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Hybrid allele expression development

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https://www.readbyqxmd.com/read/27899656/idp-ase-haplotyping-and-quantifying-allele-specific-expression-at-the-gene-and-gene-isoform-level-by-hybrid-sequencing
#1
Benjamin Deonovic, Yunhao Wang, Jason Weirather, Xiu-Jie Wang, Kin Fai Au
Allele-specific expression (ASE) is a fundamental problem in studying gene regulation and diploid transcriptome profiles, with two key challenges: (i) haplotyping and (ii) estimation of ASE at the gene isoform level. Existing ASE analysis methods are limited by a dependence on haplotyping from laborious experiments or extra genome/family trio data. In addition, there is a lack of methods for gene isoform level ASE analysis. We developed a tool, IDP-ASE, for full ASE analysis. By innovative integration of Third Generation Sequencing (TGS) long reads with Second Generation Sequencing (SGS) short reads, the accuracy of haplotyping and ASE quantification at the gene and gene isoform level was greatly improved as demonstrated by the gold standard data GM12878 data and semi-simulation data...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27880012/patterns-of-gene-expression-in-developing-embryos-of-arabidopsis-hybrids
#2
Maria M Alonso-Peral, Marina Trigueros, Bjorg Sherman, Hua Ying, Jennifer M Taylor, W James Peacock, Elizabeth S Dennis
Hybrids between the Arabidopsis ecotypes C24 and Ler have high levels of hybrid vigour, heterosis, in both biomass and seed yield. Heterosis can be detected throughout the development of the plant and in different tissues. We examined developing embryos and seeds of C24/Ler reciprocal hybrids with the aim of detecting the earliest time at which heterotic gene activity occurs. In the transcriptomes of 4 dap (dermatogen to globular) and 6 dap (heart) embryos from both parents and hybrids, 95% of expressed genes were at the Mid Parent Value (MPV) and 95% of the genes with SNPs between C24 and Ler retained the same relative allelic expression levels in the hybrids as existed in the parents...
November 23, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27875998/transcriptome-profiling-and-comparison-of-maize-ear-heterosis-during-the-spikelet-and-floret-differentiation-stages
#3
Xiaojiao Hu, Hongwu Wang, Xizhou Diao, Zhifang Liu, Kun Li, Yujin Wu, Qianjin Liang, Hui Wang, Changling Huang
BACKGROUND: Hybridization is a prominent process in the evolution of crop plants that can give rise to gene expression variation, phenotypic novelty and heterosis. Maize is the most successful crop in utilizing heterosis. The development of hybrid maize ears exhibits strong heterotic vigor and greatly affects maize yield. However, a comprehensive perspective on transcriptional variation and its correlation with heterosis during maize ear development is not available. RESULTS: Using RNA sequencing technology, we investigated the transcriptome profiles of maize ears in the spikelet and floret differentiation stages of hybrid ZD808 and its parents CL11 and NG5...
November 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27871306/akirin2-is-essential-for-the-formation-of-the-cerebral-cortex
#4
Peter J Bosch, Leah C Fuller, Carolyn M Sleeth, Joshua A Weiner
BACKGROUND: The proper spatial and temporal regulation of dorsal telencephalic progenitor behavior is a prerequisite for the formation of the highly-organized, six-layered cerebral cortex. Premature differentiation of cells, disruption of cell cycle timing, excessive apoptosis, and/or incorrect neuronal migration signals can have devastating effects, resulting in a number of neurodevelopmental disorders involving microcephaly and/or lissencephaly. Though genes encoding many key players in cortical development have been identified, our understanding remains incomplete...
November 21, 2016: Neural Development
https://www.readbyqxmd.com/read/27861562/digitor-dasciz-has-multiple-roles-in-drosophila-development
#5
Saheli Sengupta, Uttama Rath, Changfu Yao, Michael Zavortink, Chao Wang, Jack Girton, Kristen M Johansen, Jørgen Johansen
In this study we provide evidence that the spindle matrix protein Skeletor in Drosophila interacts with the human ASCIZ (also known as ATMIN and ZNF822) ortholog, Digitor/dASCIZ. This interaction was first detected in a yeast two-hybrid screen and subsequently confirmed by pull-down assays. We also confirm a previously documented function of Digitor/dASCIZ as a regulator of Dynein light chain/Cut up expression. Using transgenic expression of a mCitrine-labeled Digitor construct, we show that Digitor/dASCIZ is a nuclear protein that is localized to interband and developmental puff chromosomal regions during interphase but redistributes to the spindle region during mitosis...
