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Hybrid allele expression development

Sebastian Maciak, Katarzyna Michalak, Shiv D Kale, Pawel Michalak
Nucleolar dominance is a dramatic disruption in the formation of nucleoli and the expression of ribosomal RNA (rRNA) genes, characteristic of some plant and animal hybrids. Here, we report that F1 hybrids produced from reciprocal crosses between 2 sister species of Xenopus clawed frogs, X. muelleri and X. borealis, undergo nucleolar dominance somewhat distinct from a pattern previously reported in hybrids between phylogenetically more distant Xenopus species. Patterns of nucleolar development, 45S rRNA expression, and gene copy inheritance were investigated using a combination of immunostaining, pyrosequencing, droplet digital PCR, flow cytometry, and epigenetic inhibition...
October 12, 2016: Cytogenetic and Genome Research
Thomas D Brekke, Lindy A Henry, Jeffrey M Good
The importance of regulatory incompatibilities to the early stages of speciation remains unclear. Hybrid mammals often show extreme parent-of-origin growth effects that are thought to be a consequence of disrupted genetic imprinting (parent-specific epigenetic gene silencing) during early development. Here we test the long-standing hypothesis that abnormal hybrid growth reflects disrupted gene expression due to loss of imprinting (LOI) in hybrid placentas, resulting in dosage imbalances between paternal growth factors and maternal growth repressors...
October 7, 2016: Evolution; International Journal of Organic Evolution
Vasundhara Sharma, Paola Monti, Gilberto Fronza, Alberto Inga
The observation that human transcription factors (TFs) can function when expressed in yeast cells has stimulated the development of various functional assays to investigate (i) the role of binding site sequences (herein referred to as response elements, REs) in transactivation specificity, (ii) the impact of polymorphic nucleotide variants on transactivation potential, (iii) the functional consequences of mutations in TFs and (iv) the impact of cofactors or small molecules. These approaches have found applications in basic as well as applied research, including the identification and the characterisation of mutant TF alleles from clinical samples...
November 2016: FEMS Yeast Research
Pierre Mélard, Yamina Idrissi, Laetitia Andrique, Sandrine Poglio, Martina Prochazkova-Carlotti, Sabine Berhouet, Cécile Boucher, Elodie Laharanne, Edith Chevret, Anne Pham-Ledard, Andréa Carla De Souza Góes, Véronique Guyonnet-Duperat, Alice Bibeyran, François Moreau-Gaudry, Béatrice Vergier, Marie Beylot-Barry, Jean-Philippe Merlio, David Cappellen
Monoallelic 6p25.3 rearrangements associated with DUSP22 (Dual Specificity Phosphatase 22) gene silencing have been reported in CD30+ peripheral T-cell lymphomas (PTCL), mostly with anaplastic morphology and of cutaneous origin. However, the mechanism of second allele silencing and the putative tumor suppressor function of DUSP22 have not been investigated so far. Here, we show that the presence, in most individuals, of an inactive paralog hampers genetic and epigenetic evaluation of the DUSP22 gene. Identification of DUSP22-specific single-nucleotide polymorphisms haplotypes and fluorescence in situ hybridization and epigenetic characterization of the paralog status led us to develop a comprehensive strategy enabling reliable identification of DUSP22 alterations...
September 10, 2016: Oncotarget
N N Fesenko, I N Fesenko
Fagopyrum homotropicum Ohnishi is a very polymorphic self-pollinating species with homostylous flowers, which morphologically different lineages are differ also in ability to hybridize with F. esculentum Moench. (closely related outcrosser with heterostyly). A lineage C2026 F. homotropicum diverged from F. esculentum with forming noticeable pre-zygotic and post-zygotic barriers: the most successful interspecific crossing F esculentum x C2026 resulted wrinkled hybrid seeds germinated in Petri dishes. These interspecific hybrids and backcrosses F...
April 2016: Genetika
Li-Li Li, Pei-Hong Liu, Xiao-Hua Xie, Su Ma, Chao Liu, Li Chen, Chun-Lin Qin
FAM20A has been studied to a very limited extent. Mutations in human FAM20A cause amelogenesis imperfecta, gingival fibromatosis and kidney problems. It would be desirable to systemically analyse the expression of FAM20A in dental tissues and to assess the pathological changes when this molecule is specifically nullified in individual tissues. Recently, we generated mice with a Fam20A-floxed allele containing the beta-galactosidase reporter gene. We analysed FAM20A expression in dental tissues using X-Gal staining, immunohistochemistry and in situ hybridization, which showed that the ameloblasts in the mouse mandibular first molar began to express FAM20A at 1 day after birth, and the reduced enamel epithelium in erupting molars expressed a significant level of FAM20A...
