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Developmental transcriptome

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https://www.readbyqxmd.com/read/28229527/melanotransferrin-new-homolog-genes-and-their-differential-expression-during-intestinal-regeneration-in-the-sea-cucumber-holothuria-glaberrima
#1
Josué Hernández-Pasos, Griselle Valentín-Tirado, José E García-Arrarás
Melanotransferrin (MTf) is a protein associated with oncogenetic, developmental, and immune processes which function remains unclear. The MTf gene has been reported in numerous vertebrate and invertebrate species, including echinoderms. We now report the finding of four different MTfs in the transcriptome of the sea cucumber Holothuria glaberrima. Sequence studies and phylogenetic analyses were done to ascertain the similarities among the putative proteins and their relationship with other transferrin family members...
February 23, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28228259/sirt1-regulates-dna-methylation-and-differentiation-potential-of-embryonic-stem-cells-by-antagonizing-dnmt3l
#2
Jinbeom Heo, Jisun Lim, Seungun Lee, Jaeho Jeong, Hyunsook Kang, YongHwan Kim, Jeong Wook Kang, Hwan Yeul Yu, Eui Man Jeong, Kyunggon Kim, Magda Kucia, Sabine J Waigel, Wolfgang Zacharias, Yinlu Chen, In-Gyu Kim, Mariusz Z Ratajczak, Dong-Myung Shin
Embryonic stem cell (ESC) abnormalities in genome methylation hamper the utility of their therapeutic derivatives; however, the underlying mechanisms are unknown. Here, we show that the nicotinamide adenine dinucleotide (NAD)-dependent deacetylase, Sirt1, selectively prevents abnormal DNA methylation of some developmental genes in murine ESCs by antagonizing Dnmt3l. Transcriptome and DNA methylome analyses demonstrated that Sirt1-null (Sirt1(-/-)) ESCs repress expression of a subset of imprinted and germline genes concomitant with increased DNA methylation of regulatory elements...
February 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28226203/characteristic-changes-in-decidual-gene-expression-signature-in-spontaneous-term-parturition
#3
Haidy El-Azzamy, Andrea Balogh, Roberto Romero, Yi Xu, Christopher LaJeunesse, Olesya Plazyo, Zhonghui Xu, Theodore G Price, Zhong Dong, Adi L Tarca, Zoltan Papp, Sonia S Hassan, Tinnakorn Chaiworapongsa, Chong Jai Kim, Nardhy Gomez-Lopez, Nandor Gabor Than
Background: The decidua has been implicated in the "terminal pathway" of human term parturition, which is characterized by the activation of pro-inflammatory pathways in gestational tissues. However, the transcriptomic changes in the decidua leading to terminal pathway activation have not been systematically explored. This study aimed to compare the decidual expression of developmental signaling and inflammation-related genes before and after spontaneous term labor in order to reveal their involvement in this process...
February 22, 2017: Journal of Pathology and Translational Medicine
https://www.readbyqxmd.com/read/28225056/comparative-rna-seq-analysis-of-transcriptome-dynamics-during-petal-development-in-rosa-chinensis
#4
Yu Han, Huihua Wan, Tangren Cheng, Jia Wang, Weiru Yang, Huitang Pan, Qixiang Zhang
The developmental process that produces the ornate petals of the China rose (Rosa chinensis) is complex and is thought to depend on the balanced expression of a functionally diverse array of genes; however, the molecular basis of rose petal development is largely unknown. Here, petal growth of the R. chinensis cultivar 'Old Blush' was divided into four developmental stages, and RNA-seq technology was used to analyse the dynamic changes in transcription that occur as development progresses. In total, 598 million clean reads and 61,456 successfully annotated unigenes were obtained...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223441/rima-dependent-nuclear-accumulation-of-iyo-triggers-auxin-irreversible-cell-differentiation-in-arabidopsis
#5
Alfonso Muñoz, Silvina Mangano, Mary Paz González-García, Ramón Contreras, Michael B Sauer, Bert De Rybel, Dolf Weijers, José J Sánchez-Serrano, Maite Sanmartín, Enrique Rojo
The transcriptional regulator MINIYO (IYO) is essential and rate-limiting for initiating cell differentiation in Arabidopsis thaliana. Moreover, IYO moves from the cytosol into the nucleus in cells at the meristem periphery, possibly triggering their differentiation. However, the genetic mechanisms controlling IYO nuclear accumulation were unknown and the evidence that increased nuclear IYO levels trigger differentiation remained correlative. Searching for IYO interactors, we have identified RPAP2 IYO Mate (RIMA), a homologue of yeast and human proteins linked to nuclear import of selective cargo...
