clusters were the key domains in ABCE1 involved in binding to β-actin. The proliferative and migratory capacity increased in cells overexpressing ABCE1. However, the absence of Fe-S clusters reversed these effects. A549 cells overexpressing ABCE1 exhibited irregular morphology and increased levels of cytoskeletal polymerization as indicated by the immunofluorescence images. In contrast, cells expressing the Fe-S cluster deletion mutant presented opposing effects. Conclusion: These results demonstrate the indispensable role of Fe-S clusters when ABCE1 participates in the proliferation and migration of LUADs by interacting with β-actin. The Fe-S clusters of ABCE1 may be potential targets for the prevention of lung cancer metastasis.

Enhanced production of avermectin by deletion of type III polyketide synthases biosynthetic cluster rpp in Streptomyces avermitilis.

Because of the wide use of avermectins, many efforts have been made to improve the productivity via conventional genetic engineering technique. However, due to the lack of the molecular and genetic basis underlying such a yield enhancement after iterative rounds of mutagenesis and selection, it is often difficult to improve the titre in overproducers. Here, we report knocking out rpp biosynthetic gene cluster improved the production of an industrial overproducer by 24%. This work enriched the strategy to improve the production of antibiotics in industrial strains and may help further understanding of the interaction between type III polyketide synthases and other types.

Variation in Fumonisin and Ochratoxin Production Associated with Differences in Biosynthetic Gene Content in Aspergillus niger and A. welwitschiae Isolates from Multiple Crop and Geographic Origins.

The fungi Aspergillus niger and A. welwitschiae are morphologically indistinguishable species used for industrial fermentation and for food and beverage production. The fungi also occur widely on food crops. Concerns about their safety have arisen with the discovery that some isolates of both species produce fumonisin (FB) and ochratoxin A (OTA) mycotoxins. Here, we examined FB and OTA production as well as the presence of genes responsible for synthesis of the mycotoxins in a collection of 92 A. niger/A. welwitschiae isolates from multiple crop and geographic origins. The results indicate that (i) isolates of both species differed in ability to produce the mycotoxins; (ii) FB-nonproducing isolates of A. niger had an intact fumonisin biosynthetic gene (fum) cluster; (iii) FB-nonproducing isolates of A. welwitschiae exhibited multiple patterns of fum gene deletion; and (iv) OTA-nonproducing isolates of both species lacked the ochratoxin A biosynthetic gene (ota) cluster. Analysis of genome sequence data revealed a single pattern of ota gene deletion in the two species. Phylogenetic analysis suggest that the simplest explanation for this is that ota cluster deletion occurred in a common ancestor of A. niger and A. welwitschiae, and subsequently both the intact and deleted cluster were retained as alternate alleles during divergence of the ancestor into descendent species. Finally, comparison of results from this and previous studies indicate that a majority of A. niger isolates and a minority of A. welwitschiae isolates can produce FBs, whereas, a minority of isolates of both species produce OTA. The comparison also suggested that the relative abundance of each species and frequency of FB/OTA-producing isolates can vary with crop and/or geographic origin.

Characterisation of the genes involved in the biosynthesis and attachment of the aminodeoxysugar D-forosamine in the auricin gene cluster of Streptomyces aureofaciens CCM3239.

We previously identified the aur1 gene cluster which produces the angucycline antibiotic auricin. Preliminary characterisation of auricin revealed that it is modified by a single aminodeoxysugar, D-forosamine. Here we characterise the D-forosamine-specific genes. The four close tandem genes, aur1TQSV, encoding enzymes involved in the initial steps of the deoxysugar biosynthesis, were located on a large operon with other core auricin biosynthetic genes. Deleting these genes resulted in the absence of auricin and the production of deglycosylated auricin intermediates. The two final D-forosamine biosynthetic genes, sa59, an NDP-hexose aminotransferase, and sa52, an NDP-aminohexose N-dimethyltransferase, are located in a region rather distant from the core auricin genes. A deletion analysis of these genes confirmed their role in D-forosamine biosynthesis. The Δsa59 mutant had a phenotype similar to that of the cluster deletion mutant, while the Δsa52 mutant produced an auricin with a demethylated D-forosamine. Although auricin contains a single deoxyhexose, two glycosyltransferase genes were found to participate in the attachment of D-forosamine to the auricin aglycon. An analysis of the expression of the D-forosamine biosynthesis genes revealed that the initial D-forosamine biosynthetic genes aur1TQSV are regulated together with the other auricin core genes by the aur1Ap promoter under the control of the auricin-specific activator Aur1P. The expression of the other D-forosamine genes, however, is governed by promoters differentially dependent upon the two SARP family auricin-specific activators Aur1PR3 and Aur1PR4. These promoters contain direct repeats similar to the SARP consensus sequence and are involved in the interaction with both regulators.

