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https://www.readbyqxmd.com/read/28220433/small-rna-and-mrna-profiling-of-arabidopsis-in-response-to-phytophthora-infection-and-pamp-treatment
#1
Yingnan Hou, Wenbo Ma
Small non-coding RNAs (smRNAs) regulate gene expression at both transcriptional and post-transcriptional levels. Well known for their roles in development, smRNAs have emerged as important regulators of plant immunity. Upon pathogen perception, accumulation of specific smRNAs are found to be altered, presumably as a host defense response. Therefore, identification of differentially accumulated smRNAs and their target genes would provide important insight into the regulation mechanism of immune responses. Here, we describe the detailed experimental procedure using Illumina sequencing to analyze the expression profiles of smRNAs and mRNAs in Arabidopsis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28220336/micrornas-in-model-and-complex-organisms
#2
EDITORIAL
Hikmet Budak, Baohong Zhang
Non-coding RNAs such as microRNAs (miRNAs) are very tiny ribonucleotides having an essential role in gene regulation at both post-transcriptional and translational levels. They are very conserved and expressed in worms, flies, plants, and mammals in a sequence-specific manner. Furthermore, it is now possible to clone miRNAs using the new genome editing tool CRISPR/cas9, which shows benefit in control of untargeted effect. In this special issue, we tried to cover researches associated with functional roles of miRNAs accross model and complex organisms...
February 20, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28218277/mir-203-enhances-let-7-biogenesis-by-targeting-lin28b-to-suppress-tumor-growth-in-lung-cancer
#3
Yong Zhou, Hongwei Liang, Zhicong Liao, Yanbo Wang, Xiuting Hu, Xi Chen, Lin Xu, Zhibin Hu
Human cancers often exhibit increased microRNA (miRNA) biogenesis and global aberrant expression of miRNAs; thus, targeting the miRNA biogenesis pathway represents a novel strategy for cancer therapy. Here, we report that miR-203 enhances the biogenesis of tumor suppressor let-7 in lung cancer by directly targeting LIN28B. Specially, we found that the LIN28B protein levels were dramatically increased in lung cancer tissues, but its mRNA levels did not differ significantly, suggesting that a post-transcriptional mechanism is involved in LIN28B regulation...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28217707/microrna-regulation-of-human-pancreatic-cancer-stem-cells
#4
REVIEW
Yi-Fan Xu, Bethany N Hannafon, Wei-Qun Ding
microRNAs (miRNAs) are a group of small non-coding RNAs that function primarily in the post transcriptional regulation of gene expression in plants and animals. Deregulation of miRNA expression in cancer cells, including pancreatic cancer cells, is well documented, and the involvement of miRNAs in orchestrating tumor genesis and cancer progression has been recognized. This review focuses on recent reports demonstrating that miRNAs are involved in regulation of pancreatic cancer stem cells (CSCs). A number of miRNA species have been identified to be involved in regulating pancreatic CSCs, including miR-21, miR-34, miR-1246, miR-221, the miR-17-92 cluster, the miR-200 and let-7 families...
2017: Stem Cell Investigation
https://www.readbyqxmd.com/read/28217257/regulation-of-hepatic-microrna-expression-by-hepatocyte-nuclear-factor-4-alpha
#5
Hong Lu, Xiaohong Lei, Jerry Liu, Curtis Klaassen
AIM: To uncover the role of hepatocyte nuclear factor 4 alpha (HNF4α) in regulating hepatic expression of microRNAs. METHODS: Microarray and real-time PCR were used to determine hepatic expression of microRNAs in young-adult mice lacking Hnf4α expression in liver (Hnf4α-LivKO). Integrative genomics viewer software was used to analyze the public chromatin immunoprecipitation-sequencing datasets for DNA-binding of HNF4α, RNA polymerase-II, and histone modifications to loci of microRNAs in mouse liver and human hepatoma cells...