February 21, 2017: Plant Cell
https://www.readbyqxmd.com/read/28223401/transcriptome-analyses-of-rhesus-monkey-pre-implantation-embryos-reveal-a-reduced-capacity-for-dna-double-strand-break-repair-in-primate-oocytes-and-early-embryos
#6
Xinyi Wang, Denghui Liu, Dajian He, Shengbo Suo, Xian Xia, Xiechao He, Jing-Dong Han, Ping Zheng
Pre-implantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA), and cell fate commitment, most of which remain mechanistically unclear in primates. In addition, primates display a high rate of embryo wastage without any clear molecular basis. Understanding the factors involved in genome reprogramming and ZGA will help the generation of induced pluripotent stem cells with high efficiency. Moreover, explaining the molecular basis responsible for embryo wastage in primates will greatly expand our knowledge of species evolution...
February 21, 2017: Genome Research
https://www.readbyqxmd.com/read/28219335/stress-responsive-pathways-and-small-rna-changes-distinguish-variable-developmental-phenotypes-caused-by-msh1-loss
#7
Mon-Ray Shao, Sunil Kumar Kenchanmane Raju, John D Laurie, Robersy Sanchez, Sally A Mackenzie
BACKGROUND: Proper regulation of nuclear-encoded, organelle-targeted genes is crucial for plastid and mitochondrial function. Among these genes, MutS Homolog 1 (MSH1) is notable for generating an assortment of mutant phenotypes with varying degrees of penetrance and pleiotropy. Stronger phenotypes have been connected to stress tolerance and epigenetic changes, and in Arabidopsis T-DNA mutants, two generations of homozygosity with the msh1 insertion are required before severe phenotypes begin to emerge...
February 20, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28212397/a-targeted-gene-expression-platform-allows-for-rapid-analysis-of-chemical-induced-antioxidant-mrna-expression-in-zebrafish-larvae
#8
Margaret G Mills, Evan P Gallagher
Chemical-induced oxidative stress and the biochemical pathways that protect against oxidative damage are of particular interest in the field of toxicology. To rapidly identify oxidative stress-responsive gene expression changes in zebrafish, we developed a targeted panel of antioxidant genes using the Affymetrix QuantiGene Plex (QGP) platform. The genes contained in our panel include eight putative Nrf2 (Nfe2l2a)-dependent antioxidant genes (hmox1a, gstp1, gclc, nqo1, prdx1, gpx1a, sod1, sod2), a stress response gene (hsp70), an inducible DNA damage repair gene (gadd45bb), and three reference genes (actb1, gapdh, hprt1)...
2017: PloS One
https://www.readbyqxmd.com/read/28209181/de-novo-sequencing-and-comparative-transcriptome-analysis-of-adventitious-root-development-induced-by-exogenous-indole-3-butyric-acid-in-cuttings-of-tetraploid-black-locust
#9
Jine Quan, Seng Meng, Erhui Guo, Sheng Zhang, Zhong Zhao, Xitian Yang
BACKGROUND: Indole-3-butyric acid (IBA) is applied to the cuttings of various plant species to induce formation of adventitious roots (ARs) in commercial settings. Tetraploid black locust is an attractive ornamental tree that is drought resistant, sand tolerant, can prevent sand erosion and has various commercial uses. To further elucidate the mechanisms of AR formation, we used Illumina sequencing to analyze transcriptome dynamics and differential gene expression at four developmental stages in control (CK) and IBA-treated groups...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28208659/developmental-origins-of-chronic-kidney-disease-should-we-focus-on-early-life
#10
REVIEW
You-Lin Tain, Chien-Ning Hsu
Chronic kidney disease (CKD) is becoming a global burden, despite recent advances in management. CKD can begin in early life by so-called "developmental programming" or "developmental origins of health and disease" (DOHaD). Early-life insults cause structural and functional changes in the developing kidney, which is called renal programming. Epidemiological and experimental evidence supports the proposition that early-life adverse events lead to renal programming and make subjects vulnerable to developing CKD and its comorbidities in later life...
