9 results on '"Medina-Ruiz S"'
Search Results
2. Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs.
- Author
-
Bredeson JV, Mudd AB, Medina-Ruiz S, Mitros T, Smith OK, Miller KE, Lyons JB, Batra SS, Park J, Berkoff KC, Plott C, Grimwood J, Schmutz J, Aguirre-Figueroa G, Khokha MK, Lane M, Philipp I, Laslo M, Hanken J, Kerdivel G, Buisine N, Sachs LM, Buchholz DR, Kwon T, Smith-Parker H, Gridi-Papp M, Ryan MJ, Denton RD, Malone JH, Wallingford JB, Straight AF, Heald R, Hockemeyer D, Harland RM, and Rokhsar DS
- Subjects
- Animals, Genome genetics, Anura genetics, Xenopus genetics, Centromere genetics, Chromatin genetics, Evolution, Molecular
- Abstract
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
3. Genome and transcriptome mechanisms driving cephalopod evolution.
- Author
-
Albertin CB, Medina-Ruiz S, Mitros T, Schmidbaur H, Sanchez G, Wang ZY, Grimwood J, Rosenthal JJC, Ragsdale CW, Simakov O, and Rokhsar DS
- Subjects
- Animals, Decapodiformes genetics, Genome genetics, RNA, Messenger genetics, Transcriptome genetics, Cephalopoda genetics
- Abstract
Cephalopods are known for their large nervous systems, complex behaviors and morphological innovations. To investigate the genomic underpinnings of these features, we assembled the chromosomes of the Boston market squid, Doryteuthis (Loligo) pealeii, and the California two-spot octopus, Octopus bimaculoides, and compared them with those of the Hawaiian bobtail squid, Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods are highly rearranged relative to other extant molluscs, indicating an intense, early burst of genome restructuring. The coleoid genomes feature multi-megabase, tandem arrays of genes associated with brain development and cephalopod-specific innovations. We find that a known coleoid hallmark, extensive A-to-I mRNA editing, displays two fundamentally distinct patterns: one exclusive to the nervous system and concentrated in genic sequences, the other widespread and directed toward repetitive elements. We conclude that coleoid novelty is mediated in part by substantial genome reorganization, gene family expansion, and tissue-dependent mRNA editing., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
4. ITGBL1 modulates integrin activity to promote cartilage formation and protect against arthritis.
- Author
-
Song EK, Jeon J, Jang DG, Kim HE, Sim HJ, Kwon KY, Medina-Ruiz S, Jang HJ, Lee AR, Rho JG, Lee HS, Kim SJ, Park CY, Myung K, Kim W, Kwon T, Yang S, and Park TJ
- Subjects
- Aged, Animals, Cell Differentiation, Cell Line, Tumor, Chondrocytes metabolism, Disease Models, Animal, Embryo, Nonmammalian metabolism, Extracellular Matrix metabolism, Face embryology, Gene Expression Regulation, Humans, Joints pathology, Mesenchymal Stem Cells cytology, Mesenchymal Stem Cells metabolism, Mice, Middle Aged, Osteoarthritis genetics, Osteoarthritis pathology, Xenopus embryology, Cartilage, Articular metabolism, Cartilage, Articular pathology, Chondrogenesis, Integrin beta1 metabolism, Osteoarthritis metabolism, Osteoarthritis prevention & control
- Abstract
Developing and mature chondrocytes constantly interact with and remodel the surrounding extracellular matrix (ECM). Recent research indicates that integrin-ECM interaction is differentially regulated during cartilage formation (chondrogenesis). Integrin signaling is also a key source of the catabolic reactions responsible for joint destruction in both rheumatoid arthritis and osteoarthritis. However, we do not understand how chondrocytes dynamically regulate integrin signaling in such an ECM-rich environment. Here, we found that developing chondrocytes express integrin-β-like 1 ( Itgbl1 ) at specific stages, inhibiting integrin signaling and promoting chondrogenesis. Unlike cytosolic integrin inhibitors, ITGBL1 is secreted and physically interacts with integrins to down-regulate activity. We observed that Itgbl1 expression was strongly reduced in the damaged articular cartilage of patients with osteoarthritis (OA). Ectopic expression of Itgbl1 protected joint cartilage against OA development in the destabilization of the medial meniscus-induced OA mouse model. Our results reveal ITGBL1 signaling as an underlying mechanism of protection against destructive cartilage disorders and suggest the potential therapeutic utility of targeting ITGBL1 to modulate integrin signaling in human disease., (Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
