A resource for the conditional ablation of microRNAs in the mouse

The importance of miRNAs during development and disease processes is well established. However, most studies have been done in cells or with patient tissues, and therefore the physiological roles of miRNAs are not well understood. To unravel in vivo functions of miRNAs, we have generated conditional, reporter-tagged knockout-first mice for numerous evolutionarily conserved miRNAs. Here, we report the generation of 162 miRNA targeting vectors, 64 targeted ES cell lines, and 46 germline-transmitted miRNA knockout mice. In vivo lacZ reporter analysis in 18 lines revealed highly tissue-specific expression patterns and their miRNA expression profiling matched closely with published expression data. Most miRNA knockout mice tested were viable, supporting a mechanism by which miRNAs act redundantly with other miRNAs or other pathways. These data and collection of resources will be of value for the in vivo dissection of miRNA functions in mouse models.     

BayGenomics: a resource of insertional mutations in mouse embryonic stem cells

The BayGenomics gene-trap resource (http://baygenomics.ucsf.edu) provides researchers with access to thousands of mouse embryonic stem (ES) cell lines harboring characterized insertional mutations in both known and novel genes. Each cell line contains an insertional mutation in a specific gene. The identity of the gene that has been interrupted can be determined from a DNA sequence tag. Approximately 75% of our cell lines contain insertional mutations in known mouse genes or genes that share strong sequence similarities with genes that have been identified in other organisms. These cell lines readily transmit the mutation to the germline of mice and many mutant lines of mice have already been generated from this resource. BayGenomics provides facile access to our entire database, including sequence tags for each mutant ES cell line, through the World Wide Web. Investigators can browse our resource, search for specific entries, download any portion of our database and BLAST sequences of interest against our entire set of cell line sequence tags. They can then obtain the mutant ES cell line for the purpose of generating knockout mice.     

Physiological suppression of Bacillus subtilis conditional sporulation phenotypes: RNA polymerase and ribosomal mutations

Summary The temperature-sensitive sporulation phenotype (Spo^ts) of Bacillus subtilis RNA polymerase, ribosomal and protein synthesis elongation factor G mutations can be corrected by supplementing the growth medium with carbohydrates such as ribose or glycerol, or with synthetic lipids such as Tween 40. The data suggest that these mutations affect a single common aspect of developmental cell function. It is proposed that these lesions prevent sporulation by disturbing the regulation of sporulating cell metabolic balance.     

A method for mutagenesis of mouse mtDNA and a resource of mouse mtDNA mutations for modeling human pathological conditions

Mutations in human mitochondrial DNA (mtDNA) can cause mitochondrial disease and have been associated with neurodegenerative disorders, cancer, diabetes and aging. Yet our progress toward delineating the precise contributions of mtDNA mutations to these conditions is impeded by the limited availability of faithful transmitochondrial animal models. Here, we report a method for the isolation of mutations in mouse mtDNA and its implementation for the generation of a collection of over 150 cell lines suitable for the production of transmitochondrial mice. This method is based on the limited mutagenesis of mtDNA by proofreading-deficient DNA-polymerase γ followed by segregation of the resulting highly heteroplasmic mtDNA population by means of intracellular cloning. Among generated cell lines, we identify nine which carry mutations affecting the same amino acid or nucleotide positions as in human disease, including a mutation in the ND4 gene responsible for 70% of Leber Hereditary Optic Neuropathies (LHON). Similar to their human counterparts, cybrids carrying the homoplasmic mouse LHON mutation demonstrated reduced respiration, reduced ATP content and elevated production of mitochondrial reactive oxygen species (ROS). The generated resource of mouse mtDNA mutants will be useful both in modeling human mitochondrial disease and in understanding the mechanisms of ROS production mediated by mutations in mtDNA.     

An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli

With the wide availability of whole-genome sequencing (WGS), genetic mapping has become the rate-limiting step, inhibiting unbiased forward genetics in even the most tractable model organisms. We introduce a rapid deconvolution resource and method for untagged causative mutations after mutagenesis, screens, and WGS in Escherichia coli. We created Deconvoluter—ordered libraries with selectable insertions every 50 kb in the E. coli genome. The Deconvoluter method uses these for replacement of untagged mutations in the genome using a phage-P1-based gene-replacement strategy. We validate the Deconvoluter resource by deconvolution of 17 of 17 phenotype-altering mutations from a screen of N-ethyl-N-nitrosourea-induced mutants. The Deconvoluter resource permits rapid unbiased screens and gene/function identification and will enable exploration of functions of essential genes and undiscovered genes/sites/alleles not represented in existing deletion collections. This resource for unbiased forward-genetic screens with mapping-by-sequencing (‘forward genomics’) demonstrates a strategy that could similarly enable rapid screens in many other microbes.     