2016: International Journal of Oral Science
Ho-Tak Lau, Lizhi Liu, Chelsea Ray, Fong T Bell, Xiajun Li
Parental origin-dependent expression of the imprinted genes is essential for mammalian development. Zfp57 maintains genomic imprinting in mouse embryos and ES cells. To examine the allelic expression patterns of the imprinted genes in ES cells, we obtained multiple hybrid ES clones that were directly derived from the blastocysts generated from the cross between mice on two different genetic backgrounds. The blastocyst-derived ES clones displayed largely intact DNA methylation imprint at the tested imprinted regions...
March 2016: Stem Cell Research
Paul Huber, Tanya Crum, Peter G Okkema
T-box transcription factors are important regulators of development in all animals, and altered expression of T-box factors has been identified in an increasing number of diseases and cancers. Despite these important roles, the mechanism of T-box factor activity is not well understood. We have previously shown that the Caenorhabditis elegans Tbx2 subfamily member TBX-2 functions as a transcriptional repressor to specify ABa-derived pharyngeal muscle, and that this function depends on SUMOylation. Here we show that TBX-2 function also depends on interaction with the Groucho-family corepressor UNC-37...
August 1, 2016: Developmental Biology
Susana Manzano, Encarnación Aguado, Cecilia Martínez, Zoraida Megías, Alicia García, Manuel Jamilena
Monoecious and andromonoecious cultivars of watermelon are characterised by the production of male and female flower or male and hermaphrodite flowers, respectively. The segregation analysis in the offspring of crosses between monoecious and andromonoecious lines has demonstrated that this trait is controlled by a single gene pair, being the monoecious allele M semi-dominant to the andromonoecious allele A. The two studied F1 hybrids (MA) had a predominantly monoecious phenotype since both produced not only female flowers, but also bisexual flowers with incomplete stamens, and hermaphrodite flowers with pollen...
2016: PloS One
Tristan Bouschet, Emeric Dubois, Christelle Reynès, Satya K Kota, Stéphanie Rialle, Stéphanie Maupetit-Méhouas, Mikael Pezet, Anne Le Digarcher, Sabine Nidelet, Vincent Demolombe, Patricia Cavelier, Céline Meusnier, Chloé Maurizy, Robert Sabatier, Robert Feil, Philippe Arnaud, Laurent Journot, Annie Varrault
In vitro corticogenesis from embryonic stem cells (ESCs) is an attractive model of cortical development and a promising tool for cortical therapy. It is unknown to which extent epigenetic mechanisms crucial for cortex development and function, such as parental genomic imprinting, are recapitulated by in vitro corticogenesis. Here, using genome-wide transcriptomic and methylation analyses on hybrid mouse tissues and cells, we find a high concordance of imprinting status between in vivo and ESC-derived cortices...
April 19, 2016: Cerebral Cortex
Zhijun Qiu, Zeinab Elsayed, Veronica Peterkin, Suehyb Alkatib, Dorothy Bennett, Joseph W Landry
BACKGROUND: Understanding how embryos specify asymmetric axes is a major focus of biology. While much has been done to discover signaling pathways and transcription factors important for axis specification, comparatively little is known about how epigenetic regulators are involved. Epigenetic regulators operate downstream of signaling pathways and transcription factors to promote nuclear processes, most prominently transcription. To discover novel functions for these complexes in axis establishment during early embryonic development, we characterized phenotypes of a mouse knockout (KO) allele of the chromatin remodeling Ino80 ATPase...
2016: BMC Biology
Lisheng Chen, Vanessa Martino, Alan Dombkowski, Trevor Williams, Judith West-Mays, Philip J Gage
PURPOSE: The homeodomain transcription factor, PITX2, is at the apex of a genetic pathway required for corneal development, but the critical effector genes regulated by the PITX2 remain unknown. The purpose of this study was to discover and validate PITX2-dependent mechanisms required for specifying cell lineages and establishing angiogenic privilege within the developing cornea. METHODS: Microarrays were used to compare gene expression in corneas isolated from temporal Pitx2 knockout embryos and control littermates...
March 2016: Investigative Ophthalmology & Visual Science
Emily K Don, Tanya A de Jong-Curtain, Karen Doggett, Thomas E Hall, Benjamin Heng, Andrew P Badrock, Claire Winnick, Garth A Nicholson, Gilles J Guillemin, Peter D Currie, Daniel Hesselson, Joan K Heath, Nicholas J Cole
Here we genetically characterise pelvic finless, a naturally occurring model of hindlimb loss in zebrafish that lacks pelvic fin structures, which are homologous to tetrapod hindlimbs, but displays no other abnormalities. Using a hybrid positional cloning and next generation sequencing approach, we identified mutations in the nuclear localisation signal (NLS) of T-box transcription factor 4 (Tbx4) that impair nuclear localisation of the protein, resulting in altered gene expression patterns during pelvic fin development and the failure of pelvic fin development...
2016: Biology Open
Joel B Berletch, Wenxiu Ma, Fan Yang, Jay Shendure, William S Noble, Christine M Disteche, Xinxian Deng
X chromosome inactivation (XCI) is a female-specific mechanism that serves to balance gene dosage between the sexes whereby one X chromosome in females is inactivated during early development. Despite this silencing, a small portion of genes escape inactivation and remain expressed from the inactive X (Xi). Little is known about the distribution of escape from XCI in different tissues in vivo and about the mechanisms that control tissue-specific differences. Using a new binomial model in conjunction with a mouse model with identifiable alleles and skewed X inactivation we are able to survey genes that escape XCI in vivo...