- Published
- 2018
- Full Text
- View/download PDF
5. A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates.
- Author
-
Plouhinec JL, Medina-Ruiz S, Borday C, Bernard E, Vert JP, Eisen MB, Harland RM, and Monsoro-Burq AH
- Subjects
- Algorithms, Animals, Cluster Analysis, Databases, Genetic, Ectoderm metabolism, Gastrulation genetics, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Ontology, Gene Regulatory Networks, Humans, Internet, Microdissection, Neoplasms genetics, Neural Crest metabolism, Neurulation genetics, Principal Component Analysis, Time Factors, Transcriptome genetics, Wnt Proteins metabolism, Xenopus laevis genetics, Ectoderm embryology, Neural Crest embryology, Neurons cytology, Stem Cells metabolism, Xenopus laevis embryology
- Abstract
During vertebrate neurulation, the embryonic ectoderm is patterned into lineage progenitors for neural plate, neural crest, placodes and epidermis. Here, we use Xenopus laevis embryos to analyze the spatial and temporal transcriptome of distinct ectodermal domains in the course of neurulation, during the establishment of cell lineages. In order to define the transcriptome of small groups of cells from a single germ layer and to retain spatial information, dorsal and ventral ectoderm was subdivided along the anterior-posterior and medial-lateral axes by microdissections. Principal component analysis on the transcriptomes of these ectoderm fragments primarily identifies embryonic axes and temporal dynamics. This provides a genetic code to define positional information of any ectoderm sample along the anterior-posterior and dorsal-ventral axes directly from its transcriptome. In parallel, we use nonnegative matrix factorization to predict enhanced gene expression maps onto early and mid-neurula embryos, and specific signatures for each ectoderm area. The clustering of spatial and temporal datasets allowed detection of multiple biologically relevant groups (e.g., Wnt signaling, neural crest development, sensory placode specification, ciliogenesis, germ layer specification). We provide an interactive network interface, EctoMap, for exploring synexpression relationships among genes expressed in the neurula, and suggest several strategies to use this comprehensive dataset to address questions in developmental biology as well as stem cell or cancer research.
- Published
- 2017
- Full Text
- View/download PDF
6. Cell-fate determination by ubiquitin-dependent regulation of translation.
- Author
-
Werner A, Iwasaki S, McGourty CA, Medina-Ruiz S, Teerikorpi N, Fedrigo I, Ingolia NT, and Rape M
- Subjects
- Adaptor Proteins, Signal Transducing metabolism, Animals, Cullin Proteins metabolism, Embryonic Stem Cells cytology, Embryonic Stem Cells metabolism, Humans, Mandibulofacial Dysostosis genetics, Nuclear Proteins genetics, Nuclear Proteins metabolism, Phosphoproteins genetics, Phosphoproteins metabolism, Proteomics, RNA Polymerase I metabolism, Ribosomes chemistry, Ribosomes metabolism, Ubiquitination, Xenopus, Cell Differentiation genetics, Neural Crest cytology, Neural Crest metabolism, Protein Biosynthesis, Ubiquitin metabolism
- Abstract
Metazoan development depends on the accurate execution of differentiation programs that allow pluripotent stem cells to adopt specific fates. Differentiation requires changes to chromatin architecture and transcriptional networks, yet whether other regulatory events support cell-fate determination is less well understood. Here we identify the ubiquitin ligase CUL3 in complex with its vertebrate-specific substrate adaptor KBTBD8 (CUL3(KBTBD8)) as an essential regulator of human and Xenopus tropicalis neural crest specification. CUL3(KBTBD8) monoubiquitylates NOLC1 and its paralogue TCOF1, the mutation of which underlies the neurocristopathy Treacher Collins syndrome. Ubiquitylation drives formation of a TCOF1-NOLC1 platform that connects RNA polymerase I with ribosome modification enzymes and remodels the translational program of differentiating cells in favour of neural crest specification. We conclude that ubiquitin-dependent regulation of translation is an important feature of cell-fate determination.
