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Hybrid allele expression development

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https://www.readbyqxmd.com/read/29149037/development-of-novel-polymorphic-est-ssr-markers-in-bailinggu-pleurotus-tuoliensis-for-crossbreeding
#1
Yueting Dai, Wenying Su, Chentao Yang, Bing Song, Yu Li, Yongping Fu
Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu). However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR) markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29138238/a-resource-for-the-allele-specific-analysis-of-dna-methylation-at-multiple-genomically-imprinted-loci-in-mice
#2
Jadiel A Wasson, Onur Birol, David J Katz
Genomically imprinted loci are expressed mono-allelically dependent upon the parent of origin. Their regulation not only illuminates how chromatin regulates gene expression but also how chromatin can be reprogrammed every generation. Because of their distinct parent of origin regulation, analysis of imprinted loci can be difficult. Single nucleotide polymorphisms (SNPs) are required to accurately assess these elements allele-specifically. However, publicly available SNP databases lack robust verification, making analysis of imprinting difficult...
November 14, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29101321/contribution-of-epigenetic-landscapes-and-transcription-factors-to-x-chromosome-reactivation-in-the-inner-cell-mass
#3
Maud Borensztein, Ikuhiro Okamoto, Laurène Syx, Guillaume Guilbaud, Christel Picard, Katia Ancelin, Rafael Galupa, Patricia Diabangouaya, Nicolas Servant, Emmanuel Barillot, Azim Surani, Mitinori Saitou, Chong-Jian Chen, Konstantinos Anastassiadis, Edith Heard
X-chromosome inactivation is established during early development. In mice, transcriptional repression of the paternal X-chromosome (Xp) and enrichment in epigenetic marks such as H3K27me3 is achieved by the early blastocyst stage. X-chromosome inactivation is then reversed in the inner cell mass. The mechanisms underlying Xp reactivation remain enigmatic. Using in vivo single-cell approaches (allele-specific RNAseq, nascent RNA-fluorescent in situ hybridization and immunofluorescence), we show here that different genes are reactivated at different stages, with more slowly reactivated genes tending to be enriched in H3meK27...
November 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/29101279/extreme-suppression-of-lateral-floret-development-by-a-single-amino-acid-change-in-the-vrs1-transcription-factor
#4
Shun Sakuma, Udda Lundqvist, Yusuke Kakei, Venkatasubbu Thirulogachandar, Takako Suzuki, Kiyosumi Hori, Jianzhong Wu, Akemi Tagiri, Twan Rutten, Ravi Koppolu, Yukihisa Shimada, Kelly Houston, William T B Thomas, Robbie Waugh, Thorsten Schnurbusch, Takao Komatsuda
Increasing grain yield is an endless challenge for cereal crop breeding. In barley, grain number is mainly controlled by Six-rowed spike 1 (Vrs1) that encodes a homeodomain leucine zipper class I transcription factor. However, little is known about the genetic basis of grain size. Here we show that extreme suppression of lateral florets contributes to enlarged grains in deficiens barley. Through a combination of fine mapping and resequencing deficiens mutants we have identified that a single amino acid substitution at a putative phosphorylation site in VRS1 is responsible for the deficiens phenotype...
November 3, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29075433/differences-in-the-genetic-control-of-early-egg-development-and-reproduction-between-c-elegans-and-its-parthenogenetic-relative-d-coronatus
#5
Christopher Kraus, Philipp H Schiffer, Hiroshi Kagoshima, Hideaki Hiraki, Theresa Vogt, Michael Kroiher, Yuji Kohara, Einhard Schierenberg
BACKGROUND: The free-living nematode Diploscapter coronatus is the closest known relative of Caenorhabditis elegans with parthenogenetic reproduction. It shows several developmental idiosyncracies, for example concerning the mode of reproduction, embryonic axis formation and early cleavage pattern (Lahl et al. in Int J Dev Biol 50:393-397, 2006). Our recent genome analysis (Hiraki et al. in BMC Genomics 18:478, 2017) provides a solid foundation to better understand the molecular basis of developmental idiosyncrasies in this species in an evolutionary context by comparison with selected other nematodes...
2017: EvoDevo
https://www.readbyqxmd.com/read/29075260/vaccine-containing-the-three-allelic-variants-of-the-plasmodium-vivax-circumsporozoite-antigen-induces-protection-in-mice-after-challenge-with-a-transgenic-rodent-malaria-parasite
#6
Alba Marina Gimenez, Luciana Chagas Lima, Katia Sanches Françoso, Priscila M A Denapoli, Raquel Panatieri, Daniel Y Bargieri, Jean-Michel Thiberge, Chiara Andolina, Francois Nosten, Laurent Renia, Ruth S Nussenzweig, Victor Nussenzweig, Rogerio Amino, Mauricio M Rodrigues, Irene S Soares
Plasmodium vivax is the most common species that cause malaria outside of the African continent. The development of an efficacious vaccine would contribute greatly to control malaria. Recently, using bacterial and adenoviral recombinant proteins based on the P. vivax circumsporozoite protein (CSP), we demonstrated the possibility of eliciting strong antibody-mediated immune responses to each of the three allelic forms of P. vivax CSP (PvCSP). In the present study, recombinant proteins representing the PvCSP alleles (VK210, VK247, and P...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29058037/epigenetic-regulation-of-agronomical-traits-in-brassicaceae
#7
REVIEW
Etsuko Itabashi, Kenji Osabe, Ryo Fujimoto, Tomohiro Kakizaki
Epigenetic regulation, covalent modification of DNA and changes in histone proteins are closely linked to plant development and stress response through flexibly altering the chromatin structure to regulate gene expression. In this review, we will illustrate the importance of epigenetic influences by discussing three agriculturally important traits of Brassicaceae. (1) Vernalization, an acceleration of flowering by prolonged cold exposure regulated through epigenetic silencing of a central floral repressor, FLOWERING LOCUS C...
