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https://www.readbyqxmd.com/read/28226240/position-and-hippo-signaling-dependent-plasticityduring-lineage-segregation-in-the-early-mouse-embryo
#1
Eszter Posfai, Sophie Petropoulos, Flavia Ro de Barros, John Paul Schell, Igor Jurisica, Rickard Sandberg, Fredrik Lanner, Janet Rossant
The segregation of the trophectoderm (TE) from the inner cell mass (ICM) in the mouse blastocyst is determined by position-dependent Hippo signaling. However, the window of responsiveness to Hippo signaling, the exact timing of lineage commitment and the overall relationship between cell commitment and global gene expression changes are still unclear. Single-cell RNA sequencing during lineage segregation revealed that the TE transcriptional profile stabilizes earlier than the ICM and prior to blastocyst formation...
February 22, 2017: ELife
https://www.readbyqxmd.com/read/28225779/combined-small-rna-and-degradome-sequencing-reveals-complex-microrna-regulation-of-catechin-biosynthesis-in-tea-camellia-sinensis
#2
Ping Sun, Chunzhen Cheng, Yuling Lin, Qiufang Zhu, Jinke Lin, Zhongxiong Lai
MicroRNAs are endogenous non-coding small RNAs playing crucial regulatory roles in plants. Tea, a globally popular non-alcoholic drink, is rich in health-enhancing catechins. In this study, 69 conserved and 47 novel miRNAs targeting 644 genes were identified by high-throughout sequencing. Predicted target genes of miRNAs were mainly involved in plant growth, signal transduction, morphogenesis and defense. To further identify targets of tea miRNAs, degradome sequencing and RNA ligase-mediated rapid amplification of 5'cDNA ends (RLM-RACE) were applied...
2017: PloS One
https://www.readbyqxmd.com/read/28225755/intragenic-dna-methylation-prevents-spurious-transcription-initiation
#3
Francesco Neri, Stefania Rapelli, Anna Krepelova, Danny Incarnato, Caterina Parlato, Giulia Basile, Mara Maldotti, Francesca Anselmi, Salvatore Oliviero
In mammals, DNA methylation occurs mainly at CpG dinucleotides. Methylation of the promoter suppresses gene expression, but the functional role of gene-body DNA methylation in highly expressed genes has yet to be clarified. Here we show that, in mouse embryonic stem cells, Dnmt3b-dependent intragenic DNA methylation protects the gene body from spurious RNA polymerase II entry and cryptic transcription initiation. Using different genome-wide approaches, we demonstrate that this Dnmt3b function is dependent on its enzymatic activity and recruitment to the gene body by H3K36me3...
February 22, 2017: Nature
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/28225006/altered-enhancer-transcription-underlies-huntington-s-disease-striatal-transcriptional-signature
#5
Stéphanie Le Gras, Céline Keime, Anne Anthony, Caroline Lotz, Lucie De Longprez, Emmanuel Brouillet, Jean-Christophe Cassel, Anne-Laurence Boutillier, Karine Merienne
Epigenetic and transcriptional alterations are both implicated in Huntington's disease (HD), a progressive neurodegenerative disease resulting in degeneration of striatal neurons in the brain. However, how impaired epigenetic regulation leads to transcriptional dysregulation in HD is unclear. Here, we investigated enhancer RNAs (eRNAs), a class of long non-coding RNAs transcribed from active enhancers. We found that eRNAs are expressed from many enhancers of mouse striatum and showed that a subset of those eRNAs are deregulated in HD vs control mouse striatum...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224923/high-throughput-sequencing-reveals-modulation-of-micrornas-in-vigna-mungo-upon-mungbean-yellow-mosaic-india-virus-inoculation-highlighting-stress-regulation
#6
Anirban Kundu, Sujay Paul, Avishek Dey, Amita Pal