February 8, 2017: World Journal of Hepatology
https://www.readbyqxmd.com/read/28217095/endogenous-protein-interactome-of-human-udp-glucuronosyltransferases-exposed-by-untargeted-proteomics
#6
Michèle Rouleau, Yannick Audet-Delage, Sylvie Desjardins, Mélanie Rouleau, Camille Girard-Bock, Chantal Guillemette
The conjugative metabolism mediated by UDP-glucuronosyltransferase enzymes (UGTs) significantly influences the bioavailability and biological responses of endogenous molecule substrates and xenobiotics including drugs. UGTs participate in the regulation of cellular homeostasis by limiting stress induced by toxic molecules, and by controlling hormonal signaling networks. Glucuronidation is highly regulated at genomic, transcriptional, post-transcriptional and post-translational levels. However, the UGT protein interaction network, which is likely to influence glucuronidation, has received little attention...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28217005/chromatin-based-epigenetic-regulation-of-plant-abiotic-stress-response
#7
Garima Pandey, Namisha Sharma, Pranav Pankaj Sahu, Manoj Prasad
Plants are continuously exposed to various abiotic and biotic factors limiting their growth and reproduction. In response, they need various sophisticated ways to adapt to adverse environmental conditions without compromising their proper development, reproductive success and eventually survival. This requires an intricate network to regulate gene expression at transcriptional and post-transcriptional levels, including epigenetic switches. Changes in chromatin modifications such as DNA and histone methylation have been observed in plants upon exposure to several abiotic stresses...
December 2016: Current Genomics
https://www.readbyqxmd.com/read/28216634/detecting-rna-modifications-in-the-epitranscriptome-predict-and-validate
#8
REVIEW
Mark Helm, Yuri Motorin
RNA modifications are emerging players in the field of post-transcriptional regulation of gene expression, and are attracting a comparable degree of research interest to DNA and histone modifications in the field of epigenetics. We now know of more than 150 RNA modifications and the true potential of a few of these is currently emerging as the consequence of a leap in detection technology, principally associated with high-throughput sequencing. This Review outlines the major developments in this field through a structured discussion of detection principles, lays out advantages and drawbacks of new high-throughput methods and presents conventional biophysical identification of modifications as meaningful ways for validation...
February 20, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28216628/genome-wide-primary-transcriptome-analysis-of-h2-producing-archaeon-thermococcus-onnurineus-na1
#9
Suhyung Cho, Min-Sik Kim, Yujin Jeong, Bo-Rahm Lee, Jung-Hyun Lee, Sung Gyun Kang, Byung-Kwan Cho
In spite of their pivotal roles in transcriptional and post-transcriptional processes, the regulatory elements of archaeal genomes are not yet fully understood. Here, we determine the primary transcriptome of the H2-producing archaeon Thermococcus onnurineus NA1. We identified 1,082 purine-rich transcription initiation sites along with well-conserved TATA box, A-rich B recognition element (BRE), and promoter proximal element (PPE) motif in promoter regions, a high pyrimidine nucleotide content (T/C) at the -1 position, and Shine-Dalgarno (SD) motifs (GGDGRD) in 5' untranslated regions (5' UTRs)...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28216286/rnf8-identified-as-a-co-activator-of-estrogen-receptor-%C3%AE-promotes-cell-growth-in-breast-cancer
#10
Shengli Wang, Hao Luo, Chunyu Wang, Hongmiao Sun, Ge Sun, Ning Sun, Kai Zeng, Huijuan Song, Renlong Zou, Tingting Zhou, Rijiao Cong, Wei Liu, Lei Yang, Da Li, Xin Zhou, Xinping Zhong, Lin Lin, Jiao Jiao, Guangqi Yan, Xue Wang, Xiaojie Min, Liu Cao, Yue Zhao
The ring finger protein 8 (RNF8), a key component of protein complex crucial for DNA-damage response, consists of a forkhead-associated (FHA) domain and a really interesting new gene (RING) domain that enables it to function as an E3 ubiquitin ligase. However, the biological functions of RNF8 in estrogen receptor α (ERα)-positive breast cancer and underlying mechanisms have not been fully defined. Here, we have explored RNF8 as an associated partner of ERα in breast cancer cells, and co-activates ERα-mediated transactivation...
