Taichi Noda

Feasibility for a large scale mouse mutagenesis by injecting CRISPR/Cas plasmid into zygotes

The recombinant clustered regulatory interspaced short palindromic repeats (CRISPR)/Cas system has opened a new era for mammalian genome editing. Here, we constructed pX330 plasmids expressing humanized Cas9 (hCas9) and single guide RNAs (sgRNAs) against mouse genes and validated them both in vitro and in vivo. When we randomly chose 291 target sequences within protein coding regions of 73 genes, an average number of off‐target candidates (exact match 13 nucleotides from 3′ target and NGG) found by Bowtie software was 9.2 ± 21.0 (~1.8 times more than the estimated value, 5.2). We next validated their activity by observing green fluorescence reconstituted by homology dependent repair (HDR) of an EGFP expression cassette in HEK293T cells. Of the pX330 plasmids tested, 81.8% (238/291) were found to be functional in vitro. We finally injected the validated pX330 plasmids into mouse zygotes in its circular form against 32 genes (including two genes previously tested) and obtained mutant mice at a 52.9 ± 22.3% (100/196) mutation frequency. Among the pups carrying mutations on the autosomes, 43.6% (47/96) carried the mutations in both alleles. When off‐target candidate sites were examined in 63 mutant mice, 0.8% (3/382) were mutated. We conclude that our method provides a simple, efficient, and cost‐effective way for mammalian gene editing that is applicable for large scale mutagenesis in mammals.

CRISPR/Cas9 mediated genome editing in ES cells and its application for chimeric analysis in mice

Targeted gene disrupted mice can be efficiently generated by expressing a single guide RNA (sgRNA)/CAS9 complex in the zygote. However, the limited success of complicated genome editing, such as large deletions, point mutations, and knockins, remains to be improved. Further, the mosaicism in founder generations complicates the genotypic and phenotypic analyses in these animals. Here we show that large deletions with two sgRNAs as well as dsDNA-mediated point mutations are efficient in mouse embryonic stem cells (ESCs). The dsDNA-mediated gene knockins are also feasible in ESCs. Finally, we generated chimeric mice with biallelic mutant ESCs for a lethal gene, Dnajb13, and analyzed their phenotypes. Not only was the lethal phenotype of hydrocephalus suppressed, but we also found that Dnajb13 is required for sperm cilia formation. The combination of biallelic genome editing in ESCs and subsequent chimeric analysis provides a useful tool for rapid gene function analysis in the whole organism.

Genome engineering uncovers 54 evolutionarily conserved and testis-enriched genes that are not required for male fertility in mice.

Significance In the mouse genome, thousands of genes are predominantly expressed in the testis, where these genes are thought to play important roles in spermatogenesis and fertilization. However, in this study, we report that 54 evolutionarily conserved and testis-enriched genes are not essential individually for male mouse fertility. Because the recent development of the CRISPR/Cas9 system has made it faster and easier to produce knockout mice, our results suggest that one should determine whether a gene of interest is essential for male fertility in vivo before spending significant effort to analyze the molecular function of the gene in vitro. Gene-expression analysis studies from Schultz et al. estimate that more than 2,300 genes in the mouse genome are expressed predominantly in the male germ line. As of their 2003 publication [Schultz N, Hamra FK, Garbers DL (2003) Proc Natl Acad Sci USA 100(21):12201–12206], the functions of the majority of these testis-enriched genes during spermatogenesis and fertilization were largely unknown. Since the study by Schultz et al., functional analysis of hundreds of reproductive-tract–enriched genes have been performed, but there remain many testis-enriched genes for which their relevance to reproduction remain unexplored or unreported. Historically, a gene knockout is the “gold standard” to determine whether a gene’s function is essential in vivo. Although knockout mice without apparent phenotypes are rarely published, these knockout mouse lines and their phenotypic information need to be shared to prevent redundant experiments. Herein, we used bioinformatic and experimental approaches to uncover mouse testis-enriched genes that are evolutionarily conserved in humans. We then used gene-disruption approaches, including Knockout Mouse Project resources (targeting vectors and mice) and CRISPR/Cas9, to mutate and quickly analyze the fertility of these mutant mice. We discovered that 54 mutant mouse lines were fertile. Thus, despite evolutionary conservation of these genes in vertebrates and in some cases in all eukaryotes, our results indicate that these genes are not individually essential for male mouse fertility. Our phenotypic data are highly relevant in this fiscally tight funding period and postgenomic age when large numbers of genomes are being analyzed for disease association, and will prevent unnecessary expenditures and duplications of effort by others.