Sufficient conditions for edit-optimal clusters

Cluster Editing is the problem of turning a graph into a cluster graph, that is, a disjoint union of cliques, by a minimum number of edge edits. Cluster Deletion is similarly defined, with edge deletions only. We propose a local notion of edit-optimality: Informally, we say that a crown (a certain type of labeled graph) is edit-optimal if it yields a cluster in some optimal solution to Cluster Editing, in every graph containing this crown as a subgraph. Then we give sufficient conditions for edit-optimality, e.g., in terms of vertex degrees. A condition for Cluster Deletion applies a theorem of Landau (1953) [7] on degree sequences of tournaments. The conditions are particularly suited for planted models of clusterings, and for networks that only partially exhibit a clear cluster structure.

Conditional Deletion of the Hoxa Cluster in MLL-AF9 Is Incompatible with Leukemia Maintenance

IntroductionHox gene expression is high in hematopoietic stem/progenitor cells (HSPCs), decreases during normal differentiation but remains elevated in leukemia subtypes. Polycomb repressor complexes and histone modifiers, e.g. Mixed Lineage Leukemia (MLL), are key regulators of Hox expression. MLL rearrangements, frequent in acute leukemia, are associated high HOXA expression. However, necessity for the HoxA cluster in MLL-leukemia maintenance is not fully elucidated.MethodologyEctopic overexpression of MLL-AF9 (MA9) in HSPCs in conditional compound transgenic mouse backgrounds MxCre+/HoxAflox/flox (MAFF) or HoxAflox/flox (AFlox) models resulted in increased colony formation and growth in liquid culture. Transformed colonies, serially re-plated (n=5) in methylcellulose and transplanted into sub-lethally irradiated recipient mice, resulted in primary leukemia. Initially, MAFF-MA9 leukemias were used to examine in vivo deletion of the HoxA cluster using intraperitoneal injections of Poly(I:C) to initiate an interferon response. To further examine the necessity for the HoxA cluster in disease maintenance, AFlox-MA9 leukemias were treated ex vivo with Cre-recombinase (MSCV-Cre-GFP) or vector control (MSCV-GFP), sorted based on GFP expression and used for gDNA-PCR, gene expression (Illumina BeadArray) and transplantation into sub-lethally irradiated recipient mice (500 cGy).ResultsGeneration of MLL-AF9 leukemias in the MAFF background (MAFF-MA9) resulted in deletion of one HoxA cluster allele (HoxA+/-), validated by genomic PCR and gDNA sequencing from expanded single colonies (Figure 1) presumably due to viral-induced activation of the Mx1 promoter. PolyI:C treatment of these mice resulted in a modest extension in survival (1-2 days) compared to controls. Luciferase labelling and transplantation of MAFF-MA9 leukemias into NSG mice, followed by PolyI:C treatment, showed a measurable decrease in disease burden compared to control, however this did not correlate with overall survival. Direct treatment of MAFF-MA9 cells with interferon-α (in vitro) resulted in further deletion of the HoxA cluster (HoxA-/hypo) and significant reduction in colony formation compared to controls. Although non-leukemic MAFF HSPCs retained colony forming ability after complete HoxA cluster deletion (HoxA-/-) no HoxA-/- colonies were recovered from the interferon-α treated MAFF-MA9 cultures. Cre-recombinase-induced deletion of the Hoxa cluster from AFlox-MA9 leukemia cells was confirmed by gDNA-PCR and sequencing (Figure 1). Transplantation of Cre-treated AFlox-MA9 cells resulted in significant increased survival (P<0.002) by up to 74 days in recipient mice, compared to controls (Figure 2). Further examination of the leukemias that developed from these Cre-treated AFlox-MA9 cells demonstrated retention of one allele of the HoxA cluster, as a result of escapees. To gain insight into the molecular mechanisms underlying the HoxA requirement for MLL-AF9 maintenance, matched Cre- or control treated AFlox-MA9 samples used for the transplantation were further examined for differential gene expression by Illumina BeadArray analysis. Preliminary analysis of the data has confirmed significant reduction in the expression of HoxA cluster genes (a2, a4, a5, a7, a9) and increased expression of several genes involved in adhesion, differentiation or immune response (e.g. Itgb3bp, Mpo, Cxcl2). Further analysis including submission of gene signatures to the LINCS database (https://www.broadinstitute.org/software/cprg/?q=node/40) will be done to identify candidate small molecules that mimic HoxA deletion in MLL-AF9.ConclusionTogether these data support a fundamental role for the HoxA cluster in MLL-AF9 maintenance indicating dependency for this leukemia subtype which may be exploited for therapeutic benefit. [Display omitted] [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Complexity of the cluster deletion problem on subclasses of chordal graphs

We consider the following vertex-partition problem on graphs, known as the CLUSTER DELETION (CD) problem: given a graph with real nonnegative edge weights, partition the vertices into clusters (in this case, cliques) to minimize the total weight of edges outside the clusters. The decision version of this optimization problem is known to be NP-complete even for unweighted graphs and has been studied extensively. We investigate the complexity of the decision CD problem for the family of chordal graphs, showing that it is NP-complete for weighted split graphs, weighted interval graphs and unweighted chordal graphs. We also prove that the problem is NP-complete for weighted cographs. Some polynomial-time solvable cases of the optimization problem are also identified, in particular CD for unweighted split graphs, unweighted proper interval graphs and weighted block graphs.

