Functional validation of mouse tyrosinase non-coding regulatory DNA elements by CRISPR-Cas9-mediated mutagenesis

Newly developed genome-editing tools, such as the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system, allow simple and rapid genetic modification in most model organisms and human cell lines. Here, we report the production and analysis of mice carrying the inactivation via deletion of a genomic insulator, a key non-coding regulatory DNA element found 5′ upstream of the mouse tyrosinase (Tyr) gene. Targeting sequences flanking this boundary in mouse fertilized eggs resulted in the efficient deletion or inversion of large intervening DNA fragments delineated by the RNA guides. The resulting genome-edited mice showed a dramatic decrease in Tyr gene expression as inferred from the evident decrease of coat pigmentation, thus supporting the functionality of this boundary sequence in vivo, at the endogenous locus. Several potential off-targets bearing sequence similarity with each of the two RNA guides used were analyzed and found to be largely intact. This study reports how non-coding DNA elements, even if located in repeat-rich genomic sequences, can be efficiently and functionally evaluated in vivo and, furthermore, it illustrates how the regulatory elements described by the ENCODE and EPIGENOME projects, in the mouse and human genomes, can be systematically validate

Hormonal and metabolic responses of Mexican lime plants to CTV infection

Plant viral infections alter gene expression and metabolism in infected host. To study the molecular responses of Mexican lime to CTV infection, an analysis of plant metabolome in response to infection with severe (T318) or mild (T385) isolates of CTV was performed. Healthy plants and those infected with any of the two virus strains showed different metabolite profiles, at different stages of new sprout development. Proline content increased in plants infected with CTV, proportionally to the virulence of the virus strain. Abscisic acid content decreased after virus infection whereas jasmonic and salicylic acid levels increased. CTV infection had an impact on plant secondary metabolism, by stimulating the synthesis of different metabolites such as l-methylhistidine, phenylpropanoid derivatives. These metabolites are common responses of different organisms, including higher mammals, to viral diseases, and its presence in this system points to the existence of universal responses to virus infection among different kingdoms

Photosynthetic and antioxidant responses of Mexican lime (Citrus aurantifolia) plants to Citrus tristeza virus infection

The effect of Citrus tristeza virus (CTV) infection on photosynthetic activity and antioxidant metabolism was analysedin plants of the highly susceptible citrus genotype Mexican lime (Citrus aurantifolia). Two virus isolates differing intheir virulence (the severe T318 and the mild T385) were used in the experiments. CTV infection caused a reduction inphotosynthetic capacity in infected plants. This limitation was mainly due to a reduction in the carboxylative efficiencywhereas the limitation of CO2diffusion through the stoma had lower impact. The virus did not damage the antennaeand did not reduce the efficiency of light harvesting complexes. Oxidative damage occurred in infected plants, as evi-denced by the increase in malondialdehyde levels. Indeed, CTV infection caused an increase in ascorbate peroxidaseactivity in new shoots developed in infected plants during the 2 years of the experiment. Data suggest that the H2O2removal machinery was not damaged as a result of stress but the defence mechanism was overwhelmed with time dueto the continuing pressure of biotic stressUniversitat Jaume I (SPAIN) P1IB2012-06 P1IB2013-23 Spanish Ministerio de Economia y Competitividad (MINECO) AGL2010-22195-C03-0

A novel in vitro tissue culture approach to study salt stress responses in citrus

In citrus, a major crop throughout the world, growth and yield are seriously affected by salinity. Different approaches, including agronomical, physiological and molecular methods, have been used to address this problem. In this work, an in vitro experimental system has been developed to study the toxic effect of NaCl on three citrus genotypes, avoiding the ion filter that represents the root system. To carry out the experiments, shoots were obtained from nodal segments of Cleopatra mandarin, Carrizo citrange and citrumelo CPB4475 plants growing in a greenhouse. Shoots were cultured in control or NaCl-supplemented media. After testing several salt concentrations, 60 mM NaCl was selected as saline treatment. Shoots accumulated similar levels of chloride when cultured without roots and exhibited similar leaf damage. No increases in malondialdehyde levels were observed in any genotype (as a measure of oxidative stress). Similar patterns of hormonal signalling (in terms of abscisic acid and salicylic acid contents) were exhibited in the three genotypes, despite their different tolerance under field conditions. All data together indicate that, without root system, all genotypes had the same behaviour under salt stress. The in vitro culture system has been proved as a useful tool to study biochemical processes involved in the response of citrus to salt stres

