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gene expression in embryonic development

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https://www.readbyqxmd.com/read/27922056/identification-and-functional-analysis-of-long-intergenic-noncoding-rna-genes-in-porcine-pre-implantation-embryonic-development
#1
Jingyu Li, Zhengling Gao, Xingyu Wang, Hongbo Liu, Yan Zhang, Zhonghua Liu
Genome-wide transcriptome studies have identified thousands of long intergenic noncoding RNAs (lincRNAs), some of which play important roles in pre-implantation embryonic development (PED). Pig is an ideal model for reproduction, however, porcine lincRNAs are still poorly characterized and it is unknown if they are associated with porcine PED. Here we reconstructed 195,531 transcripts in 122,007 loci, and identified 7,618 novel lincRNAs from 4,776 loci based on published RNA-seq data. These lincRNAs show low exon number, short length, low expression level, tissue-specific expression and cis-acting, which is consistent with previous reports in other species...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920155/sos2-and-acp1-loci-identified-through-large-scale-exome-chip-analysis-regulate-kidney-development-and-function
#2
Man Li, Yong Li, Olivia Weeks, Vladan Mijatovic, Alexander Teumer, Jennifer E Huffman, Gerard Tromp, Christian Fuchsberger, Mathias Gorski, Leo-Pekka Lyytikäinen, Teresa Nutile, Sanaz Sedaghat, Rossella Sorice, Adrienne Tin, Qiong Yang, Tarunveer S Ahluwalia, Dan E Arking, Nathan A Bihlmeyer, Carsten A Böger, Robert J Carroll, Daniel I Chasman, Marilyn C Cornelis, Abbas Dehghan, Jessica D Faul, Mary F Feitosa, Giovanni Gambaro, Paolo Gasparini, Franco Giulianini, Iris Heid, Jinyan Huang, Medea Imboden, Anne U Jackson, Janina Jeff, Min A Jhun, Ronit Katz, Annette Kifley, Tuomas O Kilpeläinen, Ashish Kumar, Markku Laakso, Ruifang Li-Gao, Kurt Lohman, Yingchang Lu, Reedik Mägi, Giovanni Malerba, Evelin Mihailov, Karen L Mohlke, Dennis O Mook-Kanamori, Antonietta Robino, Douglas Ruderfer, Erika Salvi, Ursula M Schick, Christina-Alexandra Schulz, Albert V Smith, Jennifer A Smith, Michela Traglia, Laura M Yerges-Armstrong, Wei Zhao, Mark O Goodarzi, Aldi T Kraja, Chunyu Liu, Jennifer Wessel, Eric Boerwinkle, Ingrid B Borecki, Jette Bork-Jensen, Erwin P Bottinger, Daniele Braga, Ivan Brandslund, Jennifer A Brody, Archie Campbell, David J Carey, Cramer Christensen, Josef Coresh, Errol Crook, Gary C Curhan, Daniele Cusi, Ian H de Boer, Aiko P J de Vries, Joshua C Denny, Olivier Devuyst, Albert W Dreisbach, Karlhans Endlich, Tõnu Esko, Oscar H Franco, Tibor Fulop, Glenn S Gerhard, Charlotte Glümer, Omri Gottesman, Niels Grarup, Vilmundur Gudnason, Tamara B Harris, Caroline Hayward, Lynne Hocking, Albert Hofman, Frank B Hu, Lise Lotte N Husemoen, Rebecca D Jackson, Torben Jørgensen, Marit E Jørgensen, Mika Kähönen, Sharon L R Kardia, Wolfgang König, Charles Kooperberg, Jennifer Kriebel, Lenore J Launer, Torsten Lauritzen, Terho Lehtimäki, Daniel Levy, Pamela Linksted, Allan Linneberg, Yongmei Liu, Ruth J F Loos, Antonio Lupo, Christine Meisinger, Olle Melander, Andres Metspalu, Paul Mitchell, Matthias Nauck, Peter Nürnberg, Marju Orho-Melander, Afshin Parsa, Oluf Pedersen, Annette Peters, Ulrike Peters, Ozren Polasek, David Porteous, Nicole M Probst-Hensch, Bruce M Psaty, Lu Qi, Olli T Raitakari, Alex P Reiner, Rainer Rettig, Paul M Ridker, Fernando Rivadeneira, Jacques E Rossouw, Frank Schmidt, David Siscovick, Nicole Soranzo, Konstantin Strauch, Daniela Toniolo, Stephen T Turner, André G Uitterlinden, Sheila Ulivi, Dinesh Velayutham, Uwe Völker, Henry Völzke, Melanie Waldenberger, Jie Jin Wang, David R Weir, Daniel Witte, Helena Kuivaniemi, Caroline S Fox, Nora Franceschini, Wolfram Goessling, Anna Köttgen, Audrey Y Chu
