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https://www.readbyqxmd.com/read/28343982/single-cell-5-formylcytosine-landscapes-of-mammalian-early-embryos-and-escs-at-single-base-resolution
#1
Chenxu Zhu, Yun Gao, Hongshan Guo, Bo Xia, Jinghui Song, Xinglong Wu, Hu Zeng, Kehkooi Kee, Fuchou Tang, Chengqi Yi
Active DNA demethylation in mammals involves ten-eleven translocation (TET) family protein-mediated oxidation of 5-methylcytosine (5mC). However, base-resolution landscapes of 5-formylcytosine (5fC) (an oxidized derivative of 5mC) at the single-cell level remain unexplored. Here, we present "CLEVER-seq" (chemical-labeling-enabled C-to-T conversion sequencing), which is a single-cell, single-base resolution 5fC-sequencing technology, based on biocompatible, selective chemical labeling of 5fC and subsequent C-to-T conversion during amplification and sequencing...
March 15, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28341363/a-gene-regulatory-program-controlling-early-xenopus-mesendoderm-formation-network-conservation-and-motifs
#2
REVIEW
Rebekah M Charney, Kitt D Paraiso, Ira L Blitz, Ken W Y Cho
Germ layer formation is among the earliest differentiation events in metazoan embryos. In triploblasts, three germ layers are formed, among which the endoderm gives rise to the epithelial lining of the gut tube and associated organs including the liver, pancreas and lungs. In frogs (Xenopus), where early germ layer formation has been studied intensively, the process of endoderm specification involves the interplay of dozens of transcription factors. Here, we review the interactions between these factors, summarized in a transcriptional gene regulatory network (GRN)...
March 21, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28340616/lacking-of-palladin-leads-to-multiple-cellular-events-changes-which-contribute-to-ntd
#3
Juan Tan, Xue-Jiao Chen, Chun-Ling Shen, Hong-Xin Zhang, Ling-Yun Tang, Shun-Yuan Lu, Wen-Ting Wu, Ying Kuang, Jian Fei, Zhu-Gang Wang
BACKGROUND: The actin cytoskeleton-associated protein palladin plays an important role in cell motility, morphogenesis and adhesion. In mice, Palladin deficient embryos are lethal before embryonic day (E) 15.5, and exhibit severe cranial neural tube and body wall closure defects. However, the mechanism how palladin regulates the process of cranial neural tube closure (NTC) remains unknown. METHODS: In this paper, we use gene knockout mouse to elucidate the function of palladin in the regulation of NTC process...
March 24, 2017: Neural Development
https://www.readbyqxmd.com/read/28339658/acute-cell-volume-regulation-by-janus-kinase-2-mediated-sodium-hydrogen-exchange-activation-develops-at-the-late-one-cell-stage-in-mouse-preimplantation-embryos%C3%A2
#4
Baozeng Xu, Chenxi Zhou, Megan Meredith, Jay M Baltz
Early preimplantation embryos are extremely sensitive to dysregulation of cell volume, which can lead to developmental arrest. It was previously shown that mouse embryos at the two-cell stage respond to a cell volume decrease by quickly activating Na+/H+ exchange via a signaling mechanism that involves the tyrosine kinase Janus kinase 2 (JAK2). However, it was not known whether this mechanism is active at the one-cell stage, when embryos are most sensitive to perturbed cell volume. Na+/H+ exchanger activity elicited by an induced cell volume decrease was significantly lower at the mid one-cell stage than at the late one-cell stage or during the two-cell stage...
February 17, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28335020/znhit3-is-defective-in-peho-syndrome-a-severe-encephalopathy-with-cerebellar-granule-neuron-loss
#5
Anna-Kaisa Anttonen, Anni Laari, Maria Kousi, Yawei J Yang, Tiina Jääskeläinen, Mirja Somer, Eija Siintola, Eveliina Jakkula, Mikko Muona, Saara Tegelberg, Tuula Lönnqvist, Helena Pihko, Leena Valanne, Anders Paetau, Melody P Lun, Johanna Hästbacka, Outi Kopra, Tarja Joensuu, Nicholas Katsanis, Maria K Lehtinen, Jorma J Palvimo, Anna-Elina Lehesjoki
Progressive encephalopathy with oedema, hypsarrhythmia, and optic atrophy (PEHO) syndrome is an early childhood onset, severe autosomal recessive encephalopathy characterized by extreme cerebellar atrophy due to almost total granule neuron loss. By combining homozygosity mapping in Finnish families with Sanger sequencing of positional candidate genes and with exome sequencing a homozygous missense substitution of leucine for serine at codon 31 in ZNHIT3 was identified as the primary cause of PEHO syndrome. ZNHIT3 encodes a nuclear zinc finger protein previously implicated in transcriptional regulation and in small nucleolar ribonucleoprotein particle assembly and thus possibly to pre-ribosomal RNA processing...