Utilización del cultivo de tejidos vegetales in vitro para el estudio de la respuesta de los cítricos al estrés salino

Este trabajo describe la puesta a punto de un sistema in vitro para el estudio de la toxicidad del NaCl en tres genotipos de cítricos, evitando el filtro de iones que constituye la raíz. Los cultivos se establecieron a partir de plantas de mandarino Cleopatra, citrange Carrizo y citrumelo CPB4475 cultivadas en invernadero. Se ensayaron diferentes concentraciones de NaCl y se seleccionó 60 mM como tratamiento salino para los diferentes experimentos. Los brotes de todos los genotipos estudiados acumularon concentraciones similares de iones cloruro cuando se cultivaron desprovistos del sistema radicular y mostraron los mismos daños foliares. No se observó incremento en la concentración de malondialdehido (como indicador del daño oxidativo) en ninguno de los genotipos y todos ellos mostraron patrones similares de señalización hormonal, con independencia de su tolerancia o sensibilidad cuando se cultivan en campo. El sistema in vitro descrito se postula como una herramienta útil para el estudio de los procesos bioquímicos implicados en la respuesta de los cítricos al estrés salino.In this work, an in vitro experimental system has been developed to study the toxic effect of NaCl on three citrus genotypes, avoiding the ion filter that represents the root system. Cultures were established from greenhouse growing plants of Cleopatra mandarin, Carrizo citrange and citrumelo CPB4475. Several salt concentrations were tested and 60 mM NaCl was selected as saline treatment. Shoots from all studied genotypes accumulated similar levels of chloride when cultured without roots and exhibited similar leaf damage. No increases in malondialdehyde levels (as a measure of oxidative stress) were observed in any genotype and similar patterns of hormonal signalling were exhibited in the three genotypes, despite their different tolerance under field conditions. The in vitro culture system has been proved as a useful tool to study biochemical processes involved in the response of citrus to salt stress.Este estudio fue financiado por el Ministerio de Ciencia e Innovación y la Fundació Bancaixa/Universitat Jaume I a través de la concesión de los proyectos AGL2010-22195-C03-01/AGR y P1 1B2009-01, respectivament

A Slc38a8 Mouse Model of FHONDA Syndrome Faithfully Recapitulates the Visual Deficits of Albinism Without Pigmentation Defects

Purpose: We aimed to generate and phenotype a mouse model of foveal hypoplasia, optic nerve decussation defects, and anterior segment dysgenesis (FHONDA), a rare disease associated with mutations in Slc38a8 that causes severe visual alterations similar to albinism without affecting pigmentation. Methods: The FHONDA mouse model was generated with clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology using an RNA guide targeting the Scl38a8 murine locus. The resulting mice were backcrossed to C57BL/6J. Melanin content was measured using spectrophotometry. Retinal cell architecture was analyzed through light and electron microscopy. Retinal projections to the brain were evaluated with anterograde labelling in embryos and adults. Visual function was assessed by electroretinography (ERG) and the optomotor test (OT). Results: From numerous Slc38a8 mouse mutant alleles generated, we selected one that encodes a truncated protein (p.196Pro*, equivalent to p.199Pro* in the human protein) closely resembling a mutant allele described in patients (p.200Gln*). Slc38a8 mutant mice exhibit wild-type eye and coat pigmentation with comparable melanin content. Subcellular abnormalities were observed in retinal pigment epithelium cells of Slc38a8 mutant mice. Anterograde labeling experiments of retinal projections in embryos and adults showed a reduction of ipsilateral fibers. Functional visual analyses revealed a decreased ERG response in scotopic conditions and a reduction of visual acuity in mutant mice measured by OT. Conclusions: Slc38a8 mutant mice recapitulate the phenotype of patients with FHONDA concerning their normal pigmentation and their abnormal visual system, in the latter being a hallmark of all types of albinism. These mice will be helpful in better understanding the pathophysiology of this genetic condition.Funded by the Spanish Ministry of Economy and Competitiveness under BIO2015-70978-R, the Spanish Ministry of Science and Innovation under RTI2018-101223-B-I00, CIBERER and Fundación Ramón Areces to L.M. Additionally, Spanish Ministry of Science and Innovation (FEDER-PID2019-106230RB-I00, 2019) and Generalitat Valenciana IDIFEDER/2017/064, 2017, PROMETEO/2021/024, 2021 supported the work of N.C. Funds from INSERM, Sorbonne Université, Retina France and Genespoir supported the work of A.R., as well as LabEx LIFESENSES (ANR-10-LABX-65) and IHU FOReSIGHT (ANR-18-IAHU-01) for the Institut de la Vision, a doctoral fellowship from the French Ministry of Education and Research to V.C

