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Hybrid allele expression development

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https://www.readbyqxmd.com/read/28729899/evolutionary-loss-of-melanogenesis-in-the-tunicate-molgula-occulta
#1
Claudia Racioppi, Maria Carmen Valoroso, Ugo Coppola, Elijah K Lowe, C Titus Brown, Billie J Swalla, Lionel Christiaen, Alberto Stolfi, Filomena Ristoratore
BACKGROUND: Analyzing close species with diverse developmental modes is instrumental for investigating the evolutionary significance of physiological, anatomical and behavioral features at a molecular level. Many examples of trait loss are known in metazoan populations living in dark environments. Tunicates are the closest living relatives of vertebrates and typically present a lifecycle with distinct motile larval and sessile adult stages. The nervous system of the motile larva contains melanized cells associated with geotactic and light-sensing organs...
2017: EvoDevo
https://www.readbyqxmd.com/read/28705894/genome-wide-analysis-of-facial-skeletal-regionalization-in-zebrafish
#2
Amjad Askary, Pengfei Xu, Lindsey Barske, Maxwell Bay, Paul Bump, Bartosz Balczerski, Michael A Bonaguidi, J Gage Crump
Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite the significance for craniofacial development, how genetic programs drive this regionalization remains incompletely understood. Here we use combinatorial labeling of zebrafish cranial neural crest-derived cells (CNCCs) to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region-specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin 1 (Edn1) signaling in the intermediate joint-forming region, yet a surprisingly minor role in ventralmost regions...
August 15, 2017: Development
https://www.readbyqxmd.com/read/28696287/genomic-architecture-of-biomass-heterosis-in-arabidopsis
#3
Mei Yang, Xuncheng Wang, Diqiu Ren, Hao Huang, Miqi Xu, Guangming He, Xing Wang Deng
Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200 Arabidopsis hybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids...
July 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28657614/genetic-analysis-of-a-hybrid-sterility-gene-that-causes-both-pollen-and-embryo-sac-sterility-in-hybrids-between-oryza-sativa-l-and-oryza-longistaminata
#4
H Chen, Z Zhao, L Liu, W Kong, Y Lin, S You, W Bai, Y Xiao, H Zheng, L Jiang, J Li, J Zhou, D Tao, J Wan
Oryza longistaminata originates from African wild rice and contains valuable traits conferring tolerance to biotic and abiotic stress. However, interspecific crosses between O. longistaminata and Oryza sativa cultivars are hindered by reproductive barriers. To dissect the mechanism of interspecific hybrid sterility, we developed a near-isogenic line (NIL) using indica variety RD23 as the recipient parent and O. longistaminata as the donor parent. Both pollen and embryo sac semi-sterility were observed in F1 hybrids between RD23 and NIL...
September 2017: Heredity
https://www.readbyqxmd.com/read/28649253/variable-level-of-dominance-of-candidate-genes-controlling-drought-functional-traits-in-maize-hybrids
#5
Ha Van Gioi, Mallana Gowdra Mallikarjuna, Mittal Shikha, Banduni Pooja, Shailendra K Jha, Prasanta K Dash, Arunkumar M Basappa, Raveendra N Gadag, Atmakuri Ramakrishna Rao, Thirunavukkarasu Nepolean
Breeding maize for drought tolerance necessitates the knowledge on tolerant genotypes, molecular basis of drought tolerance mechanism, action, and expression pattern of genes. Studying the expression pattern and gene action of candidate genes during drought stress in the hybrids will help in choosing target genes for drought tolerance breeding. In the present investigation, a set of five hybrids and their seven parents with a variable level of tolerance to drought stress was selected to study the magnitude and the direction of 52 drought-responsive candidate genes distributed across various biological functions, viz...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28555639/clonally-stable-v%C3%AE%C2%BA-allelic-choice-instructs-ig%C3%AE%C2%BA-repertoire
#6
Rena Levin-Klein, Shira Fraenkel, Michal Lichtenstein, Louise S Matheson, Osnat Bartok, Yuval Nevo, Sebastian Kadener, Anne E Corcoran, Howard Cedar, Yehudit Bergman
Although much has been done to understand how rearrangement of the Igκ locus is regulated during B-cell development, little is known about the way the variable (V) segments themselves are selected. Here we show, using B6/Cast hybrid pre-B-cell clones, that a limited number of V segments on each allele is stochastically activated as characterized by the appearance of non-coding RNA and histone modifications. The activation states are clonally distinct, stable across cell division and developmentally important in directing the Ig repertoire upon differentiation...
