Ramiro Ramirez-Solis

• PhD
• Director of Institutional Core Laboratories at The University of Texas Health Science Center at San Antonio

The International Mouse Phenotyping Consortium (IMPC) systematically produces and phenotypes mouse lines with presumptive null mutations to provide insight into gene function. The IMPC now uses the programmable RNA-guided nuclease Cas9 for its increased capacity and flexibility to efficiently generate null alleles in the C57BL/6N strain. In additio...

Genomic instability arising from defective responses to DNA damage ¹ or mitotic chromosomal imbalances ² can lead to the sequestration of DNA in aberrant extranuclear structures called micronuclei (MN). Although MN are a hallmark of ageing and diseases associated with genomic instability, the catalogue of genetic players that regulate the generatio...

Aortic aneurysms, which may dissect or rupture acutely and be lethal, can be a part of multisystem disorders that have a heritable basis. We report four patients with deficiency of selenocysteine-containing proteins due to selenocysteine Insertion Sequence Binding Protein 2 ( SECISBP2) mutations who show early-onset, progressive, aneurysmal dilatat...

Meiosis has a principal role in sexual reproduction to generate haploid gametes in both sexes. During meiosis, the cell nucleus hosts a dynamic environment where some genes are transcriptionally activated, and some are inactivated at the same time. This becomes possible through subnuclear compartmentalization. The sex body, sequestering X and Y chr...

The International Mouse Phenotyping Consortium (IMPC) is generating and phenotyping null mutations for every protein-coding gene in the mouse 1,2 . The IMPC now uses Cas9, a programmable RNA-guided nuclease that has revolutionized mouse genome editing ³ and increased capacity and flexibility to efficiently generate null alleles in the C57BL/6N stra...

The International Mouse Phenotyping Consortium reports the generation of new mouse mutant strains for more than 5,000 genes, including 2,850 novel null, 2,987 novel conditional-ready and 4,433 novel reporter alleles.

By developing a high-density murine immunophenotyping platform compatible with high-throughput genetic screening, we have established profound contributions of genetics and structure to immune variation (http://www.immunophenotype.org). Specifically, high-throughput phenotyping of 530 unique mouse gene knockouts identified 140 monogenic ‘hits’, of...

The International Mouse Phenotyping Consortium reports the generation of new mouse mutant strains for over 5,000 genes from targeted embryonic stem cells on the C57BL/6N genetic background. This includes 2,850 null alleles for which no equivalent mutant mouse line exists, 2,987 novel conditional-ready alleles, and 4,433 novel reporter alleles. This...

By developing a high-density murine immunophenotyping platform compatible with high-throughput genetic screening, we have established profound contributions of genetics and structure to immune variation. Specifically, high-throughput phenotyping of 530 knockout mouse lines identified 140 monogenic "hits" (>25%), most of which had never hitherto bee...

The relationship between the mechanisms that underlie longevity and aging and the metabolic alterations due to feeding conditions has not been completely defined. In the present work, through the deletion of the gene encoding catalase, hydrogen peroxide (H 2 O 2 ) was uncovered as a relevant regulator of longevity and of liver metabolism. Mice lack...

Most human genes are associated with promoters embedded in non-methylated, G + C-rich CpG islands (CGIs). Not all CGIs are found at annotated promoters, however, raising the possibility that many serve as promoters for transcripts that do not code for proteins. To test this hypothesis, we searched for novel transcripts in embryonic stem cells (ESCs...

[This corrects the article DOI: 10.1038/s42003-018-0226-0.]. Despite advances in next generation sequencing technologies, determining the genetic basis of ocular disease remains a major challenge due to the limited access and prohibitive cost of human forward genetics. Thus, less than 4,000 genes currently have available phenotype information for a...

Despite advances in next generation sequencing technologies, determining the genetic basis of ocular disease remains a major challenge due to the limited access and prohibitive cost of human forward genetics. Thus, less than 4,000 genes currently have available phenotype information for any organ system. Here we report the ophthalmic findings from...

Antithrombotic therapies reduce cardiovascular diseases by preventing arterial thrombosis and thromboembolism, but at expense of increased bleeding risks. Arterial thrombosis studies using genetically modified mice have been invaluable for identification of new molecular targets. Because of low sample sizes and heterogeneity in approaches or method...

This corrects the article DOI: 10.1038/nature19356.

Mouse embryonic stem cells derived from the epiblast contribute to the somatic lineages and the germline but are excluded from the extra-embryonic tissues that are derived from the trophectoderm and the primitive endoderm upon reintroduction to the blastocyst. Here we report that cultures of expanded potential stem cells can be established from ind...

The International Knockout Mouse Consortium (IKMC) developed high throughput gene trapping and gene targeting pipelines that produced mostly conditional mutations of more than 18,500 genes in C57BL/6N mouse embryonic stem (ES) cells which have been archived and are freely available to the research community as a frozen resource. From this unprecede...

The role of sex in biomedical studies has often been overlooked, despite evidence of sexually dimorphic effects in some biological studies. Here, we used high-throughput phenotype data from 14,250 wildtype and 40,192 mutant mice (representing 2,186 knockout lines), analysed for up to 234 traits, and found a large proportion of mammalian traits both...