Lack of EGFR catalytic activity in hepatocytes improves liver regeneration following DDC-induced cholestatic injury by promoting a pro-restorative inflammatory response

Despite the well-known hepatoprotective role of the epidermal growth factor receptor (EGFR) pathway upon acute damage, its specific actions during chronic liver disease, particularly cholestatic injury, remain ambiguous and unresolved. Here, we analyzed the consequences of inactivating EGFR signaling in the liver on the regenerative response following cholestatic injury. For that, transgenic mice overexpressing a dominant negative mutant human EGFR lacking tyrosine kinase activity (ΔEGFR) in albumin-positive cells were submitted to liver damage induced by 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC), an experimental model resembling human primary sclerosing cholangitis. Our results show an early activation of EGFR after 1–2 days of a DDC-supplemented diet, followed by a signaling switch-off. Furthermore, ΔEGFR mice showed less liver damage and a more efficient regeneration following DDC injury. Analysis of the mechanisms driving this effect revealed an enhanced activation of mitogenic/survival signals, AKT and ERK1/2-MAPKs, and changes in cell turnover consistent with a quicker resolution of damage in response to DDC. These changes were concomitant with profound differences in the profile of intrahepatic immune cells, consisting of a shift in the M1/M2 balance towards M2 polarity, and the Cd4/Cd8 ratio in favor of Cd4 lymphocytes, overall supporting an immune cell switch into a pro-restorative phenotype. Interestingly, ΔEGFR livers also displayed an amplified ductular reaction, with increased expression of EPCAM and an increased number of CK19-positive ductular structures in portal areas, demonstrating an overexpansion of ductular progenitor cells. In summary, our work supports the notion that hepatocyte-specific EGFR activity acts as a key player in the crosstalk between parenchymal and non-parenchymal hepatic cells, promoting the pro-inflammatory response activated during cholestatic injury and therefore contributing to the pathogenesis of cholestatic liver disease. © 2022 The Pathological Society of Great Britain and Ireland.This work was supported by the Ministry of Science,Innovation and Universities (MICIU) and AgenciaEstatal de Investigacion (AEI), Spain (co-funded byFEDER funds/Development Fund–a Way to BuildEurope): RTI2018-099098-B-100 to AS/BH andRTI2018-094052-B-100 to AMV; and the RamonAreces Foundation: 20th National Competition forScientific and Technical Research in Life and MatterScience (2020) to IF. NL and JGS were recipients ofresearch assistant contracts linked to grant SAF2015-69145-R and RTI2018-099098-B-100, respectively. CMR was the recipient of a researchcontract (PEJD-2019-POST/BMD-16090) from the Education, Universities, Research and Spokesperson Counseling of the Community of Madrid

diverse human vh antibody fragments with bio therapeutic properties from the crescendo mouse