PP14.13 – 2765: SCN cluster deletions: More than the classic Dravet syndrome?

Objective Dravet syndrome is a severe epileptic encephalopathy beginning in infancy. The characteristic electroclinical picture is well known. With the discovery of SCN1A, molecular confirmation is possible in 75% of the patients. In approximately 70% a mutation is found and in 3–5% a copy number variant (CNV). CNVs frequently involve deletions, which not only contain SCN1A but the whole SCN gene cluster. This cluster contains five sodium channel genes (SCN3A, SCN2A, SCN1A, SCNC9A and SCN7A) along with GRB14 and GALNT3. The aim of this study was to determine whether patients with a SCN cluster deletion show a more severe form of the Dravet syndrome or have a specific continuous gene deletion syndrome. Methods We retrospectively reviewed the files of children with a deletion of the SCN gene cluster. Results We report six patients with a SCN cluster deletion (5 confirmed by aCGH, one with MLPA). All patients have a large de novo deletion (mean 5.6 Mb, SD 2.5). The mean age of presentation was 14.8 w (SD 7.3 w). Four infants presented with myoclonus, one with a febrile status epilepticus and one with an afebrile focal seizure with secondary generalization. Three had dysmorphic features and an abnormal development prior to the onset of convulsions. All patients showed a disastrous course with a severe mental retardation, hypotonia, failure to thrive and therapy resistant epilepsy in infancy. Two patients died around the age of one year, one at the age of 15 years. Three patients (8m, 20m and 4y of age) are still in follow-up. Conclusion Patients with a SCN cluster deletion frequently show a more severe form than the classic Dravet syndrome phenotype. The slightly earlier presentations with myoclonic seizures, abnormal development prior to the onset of convulsions, severe developmental delay or dead in infancy are suggestive for the SCN cluster deletion syndrome.

De novo deletion of HOXB gene cluster in a patient with failure to thrive, developmental delay, gastroesophageal reflux and bronchiectasis

We report a female patient with a complex phenotype consisting of failure to thrive, developmental delay, congenital bronchiectasis, gastroesophageal reflux and bilateral inguinal hernias. Chromosomal microarray analysis revealed a 230 kilobase deletion in chromosomal region 17q21.32 (arr[hg19] 17q21.32(46 550 362–46 784 039)×1) encompassing only 9 genes – HOXB1 to HOXB9. The deletion was not found in her mother or father. This is the first report of a patient with a HOXB gene cluster deletion involving only HOXB1 to HOXB9 genes. By comparing our case to previously reported five patients with larger chromosomal aberrations involving the HOXB gene cluster, we can suppose that HOXB gene cluster deletions are responsible for growth retardation, developmental delay, and specific facial dysmorphic features. Also, we suppose that bilateral inguinal hernias, tracheo-esophageal abnormalities, and lung malformations represent features with incomplete penetrance. Interestingly, previously published knock-out mice with targeted heterozygous deletion comparable to our patient did not show phenotypic alterations.

One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces.

The RNA-guided DNA editing technology CRISPRs (clustered regularly interspaced short palindromic repeats)/Cas9 had been used to introduce double-stranded breaks into genomes and to direct subsequent site-specific insertions/deletions or the replacement of genetic material in bacteria, such as Escherichia coli, Streptococcus pneumonia, and Lactobacillus reuteri. In this study, we established a high-efficiency CRISPR/Cas9 genome editing plasmid pKCcas9dO for use in Streptomyces genetic manipulation, which comprises a target-specific guide RNA, a codon-optimized cas9, and two homology-directed repair templates. By delivering pKCcas9dO series editing plasmids into the model strain Streptomyces coelicolor M145, through one-step intergeneric transfer, we achieved the genome editing at different levels with high efficiencies of 60%-100%, including single gene deletion, such as actII-orf4, redD, and glnR, and single large-size gene cluster deletion, such as the antibiotic biosynthetic clusters of actinorhodin (ACT) (21.3 kb), undecylprodigiosin (RED) (31.6 kb), and Ca(2+)-dependent antibiotic (82.8 kb). Furthermore, we also realized simultaneous deletions of actII-orf4 and redD, and of the ACT and RED biosynthetic gene clusters with high efficiencies of 54% and 45%, respectively. Finally, we applied this system to introduce nucleotide point mutations into the rpsL gene, which conferred the mutants with resistance to streptomycin. Notably, using this system, the time required for one round of genome modification is reduced by one-third or one-half of those for conventional methods. These results clearly indicate that the established CRISPR/Cas9 genome editing system substantially improves the genome editing efficiency compared with the currently existing methods in Streptomyces, and it has promise for application to genome modification in other Actinomyces species.

A one-to-one correspondence between potential solutions of the cluster deletion problem and the minimum sum coloring problem, and its application to [formula omitted]-sparse graphs

In this note we show a one-to-one correspondence between potentially optimal solutions to the cluster deletion problem in a graph G and potentially optimal solutions for the minimum sum coloring problem in G¯ (i.e. the complement graph of G). We apply this correspondence to polynomially solve the cluster deletion problem in a subclass of P4-sparse graphs that strictly includes P4-reducible graphs.