March 1, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334846/dapl1-a-susceptibility-locus-for-age-related-macular-degeneration-acts-as-a-novel-suppressor-of-cell-proliferation-in-the-retinal-pigment-epithelium
#6
Xiaoyin Ma, Huirong Li, Yipin Wang, Jing Wang, Qinxiang Zheng, Jiajia Hua, Juan Yang, Li Pan, Fan Lu, Jia Qu, Ling Hou
The retinal pigment epithelium (RPE) forms a monolayer at the back of the vertebrate eye and is fundamental to retinal function and homoeostasis. During early development, RPE cells undergo rapid proliferation, but in the adult, they remain normally nonproliferative throughout life. Nevertheless, under pathological conditions such as in proliferative vitreoretinopathy or after retinal ablation, mature RPE cells can re-enter the cell cycle and form nodules or multiple cell layers. Here we show that Dapl1, whose human homolog represents a susceptibility locus for age-related macular degeneration (AMD), is highly up-regulated in quiescent but not proliferating RPE cells and that experimental overexpression of DAPL1 in proliferating RPE cells inhibits their proliferation...
February 22, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28333934/visualizing-the-structure-of-rna-seq-expression-data-using-grade-of-membership-models
#7
Kushal K Dey, Chiaowen Joyce Hsiao, Matthew Stephens
Grade of membership models, also known as "admixture models", "topic models" or "Latent Dirichlet Allocation", are a generalization of cluster models that allow each sample to have membership in multiple clusters. These models are widely used in population genetics to model admixed individuals who have ancestry from multiple "populations", and in natural language processing to model documents having words from multiple "topics". Here we illustrate the potential for these models to cluster samples of RNA-seq gene expression data, measured on either bulk samples or single cells...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28323620/discovery-of-novel-determinants-of-endothelial-lineage-using-chimeric-heterokaryons
#8
Wing Tak Wong, Gianfranco Matrone, XiaoYu Tian, Simion Alin Tomoiaga, Kin Fai Au, Shu Meng, Sayumi Yamazoe, Daniel Sieveking, Kaifu Chen, David M Burns, James K Chen, Helen M Blau, John P Cooke
We wish to identify determinants of endothelial lineage. Murine embryonic stem cells (mESC) were fused with human endothelial cells in stable, non-dividing, heterokaryons. Using RNA-seq it is possible to discriminate between human and mouse transcripts in these chimeric heterokaryons. We observed a temporal pattern of gene expression in the ESCs of the heterokaryons that recapitulated ontogeny, with early mesodermal factors being expressed before mature endothelial genes. A set of transcriptional factors not known to be involved in endothelial development was upregulated, one of which was POU class 3 homeobox 2 (Pou3f2)...
March 21, 2017: ELife
https://www.readbyqxmd.com/read/28298438/single-cell-analysis-reveals-lineage-segregation-in-early-post-implantation-mouse-embryos
#9
Jing Wen, Yanwu Zeng, Zhuoqing Fang, Junjie Gu, Laixiang Ge, Fan Tang, Zepeng Qu, Jing Hu, Yaru Cui, Kunshan Zhang, Junbang Wang, Siguang Li, Yi Sun, Ying Jin
The mammalian post-implantation embryo has been extensively investigated at the tissue level. However, to unravel the molecular basis for the cell-fate plasticity and determination, it is essential to study the characteristics of individual cells. Especially, the individual definitive endoderm (DE) cells have not been characterized in vivo. Here, we report gene expression patterns in single cells freshly isolated from mouse embryos on days 5.5 and 6.5. Initial transcriptome data from 124 single cells yielded signature genes for the epiblast, visceral endoderm, and extra-embryonic ectoderm and revealed a unique distribution pattern of fibroblast growth factor (Fgf) ligands and receptors...
