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RNA methylation

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https://www.readbyqxmd.com/read/29352065/a-role-for-miniyo-and-quatre-quart-2-in-the-assembly-of-rna-polymerases-ii-iv-and-v-in-arabidopsis
#1
Yaoxi Li, Yuxiang Yuan, Xiaofeng Fang, Xiuli Lu, Bi Lian, Gaozhan Zhao, Yijun Qi
RNA polymerases IV and V (Pol IV and Pol V) are required for the generation of noncoding RNAs in RNA-directed DNA methylation (RdDM). Their subunit compositions resemble that of Pol II. The mechanism and accessory factors involved in their assembly remain largely unknown. In this study, we identified mutant alleles of MINIYO (IYO), QUATRE-QUART 2 (QQT2) and NUCLEAR RNA POLYMERASE B11/D11/E11 (NRPB/D/E11) that cause defects in RdDM in Arabidopsis. We found that Pol IV-dependent small interfering RNAs (siRNAs) and Pol V-dependent transcripts were greatly reduced in the mutants...
January 18, 2018: Plant Cell
https://www.readbyqxmd.com/read/29351348/interactions-of-2-o-methyl-oligoribonucleotides-with-the-rna-models-of-the-30s-subunit-a-site
#2
Maciej Jasiński, Marta Kulik, Monika Wojciechowska, Ryszard Stolarski, Joanna Trylska
Synthetic oligonucleotides targeting functional regions of the prokaryotic rRNA could be promising antimicrobial agents. Indeed, such oligonucleotides were proven to inhibit bacterial growth. 2'-O-methylated (2'-O-Me) oligoribonucleotides with a sequence complementary to the decoding site in 16S rRNA were reported as inhibitors of bacterial translation. However, the binding mode and structures of the formed complexes, as well as the level of selectivity of the oligonucleotides between the prokaryotic and eukaryotic target, were not determined...
2018: PloS One
https://www.readbyqxmd.com/read/29348729/panax-ginseng-exerts-antidepressant-like-effects-by-suppressing-neuroinflammatory-response-and-upregulating-nuclear-factor-erythroid-2-related-factor-2-signaling-in-the-amygdala
#3
Jong Hee Choi, Min Jung Lee, Minhee Jang, Hak-Jae Kim, Sanghyun Lee, Sang Won Lee, Young Ock Kim, Ik-Hyun Cho
Background: Depression is one of the most commonly diagnosed neuropsychiatric diseases, but the underlying mechanism and medicine are not well-known. Although Panax ginseng has been reported to exert protective effects in various neurological studies, little information is available regarding its antidepressant effects. Methods: Here, we examined the antidepressant effect and underlying mechanism of P. ginseng extract (PGE) in a chronic restraint stress (CRS)-induced depression model in mice...
January 2018: Journal of Ginseng Research
https://www.readbyqxmd.com/read/29348610/the-histone-methyltransferase-dot1l-inhibits-osteoclastogenesis-and-protects-against-osteoporosis
#4
Yanpan Gao, Wei Ge
Osteoclasts are absorptive cells that play a critical role in homeostatic bone remodeling and pathological bone resorption. Emerging evidence suggests an important role of epigenetic regulation in osteoclastogenesis. In this study, we investigated the role of DOT1L, which regulates gene expression epigenetically by histone H3K79 methylation (H3K79me), during osteoclast formation. Using RANKL-induced RAW264.7 macrophage cells as an osteoclast differentiation model, we found that DOT1L and H3K79me2 levels were upregulated during osteoclast differentiation...
January 18, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29348366/structures-of-human-prc2-with-its-cofactors-aebp2-and-jarid2
#5
Vignesh Kasinath, Marco Faini, Simon Poepsel, Dvir Reif, Xinyu Ashlee Feng, Goran Stjepanovic, Ruedi Aebersold, Eva Nogales
Transcriptionally repressive histone H3K27 methylation by PRC2 (Polycomb repressive complex 2) is essential for cellular differentiation and development. Here we report cryo-EM structures of human PRC2 in two distinct, active states, while in complex with its cofactors JARID2 and AEBP2. Both cofactors mimic the binding of histone H3 tails. JARID2, methylated by PRC2, mimics a methylated H3 tail to stimulate PRC2 activity, while AEBP2 interacts with the RBAP48 subunit mimicking an unmodified H3 tail. SUZ12 interacts with all other subunits within the assembly and thus contributes to the stability of the complex...