December 2015: Data in Brief
Geraldo Carvalho, Robert Eugene Schaffert, Marcos Malosetti, Joao Herbert Moreira Viana, Cicero Bezerra Menezes, Lidianne Assis Silva, Claudia Teixeira Guimaraes, Antonio Marcos Coelho, Leon V Kochian, Fred A van Eeuwijk, Jurandir Vieira Magalhaes
Aluminum (Al) toxicity damages plant roots and limits crop production on acid soils, which comprise up to 50% of the world's arable lands. A major Al tolerance locus on chromosome 3, AltSB, controls aluminum tolerance in sorghum [Sorghum bicolor (L.) Moench] via SbMATE, an Al-activated plasma membrane transporter that mediates Al exclusion from sensitive regions in the root apex. As is the case with other known Al tolerance genes, SbMATE was cloned based on studies conducted under controlled environmental conditions, in nutrient solution...
February 2016: G3: Genes—Genomes—Genetics
H S Nie, S P Li, X H Shan, Y Wu, S Z Su, H K Liu, J Y Han, Y P Yuan
Heterosis has greatly contributed to conventional plant breeding and is widely used to increase crop plant productivity. However, although some studies have explored the mechanisms of heterosis at the genomic and transcriptome level, these mechanisms still remain unclear. The growth and development of maize seedlings and immature embryos have an important impact on subsequent production. This study investigated differentially expressed genes (DEGs) between parents and reciprocal hybrids in the seedling leaves, roots, and immature embryo 15 days after pollination using amplified fragment length polymorphism (AFLP)-based transcript profiling (cDNA-AFLP)...
2015: Genetics and Molecular Research: GMR
Christina Doxaki, Sotirios C Kampranis, Aristides G Eliopoulos, Charalampos Spilianakis, Christos Tsatsanis
Endotoxin tolerance occurs to protect the organism from hyperactivation of innate immune responses, primarily mediated by macrophages. Regulation of endotoxin tolerance occurs at multiple levels of cell responses and requires significant changes in gene expression. In the process of macrophage activation, induced expression of microRNA (miR)-155 and miR-146a contributes to the regulation of the inflammatory response and endotoxin tolerance. In this article, we demonstrate that expression of both miRNAs is coordinately regulated during endotoxin tolerance by a complex mechanism that involves monoallelic interchromosomal association, alterations in histone methyl marks, and transcription factor binding...
December 15, 2015: Journal of Immunology: Official Journal of the American Association of Immunologists
Michael A Caprio, Jeannette C Martinez, Patrick A Porter, Ed Bynum
Seeds or kernels on hybrid plants are primarily F(2) tissue and will segregate for heterozygous alleles present in the parental F(1) hybrids. In the case of plants expressing Bt-toxins, the F(2) tissue in the kernels will express toxins as they would segregate in any F(2) tissue. In the case of plants expressing two unlinked toxins, the kernels on a Bt plant fertilized by another Bt plant would express anywhere from 0 to 2 toxins. Larvae of corn earworm [Helicoverpa zea (Boddie)] feed on a number of kernels during development and would therefore be exposed to local habitats (kernels) that varied in their toxin expression...
February 2016: Journal of Economic Entomology
Jinwen Wu, Muhammad Qasim Shahid, Lin Chen, Zhixiong Chen, Lan Wang, Xiangdong Liu, Yonggen Lu
Intersubspecific autotetraploid rice (Oryza sativa ssp. indica × japonica) hybrids have greater biological and yield potentials than diploid rice. However, the low fertility of intersubspecific autotetraploid hybrids, which is largely caused by high pollen abortion rates, limits their commercial utility. To decipher the cytological and molecular mechanisms underlying allelic interactions in autotetraploid rice, we developed an autotetraploid rice hybrid that was heterozygous (S(i)S(j)) at F1 pollen sterility loci (Sa, Sb, and Sc) using near-isogenic lines...
December 2015: Plant Physiology
Kevin D Wright, Amanda A Mahoney Rogers, Jian Zhang, Katherine Shim
BACKGROUND: In multiple vertebrate organisms, including chick, Xenopus, and zebrafish, Fibroblast Growth Factor (FGF) and Wnt signaling cooperate during formation of the otic placode. However, in the mouse, although FGF signaling induces Wnt8a expression during induction of the otic placode, it is unclear whether these two signaling pathways functionally cooperate. Sprouty (Spry) genes encode intracellular antagonists of receptor tyrosine kinase signaling, including FGF signaling. We previously demonstrated that the Sprouty1 (Spry1) and Sprouty2 (Spry2) genes antagonize FGF signaling during induction of the otic placode...
October 6, 2015: BMC Developmental Biology
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