May 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/28424873/the-changes-in-the-reproductive-barrier-between-hexaploid-wheat-triticum-aestivum-l-and-rye-secale-cereale-l-different-states-lead-to-different-fates
#7
Natalia Tikhenko, Twan Rutten, Angelika Senula, Myroslava Rubtsova, E R Joachim Keller, Andreas Börner
The changes in the reproductive barrier between hexaploid wheat ( Triticum aestivum L.) and rye ( Secale cereale L.) can be induced using in situ embryo rescue of abnormal embryos, yielding stable fertile amphidiploid plants. In intergeneric crosses between hexaploid wheat (Triticum aestivum L.) and rye (Secale cereale L.), postzygotic barriers may occur at different stages of hybrid development. One such mechanism is embryo lethality, which is genetically determined by the interaction and expression of two incompatible genes in wheat (Eml-A1) and rye (Eml-R1)...
April 19, 2017: Planta
https://www.readbyqxmd.com/read/28381549/a-dominant-mutation-in-nuclear-receptor-interacting-protein-1-causes-urinary-tract-malformations-via-dysregulation-of-retinoic-acid-signaling
#8
Asaf Vivante, Nina Mann, Hagith Yonath, Anna-Carina Weiss, Maike Getwan, Michael M Kaminski, Tobias Bohnenpoll, Catherine Teyssier, Jing Chen, Shirlee Shril, Amelie T van der Ven, Hadas Ityel, Johanna Magdalena Schmidt, Eugen Widmeier, Stuart B Bauer, Simone Sanna-Cherchi, Ali G Gharavi, Weining Lu, Daniella Magen, Rachel Shukrun, Richard P Lifton, Velibor Tasic, Horia C Stanescu, Vincent Cavaillès, Robert Kleta, Yair Anikster, Benjamin Dekel, Andreas Kispert, Soeren S Lienkamp, Friedhelm Hildebrandt
Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause of CKD in the first three decades of life. However, for most patients with CAKUT, the causative mutation remains unknown. We identified a kindred with an autosomal dominant form of CAKUT. By whole-exome sequencing, we identified a heterozygous truncating mutation (c.279delG, p.Trp93fs*) of the nuclear receptor interacting protein 1 gene (NRIP1) in all seven affected members. NRIP1 encodes a nuclear receptor transcriptional cofactor that directly interacts with the retinoic acid receptors (RARs) to modulate retinoic acid transcriptional activity...
August 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28369525/the-mads-box-gene-agamous-like-11-is-essential-for-seed-morphogenesis-in-grapevine
#9
Jaiana Malabarba, Vanessa Buffon, Jorge E A Mariath, Marcos L Gaeta, Marcelo C Dornelas, Márcia Margis-Pinheiro, Giancarlo Pasquali, Luís F Revers
Despite the wide appreciation of seedless grapes, little is known about the molecular mechanisms that drive the stenospermocarpic seedless-type phenotype in grapevine. In order to address the molecular mechanisms that control seedlessness in grapevine, our study aimed to characterize VviAGL11, a class D MADS-box transcription factor gene that has been proposed as the major candidate gene involved in Vitis vinifera seed morphogenesis. VviAGL11 allelic variations in seeded and seedless grapevine cultivars were determined, and its correlations with allele-specific steady-state mRNA levels were investigated...