Call behaviour at the gene level

Supplementary Figures and Supplementary Tables

Significance Infertility is a global problem that afflicts 15% of couples, and in 50% of cases, the attributing factor is linked to men. Among these infertile men, 18% specifically exhibit decreased motility of sperm (asthenozoospermia). Sperm motility is dependent on the formation and functioning of the flagellum, a modified cilium used for locomo...

Mouse embryonic stem cells are derived from in vitro explantation of blastocyst epiblasts 1,2 and contribute to both the somatic lineage and germline when returned to the blastocyst ³ but are normally excluded from the trophoblast lineage and primitive endoderm 4–6 . Here, we report that cultures of expanded potential stem cells (EPSCs) can be esta...

Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their...

We present a simple and quick system for accurately scoring the developmental progress of mouse embryos harvested on embryonic day 14 (E14.5). Based solely on the external appearance of the maturing forelimb, we provide a convenient way to distinguish six developmental sub-stages. Using a variety of objective morphometric data obtained from the com...

Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their...

Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here...

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...

Zinc finger motifs are distributed amongst many eukaryotic protein families, directing nucleic acid–protein and protein–protein interactions. Zinc finger protein 106 (ZFP106) has previously been associated with roles in immune response, muscle differentiation, testes development and DNA damage, although little is known about its specific function....

Knowledge of the expression profile of a gene is a critical piece of information required to build an understanding of the normal and essential functions of that gene, and any role it may play in the development or progression of disease. High throughput, large scale efforts are on-going internationally to characterise reporter tagged knockout mous...

The function of the majority of genes in the mouse and human genomes remains unknown. The mouse embryonic stem cell knockout resource provides a basis for the characterization of relationships between genes and phenotypes. The EUMODIC consortium developed and validated robust methodologies for the broad-based phenotyping of knockouts through a pipe...

The function of the majority of genes in the mouse and human genomes remains unknown. The mouse embryonic stem cell knockout resource provides a basis for the characterization of relationships between genes and phenotypes. The EUMODIC consortium developed and validated robust methodologies for the broad-based phenotyping of knockouts through a pipe...

With the advent of modern developmental biology and molecular genetics, the scientific community has generated thousands of newly genetically altered strains of laboratory mice with the aim of elucidating gene function. To this end, a large group of Institutions which form the International Mouse Phenotyping Consortium is generating and phenotyping...

Iron homeostasis is a dynamic process that is tightly controlled to balance iron uptake, storage and export. Reduction of dietary iron from the ferric to the ferrous form is required for uptake by solute carrier family 11 (proton-coupled divalent metal ion transporters) member 2 (Slc11a2) into the enterocytes. Both processes are proton dependent, a...

10.1093/nar/gku1193 INFRAFRONTIER––providing mutant mouse resources as research tools for the international scientific community INFRAFRONTIER Consortium *, ABSTRACT The laboratory mouse is a key model organism to in-vestigate mechanism and therapeutics of human dis-ease. The number of targeted genetic mouse models of disease is growing rapidly due...

The skin is a highly regenerative organ which plays critical roles in protecting the body and sensing its environment. Consequently, morbidity and mortality associated with skin defects represent a significant health issue. To identify genes important in skin development and homeostasis, we have applied a high throughput, multi-parameter phenotype...

Permanent stop-and-shop large-scale mouse mutant resources provide an excellent platform to decipher tissue phenogenomics. Here we analyse skin from 538 knockout mouse mutants generated by the Sanger Institute Mouse Genetics Project. We optimize immunolabelling of tail epidermal wholemounts to allow systematic annotation of hair follicle, sebaceous...

We describe here use of a cell-permeable Cre to efficiently convert the EUCOMM/KOMP-CSD tm1a allele to the tm1b form in preimplantation mouse embryos in a high-throughput manner, consistent with the requirements of the International Mouse Phenotyping Consortium-affiliated NIH KOMP2 project. This method results in rapid allele conversion and minimiz...

The Sanger Mouse Genetics Project generates knockout mice strains using the EUCOMM/KOMP-CSD embryonic stem (ES) cell collection and characterizes the consequences of the mutations using a high-throughput primary phenotyping screen. Upon achieving germline transmission, new strains are subject to a panel of quality control (QC) PCR- and qPCR-based a...

The mouse inbred line C57BL/6J is widely used in mouse genetics and its genome has been incorporated into many genetic reference populations. More recently large initiatives such as The International Knockout Mouse Consortium (IKMC) are using the C57BL/6N mouse strain to generate null alleles for all mouse genes. Hence both strains are now widely u...

We report an albino C57BL/6N mouse strain carrying a spontaneous mutation in the Tyrosinase gene (C57BL/6N-Tyr(cWTSI) ). Deep whole genome sequencing of founder mice revealed very little divergence from C57BL/6NJ and C57BL/6N (Taconic). This co-isogenic strain will be of great utility for the International Mouse Phenotyping Consortium (IMPC), which...