February 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28203244/pistil-transcriptome-analysis-to-disclose-genes-and-gene-products-related-to-aposporous-apomixis-in-hypericum-perforatum-l
#11
Giulio Galla, Sara Zenoni, Linda Avesani, Lothar Altschmied, Paride Rizzo, Timothy F Sharbel, Gianni Barcaccia
Unlike sexual reproduction, apomixis encompasses a number of reproductive strategies, which permit maternal genome inheritance without genetic recombination and syngamy. The key biological features of apomixis are the circumvention of meiosis (i.e., apomeiosis), the differentiation of unreduced embryo sacs and egg cells, and their autonomous development in functional embryos through parthenogenesis, and the formation of viable endosperm either via fertilization-independent means or following fertilization with a sperm cell...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28202034/transcriptomic-signatures-shaped-by-cell-proportions-shed-light-on-comparative-developmental-biology
#12
Sophie Pantalacci, Laurent Guéguen, Coraline Petit, Anne Lambert, Renata Peterkovà, Marie Sémon
BACKGROUND: Comparative transcriptomics can answer many questions in developmental and evolutionary developmental biology. Most transcriptomic studies start by showing global patterns of variation in transcriptomes that differ between species or organs through developmental time. However, little is known about the kinds of expression differences that shape these patterns. RESULTS: We compared transcriptomes during the development of two morphologically distinct serial organs, the upper and lower first molars of the mouse...
February 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28197155/dissecting-the-biochemical-and-transcriptomic-effects-of-a-locally-applied-heat-treatment-on-developing-cabernet-sauvignon-grape-berries
#13
Fatma Lecourieux, Christian Kappel, Philippe Pieri, Justine Charon, Jérémy Pillet, Ghislaine Hilbert, Christel Renaud, Eric Gomès, Serge Delrot, David Lecourieux
Reproductive development of grapevine and berry composition are both strongly influenced by temperature. To date, the molecular mechanisms involved in grapevine berries response to high temperatures are poorly understood. Unlike recent data that addressed the effects on berry development of elevated temperatures applied at the whole plant level, the present work particularly focuses on the fruit responses triggered by direct exposure to heat treatment (HT). In the context of climate change, this work focusing on temperature effect at the microclimate level is of particular interest as it can help to better understand the consequences of leaf removal (a common viticultural practice) on berry development...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28196854/hypothalamic-transcriptomic-alterations-in-male-and-female-california-mice-peromyscus-californicus-developmentally-exposed-to-bisphenol-a-or-ethinyl-estradiol
#14
Sarah A Johnson, William G Spollen, Lindsey K Manshack, Nathan J Bivens, Scott A Givan, Cheryl S Rosenfeld
Bisphenol A (BPA) is an endocrine-disrupting chemical (EDC) prevalent in many household items. Rodent models and human epidemiological studies have linked this chemical to neurobehavior impairments. In California mice, developmental exposure to BPA results in sociosexual disorders at adulthood, including communication and biparental care deficits, behaviors that are primarily regulated by the hypothalamus. Thus, we sought to examine the transcriptomic profile in this brain region of juvenile male and female California mice offspring exposed from periconception through lactation to BPA or ethinyl estradiol (EE, estrogen present in birth control pills and considered a positive estrogen control for BPA studies)...
February 2017: Physiological Reports
https://www.readbyqxmd.com/read/28193317/identification-of-differentially-expressed-placental-transcripts-during-multiple-gestations-in-the-eurasian-beaver-castor-fiber-l
#15
A Lipka, L Paukszto, M Majewska, J P Jastrzebski, K Myszczynski, G Panasiewicz, B Szafranska
The Eurasian beaver is one of the largest rodents that, despite its high impact on the environment, is a non-model species that lacks a reference genome. Characterising genes critical for pregnancy outcome can serve as a basis for identifying mechanisms underlying effective reproduction, which is required for the success of endangered species conservation programs. In the present study, high-throughput RNA sequencing (RNA-seq) was used to analyse global changes in the Castor fiber subplacenta transcriptome during multiple pregnancy...