March 1, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28345808/molecular-genetic-analysis-of-the-melanoma-regulatory-locus-in-xiphophorus-interspecies-hybrids
#10
Yuan Lu, Mikki Boswell, William Boswell, Susanne Kneitz, Michael Hausmann, Barbara Klotz, Janine Regneri, Markita Savage, Angel Amores, John Postlethwait, Wesley Warren, Manfred Schartl, Ronald Walter
Development of spontaneous melanoma in Xiphophorus interspecies backcross hybrid progeny, (X. hellerii × [X. maculatus Jp 163 A × X. hellerii]) is due to Mendelian segregation of a oncogene (xmrk) and a molecularly uncharacterized locus, called R(Diff), on LG5. R(Diff) is thought to suppresses the activity of xmrk in healthy X. maculatus Jp 163 A parental species that rarely develop melanoma. To better understand the molecular genetics of R(Diff), we utilized RNA-Seq to study allele-specific gene expression of spontaneous melanoma tumors and corresponding normal skin samples derived from 15 first generation backcross (BC1 ) hybrids and 13 fifth generation (BC5 ) hybrids...
August 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28248994/hybrid-weakness-in-a-rice-interspecific-hybrid-is-nitrogen-dependent-and-accompanied-by-changes-in-gene-expression-at-both-total-transcript-level-and-parental-allele-partitioning
#11
Shuai Sun, Ying Wu, Xiuyun Lin, Jie Wang, Jiamiao Yu, Yue Sun, Yiling Miao, Qiuping Li, Karen A Sanguinet, Bao Liu
BACKGROUND: Hybrid weakness, a phenomenon opposite to heterosis, refers to inferior growth and development in a hybrid relative to its pure-line parents. Little attention has been paid to the phenomenological or mechanistic aspect of hybrid weakness, probably due to its rare occurrence. METHODOLOGY/PRINCIPAL FINDINGS: Here, using a set of interspecific triploid F1 hybrids between Oryza sativa, ssp. japonica (genome AA) and a tetraploid wild rice species, O. alta (genome, CCDD), we investigated the phenotypic and physiological differences between the F1 hybrids and their parents under normal and nitrogen-limiting conditions...
2017: PloS One
https://www.readbyqxmd.com/read/28237997/umtco1-a-hybrid-histidine-kinase-gene-is-essential-for-the-sexual-development-and-virulence-of-ustilago-maydis
#12
Yeo Hong Yun, Man Hwan Oh, Jun Young Kim, Seong Hwan Kim
Hybrid histidine kinase is part of a two-component system that is required for various stress responses and pathogenesis of pathogenic fungi. The Tco1 gene in human pathogen Cryptococcus neoformans encodes a hybrid histidine kinase and is important for pathogenesis. In this study, we identified a Tco1 homolog, UmTco1, in the maize pathogen Ustilago maydis by bioinformatics analysis. To explore the role of UmTco1 in the survival of U. maydis under environmental stresses and its pathogenesis, Δumtco1 mutants were constructed by allelic exchange...
May 28, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28188885/trpm5-expression-in-the-olfactory-epithelium
#13
Martina Pyrski, Eugenia Eckstein, Andreas Schmid, Bernd Bufe, Jan Weiss, Vladimir Chubanov, Ulrich Boehm, Frank Zufall
The Ca(2+)-activated monovalent cation channel Trpm5 is a key element in chemotransduction of taste receptor cells of the tongue, but the extent to which Trpm5 channels are expressed in olfactory sensory neurons (OSNs) of the main olfactory epithelium (MOE) of adult mice as part of a specific pheromonal detection system is debated. Here, we used a novel Trpm5-IRES-Cre knockin strain to drive Cre recombinase expression, employed previously validated Trpm5 antibodies, performed in situ hybridization experiments to localize Trpm5 RNA, and searched extensively for Trpm5 splice variants in genetically-labeled, Trpm5-expressing MOE cells...
February 8, 2017: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/28112738/landscape-of-monoallelic-dna-accessibility-in-mouse-embryonic-stem-cells-and-neural-progenitor-cells
#14
Jin Xu, Ava C Carter, Anne-Valerie Gendrel, Mikael Attia, Joshua Loftus, William J Greenleaf, Robert Tibshirani, Edith Heard, Howard Y Chang
We developed an allele-specific assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to genotype and profile active regulatory DNA across the genome. Using a mouse hybrid F1 system, we found that monoallelic DNA accessibility across autosomes was pervasive, developmentally programmed and composed of several patterns. Genetically determined accessibility was enriched at distal enhancers, but random monoallelically accessible (RAMA) elements were enriched at promoters and may act as gatekeepers of monoallelic mRNA expression...