March 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28291811/systematic-identification-and-characterization-of-long-non-coding-rnas-in-mouse-mature-sperm
#10
Xiaoning Zhang, Fengxin Gao, Jianbo Fu, Peng Zhang, Yuqing Wang, Xuhui Zeng
Increasing studies have shown that mature spermatozoa contain many transcripts including mRNAs and miRNAs. However, the expression profile of long non-coding RNAs (lncRNAs) in mammalian sperm has not been systematically investigated. Here, we used highly purified RNA to investigate lncRNA expression profiles in mouse mature sperm by stranded-specific RNA-seq. We identified 20,907 known and 4,088 novel lncRNAs transcripts, and the existence of intact lncRNAs was confirmed by RT-PCR and fluorescence in situ hybridization on two representative lncRNAs...
2017: PloS One
https://www.readbyqxmd.com/read/28290521/ndrg3-gene-regulates-dsb-repair-during-meiosis-through-modulation-the-erk-signal-pathway-in-the-male-germ-cells
#11
Hongjie Pan, Xuan Zhang, Hanwei Jiang, Xiaohua Jiang, Liu Wang, Qi Qi, Yuan Bi, Jian Wang, Qinghua Shi, Runsheng Li
The N-myc downstream regulated gene (NDRG) family consists of 4 members, NDRG-1, -2, -3, -4. Physiologically, we found Ndrg3, a critical gene which led to homologous lethality in the early embryo development, regulated the male meiosis in mouse. The expression of Ndrg3 was enhanced specifically in germ cells, and reached its peak level in the pachytene stage spermatocyte. Haplo-insufficiency of Ndrg3 gene led to sub-infertility during the male early maturation. In the Ndrg3(+/-) germ cells, some meiosis events such as DSB repair and synaptonemal complex formation were impaired...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28289135/the-chromatin-modifier-satb1-regulates-cell-fate-through-fgf-signalling-in-the-early-mouse-embryo
#12
Mubeen Goolam, Magdalena Zernicka-Goetz
The separation of embryonic from extra-embryonic tissues within the inner-cell-mass (ICM) to generate the epiblast (EPI), that will form the new organism, from the primitive endoderm (PE), that will form the yolk sac, is a crucial developmental decision. Here we identify a chromatin modifier, Satb1, with a distinct role in this decision. Satb1 is differentially expressed within 16-cell-stage embryos with higher expression levels in the ICM progenitor cells. Depleting Satb1 increases the number of EPI cells at the expense of PE...
March 13, 2017: Development
https://www.readbyqxmd.com/read/28288969/visualizing-endoderm-cell-populations-and-their-dynamics-in-the-mouse-embryo-with-a-hex-tdtomato-reporter
#13
Tao Wu, Anna-Katerina Hadjantonakis, Sonja Nowotschin
Live imaging is the requisite tool for studying cell behaviors driving embryonic development and tissue formation. Genetically-encoded reporters expressed under cell type-specific cis-regulatory elements that drive fluorescent protein expression at sufficient levels for visualization in living specimens have become indispensable for these studies. Increasingly dual-color (red-green) imaging is used for studying the coordinate behaviors if two cell populations of interest, identifying and characterizing subsets of within broader cell populations or subcellular features...
March 13, 2017: Biology Open
https://www.readbyqxmd.com/read/28283910/hyperglycemia-impedes-definitive-endoderm-differentiation-of-human-embryonic-stem-cells-by-modulating-histone-methylation-patterns
#14
A C H Chen, Y L Lee, S W Fong, C C Y Wong, E H Y Ng, W S B Yeung
Exposure to maternal diabetes during fetal growth is a risk factor for the development of type II diabetes (T2D) in later life. Discovery of the mechanisms involved in this association should provide valuable background for therapeutic treatments. Early embryogenesis involves epigenetic changes including histone modifications. The bivalent histone methylation marks H3K4me3 and H3K27me3 are important for regulating key developmental genes during early fetal pancreas specification. We hypothesized that maternal hyperglycemia disrupted early pancreas development through changes in histone bivalency...