Relationship between cyclic AMP-dependent protein tyrosine phosphorylation and extracellular calcium during hyperactivation of boar spermatozoa

In mammalian spermatozoa, the state of protein tyrosine phosphorylation is modulated by protein tyrosine kinases and protein tyrosine phosphatases that are controlled via cyclic AMP (cAMP)‐protein kinase A (PKA) signaling cascades. The aims of this study were to examine the involvement of cAMP‐induced protein tyrosine phosphorylation in response to extracellular calcium and to characterize effects of pharmacological modulation of the cAMP‐induced protein phosphorylation state and calmodulin activity during hyperactivation in boar spermatozoa. Ejaculated spermatozoa were incubated with cBiMPS (a cell‐permeable cAMP analog) and CaCl2 at 38.5°C to induce hyperactivation, and then used for Western blotting and indirect immunofluorescence of phosphorylated proteins and for the assessment of motility. Both cBiMPS and CaCl2 were necessary for hyperactivation. The increase in hyperactivated spermatozoa exhibited a dependence on the state of cBiMPS‐induced protein tyrosine phosphorylation in the connecting and principal pieces. The addition of calyculin A (an inhibitor for protein phosphatases 1/2A (PP1/PP2A), 50–100 nM) coincidently promoted hyperactivation and cAMP‐induced protein tyrosine phosphorylation in the presence of cBiMPS and CaCl2. Moreover, the addition of W‐7 (a calmodulin antagonist, 2–4 µM) enhanced the percentages of hyperactivated spermatozoa after incubation with cBiMPS and CaCl2, independently of protein tyrosine phosphorylation. These findings indicate that cAMP‐induced protein tyrosine phosphorylation in the connecting and principal pieces is involved in hyperactivation in response to extracellular calcium, and that calmodulin may suppress hyperactivation via the signaling cascades that are independent of cAMP‐induced protein tyrosine phosphorylation. Mol. Reprod. Dev. 79: 727–739, 2012.

Distinct segment‐specific functions of calyculin A‐sensitive protein phosphatases in the regulation of cAMP‐triggered events in ejaculated bull spermatozoa

Livestock spermatozoa possess more tenacious suppressors of cAMP‐triggered events—including capacitation‐associated changes—than laboratory animal spermatozoa, leading to flagellar hyperactivation. In order to identify the suppressors, we examined effects of an inhibitor of serine/threonine protein phosphatases (calyculin A) on cAMP‐triggered changes in the protein phosphorylation state, and subsequent occurrence of hyperactivation and acrosome reaction in ejaculated bull spermatozoa. Ejaculated spermatozoa were incubated in cAMP‐supplemented medium, then assessed for motility, acrosome morphology, and phosphorylated protein localization. The addition of calyculin A greatly enhanced cAMP‐triggered protein phosphorylation at serine/threonine and tyrosine residues in the connecting piece and induction of flagellar hyperactivation. Most hyperactivated spermatozoa exhibited extremely asymmetrical bends at the middle piece, which produced intensive twisting or figure‐eight movements. In the sperm head, however, cAMP‐triggered dephosphorylation of serine/threonine‐phosphorylated proteins and subsequent acrosome reaction were abolished by the addition of calyculin A. Based on these results, we suggest that calyculin A‐sensitive protein phosphatases in the connecting piece are suppressors of cAMP‐triggered events leading to hyperactivation. By contrast, similar protein phosphatases in the sperm head accelerate cAMP‐triggered events leading to the acrosome reaction. These findings are consistent with the indication that calyculin A‐sensitive protein phosphatases have distinct functions in the regulation of cAMP‐triggered events in different regions of ejaculated bull spermatozoa. Mol. Reprod. Dev. 82: 232–250, 2015.