March 2017: Nature Genetics
https://www.readbyqxmd.com/read/28055137/a-single-point-mutation-in-ms44-results-in-dominant-male-sterility-and-improves-nitrogen-use-efficiency-in-maize
#15
Tim Fox, Jason DeBruin, Kristin Haug Collet, Mary Trimnell, Joshua Clapp, April Leonard, Bailin Li, Eric Scolaro, Sarah Collinson, Kimberly Glassman, Michael Miller, Jeff Schussler, Dennis Dolan, Lu Liu, Carla Gho, Marc Albertsen, Dale Loussaert, Bo Shen
Application of nitrogen fertilizer in the past 50 years has resulted in significant increases in crop yields. However, loss of nitrogen from crop fields has been associated with negative impacts on the environment. Developing maize hybrids with improved nitrogen use efficiency is a cost-effective strategy for increasing yield sustainably. We report that a dominant male-sterile mutant Ms44 encodes a lipid transfer protein which is expressed specifically in the tapetum. A single amino acid change from alanine to threonine at the signal peptide cleavage site of the Ms44 protein abolished protein processing and impeded the secretion of protein from tapetal cells into the locule, resulting in dominant male sterility...
August 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28041834/the-hla-g-14-base-pair-deletion-allele-and-the-deletion-deletion-genotype-are-associated-with-persistent-hbe-antigenemia-in-chronic-hepatis-b-infection
#16
Sandro da Costa Ferreira, Silvana Gama Florêncio Chachá, Fernanda Fernandes Souza, Andreza Corrêa Teixeira, Rodrigo de Carvalho Santana, Neifi Hassan Saloun Deghaide, Sandra Rodrigues, Leonardo A Marano, Celso Teixeira Mendes-Junior, Leandra Naira Zambelli Ramalho, Sérgio Zucoloto, Eduardo Antônio Donadi, Ana de Lourdes Candolo Martinelli
BACKGROUND AND AIMS: HLA-G has well-recognized immunomodulatory properties, and this molecule is frequently expressed in the livers of hepatitis B virus (HBV)-infected patients. Because the HLA-G 14 bp-insertion/deletion polymorphism (rs371194629) has been associated with the magnitude of HLA-G expression, we evaluated this polymorphism in the recognized evolutionary forms of chronic HBV infection. METHODS: We studied 196 chronic HBV-infected patients (118 HBeAg-negative chronic hepatitis, 53 HBeAg-positive chronic hepatitis and 25 inactive carriers exhibiting low levels of serum HBVDNA and persistently normal ALT levels), and 202 healthy individuals...
February 2017: Human Immunology
https://www.readbyqxmd.com/read/27965404/targeted-genome-editing-in-a-quail-cell-line-using-a-customized-crispr-cas9-system
#17
Jinsoo Ahn, Joonbum Lee, Ju Yeon Park, Keon Bong Oh, Seongsoo Hwang, Chang-Won Lee, Kichoon Lee
Soon after RNA-guided Cas9 (CRISPR-associated protein 9) endonuclease opened a new era of targeted genome editing, the CRISPR/Cas9 platform began to be extensively used to modify genes in various types of cells and organisms. However, successful CRISPR/Cas9-mediated insertion/deletion (indel) mutation remains to be demonstrated in avian cell lines. The objective of this study was to design a poultry-specific CRISPR/Cas9 system to efficiently introduce targeted deletion mutation in chromosomes of the quail muscle clone 7 (QM7) cell line using a customized quail CRISPR vector...
May 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/27899656/idp-ase-haplotyping-and-quantifying-allele-specific-expression-at-the-gene-and-gene-isoform-level-by-hybrid-sequencing
#18
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...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27880012/patterns-of-gene-expression-in-developing-embryos-of-arabidopsis-hybrids
#19
Maria M Alonso-Peral, Marina Trigueros, Bjorg Sherman, Hua Ying, Jennifer M Taylor, William J Peacock, Elizabeth S Dennis
Hybrids between the Arabidopsis ecotypes C24 and Ler have high levels of hybrid vigour, or 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 (days after pollination; 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 single nucleotide polymorphisms between C24 and Ler retained the same relative allelic expression levels in the hybrids as existed in the parents...
March 2017: 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
#20
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
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