Mutations in whole organisms are powerful ways of interrogating gene function in a realistic context. We describe a program, the Sanger Institute Mouse Genetics Project, that provides a step toward the aim of knocking out all genes and screening each line for a broad range of traits. We found that hitherto unpublished genes were as likely to reveal...

C57BL/6N (B6N) is becoming the standard background for genetic manipulation of the mouse genome. The B6N, whose genome is very closely related to the reference C57BL/6J genome, is versatile in a wide range of phenotyping and experimental settings and large repositories of B6N ES cells have been developed. Here, we present a series of studies showin...

Anaemia is a chief determinant of global ill health, contributing to cognitive impairment, growth retardation and impaired physical capacity. To understand further the genetic factors influencing red blood cells, we carried out a genome-wide association study of haemoglobin concentration and related parameters in up to 135,367 individuals. Here we...

Ubiquitination plays a crucial role in neurodevelopment as exemplified by Angelman syndrome, which is caused by genetic alterations of the ubiquitin ligase-encoding UBE3A gene. Although the function of UBE3A has been widely studied, little is known about its paralog UBE3B. By using exome and capillary sequencing, we here identify biallelic UBE3B mu...

Analyses of Cenpjtm/tm mice A. LacZ staining in the brain was restricted to the lining of the cerebellar aqueduct and the fourth ventricle, which connected to a focus of staining at the precommissural nucleus. Weak staining was observed around the ventromedial preoptic nucleus. Strong LacZ staining was observed in the testes (the epididymus contain...

Apoptotic cells are scattered throughout Cenpjtm/tm embryos. Representative whole embryo (14.5 d.p.c.) images show immunohistochemical staining for Cenpj, Ki67 as a marker of proliferation, cleaved (activated) caspase-3 as a marker of apoptosis and Ser139-phosphorylated H2AX (γH2AX) as a marker of DNA damage. Apoptotic cells were scattered througho...

Protein interaction network. Using gene ontology enrichment analysis of the Seckel syndrome protein-protein interaction network. 265 biological processes (level 3 classification) are over-represented and many are related to the regulation of the cell cycle, cell growth and cell death (q-val<0.01). (XLSX)

A. Design and validation of the Cenpj allele. The L1L2_gt1 cassette was inserted at basepair 57174548 of chromosome 14 upstream of a Cenpj critical exon (exon 5, Build 37). The cassette is composed of an FRT-flanked lacZ/neomycin sequence followed by a loxP site. An additional loxP site is inserted downstream of the targeted exon at basepair 571736...

Brain measurement analysis. Diagram to show the measurements of adult brains taken at 16 weeks of age. Thalamus, mammillothalamic tracts and caudate were used as markers. (PDF)

Proposed mechanism of cell death of CENPJ-SECKEL cells and SECKEL protein interaction network. A. Flow diagram to illustrate the sequence of events that may lead to chromosomal instability, polyploidy or cell death of CENPJ-SECKEL cells. Aberrant or supernumerary centrosomes are likely to increase the frequency of multipolar spindle cell intermedia...

Centrosomal abnormalities of Cenpjtm/tm cells. A. Images show examples of centrin-3 staining in centrosomes of Cenpj+/+ and Cenpjtm/tm mouse embryonic fibroblasts (MEFs). Cells were stained with antibodies against centrin-3 (red in merge) and the mitotic spindle protein TPX-2 (green in merge). DNA is in blue. Framed areas are shown at higher magnif...

Peripheral blood leukocyte analyses: Staining panel 1. A list of antibodies use in the peripheral blood straining 1, the dilution they were used at, and the suppliers of these antibodies. (DOCX)

Peripheral blood leukocyte analyses: Staining panel 2. A list of antibodies use in the peripheral blood straining 2, the dilution they were used at, and the suppliers of these antibodies. (DOCX)

Standardized phenotypic analysis of mutant forms of every gene in the mouse genome will provide fundamental insights into mammalian gene function and advance human and animal health. The availability of the human and mouse genome sequences, the development of embryonic stem cell mutagenesis technology, the standardization of phenotypic analysis pip...

Disruption of the centromere protein J gene, CENPJ (CPAP, MCPH6, SCKL4), which is a highly conserved and ubiquitiously expressed centrosomal protein, has been associated with primary microcephaly and the microcephalic primordial dwarfism disorder Seckel syndrome. The mechanism by which disruption of CENPJ causes the proportionate, primordial growth...

In 2007, the International Knockout Mouse Consortium (IKMC) made the ambitious promise to generate mutations in virtually every protein-coding gene of the mouse genome in a concerted worldwide action. Now, 5 years later, the IKMC members have developed high-throughput gene trapping and, in particular, gene-targeting pipelines and generated more tha...

Two large-scale phenotyping efforts, the European Mouse Disease Clinic (EUMODIC) and the Wellcome Trust Sanger Institute Mouse Genetics Project (SANGER-MGP), started during the late 2000s with the aim to deliver a comprehensive assessment of phenotypes or to screen for robust indicators of diseases in mouse mutants. They both took advantage of avai...