2016: PloS One
https://www.readbyqxmd.com/read/27832742/comparative-transcriptome-profiling-of-the-fertile-and-sterile-flower-buds-of-a-dominant-genic-male-sterile-line-in-sesame-sesamum-indicum-l
#6
Hongyan Liu, Mingpu Tan, Haijuan Yu, Liang Li, Fang Zhou, Minmin Yang, Ting Zhou, Yingzhong Zhao
BACKGROUND: Sesame (Sesamum indicum L.) is a globally important oilseed crop with highly-valued oil. Strong hybrid vigor is frequently observed within this crop, which can be exploited by the means of genic male sterility (GMS). We have previously developed a dominant GMS (DGMS) line W1098A that has great potential for the breeding of F1 hybrids. Although it has been genetically and anatomically characterized, the underlying molecular mechanism for male sterility remains unclear and therefore limits the full utilization of such GMS line...
November 10, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27801963/nbp35-interacts-with-dre2-in-the-maturation-of-cytosolic-iron-sulfur-proteins-in-arabidopsis-thaliana
#7
Emma L Bastow, Katrine Bych, Jason C Crack, Nick E Le Brun, Janneke Balk
Proteins of the cytosolic pathway for iron-sulfur (FeS) cluster assembly are conserved, except that plants lack a gene for CFD1 (Cytosolic FeS cluster Deficient 1). This poses the question of how NBP35 (Nucleotide-Binding Protein 35 kDa), the heteromeric partner of CFD1 in metazoa, functions on its own in plants. Firstly, we created viable mutant alleles of NBP35 in Arabidopsis to overcome embryo lethality of previously reported knockout mutations. RNAi knockdown lines with less than 30% NBP35 protein surprisingly showed no developmental or biochemical differences to wild type...
November 1, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27728911/nucleolar-dominance-and-repression-of-45s-ribosomal-rna-genes-in-hybrids-between-xenopus-borealis-and-x-muelleri-2n-36
#8
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
https://www.readbyqxmd.com/read/27714796/genomic-imprinting-disrupted-placental-expression-and-speciation
#9
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...
December 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27683095/human-transcription-factors-in-yeast-the-fruitful-examples-of-p53-and-nf-%C3%B0%C2%BAb
#10
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
https://www.readbyqxmd.com/read/27626696/molecular-alterations-and-tumor-suppressive-function-of-the-dusp22-dual-specificity-phosphatase-22-gene-in-peripheral-t-cell-lymphoma-subtypes
#11
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
https://www.readbyqxmd.com/read/27529977/-silencing-of-dominant-genes-in-heterozygous-genotypes-of-interspecific-hybrids-fagopyrum-esculentum-moench-x-c2026-f-homotropicum-ohnishi
#12
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
https://www.readbyqxmd.com/read/27281036/loss-of-epithelial-fam20a-in-mice-causes-amelogenesis-imperfecta-tooth-eruption-delay-and-gingival-overgrowth
#13
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
https://www.readbyqxmd.com/read/27280270/derivation-of-hybrid-es-cell-lines-from-two-different-strains-of-mice
#14
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
https://www.readbyqxmd.com/read/27265867/function-of-the-c-elegans-t-box-factor-tbx-2-depends-on-interaction-with-the-unc-37-groucho-corepressor
#15
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
https://www.readbyqxmd.com/read/27149159/the-ethylene-biosynthesis-gene-citacs4-regulates-monoecy-andromonoecy-in-watermelon-citrullus-lanatus
#16
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
https://www.readbyqxmd.com/read/27095822/in-vitro-corticogenesis-from-embryonic-stem-cells-recapitulates-the-in-vivo-epigenetic-control-of-imprinted-gene-expression
#17
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
https://www.readbyqxmd.com/read/26975355/ino80-is-essential-for-proximal-distal-axis-asymmetry-in-part-by-regulating-bmp4-expression
#18
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
https://www.readbyqxmd.com/read/26968737/ap-2%C3%AE-is-a-downstream-effector-of-pitx2-required-to-specify-endothelium-and-establish-angiogenic-privilege-during-corneal-development
#19
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
https://www.readbyqxmd.com/read/26892237/genetic-basis-of-hindlimb-loss-in-a-naturally-occurring-vertebrate-model
#20
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
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