Abstract We describe the 'Crescendo Mouse', a human VH transgenic platform combining an engineered heavy chain locus with diverse human heavy chain V, D and J genes, a modified mouse Cγ1 gene and complete 3' regulatory region, in a triple knock-out (TKO) mouse background devoid of endogenous immunoglobulin expression. The addition of the engineered heavy chain locus to the TKO mouse restored B cell development, giving rise to functional B cells that responded to immunization with a diverse response that comprised entirely 'heavy chain only' antibodies. Heavy chain variable (VH) domain libraries were rapidly mined using phage display technology, yielding diverse high-affinity human VH that had undergone somatic hypermutation, lacked aggregation and showed enhanced expression in E. coli. The Crescendo Mouse produces human VH fragments, or Humabody® VH, with excellent bio-therapeutic potential, as exemplified here by the generation of antagonistic Humabody® VH specific for human IL17A and IL17RA

Evolution of CRISPR-associated endonucleases as inferred from resurrected proteins

Clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas9 is an effector protein that targets invading DNA and plays a major role in the prokaryotic adaptive immune system. Although Streptococcus pyogenes CRISPR–Cas9 has been widely studied and repurposed for applications including genome editing, its origin and evolution are poorly understood. Here, we investigate the evolution of Cas9 from resurrected ancient nucleases (anCas) in extinct firmicutes species that last lived 2.6 billion years before the present. We demonstrate that these ancient forms were much more flexible in their guide RNA and protospacer-adjacent motif requirements compared with modern-day Cas9 enzymes. Furthermore, anCas portrays a gradual palaeoenzymatic adaptation from nickase to double-strand break activity, exhibits high levels of activity with both single-stranded DNA and single-stranded RNA targets and is capable of editing activity in human cells. Prediction and characterization of anCas with a resurrected protein approach uncovers an evolutionary trajectory leading to functionally flexible ancient enzymes.This work has been supported by grant nos. PID2019-109087RB-I00 (to R.P.-J.) and RTI2018-101223-B-I00 and PID2021-127644OB-I00 (to L.M.) from the Spanish Ministry of Science and Innovation. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 964764 (to R.P.-J.). The content presented in this document represents the views of the authors, and the European Commission has no liability in respect to the content. We acknowledge financial support from the Spanish Foundation for the Promotion of Research of Amyotrophic Lateral Sclerosis. A.F. acknowledges Spanish Center for Biomedical Network Research on Rare Diseases (CIBERE) intramural funds (no. ER19P5AC756/2021). F.J.M.M. acknowledges research support by Conselleria d’Educació, Investigació, Cultura i Esport from Generalitat Valenciana, research project nos. PROMETEO/2017/129 and PROMETEO/2021/057. M.M. acknowledges funding from CIBERER (grant no. ER19P5AC728/2021). The work has received funding from the Regional Government of Madrid (grant no. B2017/BMD3721 to M.A.M.-P.) and from Instituto de Salud Carlos III, cofounded with the European Regional Development Fund ‘A way to make Europe’ within the National Plans for Scientific and Technical Research and Innovation 2017–2020 and 2021–2024 (nos. PI17/1659, PI20/0429 and IMP/00009; to M.A.M.-P. B.P.K. was supported by an MGH ECOR Howard M. Goodman Award and NIH P01 HL142494

An insulator embedded in the chicken α-globin locus regulates chromatin domain configuration and differential gene expression

Genome organization into transcriptionally active domains denotes one of the first levels of gene expression regulation. Although the chromatin domain concept is generally accepted, only little is known on how domain organization impacts the regulation of differential gene expression. Insulators might hold answers to address this issue as they delimit and organize chromatin domains. We have previously identified a CTCF-dependent insulator with enhancer-blocking activity embedded in the 5′ non-coding region of the chicken α-globin domain. Here, we demonstrate that this element, called the αEHS-1.4 insulator, protects a transgene against chromosomal position effects in stably transfected cell lines and transgenic mice. We found that this insulator can create a regulated chromatin environment that coincides with the onset of adult α-globin gene expression. Furthermore, such activity is in part dependent on the in vivo regulated occupancy of CTCF at the αEHS-1.4 element. Insulator function is also regulated by CTCF poly(ADP-ribosyl)ation. Our results suggest that the αEHS-1.4 insulator contributes in organizing the chromatin structure of the α-globin gene domain and prevents activation of adult α-globin gene expression at the erythroblast stage via CTCF