Genome-wide association studies have identified >50 common variants associated with kidney function, but these variants do not fully explain the variation in eGFR. We performed a two-stage meta-analysis of associations between genotypes from the Illumina exome array and eGFR on the basis of serum creatinine (eGFRcrea) among participants of European ancestry from the CKDGen Consortium (nStage1: 111,666; nStage2: 48,343). In single-variant analyses, we identified single nucleotide polymorphisms at seven new loci associated with eGFRcrea (PPM1J, EDEM3, ACP1, SPEG, EYA4, CYP1A1, and ATXN2L; PStage1<3...
December 5, 2016: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/27915011/determinants-of-orofacial-clefting-i-effects-of-5-aza-2-deoxycytidine-on-cellular-processes-and-gene-expression-during-development-of-the-first-branchial-arch
#3
Partha Mukhopadhyay, Ratnam S Seelan, Francine Rezzoug, Dennis R Warner, Irina A Smolenkova, Guy Brock, M Michele Pisano, Robert M Greene
In this study, we identify gene targets and cellular events mediating the teratogenic action(s) of 5-Aza-2'-deoxycytidine (AzaD), an inhibitor of DNA methylation, on secondary palate development. Exposure of pregnant mice (on gestation day (GD) 9.5) to AzaD for 12hrs resulted in the complete penetrance of cleft palate (CP) in fetuses. Analysis of cells of the embryonic first branchial arch (1-BA), in fetuses exposed to AzaD, revealed: 1) significant alteration in expression of genes encoding several morphogenetic factors, cell cycle inhibitors and regulators of apoptosis; 2) a decrease in cell proliferation; and, 3) an increase in apoptosis...
November 30, 2016: Reproductive Toxicology
https://www.readbyqxmd.com/read/27914912/identification-of-foxj1-effectors-during-ciliogenesis-in-the-foetal-respiratory-epithelium-and-embryonic-left-right-organiser-of-the-mouse
#4
Michael Stauber, Marina Weidemann, Oliver Dittrich-Breiholz, Katharina Lobschat, Leonie Alten, Michaela Mai, Anja Beckers, Michael Kracht, Achim Gossler
Formation of motile cilia in vertebrate embryos is essential for proper development and tissue function. Key regulators of motile ciliogenesis are the transcription factors FOXJ1 and NOTO, which are conserved throughout vertebrates. Downstream target genes of FOXJ1 have been identified in a variety of species, organs and cultured cell lines; in murine embryonic and foetal tissues, however, FOXJ1 and NOTO effectors have not been comprehensively analysed and our knowledge of the downstream genetic programme driving motile ciliogenesis in the mammalian lung and ventral node is fragmentary...
November 30, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27912755/establishment-of-high-reciprocal-connectivity-between-clonal-cortical-neurons-is-regulated-by-the-dnmt3b-dna-methyltransferase-and-clustered-protocadherins
#5
Etsuko Tarusawa, Makoto Sanbo, Atsushi Okayama, Toshio Miyashita, Takashi Kitsukawa, Teruyoshi Hirayama, Takahiro Hirabayashi, Sonoko Hasegawa, Ryosuke Kaneko, Shunsuke Toyoda, Toshihiro Kobayashi, Megumi Kato-Itoh, Hiromitsu Nakauchi, Masumi Hirabayashi, Takeshi Yagi, Yumiko Yoshimura
BACKGROUND: The specificity of synaptic connections is fundamental for proper neural circuit function. Specific neuronal connections that underlie information processing in the sensory cortex are initially established without sensory experiences to a considerable extent, and then the connections are individually refined through sensory experiences. Excitatory neurons arising from the same single progenitor cell are preferentially connected in the postnatal cortex, suggesting that cell lineage contributes to the initial wiring of neurons...