October 20, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29040498/genome-stability-of-bovine-in-vivo-conceived-cleavage-stage-embryos-is-higher-compared-to-in-vitro-produced-embryos
#8
Olga Tšuiko, Maaike Catteeuw, Masoud Zamani Esteki, Aspasia Destouni, Osvaldo Bogado Pascottini, Urban Besenfelder, Vitezslav Havlicek, Katrien Smits, Ants Kurg, Andres Salumets, Thomas D'Hooghe, Thierry Voet, Ann Van Soom, Joris Robert Vermeesch
STUDY QUESTION: Is the rate and nature of chromosome instability (CIN) similar between bovine in vivo-derived and in vitro-cultured cleavage-stage embryos? SUMMARY ANSWER: There is a major difference regarding chromosome stability of in vivo-derived and in vitro-cultured embryos, as CIN is significantly lower in in vivo-derived cleavage-stage embryos compared to in vitro-cultured embryos. WHAT IS KNOWN ALREADY: CIN is common during in vitro embryogenesis and is associated with early embryonic loss in humans, but the stability of in vivo-conceived cleavage-stage embryos remains largely unknown...
November 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28912827/development-of-taqman-probes-targeting-the-four-major-celiac-disease-epitopes-found-in-%C3%AE-gliadin-sequences-of-spelt-triticum-aestivum-ssp-spelta-and-bread-wheat-triticum-aestivum-ssp-aestivum
#9
Benjamin Dubois, Pierre Bertin, Yordan Muhovski, Emmanuelle Escarnot, Dominique Mingeot
BACKGROUND: Celiac disease (CD) is caused by specific sequences of gluten proteins found in cereals such as bread wheat (Triticum aestivum ssp. aestivum) and spelt (T. aestivum ssp. spelta). Among them, the α-gliadins display the highest immunogenicity, with four T-cell stimulatory epitopes. The toxicity of each epitope sequence can be reduced or even suppressed according to the allelic form of each sequence. One way to address the CD problem would be to make use of this allelic variability in breeding programs to develop safe varieties, but tools to track the presence of toxic epitopes are required...
2017: Plant Methods
https://www.readbyqxmd.com/read/28912108/leptospira-borgpetersenii-hybrid-leucine-rich-repeat-protein-cloning-and-expression-immunogenic-identification-and-molecular-docking-evaluation
#10
Tepyuda Sritrakul, Supachai Nitipan, Worawidh Wajjwalku, Anchalee La-Ard, Chattip Suphatpahirapol, Wimol Petkarnjanapong, Boonsong Ongphiphadhanakul, Siriwan Prapong
Leptospirosis is an important zoonotic disease, and the major outbreak of this disease in Thailand in 1999 was due largely to the Leptospira borgpetersenii serovar Sejroe. Identification of the leucine-rich repeat (LRR) LBJ_2271 protein containing immunogenic epitopes and the discovery of the LBJ_2271 ortholog in Leptospira serovar Sejroe, KU_Sej_R21_2271, led to further studies of the antigenic immune properties of KU_Sej_LRR_2271. The recombinant hybrid (rh) protein was created and expressed from a hybrid PCR fragment of KU_Sej_R21_2271 fused with DNA encoding the LBJ_2271 signal sequence for targeting protein as a membrane-anchoring protein...
November 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28874509/the-maize-imprinted-gene-floury3-encodes-a-platz-protein-required-for-trna-and-5s-rrna-transcription-through-interaction-with-rna-polymerase-iii
#11
Qi Li, Jiechen Wang, Jianwei Ye, Xixi Zheng, Xiaoli Xiang, Changsheng Li, Miaomiao Fu, Qiong Wang, Zhi-Yong Zhang, Yongrui Wu
Maize (Zea mays) floury3 (fl3) is a classic semi-dominant negative mutant that exhibits severe defects in the endosperm but fl3 plants otherwise appear normal. We cloned the fl3 gene and determined that it encodes a PLATZ (plant AT-rich sequence- and zinc-binding) protein. The mutation in fl3 resulted in an Asn to His replacement in the conserved PLATZ domain, creating a dominant allele. Fl3 is specifically expressed in starchy endosperm cells and regulated by genomic imprinting, which leads to the suppressed expression of fl3 when transmitted through the male, perhaps as a consequence the semi-dominant behavior...
September 5, 2017: Plant Cell
https://www.readbyqxmd.com/read/28864017/maternal-grb10-microdeletion-is-a-novel-cause-of-cystic-placenta-spectrum-of-genomic-changes-in-the-etiology-of-enlarged-cystic-placenta
#12
Urvashi Surti, Svetlana Yatsenko, Jie Hu, Daniel Bellissimo, W Tony Parks, Lori Hoffner
INTRODUCTION: The genetics and pathology of diploid complete and triploid partial hydatidiform moles have been well established. Enlarged cystic placenta often indicates an underlying etiology and is frequently associated with adverse pregnancy outcome. Several imprinted genes are strongly expressed in placental tissues and essential for normal placental growth and development. Disruption of these imprinted genes can lead to abnormal placental pathology and placental stunting or overgrowth...
September 2017: Placenta
https://www.readbyqxmd.com/read/28729899/evolutionary-loss-of-melanogenesis-in-the-tunicate-molgula-occulta
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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