March 10, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/28280571/a-full-lifespan-model-of-vertebrate-lens-growth
#15
Hrvoje Šikić, Yanrong Shi, Snježana Lubura, Steven Bassnett
The mathematical determinants of vertebrate organ growth have yet to be elucidated fully. Here, we utilized empirical measurements and a dynamic branching process-based model to examine the growth of a simple organ system, the mouse lens, from E14.5 until the end of life. Our stochastic model used difference equations to model immigration and emigration between zones of the lens epithelium and included some deterministic elements, such as cellular footprint area. We found that the epithelial cell cycle was shortened significantly in the embryo, facilitating the rapid growth that marks early lens development...
January 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28273703/-the-composition-of-the-gastrointestinal-bacterial-flora-of-mouse-embryos-and-the-placenta-tissue-bacterial-flora
#16
D Lei, Y Lin, X Jiang, L Lan, W Zhang, B X Wang
Objective: To explore the composition of the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora. Method: Twenty-four specimens were collected from pregnant Kunming mouse including 8 mice of early embryonic (12-13 days) gastrointestinal tissues, 8 cases of late embryonic (19-20 days)gastrointestinal tissues, 8 of late pregnancy placental tissues.The 24 samples were extracted by DNeasy Blood & Tissue kit for high-throughput DNA sequencing. Result: The level of Proteobacteria, Bacteroidetes, Actino-bacteria and Firmicutes were predominantin all specimens...
March 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/28272511/non-destructive-monitoring-of-mouse-embryo-development-and-its-qualitative-evaluation-at-the-molecular-level-using-raman-spectroscopy
#17
Mika Ishigaki, Kosuke Hashimoto, Hidetoshi Sato, Yukihiro Ozaki
Current research focuses on embryonic development and quality not only by considering fundamental biology, but also by aiming to improve assisted reproduction technologies, such as in vitro fertilization. In this study, we explored the development of mouse embryo and its quality based on molecular information, obtained nondestructively using Raman spectroscopy. The detailed analysis of Raman spectra measured in situ during embryonic development revealed a temporary increase in protein content after fertilization...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28270748/huntingtin-is-required-for-neural-but-not-cardiac-pancreatic-progenitor-differentiation-of-mouse-embryonic-stem-cells-in-vitro
#18
Man Shan Yu, Naoko Tanese
Mutation in the huntingtin (HTT) gene causes Huntington's disease (HD). It is an autosomal dominant trinucleotide-repeat expansion disease in which CAG repeat sequence expands to >35. This results in the production of mutant HTT protein with an increased stretch of glutamines near the N-terminus. The wild type HTT gene encodes a 350 kD protein whose function remains elusive. Mutant HTT protein has been implicated in transcription, axonal transport, cytoskeletal structure/function, signal transduction, and autophagy...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28268375/directing-the-spatial-patterning-of-motor-neuron-differentiation-in-engineered-microenvironments
#19
Christopher J Demers, Greg Cox, Scott D Collins, Rosemary L Smith
Embryonic development of the spinal cord proceeds through a carefully orchestrated temporal and spatial sequence of chemical cues to provide precise patterning of adult cell types. Recreating this complex microenvironment in a standard cell culture dish is difficult, if not impossible. In this paper, a microfluidic device is used to recapitulate, in vitro, the graded patterning events which occur during early spinal cord development. The microdevice design is developed using COMSOL modeling, with which the spatiotemporal profiles of multiple, diffusible morphogens are simulated...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28260557/the-influence-of-in-vitro-fertilization-and-embryo-culture-on-the-embryo-epigenetic-constituents-and-the-possible-consequences-in-the-bovine-model
#20
M-A Sirard
Medically assisted reproductive technologies, such as in vitro embryo production, are increasingly being used to palliate infertility. Eggs are produced following a hormonal regimen that stimulates the ovaries to produce a large number of oocytes. Collected oocytes are then fertilized in vitro and allowed to develop in vitro until they are either frozen or transferred to mothers. There are controversial reports on the adverse impacts of these technologies on early embryos and their potential long-term effects...
March 6, 2017: Journal of Developmental Origins of Health and Disease
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