January 18, 2018: Science
https://www.readbyqxmd.com/read/29348140/interactions-localization-and-phosphorylation-of-the-m6a-generating-mettl3-mettl14-wtap-complex
#6
Eva Schöller, Franziska Weichmann, Thomas Treiber, Sam Ringle, Nora Treiber, Andrew Flatley, Regina Feederle, Astrid Bruckmann, Gunter Meister
N6-methyladenine (m6A) is found on many eukaryotic RNAs including mRNAs. M6A modification has been implicated in mRNA stability and turn over, localization or translation efficiency. A heterodimeric enzyme complex composed of METTL3 and METTL14 generates m6A on mRNAs. METTL3/14 is found in the nucleus where it is localized to nuclear speckles and the splicing regulator WTAP is required for this distinct nuclear localization pattern. Although recent crystal structures revealed how the catalytic MT-A70 domains of METTL3 and METTL14 interact with each other, a more global architecture including WTAP and RNA interactions has not been reported so far...
January 18, 2018: RNA
https://www.readbyqxmd.com/read/29346625/complete-genomic-and-transcriptional-landscape-analysis-using-third-generation-sequencing-a-case-study-of-saccharomyces-cerevisiae-cen-pk113-7d
#7
Piroon Jenjaroenpun, Thidathip Wongsurawat, Rui Pereira, Preecha Patumcharoenpol, David W Ussery, Jens Nielsen, Intawat Nookaew
Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29344314/aberrant-expression-and-dna-methylation-of-lipid-metabolism-genes-in-pcos-a-new-insight-into-its-pathogenesis
#8
Jie-Xue Pan, Ya-Jing Tan, Fang-Fang Wang, Ning-Ning Hou, Yu-Qian Xiang, Jun-Yu Zhang, Ye Liu, Fan Qu, Qing Meng, Jian Xu, Jian-Zhong Sheng, He-Feng Huang
Background: Polycystic ovary syndrome (PCOS), whose etiology remains uncertain, is a highly heterogenous and genetically complex endocrine disorder. The aim of this study was to identify differentially expressed genes (DEGs) in granulosa cells (GCs) from PCOS patients and make epigenetic insights into the pathogenesis of PCOS. Results: Included in this study were 110 women with PCOS and 119 women with normal ovulatory cycles undergoing in vitro fertilization acting as the control group...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29343504/canonical-and-non-canonical-actions-of-arabidopsis-histone-deacetylases-in-ribosomal-rna-processing
#9
Xiangsong Chen, Li Lu, Shuiming Qian, Mark Scalf, Lloyd M Smith, Xuehua Zhong
Ribosome biogenesis is a fundamental process required for all cellular activities. Histone deacetylases play critical roles in many biological processes including transcriptional repression and rDNA silencing. However, their function in pre-rRNA processing remains poorly understood. Here, we discovered a previously uncharacterized role of Arabidopsis thaliana histone deacetylase HD2C in pre-rRNA processing via both canonical and non-canonical manners. HD2C interacts with another histone deacetylase HD2B and forms homo- and/or hetero-oligomers in the nucleolus...
January 17, 2018: Plant Cell
https://www.readbyqxmd.com/read/29341505/stability-integrity-and-recovery-rate-of-cellular-nucleic-acids-preserved-in-a-new-liquid-based-cytology-medium
#10
Guodong Zhao, Zhaocheng Liu, Yaping Tian, Minsheng Zhu, Shouli Wang, Hui Wang, Shen Gao, Yong Ma, Minxue Zheng
BACKGROUND: Liquid-based cytology (LBC) has replaced the conventional Papanicolaou test in cervical cancer screening. The cervical swab specimens collected in LBC media can also be used for additional analyses including high-risk HPV (HR-HPV) test, DNA methylation analysis, and HPV E6/E7 mRNA test. METHODS: The stability, integrity, and recovery rate of cellular DNA and RNA after storage at different conditions were evaluated by a quantitative real-time PCR (qPCR) based HR-HPV test, reverse transcription qPCR (RT-qPCR), and agarose gel electrophoresis...