December 2, 2016: BMC Biology
https://www.readbyqxmd.com/read/27909049/control-of-secreted-protein-gene-expression-and-the-mammalian-secretome-by-the-metabolic-regulator-pgc-1%C3%AE
#6
Neri Minsky, Robert G Roeder
Secreted proteins serve pivotal roles in the development of multicellular organisms, acting as structural matrix, extracellular enzymes and signal molecules. However, how the secretome is regulated remains incompletely understood. Here we demonstrate, unexpectedly, that peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α), a critical transcriptional co-activator of metabolic gene expression, functions to down-regulate expression of diverse genes encoding secreted molecules and extracellular matrix (ECM) components to modulate the secretome...
December 1, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27907214/derivation-of-induced-trophoblast-cell-lines-in-cattle-by-doxycycline-inducible-piggybac-vectors
#7
Takamasa Kawaguchi, Dooseon Cho, Masafumi Hayashi, Tomoyuki Tsukiyama, Koji Kimura, Shuichi Matsuyama, Naojiro Minami, Masayasu Yamada, Hiroshi Imai
Trophectoderm lineage specification is one of the earliest differentiation events in mammalian development. The trophoblast lineage, which is derived from the trophectoderm, mediates implantation and placental formation. However, the processes involved in trophoblastic differentiation and placental formation in cattle remain unclear due to interspecies differences when compared with other model systems and the small repertoire of available trophoblast cell lines. Here, we describe the generation of trophoblast cell lines (biTBCs) from bovine amnion-derived cells (bADCs) using an induced pluripotent stem cell technique...
2016: PloS One
https://www.readbyqxmd.com/read/27907180/deep-staged-transcriptomic-resources-for-the-novel-coleopteran-models-atrachya-menetriesi-and-callosobruchus-maculatus
#8
Matthew A Benton, Nathan J Kenny, Kai H Conrads, Siegfried Roth, Jeremy A Lynch
Despite recent efforts to sample broadly across metazoan and insect diversity, current sequence resources in the Coleoptera do not adequately describe the diversity of the clade. Here we present deep, staged transcriptomic data for two coleopteran species, Atrachya menetriesi (Faldermann 1835) and Callosobruchus maculatus (Fabricius 1775). Our sampling covered key stages in ovary and early embryonic development in each species. We utilized this data to build combined assemblies for each species which were then analysed in detail...
2016: PloS One
https://www.readbyqxmd.com/read/27906584/effects-of-the-transforming-growth-factor-beta-signaling-pathway-on-the-differentiation-of-chicken-embryonic-stem-cells-into-male-germ-cells
#9
Yani Zhang, Yingjie Wang, Qisheng Zuo, Dong Li, Wenhui Zhang, Chao Lian, Beibei Tang, Tianrong Xiao, Man Wang, Kehua Wang, Bichun Li
The objectives of the present study were to screen for key gene and signaling pathways involved in the production of male germ cells in poultry and to investigate the effects of the transforming growth factor beta (TGF-β) signaling pathway on the differentiation of chicken embryonic stem cells (ESCs) into male germ cells. The ESCs, primordial germ cells, and spermatogonial stem cells (SSCs) were sorted using flow cytometry for RNA sequencing (RNA-seq) technology. Male chicken ESCs were induced using 40 ng/mL of bone morphogenetic protein 4 (BMP4)...