MicroRNAs (miRNAs) are 20-24 nucleotides long non-coding RNAs known to play important regulatory roles during biotic and abiotic stresses by controlling gene expression. Blackgram (Vigna mungo), an economically important grain legume is highly susceptible to pathogenic begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) and resulting in high yield loss. In this study two different leaf-small-RNA libraries were prepared from the pooled RNA at three different time points of resistant V. mungo inbred line VM84 inoculated either with viruliferous or non-viruliferous whiteflies carrying MYMIV and performed high-throughput Illumina sequencing...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28224916/transcriptional-markers-enable-identification-of-rye-grass-lolium-sp-plants-with-non-target-site-based-resistance-to-herbicides-inhibiting-acetolactate-synthase
#7
Arnaud Duhoux, Sébastien Carrère, Alexis Duhoux, Christophe Délye
Molecular detection of herbicide non-target-site-based resistance (NTSR) classically requires extensively validated NTSR genes. We assessed the feasibility of predicting NTSR phenotypes using expression data of NTSR transcriptional markers, i.e., transcripts which expression levels are statistically correlated to NTSR. Markers were sought by comparative RNA-Seq analysis of untreated NTSR or sensitive plants from four rye-grass populations followed by expression quantification in 299 individual plants with characterised sensitivity to two acetolactate-synthase-inhibiting herbicides...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28224733/nk1-1-cd4-nkg2d-t-cells-suppress-dss-induced-colitis-in-mice-through-production-of-tgf-%C3%AE
#8
Xingxing Qian, Chunxia Hu, Sen Han, Zhijie Lin, Weiming Xiao, Yanbing Ding, Yu Zhang, Li Qian, Xiaoqing Jia, Guoqiang Zhu, Weijuan Gong
CD4(+) NKG2D(+) T cells are associated with tumour, infection and autoimmune diseases. Some CD4(+) NKG2D(+) T cells secrete IFN-γ and TNF-α to promote inflammation, but others produce TGF-β and FasL to facilitate tumour evasion. Here, murine CD4(+) NKG2D(+) T cells were further classified into NK1.1(-) CD4(+) NKG2D(+) and NK1.1(+) CD4(+) NKG2D(+) subpopulations. The frequency of NK1.1(-) CD4(+) NKG2D(+) cells decreased in inflamed colons, whereas more NK1.1(+) CD4(+) NKG2D(+) cells infiltrated into colons of mice with DSS-induced colitis...
February 22, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28224655/rna-seq-analysis-of-transcriptional-change-in-the-freshwater-mussel-elliptio-complanata-after-environmentally-relevant-sodium-chloride-exposure
#9
Laura S Robertson, Heather S Galbraith, Deborah Iwanowicz, Carrie J Blakeslee, R Scott Cornman
To identify potential biomarkers of salt stress in a freshwater sentinel species, we examined transcriptional responses of the common mussel Elliptio complanata to controlled NaCl exposures. RNA-Seq of mantle tissue identified 481 transcripts differentially expressed in adult mussels exposed to 2 ppt NaCl (1.2 ppt chloride) for seven days, of which 290 had non-overlapping intervals. Differentially expressed gene categories included ion and transmembrane transport, oxidoreductase activity, maintenance of protein folding, and amino acid metabolism...
February 22, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28224385/evaluation-of-real-time-rt-pcr-assays-for-detection-and-quantification-of-norovirus-genogroups-i-and-ii
#10
Kitwadee Rupprom, Porntip Chavalitshewinkoon-Petmitr, Pornphan Diraphat, Leera Kittigul
Noroviruses are the leading cause of acute gastroenteritis in humans. Real-time reverse transcription-polymerase chain reaction (real-time RT-PCR) is a promising molecular method for the detection of noroviruses. In this study, the performance of three TaqMan real-time RT-PCR assays was assessed, which were one commercially available real-time RT-PCR kit (assay A: Norovirus Real Time RT-PCR kit) and two in-house real-time RT-PCR assays (assay B: LightCycler RNA Master Hybprobe and assay C: RealTime ready RNA Virus Master)...