Helicase-inactivating mutations as a basis for dominant negative phenotypes

There is ample evidence from studies of both unicellular and multicellular organisms that helicase-inactivating mutations lead to cellular dysfunction and disease phenotypes. In this review, we will discuss the mechanisms underlying the basis for abnormal phenotypes linked to mutations in genes encoding DNA helicases. Recent evidence demonstrates that a clinically relevant patient missense mutation in Fanconi Anemia Complementation Group J exerts detrimental effects on the biochemical activities of the FANC J helicase, and these molecular defects are responsible for aberrant genomic stability and a poor DNA damage response. The ability of FANC J to use the energy from AT P hydrolysis to produce the force required to unwind duplex or G-quadruplex DNA structures or destabilize protein bound to DNA is required for its DNA repair functions in vivo. Strikingly, helicase-inactivating mutations can exert a spectrum of dominant negative phenotypes, indicating that expression of the mutant helicase protein potentially interferes with normal DNA metabolism and has an effect on basic cellular processes such as DNA replication, the DNA damage response and protein trafficking. This review emphasizes that future studies of clinically relevant mutations in helicase genes will be important to understand the molecular pathologies of the associated diseases and their impact on heterozygote carriers.Key words: helicase, dominant negative, dominant lethal, DNA repair, replication, genomic stability, human disease, Fanconi anemia, FANCJ, G-quadruplexClassic genetic complementation studies in E. coli provided some of the first biological evidence that the catalytic DNA unwinding activity performed by helicases is critically important in various aspects of cellular DNA metabolism including replication, DNA repair and recombination.^1,2 Appreciation that the conserved amino acid motifs found in a variety of cellular DNA helicases compose protein domains important for ATP binding and hydrolysis, DNA binding and coupling of ATP hydrolysis to separation of complementary strands in a structured nucleic acid molecule led to new insights for how helicases function mechanistically (reviewed in ref. ^3–5). Advances in understanding the roles of helicases in DNA repair really provided a foundation for future progress in the field. The genetics in bacterial systems gradually led to similar complementation experiments in the unicellular eukaryotic model organisms Sachromyces cerevisiae and Sachromyces pombe.^6–10 In a number of cases, the underlying mechanisms whereby helicases operate to preserve genomic stability were found to be generally conserved between prokaryotes and eukaryotes. Ultimately, genetic analyses of helicase mutants in higher order eukaryotes (e.g., C. elegans,^11–13 Drosophila,¹⁴ Xenopus^15,16) have begun to pave the way for studies of mammalian DNA helicases in cell-based models and mice. As human helicase genetic disorders are continuously being discovered,^17–24 the interest and pace of investigation to understand how helicases preserve the genome continues to accelerate (reviewed in refs. ^25–31).In this review, we will focus on discussing some landmark studies that describe how helicase-inactivating mutations disrupt normal cellular DNA metabolism, with a particular emphasis on dominant negative phenotypes exerted by mutations in helicase genes. This topic deserves special attention since recent evidence from our lab and others suggests that naturally occurring mutations in helicase genes exert deleterious effects even in a wild-type background which provides insight to the molecular-genetic roles of various helicases to maintain genomic stability. We will begin by discussing genetic and biochemical studies of bacterial DNA helicases which provide an excellent foundation for this line of inquiry, and then focus on eukaryotic helicases with a particular emphasis placed on human DNA helicases, mutated in chromosomal instability and DNA repair disorders.     

Generation of a mouse for conditional excision of progesterone receptor

The progesterone receptor (PR) is required for several aspects of mammalian female reproduction. PR null mice have overlapping defects that preclude an understanding of its multiple functions in ovulation, pregnancy, mammary gland biology, and sexual behavior. We have generated a PR conditional excision (PRCE) allele in which loxP sites flank exon 1. Homozygous PRCE females are fertile and appear to be functionally normal. Global cre mediated excision of the floxed exon 1 using EIIa-cre mice resulted in systemic loss of exon 1 and PR protein. Female mice homozygous for this null allele were sterile, as expected for PR knockout (PRKO) females. Conditional loss of PR will facilitate investigation of the spatial and temporal roles of PR in both normal development and disease.     

The mouse genome database: a resource for today and tomorrow

The Mouse Genome Database supports the use of mice in genome research, offering researchers information on gene characterization, genetic maps, comparative genomic data, and phenotypes.     

Cre recombinase resources for conditional mouse mutagenesis

Large scale international activities for systematic conditional mouse mutagenesis, exploiting advances in the sophisticated manipulation of the mouse genome, has established the mouse as the premier organism for developing models of human disease and drug action. Conditional mutagenesis is critical for the elucidation of the gene functions that exert pleiotropic effects in a variety of cell types and tissues throughout the life of the animal. The majority of new mouse mutants are therefore designed as conditional, activated only in a specific tissue (spatial control) and/or life stage (temporal control) through biogenic Cre/loxP technologies. The full power of conditional mutant mice can therefore only be exploited with the availability of well characterized mouse lines expressing Cre-recombinase in tissue, organ and cell type-specific patterns, to allow the creation of somatic mutations in defined genes. This chapter provides an update on the current state of Cre driver mouse lines worldwide, and reviews the available public databases and portals that capture critical details of Cre driver lines such as the efficiency of recombination, cell tissue specificity, or genetic background effects. The continuously changing landscape of these mouse resources reflects the rapid progression of research and development in conditional and inducible mouse mutagenesis.     