November 2016: Cellular Reprogramming
https://www.readbyqxmd.com/read/27906186/preimplantation-factor-is-an-anti-apoptotic-effector-in-human-trophoblasts-involving-p53-signaling-pathway
#10
Hadia Moindjie, Esther Dos Santos, Rita-Josiane Gouesse, Nelly Swierkowski-Blanchard, Valérie Serazin, Eytan R Barnea, François Vialard, Marie-Noëlle Dieudonné
From the earliest stages of gestation, embryonic-maternal interaction has a key role in a successful pregnancy. Various factors present during gestation may significantly influence this type of juxta/paracrine interaction. PreImplantation Factor (PIF) is a recently identified factor with activity at the fetomaternal interface. PIF is secreted by viable embryos and directly controls placental development by increasing the invasive capacity of human extravillous trophoblasts (EVTs). To further specify PIF's role in the human placenta, we analyzed the genome-wide expression profile of the EVT in the presence of a synthetic PIF analog (sPIF)...
December 1, 2016: Cell Death & Disease
https://www.readbyqxmd.com/read/27904930/micrornas-in-bone-diseases
#11
REVIEW
L Gennari, S Bianciardi, D Merlotti
MicroRNAs are small, noncoding single-stranded RNAs that have emerged as important posttranscriptional regulators of gene expression, with an essential role in vertebrate development and different biological processes. This review highlights the recent advances in the function of miRNAs and their roles in bone remodeling and bone diseases. MicroRNAs (miRNAs) are a class of small (∼22 nt), noncoding single-stranded RNAs that have emerged as important posttranscriptional regulators of gene expression. They are essential for vertebrate development and play critical roles in different biological processes related to cell differentiation, activity, metabolism, and apoptosis...
November 30, 2016: Osteoporosis International
https://www.readbyqxmd.com/read/27904699/generation-of-induced-pluripotent-stem-cells-with-high-efficiency-from-human-embryonic-renal-cortical-cells
#12
Ling Yao, Ruifang Chen, Pu Wang, Qi Zhang, Hailiang Tang, Huaping Sun
Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) emerges as a prospective therapeutic angle in regenerative medicine and a tool for drug screening. Although increasing numbers of iPSCs from different sources have been generated, there has been limited progress in yield of iPSC. Here, we show that four Yamanaka factors Oct4, Sox2, Klf4 and c-Myc can convert human embryonic renal cortical cells (hERCCs) to pluripotent stem cells with a roughly 40-fold higher reprogramming efficiency compared with that of adult human dermal fibroblasts...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27904015/deletion-of-conserved-sequences-in-ig-dmr-at-dlk1-gtl2-locus-suggests-their-involvement-in-expression-of-paternally-expressed-genes-in-mice
#13
Takeshi Saito, Satoshi Hara, Moe Tamano, Hiroshi Asahara, Shuji Takada
Expression regulation of the Dlk1-Dio3 imprinted domain by the intergenic differentially methylated region (IG-DMR) is essential for normal embryonic development in mammals. In this study, we investigated conserved IG-DMR genomic sequences in eutherians to elucidate their role in genomic imprinting of the Dlk1-Dio3 domain. Using a comparative genomics approach, we identified three highly conserved sequences in IG-DMR. To elucidate the functions of these sequences in vivo, we generated mutant mice lacking each of the identified highly conserved sequences using the CRISPR/Cas9 system...
December 1, 2016: Journal of Reproduction and Development
https://www.readbyqxmd.com/read/27903222/sustained-elabela-gene-therapy-in-high-salt-induced-hypertensive-rats
#14
Claire A Schreiber, Sara J Holditch, Alex Generous, Yasuhiro Ikeda
BACKGROUND: Elabela (ELA) is a recently identified apelin receptor agonist essential for cardiac development, but its biology and therapeutic potential are unclear. In humans ELA transcripts are detected in embryonic stem cells, induced pluripotent stem cells, kidney, heart and blood vessels. ELA through the apelin receptor promotes angiogenesis in vitro, relaxes murine aortic blood vessels and attenuates high blood pressure in vivo. The apelin receptor when bound to its original ligand, apelin, exerts peripheral vasodilatory and positive inotropic effects, conferring cardioprotection in vivo...