February 20, 2017: Virologica Sinica
https://www.readbyqxmd.com/read/28224052/compacting-and-correcting-trinity-and-oases-rna-seq-de-novo-assemblies
#11
Cédric Cabau, Frédéric Escudié, Anis Djari, Yann Guiguen, Julien Bobe, Christophe Klopp
BACKGROUND: De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved...
2017: PeerJ
https://www.readbyqxmd.com/read/28223998/rna-seq-analysis-of-cold-and-drought-responsive-transcriptomes-of-zea-mays-ssp-mexicana-l
#12
Xiang Lu, Xuan Zhou, Yu Cao, Meixue Zhou, David McNeil, Shan Liang, Chengwei Yang
The annual Zea mays ssp. mexicana L. is a member of teosinte, a wild relative of the Zea mays spp. mays L. This subspecies has strong growth and regeneration ability, high tiller numbers, high protein and lysine content as well as resistance to many fungal diseases, and it can be effectively used in maize improvement. In this study, we reported a Zea mays ssp. mexicana L. transcriptome by merging data from untreated control (CK), cold (4°C) and drought (PEG2000, 20%) treated plant samples. A total of 251,145 transcripts (N50 = 1,269 bp) and 184,280 unigenes (N50 = 923 bp) were predicted, which code for homologs of near 47% of the published maize proteome...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223997/melatonin-regulates-root-architecture-by-modulating-auxin-response-in-rice
#13
Chengzhen Liang, Aifu Li, Hua Yu, Wenzhen Li, Chengzhi Liang, Sandui Guo, Rui Zhang, Chengcai Chu
It has been suggested that melatonin acts as an important regulator in controlling root growth and development, but the underlying molecular mechanism driving this relationship remains undetermined. In this study, we demonstrated that melatonin acts as a potent molecule to govern root architecture in rice. Treatments with melatonin significantly inhibited embryonic root growth, and promoted lateral root formation and development. Genome-wide expression profiling by RNA-sequencing revealed auxin-related genes were significantly activated under melatonin treatment...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223989/ufgt-the-key-enzyme-associated-with-the-petals-variegation-in-japanese-apricot
#14
Xinxin Wu, Qinghua Gong, Xiaopeng Ni, Yong Zhou, Zhihong Gao
Japanese apricot (Prunus mume Sieb.et Zucc.) is an important ornamental plant in China. One of the traits of petals color variegation is attractive, but its formation mechanism is unclear. In our study, RNA-seq technology was employed to characterize the transcriptome response to the mutation of "Fuban Tiaozhi" associated with petals variegation in Japanese apricot. As a result, 4,579,040 (white-flowered, WF) and 7,269,883 (red-flowered, RF) reads were mapped to P. persica genes, while 5,006,676 (WF) and 7,907,436 (RF) were mapped to P...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223918/rpph1-upregulates-cdc42-expression-and-promotes-hippocampal-neuron-dendritic-spine-formation-by-competing-with-mir-330-5p
#15
Yifei Cai, Ziling Sun, Huizhen Jia, Hongxue Luo, Xiaoyang Ye, Qi Wu, Yi Xiong, Wei Zhang, Jun Wan
Alzheimer's disease (AD) is a heterogeneous neurodegenerative disease. Recent studies employing microRNA-seq and genome-wide sequencing have identified some non-coding RNAs that are influentially involved in AD pathogenesis. Non-coding RNAs can compete with other endogenous RNAs by microRNA response elements (MREs) and manipulate biological processes, such as tumorigenesis. However, only a few non-coding RNAs have been reported in the pathogenesis of AD. In this study, we constructed the first competing endogenous RNA (ceRNA) network leveraging whole transcriptome sequencing and a previously studied microRNA-seq of APPswe/PS1ΔE9 transgenic mice...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28223695/the-mirnaome-of-catharanthus-roseus-identification-expression-analysis-and-potential-roles-of-micrornas-in-regulation-of-terpenoid-indole-alkaloid-biosynthesis
#16
Ethan M Shen, Sanjay K Singh, Jayadri S Ghosh, Barunava Patra, Priyanka Paul, Ling Yuan, Sitakanta Pattanaik