Roles of extracellular Ca2+ in the occurrence of full-type hyperactivation in boar ejaculated spermatozoa pre-incubated to induce the cAMP-triggered events

There are species differences in the regulatory system for sperm capacitation and subsequent hyperactivation between livestock and laboratory animals. In livestock spermatozoa, it is poorly understood when and how extracellular Ca2+ is necessary for hyperactivation, although it has been demonstrated that the [Ca2+]i increase is indispensable to occurrence of hyperactivation. In this study, we examined necessity of extracellular Ca2+ for the initiation and maintenance of hyperactivation and then sought possible target molecule of Ca2+ that was involved in hyperactivation of boar spermatozoa. Boar ejaculated spermatozoa were pre‐incubated with a cell‐permeable cyclic adenosine monophosphate (cAMP) analog ‘cBiMPS’ and without CaCl2 to induce the cAMP‐triggered events including capacitation‐associated changes. Subsequently, they were incubated with CaCl2 to induce hyperactivation and then used for motility assessment. Many of the spermatozoa after the incubation exhibited full‐type hyperactivation which was characterized by high‐amplitude and extremely asymmetrical beating of whole middle piece and principal piece. The initiation of full‐type hyperactivation required the millimolar concentration of CaCl2 in the medium. However, CaCl2 of the medium was less necessary for maintenance than initiation of full‐type hyperactivation, as hyperactivated spermatozoa were barely affected by the incubation with the Ca2+‐chelating reagent. On the other hand, the pre‐treatment with the inhibitor for Ca2+‐dependent protease ‘calpain 1 and 2’ clearly suppressed the occurrence of CaCl2‐induced hyperactivation without influences on the percentages of motile spermatozoa. Western blotting and indirect immunofluorescence showed distribution of calpain 2 in the middle and principal pieces in which full‐type hyperactivated spermatozoa exhibited extremely asymmetrical beating. On the basis of these results, we conclude that the millimolar concentration of extracellular Ca2+ is necessary for the initiation, but not for the maintenance of full‐type hyperactivation in boar spermatozoa that beforehand undergo the cAMP‐triggered events including capacitation‐associated changes. Moreover, we suggest possible involvement of calpain 2 in the intracellular Ca2+ signal transduction leading to full‐type hyperactivation.

Novel Approach for the Detection of the Vestiges of Testicular mRNA Splicing Errors in Mature Spermatozoa of Japanese Black Bulls

There is a serious problem with the reduction of male reproductive performance of the livestock in the world. We have a hypothesis that the splicing error-caused derivation of aberrant sperm motility-related proteins may be one of its causal factors. It is thought that fresh testicular tissues are necessary for the detection of splicing errors of the mRNA. However, it is difficult to obtain testicular tissues from a number of agriculturally important bulls by surgical methods, because such procedures may have deleterious effects on bulls’ reproductive performance. The aim of this study was to examine the usefulness of mRNA fragments collected from ejaculated spermatozoa as alternative analytical samples for detection of the splicing errors. In the first experiment, we characterized the alternative splicing and splicing error of bull testicular ADCY10 mRNA which coded the synthase of the regulatory molecule for sperm motility “cAMP”. In testes, the exon 11-lacking variant coding the truncated ADCY10 was derived by alternative splicing. However, splicing errors, which accompanied the frame shift in the second cyclase domain, were occasionally observed in the exon 11-lacking variant. This aberrant variant retained intronic nucleotides (4 bases, CCAG) connecting the initial part of exon 10 due to splicing errors and consequently yielded the cleavage site for a restriction enzyme (Cac8I) which recognized the nucleotide sequences (GCNNGC). In the second experiment, we recovered residual testicular mRNA fragments from ejaculated spermatozoa and observed the splicing error-caused derivation of the aberrant variant of ADCY 10. Ejaculated spermatozoa conserved mRNA fragments of the exon 11-lacking variant coding exons 9, 10, 12 and 13. Moreover, the above-mentioned aberrant variant of ADCY10 mRNA fragment was detectable by Cac8I digestion treatment using the sperm mRNAs. These results indicate the utility of sperm mRNA fragments for the detection of splicing errors in bull testicular mRNAs.