January 16, 2018: Diagnostic Cytopathology
https://www.readbyqxmd.com/read/29341452/contribution-of-mlh1-constitutional-methylation-for-lynch-syndrome-diagnosis-in-patients-with-tumor-mlh1-downregulation
#11
Diana Pinto, Carla Pinto, Joana Guerra, Manuela Pinheiro, Rui Santos, Hege Marie Vedeld, Zeremariam Yohannes, Ana Peixoto, Catarina Santos, Pedro Pinto, Paula Lopes, Ragnhild Lothe, Guro Elisabeth Lind, Rui Henrique, Manuel R Teixeira
Constitutional epimutation of the two major mismatch repair genes, MLH1 and MSH2, has been identified as an alternative mechanism that predisposes to the development of Lynch syndrome. In the present work, we aimed to investigate the prevalence of MLH1 constitutional methylation in colorectal cancer (CRC) patients with abnormal expression of the MLH1 protein in their tumors. In a series of 38 patients who met clinical criteria for Lynch syndrome genetic testing, with loss of MLH1 expression in the tumor and with no germline mutations in the MLH1 gene (35/38) or with tumors presenting the BRAF p...
January 17, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29339785/the-lncrna-gata6-as-epigenetically-regulates-endothelial-gene-expression-via-interaction-with-loxl2
#12
Philipp Neumann, Nicolas Jaé, Andrea Knau, Simone F Glaser, Youssef Fouani, Oliver Rossbach, Marcus Krüger, David John, Albrecht Bindereif, Phillip Grote, Reinier A Boon, Stefanie Dimmeler
Impaired or excessive growth of endothelial cells contributes to several diseases. However, the functional involvement of regulatory long non-coding RNAs in these processes is not well defined. Here, we show that the long non-coding antisense transcript of GATA6 (GATA6-AS) interacts with the epigenetic regulator LOXL2 to regulate endothelial gene expression via changes in histone methylation. Using RNA deep sequencing, we find that GATA6-AS is upregulated in endothelial cells during hypoxia. Silencing of GATA6-AS diminishes TGF-β2-induced endothelial-mesenchymal transition in vitro and promotes formation of blood vessels in mice...
January 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29338703/diagnostic-accuracy-and-prediction-increment-of-markers-of-epithelial-mesenchymal-transition-to-assess-cancer-cell-detachment-from-primary-tumors
#13
Evan L Busch, Prabhani Kuruppumullage Don, Haitao Chu, David B Richardson, Temitope O Keku, David A Eberhard, Christy L Avery, Robert S Sandler
BACKGROUND: Metastases play a role in about 90% of cancer deaths. Markers of epithelial-mesenchymal transition (EMT) measured in primary tumor cancer cells might provide diagnostic information about the likelihood that cancer cells have detached from the primary tumor. Used together with established diagnostic tests of detachment-lymph node evaluation and radiologic imaging-EMT marker measurements might improve the ability of clinicians to assess the patient's risk of metastatic disease...
January 16, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29338423/production-of-thermostable-multiple-enzymes-from-bacillus-amyloliquefaciens-kub29
#14
Kubendran Devaraj, Salma Aathika, Karthik Periyasamy, Premkumar Manickam Periyaraman, Shanmugam Palaniyandi, Sivanesan Subramanian
A strain of Bacillus amyloliquefaciens KUB29 was identified by 16S ribosomal RNA sequencing (Genbank: MF772779.1). Production of thermostable protease, amylase and lipase were done by the isolated strain. The produced enzymes were partially purified by ammonium precipitation followed by dialysis process. Protease and lipase enzymes are effectively used in bio-oil extraction from proteinaceous sample followed by transesterification to produce methyl ester. Amylase enzyme is widely used in food and laundry industry...
January 16, 2018: Natural Product Research
https://www.readbyqxmd.com/read/29338341/rna-sequencing-on-amomum-villosum-lour-induced-by-meja-identifies-the-genes-of-wrky-and-terpene-synthases-involved-in-terpene-biosynthesis
#15
Xueying He, Huan Wang, Jinfen Yang, Ke Deng, Teng Wang
Amomum villosum Lour. is an important Chinese medicine that has diverse medicinal functions, and mainly contains volatile terpenes This study aimed to explore the WRKY transcription factors (TFs) and terpene synthases (TPS) unigenes, which might be involved in terpene biosynthesis in A. villosum for providing some new information on the regulation of terpenes in plants. RNA sequencing of A.villosum-induced by methyl jasmonate (MeJA) revealed WRKY family was the second biggest TF family in the transcriptome...