MicroRNAs (miRNAs) regulate numerous crucial biological processes in plants. However, information is limited on their involvement in the biosynthesis of specialized metabolites in plants, including Catharanthus roseus that produces a number of pharmaceutically valuable, bioactive terpenoid indole alkaloids (TIAs). Using small RNA-sequencing, we identified 181 conserved and 173 novel miRNAs (cro-miRNAs) in C. roseus seedlings. Genome-wide expression analysis revealed that a set of cro-miRNAs are differentially regulated in response to methyl jasmonate (MeJA)...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223493/crystal-structure-of-aquifex-aeolicus-%C3%AF-n-bound-to-promoter-dna-and-the-structure-of-%C3%AF-n-holoenzyme
#17
Elizabeth A Campbell, Shreya Kamath, Kanagalaghatta R Rajashankar, Mengyu Wu, Seth A Darst
The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σ(N), is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by specialized AAA(+) ATPases. We report a 3.4-Å resolution X-ray crystal structure of a σ(N) fragment in complex with its cognate promoter DNA, revealing the molecular details of promoter recognition by σ(N) The structure allowed us to build and refine an improved σ(N)-holoenzyme model based on previously published 3...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223461/identification-of-a-pseudomonas-aeruginosa-pao1-dna-methyltransferase-its-targets-and-physiological-roles
#18
Sebastian Doberenz, Denitsa Eckweiler, Olga Reichert, Vanessa Jensen, Boyke Bunk, Cathrin Spröer, Adrian Kordes, Emanuela Frangipani, Khai Luong, Jonas Korlach, Stephan Heeb, Jörg Overmann, Volkhard Kaever, Susanne Häussler
DNA methylation is widespread among prokaryotes, and most DNA methylation reactions are catalyzed by adenine DNA methyltransferases, which are part of restriction-modification (R-M) systems. R-M systems are known for their role in the defense against foreign DNA; however, DNA methyltransferases also play functional roles in gene regulation. In this study, we used single-molecule real-time (SMRT) sequencing to uncover the genome-wide DNA methylation pattern in the opportunistic pathogen Pseudomonas aeruginosa PAO1...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223458/mutation-of-the-n-terminal-region-of-chikungunya-virus-capsid-protein-implications-for-vaccine-design
#19
Adam Taylor, Xiang Liu, Ali Zaid, Lucas Y H Goh, Jody Hobson-Peters, Roy A Hall, Andres Merits, Suresh Mahalingam
Mosquito-transmitted chikungunya virus (CHIKV) is an arthritogenic alphavirus of the Togaviridae family responsible for frequent outbreaks of arthritic disease in humans. Capsid protein, a structural protein encoded by the CHIKV RNA genome, is able to translocate to the host cell nucleolus. In encephalitic alphaviruses, nuclear translocation induces host cell transcriptional shutoff; however, the role of capsid protein nucleolar localization in arthritogenic alphaviruses remains unclear. Using recombinant enhanced green fluorescent protein (EGFP)-tagged expression constructs and CHIKV infectious clones, we describe a nucleolar localization sequence (NoLS) in the N-terminal region of capsid protein, previously uncharacterized in CHIKV...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223400/distal-cpg-islands-can-serve-as-alternative-promoters-to-transcribe-genes-with-silenced-proximal-promoters
#20
Shrutii Sarda, Avinash Das, Charles Vinson, Sridhar Hannenhalli
DNA methylation at the promoter of a gene is presumed to render it silent, yet, a sizable fraction of genes with methylated proximal-promoters exhibit elevated expression. Here, we show, through extensive analysis of the methylome and transcriptome in 34 tissues, that in many such cases, transcription is initiated by a distal upstream CpG island (CGI) located several kilobases away that functions as an alternative promoter. Specifically, such genes are expressed precisely when the neighboring CGI remains unmethylated, but remain silenced otherwise...
February 21, 2017: Genome Research
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