Generation of a conditional null allele for Dmp1 in mouse

Dentin matrix protein1 (DMP1), highly conserved in humans and mice, is highly expressed in teeth, the skeleton, and to a lesser extent in nonskeletal tissues such as brain, kidney, and salivary gland. Pathologically, DMP1 is associated with several forms of cancers and with tumor-induced osteomalacia. Conventional disruption of the murine Dmp1 gene results in defects in dentin in teeth and in the skeleton, including hypophosphatemic rickets, and abnormalities in phosphate homeostasis. Human DMP1 mutations are responsible for the condition known as autosomal recessive hypophosphatemic rickets. For better understanding of the roles of DMP1 in different tissues at different stages of development and in pathological conditions, we generated Dmp1 floxed mice in which loxP sites flank exon 6 that encodes for over 80% of DMP1 protein. We demonstrate that Cre-mediated recombination using Sox2-Cre, a Cre line expressed in epiblast during early embryogenesis, results in early deletion of the gene and protein. These homozygous Cre-recombined null mice display an identical phenotype to conventional null mice. This animal model will be useful to reveal distinct roles of DMP1 in different tissues at different ages.     

Derivation of a mouse model for conditional inactivation of Pax9

Pax9 is required for the formation of a variety of organs during mouse development. The function of Pax9 at postnatal stages is unknown since homozygosity of the null allele (Pax9(lacZ)) causes neonatal lethality. Recently, we have generated a hypomorphic Pax9 allele, Pax9(neo), which contains a removable neomycin resistance cassette (neo) and loxP sites flanking the first two exons of Pax9. Here we show that FLP-mediated in vivo excision of neo generates phenotypically normal Pax9(flox) mice. Crossing Pax9(flox) mice to PGK-Cre mice leads to efficient recombination of loxP sites and neonatal lethality in the resulting Pax9(del/del) offspring. Inactivation of Pax9 using Wnt1-Cre mice causes cleft secondary palate and tooth agenesis and reveals that the Pax9 expressing mesenchymal cells of the nose, palate, and teeth are derived from neural crest cells. The conditional Pax9 allele will be a valuable tool to study Pax9 function in specific tissues of adult mice.     

Generation of a conditional mutant allele for Tab1 in mouse

TAK1 binding protein 1 (TAB1) binds and induces autophosphorylation of TGF-beta activating kinase (TAK1). TAK1, a mitogen-activated kinase kinase kinase, is involved in several distinct signaling pathways including non-Smad pathways for TGF-beta superfamily members and inflammatory responses caused by cytokines. Conventional disruption of the murine Tab1 gene results in late gestational lethality showing intraventricular septum defects and underdeveloped lung alveoli. To gain a better understanding of the roles of TAB1 in different tissues, at different stages of development, and in pathological conditions, we generated Tab1 floxed mice in which the loxP sites flank Exons 9 and 10 to remove the C-terminal region of TAB1 protein necessary for activation of TAK1. We demonstrate that Cre-mediated recombination using Sox2-Cre, a Cre line expressed in the epiblast during early embryogenesis, results in deletion of the gene and protein. These homozygous Cre-recombined null embryos display an identical phenotype to conventional null embryos. This animal model will be useful in revealing distinct roles of TAB1 in different tissues at different stages.     

Helicase-inactivating mutations as a basis for dominant negative phenotypes

There is ample evidence from studies of both unicellular and multicellular organisms that helicase-inactivating mutations lead to cellular dysfunction and disease phenotypes. In this review, we will discuss the mechanisms underlying the basis for abnormal phenotypes linked to mutations in genes encoding DNA helicases. Recent evidence demonstrates that a clinically relevant patient missense mutation in Fanconi Anemia Complementation Group J exerts detrimental effects on the biochemical activities of the FANCJhelicase, and these molecular defects are responsible for aberrant genomic stability and a poor DNA damage response. The ability of FANCJ to use the energy from ATP hydrolysis to produce the force required to unwind duplex or G-quadruplex DNA structures or destabilize protein bound to DNA is required for its DNA repair functions in vivo. Strikingly, helicase-inactivating mutations can exert a spectrum of dominant negative phenotypes, indicating that expression of the mutant helicase protein potentially interferes with normal DNA metabolism and has an effect on basic cellular processes such as DNA replication, the DNA damage response, and protein trafficking. This review emphasizes that future studies of clinically relevant mutations in helicase genes will be important to understand the molecular pathologies of the associated diseases and their impact on heterozygote carriers.