November 21, 2016: Current Gene Therapy
https://www.readbyqxmd.com/read/27902763/temperature-shift-alters-dna-methylation-and-histone-modification-patterns-in-gonadal-aromatase-cyp19a1-gene-in-species-with-temperature-dependent-sex-determination
#15
Yuiko Matsumoto, Brette Hannigan, David Crews
The environment surrounding the embryos has a profound impact on the developmental process and phenotypic outcomes of the organism. In species with temperature-dependent sex determination, gonadal sex is determined by the incubation temperature of the eggs. A mechanistic link between temperature and transcriptional regulation of developmental genes, however, remains elusive. In this study, we examine the changes in DNA methylation and histone modification patterns of the aromatase (cyp19a1) gene in embryonic gonads of red-eared slider turtles (Trachemys scripta) subjected to a temperature shift during development...
2016: PloS One
https://www.readbyqxmd.com/read/27899656/idp-ase-haplotyping-and-quantifying-allele-specific-expression-at-the-gene-and-gene-isoform-level-by-hybrid-sequencing
#16
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/27899417/emerging-roles-of-glis3-in-neonatal-diabetes-type-1-and-type-2-diabetes
#17
Xianjie Wen, Yisheng Yang
GLI-similar 3 (GLIS3), a member of the Krüppel-like zinc finger protein subfamily, is predominantly expressed in the pancreas, thyroid, and kidney. Glis3 mRNA can be initially detected in mouse pancreas at embryonic day 11.5 and is largely restricted to β cells, pancreatic polypeptide-expressing cells, as well as ductal cells at later stage of pancreas development. Mutations in GLIS3 cause a neonatal diabetes syndrome, characterized by neonatal diabetes, congenital hypothyroidism, and polycystic kidney. Importantly, genome-wide association studies showed that variations of GLIS3 are strongly associated with both type 1 diabetes (T1D) and type 2 diabetes (T2D) in multiple populations...
November 29, 2016: Journal of Molecular Endocrinology
https://www.readbyqxmd.com/read/27899062/scleraxis-is-essential-for-tendon-differentiation-by-equine-embryonic-stem-cells-and-in-equine-fetal-tenocytes
#18
Emma Bavin, Francesca Atkinson, Tom Barsby, Debbie Guest
The transcription factor scleraxis is required for tendon development and is upregulated during embryonic stem cell (ESC) differentiation into tenocytes. However, its role beyond early embryonic development is not defined. We utilised a short hairpin RNA to knockdown scleraxis expression in ESCs, adult and fetal tenocytes. No effect on growth or morphology was observed in 2D cultures. However, scleraxis knockdown in fetal tenocytes significantly reduced COL1A1, COMP and SOX9 gene expression. Scleraxis knockdown in adult tenocytes had no effect on the expression of these genes...
November 29, 2016: Stem Cells and Development
https://www.readbyqxmd.com/read/27898696/regulation-of-gonad-morphogenesis-in-drosophila-melanogaster-by-btb-family-transcription-factors
#19
Diane Silva, Kenneth W Olsen, Magdalena N Bednarz, Andrew Droste, Christopher P Lenkeit, Edwin Chaharbakhshi, Emily R Temple-Wood, Jennifer C Jemc
During embryogenesis, primordial germ cells (PGCs) and somatic gonadal precursor cells (SGPs) migrate and coalesce to form the early gonad. A failure of the PGCs and SGPs to form a gonad with the proper architecture not only affects germ cell development, but can also lead to infertility. Therefore, it is critical to identify the molecular mechanisms that function within both the PGCs and SGPs to promote gonad morphogenesis. We have characterized the phenotypes of two genes, longitudinals lacking (lola) and ribbon (rib), that are required for the coalescence and compaction of the embryonic gonad in Drosophila melanogaster...
2016: PloS One
https://www.readbyqxmd.com/read/27898587/maternal-epigenetics-and-fetal-and-neonatal-growth
#20
Sofia Kitsiou-Tzeli, Maria Tzetis
PURPOSE OF REVIEW: The article provides an update on new insights of factors altering inherited maternal epigenome that ultimately affect fetal and neonatal growth. RECENT FINDINGS: A number of new publications have identified mechanisms through which maternal nutrition, environmental exposures such as stress and toxic substances altering expression of imprinted genes during pregnancy can influence fetal and neonatal phenotype and susceptibility to disease development later in life...
November 24, 2016: Current Opinion in Endocrinology, Diabetes, and Obesity
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