- Published
- 2015
- Full Text
- View/download PDF
7. A thioredoxin fold protein Sh3bgr regulates Enah and is necessary for proper sarcomere formation.
- Author
-
Jang DG, Sim HJ, Song EK, Medina-Ruiz S, Seo JK, and Park TJ
- Subjects
- Animals, Embryo, Nonmammalian metabolism, Female, Gene Knockdown Techniques, Humans, Muscle Development, Muscle, Striated embryology, Muscle, Striated metabolism, Myocardium metabolism, Protein Structure, Secondary, Protein Transport, Somites embryology, Somites metabolism, Thioredoxins metabolism, Xenopus embryology, Microfilament Proteins chemistry, Microfilament Proteins metabolism, Sarcomeres metabolism, Thioredoxins chemistry, Xenopus Proteins chemistry, Xenopus Proteins metabolism
- Abstract
The sh3bgr (SH3 domain binding glutamate-rich) gene encodes a small protein containing a thioredoxin-like fold, SH3 binding domain, and glutamate-rich domain. Originally, it was suggested that increased expression of Sh3bgr may cause the cardiac phenotypes in Down's syndrome. However, it was recently reported that the overexpression of Sh3bgr did not cause any disease phenotypes in mice. In this study, we have discovered that Sh3bgr is critical for sarcomere formation in striated muscle tissues and also for heart development. Sh3bgr is strongly expressed in the developing somites and heart in Xenopus. Morpholino mediated-knockdown of sh3bgr caused severe malformation of heart tissue and disrupted segmentation of the somites. Further analysis revealed that Sh3bgr specifically localized to the Z-line in mature sarcomeres and that knockdown of Sh3bgr completely disrupted sarcomere formation in the somites. Moreover, overexpression of Sh3bgr resulted in abnormally discontinues thick firmaments in the somitic sarcomeres. We suggest that Sh3bgr does its function at least partly by regulating localization of Enah for the sarcomere formation. In addition, we provide the data supporting Sh3bgr is also necessary for proper heart development in part by affecting the Enah protein level., (Copyright © 2015 Elsevier Inc. All rights reserved.)
- Published
- 2015
- Full Text
- View/download PDF
8. Sp8 regulates inner ear development.
- Author
-
Chung HA, Medina-Ruiz S, and Harland RM
- Subjects
- Animals, Base Sequence, Biomarkers metabolism, Ear, Inner embryology, Ear, Inner metabolism, Embryo, Nonmammalian metabolism, Endonucleases metabolism, Gene Expression Regulation, Developmental, Molecular Sequence Data, Morpholinos pharmacology, Mutation genetics, RNA, Messenger genetics, RNA, Messenger metabolism, Trans-Activators metabolism, Transcription Factors genetics, Xenopus embryology, Xenopus metabolism, Xenopus Proteins genetics, Ear embryology, Transcription Factors metabolism, Xenopus Proteins metabolism
- Abstract
A forward genetic screen of N-ethyl-N-nitrosourea mutagenized Xenopus tropicalis has identified an inner ear mutant named eclipse (ecl). Mutants developed enlarged otic vesicles and various defects of otoconia development; they also showed abnormal circular and inverted swimming patterns. Positional cloning identified specificity protein 8 (sp8), which was previously found to regulate limb and brain development. Two different loss-of-function approaches using transcription activator-like effector nucleases and morpholino oligonucleotides confirmed that the ecl mutant phenotype is caused by down-regulation of sp8. Depletion of sp8 resulted in otic dysmorphogenesis, such as uncompartmentalized and enlarged otic vesicles, epithelial dilation with abnormal sensory end organs. When overexpressed, sp8 was sufficient to induce ectopic otic vesicles possessing sensory hair cells, neurofilament innervation in a thickened sensory epithelium, and otoconia, all of which are found in the endogenous otic vesicle. We propose that sp8 is an important factor for initiation and elaboration of inner ear development.
- Published
- 2014
- Full Text
- View/download PDF
9. Recurrent DNA inversion rearrangements in the human genome.
- Author
-
Flores M, Morales L, Gonzaga-Jauregui C, Domínguez-Vidaña R, Zepeda C, Yañez O, Gutiérrez M, Lemus T, Valle D, Avila MC, Blanco D, Medina-Ruiz S, Meza K, Ayala E, García D, Bustos P, González V, Girard L, Tusie-Luna T, Dávila G, and Palacios R
- Subjects
- Adult, Age Factors, Cloning, Molecular, Computational Biology methods, Humans, Infant, Newborn, Polymerase Chain Reaction methods, Repetitive Sequences, Nucleic Acid genetics, Sequence Analysis, DNA, Chromosome Inversion genetics, Chromosomes, Human genetics, Gene Rearrangement genetics, Genome Components genetics, Genome, Human genetics
- Abstract
Several lines of evidence suggest that reiterated sequences in the human genome are targets for nonallelic homologous recombination (NAHR), which facilitates genomic rearrangements. We have used a PCR-based approach to identify breakpoint regions of rearranged structures in the human genome. In particular, we have identified intrachromosomal identical repeats that are located in reverse orientation, which may lead to chromosomal inversions. A bioinformatic workflow pathway to select appropriate regions for analysis was developed. Three such regions overlapping with known human genes, located on chromosomes 3, 15, and 19, were analyzed. The relative proportion of wild-type to rearranged structures was determined in DNA samples from blood obtained from different, unrelated individuals. The results obtained indicate that recurrent genomic rearrangements occur at relatively high frequency in somatic cells. Interestingly, the rearrangements studied were significantly more abundant in adults than in newborn individuals, suggesting that such DNA rearrangements might start to appear during embryogenesis or fetal life and continue to accumulate after birth. The relevance of our results in regard to human genomic variation is discussed.
- Published
- 2007
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.