January 16, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29337423/the-next-generation-of-melanocyte-data-genetic-epigenetic-and-transcriptional-resource-datasets-and-analysis-tools
#16
Stacie K Loftus
Genomics is a common thread linking all aspects of pigment cell biology, including melanocyte- and melanosome-related functions, pigmentary disorders, normal human pigmentation variation and melanoma. Recently, genomic-scale Next Generation Sequencing (NGS) analyses have rapidly expanded, because of reductions in sequencing costs, increased assay sensitivity, and smaller sample requirement. These NGS technologies have been adapted to assay RNA transcript expression, chromatin accessibility, DNA methylation, histone modifications, and transcription factor binding...
January 16, 2018: Pigment Cell & Melanoma Research
https://www.readbyqxmd.com/read/29337373/making-use-of-cancer-genomic-databases
#17
Chad J Creighton
The vast amounts of genomic data now deposited in public repositories represent rich resources for cancer researchers. Large-scale genomics initiatives such as The Cancer Genome Atlas have made available data from multiple molecular profiling platforms (e.g., somatic mutation, RNA and protein expression, and DNA methylation) for the same set of over 10,000 human tumors. There has been much collective effort toward providing user-friendly software tools for biologists lacking computational skills to ask questions of large-scale genomic datasets...
January 16, 2018: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/29336373/advances-of-long-noncoding-rnas-mediated-regulation-in-reproduction
#18
REVIEW
Kang-Sheng Liu, Tai-Ping Li, Hua Ton, Xiao-Dong Mao, Ya-Jun Chen
OBJECTIVE: Advances in genomics and molecular biology have led to the discovery of a large group of uncharacterized long noncoding RNAs (lncRNAs). Emerging evidence indicated that many lncRNAs function in multiple biological processes and its dysregulation often causes diseases. Recent studies suggested that almost all regulatory lncRNAs interact with biological macromolecules such as DNA, RNA, and protein. LncRNAs regulate gene expression mainly on three levels, including epigenetic modification, transcription, and posttranscription, through DNA methylation, histone modification, and chromatin remodeling...
January 20, 2018: Chinese Medical Journal
https://www.readbyqxmd.com/read/29336230/alterations-of-global-dna-methylation-and-dnmt-expression-in-t-and-b-lymphocytes-from-patients-with-newly-diagnosed-aitd-after-treatment-a-follow-up-study
#19
Qingling Guo, Dan Wu, Huixin Yu, Jiandong Bao, Shiqiao Peng, Zhongyan Shan, Haixia Guan, Weiping Teng
BACKGROUND: Dysregulated DNA methylation in lymphocytes has been linked to autoimmune disorders. The aims of this study were to identify global DNA methylation patterns in patients with autoimmune thyroid diseases (AITDs) and to observe methylation changes after treatment for these conditions. METHODS: We conducted a cross-sectional study design including the following patients: 51 with newly diagnosed Graves' disease (GD), 28 with autoimmune hypothyroidism (AIT), 29 with positive thyroid autoantibodies (pTAb) and 39 matched healthy volunteers...
January 16, 2018: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/29335548/paternal-easirnas-regulate-parental-genome-dosage-in-arabidopsis
#20
German Martinez, Philip Wolff, Zhenxing Wang, Jordi Moreno-Romero, Juan Santos-González, Lei Liu Conze, Christopher DeFraia, R Keith Slotkin, Claudia Köhler
The regulation of parental genome dosage is of fundamental importance in animals and plants, as exemplified by X-chromosome inactivation and dosage compensation. The 'triploid block' is a classic example of dosage regulation in plants that establishes a reproductive barrier between species differing in chromosome number1,2. This barrier acts in the embryo-nourishing endosperm tissue and induces the abortion of hybrid seeds through a yet unknown mechanism 3 . Here we show that depletion of paternal epigenetically activated small interfering RNAs (easiRNAs) bypasses the triploid block in response to increased paternal ploidy in Arabidopsis thaliana...
January 15, 2018: Nature Genetics
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