February 14, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28192787/m-6-a-dependent-maternal-mrna-clearance-facilitates-zebrafish-maternal-to-zygotic-transition
#16
Boxuan Simen Zhao, Xiao Wang, Alana V Beadell, Zhike Lu, Hailing Shi, Adam Kuuspalu, Robert K Ho, Chuan He
The maternal-to-zygotic transition (MZT) is one of the most profound and tightly orchestrated processes during the early life of embryos, yet factors that shape the temporal pattern of vertebrate MZT are largely unknown. Here we show that over one-third of zebrafish maternal messenger RNAs (mRNAs) can be N(6)-methyladenosine (m(6)A) modified, and the clearance of these maternal mRNAs is facilitated by an m(6)A-binding protein, Ythdf2. Removal of Ythdf2 in zebrafish embryos decelerates the decay of m(6)A-modified maternal mRNAs and impedes zygotic genome activation...
February 23, 2017: Nature
https://www.readbyqxmd.com/read/28191465/pedf-is-associated-with-the-termination-of-chondrocyte-phenotype-and-catabolism-of-cartilage-tissue
#17
P Klinger, S Lukassen, F Ferrazzi, A B Ekici, T Hotfiel, B Swoboda, T Aigner, K Gelse
Objective. To investigate the expression and target genes of pigment epithelium-derived factor (PEDF) in cartilage and chondrocytes, respectively. Methods. We analyzed the expression pattern of PEDF in different human cartilaginous tissues including articular cartilage, osteophytic cartilage, and fetal epiphyseal and growth plate cartilage, by immunohistochemistry and quantitative real-time (qRT) PCR. Transcriptome analysis after stimulation of human articular chondrocytes with rhPEDF was performed by RNA sequencing (RNA-Seq) and confirmed by qRT-PCR...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28187707/transcriptome-analysis-of-coding-and-long-non-coding-rnas-highlights-the-regulatory-network-of-cascade-initiation-of-permanent-molars-in-miniature-pigs
#18
Fu Wang, Yang Li, Xiaoshan Wu, Min Yang, Wei Cong, Zhipeng Fan, Jinsong Wang, Chunmei Zhang, Jie Du, Songlin Wang
BACKGROUND: In diphyodont mammals, the additional molars (permanent molars) bud off from the posterior-free end of the primary dental lamina compared with successional teeth (replacement teeth) budding off from the secondary dental lamina. The diphyodont miniature pig has proved to be a valuable model for studying human molar morphogenesis. The additional molars show a sequential initiation pattern related to the specific tooth development stage of additional molars in miniature pigs during the morphogenesis of additional molars...
February 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28186631/dna-methylation-and-gene-expression-regulation-associated-with-vascularization-in-sorghum-bicolor
#19
Gina M Turco, Kaisa Kajala, Govindarajan Kunde-Ramamoorthy, Chew-Yee Ngan, Andrew Olson, Shweta Deshphande, Denis Tolkunov, Barbara Waring, Scott Stelpflug, Patricia Klein, Jeremy Schmutz, Shawn Kaeppler, Doreen Ware, Chia-Lin Wei, J Peter Etchells, Siobhan M Brady
Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues...
February 10, 2017: New Phytologist
https://www.readbyqxmd.com/read/28186613/-circular-rna-in-human-disease-and-their-potential-clinic-significance
#20
Yonghua Chen, Cheng Li, Chunlu Tan, Gang Mai, Xubao Liu
Circular RNAs (circ RNAs) are a novel type of RNA that, unlike linear RNAs, form a covalently closed continuous loop and are highly represented in the eukaryotic transcriptome. They share a stable structure, high expression and often exhibit tissue/developmental-stage-specific expression. Emerging evidence indicates that circRNAs might play important roles in human disease, such as cancer, neurological disorders and atherosclerotic vascular disease risk. The huge potentials of circRNAs are recently being discovered from the laboratory to the clinic...
February 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
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