Detection of the activator cAMP responsive element modulator (CREM) isoform ortholog proteins in porcine spermatids and sperm

It is necessary to obtain basic information on transcription factors expressed in the spermatids of livestock to determine mechanisms of defective spermiogenesis. In this study, we characterized the activator cAMP responsive element modulator (CREM) ortholog isoforms in porcine testicular germ cells and ejaculated sperm. At least two kinds of porcine activator CREM τ family ortholog mRNAs were more strongly expressed in the testis than in kidney or liver. The activator CREM isoform ortholog proteins were localized in nuclei of round spermatids and around nuclei of elongated spermatids. Furthermore, approximately 34% of ejaculated sperm had the activator CREM isoform ortholog proteins at their connecting piece. This is apparently the first report demonstrating the expression and localization of the activator CREM isoform ortholog proteins in spermatids and ejaculated sperm of a livestock species.

Expression patterns of the activator type of cAMP-responsive element modulator in testicular germ cells of Japanese Black bulls

The characterization and quantitative analyses of the key transcription factors for spermiogenesis are necessary in the identification of causal factors for the production of the seemingly normal sperm with dysfunctions in Japanese Black bulls and further elucidation of whole aspect of molecular mechanisms for spermiogenesis in livestock. The objective of this study was to obtain the information regarding the characterization and individual changes of an activator cAMP-responsive element modulator (CREM), which is necessary to the normal progress of spermiogenesis and is required for the transcriptional activity of genes coding essential factors for the sperm fertilization ability in rodents, using testes from 21 Japanese Black bulls with the ability to produce sperm indicating the normal motility and morphology. The bull CREM ταγ (one of activator variants) was detected in testes more strongly than livers by reverse transcription-polymerase chain reaction and Northern blotting. This variant was localized in the nuclei of spermatids as shown by indirect immunofluorescence with the homemade mouse antiserum. The motility and morphology of the cauda epididymal sperm from 16 Japanese Black bulls were examined before the quantitative analyses of testicular activator CREM to confirm the ability to produce sperm with normal motility and morphology in these males. The percentages of the motile sperm, those of the sperm with the normal acrosomes, and those of morphologically normal sperm were 60.0% to 90.0%, 88.0% to 100%, and 83.0% to 97.9%, respectively. The quantitative analyses with real-time polymerase chain reaction using the testicular RNA from the same bulls revealed that the relative expression levels of activator CREM variants in testes varied significantly among these bulls in the range from 0.56 to 1.64 (P < 0.05). These results are consistent with the suggestions that CREM ταγ are involved in the spermiogenesis in the testes of Japanese Black bulls and that the expression levels of the activator CREM variant mRNAs in the testes are varied significantly among individual bulls that have the ability to produce sperm with the normal motility and morphology.

Engineered CRISPR-Cas9 nuclease with expanded targeting space

Expanding the targeting space of Cas9 CRISPR-Cas9 associates with a guide RNA to target and cleave a specific DNA site next to a protospacer adjacent motif (PAM). Streptococcus pyogenes Cas9 (SpCas9), the one most often used for genome editing, only recognizes the NGG sequence (where N is any nucleobase) as the PAM, which restricts regions in the genome that can be targeted. To address this limitation, Nishimasu et al. created a SpCas9 variant that recognizes NG rather than NGG. The SpCas9-NG variant increased the targeting range, had a specificity similar to that of the wild-type enzyme, and could be used with a base editor. Thus, SpCas9-NG is a powerful addition to the CRISPR-Cas9 genome engineering toolbox and will be useful in a broad range of applications, from basic research to clinical therapeutics. Science, this issue p. 1259 An engineered CRISPR-Cas9 nuclease increases the range of genomic sequences that can be targeted in Cas9-mediated genome engineering. The RNA-guided endonuclease Cas9 cleaves its target DNA and is a powerful genome-editing tool. However, the widely used Streptococcus pyogenes Cas9 enzyme (SpCas9) requires an NGG protospacer adjacent motif (PAM) for target recognition, thereby restricting the targetable genomic loci. Here, we report a rationally engineered SpCas9 variant (SpCas9-NG) that can recognize relaxed NG PAMs. The crystal structure revealed that the loss of the base-specific interaction with the third nucleobase is compensated by newly introduced non–base-specific interactions, thereby enabling the NG PAM recognition. We showed that SpCas9-NG induces indels at endogenous target sites bearing NG PAMs in human cells. Furthermore, we found that the fusion of SpCas9-NG and the activation-induced cytidine deaminase (AID) mediates the C-to-T conversion at target sites with NG PAMs in human cells.