February 12, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28214646/new-rna-seq-approaches-for-the-study-of-bacterial-pathogens
#11
REVIEW
Antoine-Emmanuel Saliba, Sara C Santos, Jörg Vogel
Understanding how bacteria cause disease requires knowledge of which genes are expressed and how they are regulated during infection. While RNA-seq is now a routine method for gene expression analysis in bacterial pathogens, the past years have also witnessed a surge of novel RNA-seq based approaches going beyond standard mRNA profiling. These include variations of the technique to capture post-transcriptional networks controlled by small RNAs and to discover associated RNA-binding proteins in the pathogen itself...
February 16, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28213476/editing-of-mitochondrial-transcripts-nad3-and-cox2-by-dek10-is-essential-for-mitochondrial-function-and-maize-plant-development
#12
Weiwei Qi, Zhongrui Tian, Lei Lu, Xiuzu Chen, Xinze Chen, Wei Zhang, Rentao Song
Respiration, the core of mitochondrial metabolism, depends on the function of five respiratory complexes. Many respiratory chain related proteins are encoded by the mitochondrial genome and their RNAs undergo post-transcriptional modifications by nuclear genome expressed factors, including pentatricopeptide repeat (PPR) proteins. Maize defective kernel 10 (dek10) is a classic mutant with small kernels and delayed development. Through positional cloning we found that Dek10 encodes an E-subgroup PPR protein localized in mitochondria...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28212892/atf2-a-paradigm-of-the-multifaceted-regulation-of-transcription-factors-in-biology-and-disease
#13
REVIEW
Gregory Watson, Ze'ev Ronai, Eric Lau
Stringent transcriptional regulation is crucial for normal cellular biology and organismal development. Perturbations in the proper regulation of transcription factors can result in numerous pathologies, including cancer. Thus, understanding how transcription factors are regulated and how they are dysregulated in disease states is key to the therapeutic targeting of these factors and/or the pathways that they regulate. Activating transcription factor 2 (ATF2) has been studied in a number of developmental and pathological conditions...
February 14, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28212751/stable-heritable-germline-silencing-directs-somatic-silencing-at-an-endogenous-locus
#14
Olga Minkina, Craig P Hunter
The importance of transgenerationally inherited epigenetic states to organismal fitness remains unknown as well-documented examples are often not amenable to mechanistic analysis or rely on artificial reporter loci. Here we describe an induced silenced state at an endogenous locus that persists, at 100% transmission without selection, for up to 13 generations. This unusually persistent silencing enables a detailed molecular genetic analysis of an inherited epigenetic state. We find that silencing is dependent on germline nuclear RNAi factors and post-transcriptional mechanisms...
February 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28212565/the-mir-675-5p-regulates-the-progression-and-development-of-pancreatic-cancer-via-the-ubqln1-zeb1-mir200-axis
#15
Jue Wang, Youli Zhang, Hong Wei, Xingxing Zhang, Yan Wu, Aihua Gong, Yu Xia, Wenbing Wang, Min Xu
Pancreatic cancer (PC) is a highly lethal disease due to extensive metastatic lesions. Accumulating evidence suggests that miR-675-5p plays different roles in metastasis through the regulation of epithelial to mesenchymal (EMT) and the mesenchymal to epithelial transitions (MET) in different cancers. ZEB1 promotes the EMT process by controlling the expression of E-cadherin and may have a reciprocal regulation with Ubiquilin1 (UBQLN1) and mir-200 family in cancer progression. In the present study, we showed that decreased expression of miR-675-5p is associated with the enhanced cell proliferation and survival of PC cells, while the increased expression of mir-675-5p shows the opposite one...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28212430/a-calmodulin-like-protein-suppresses-rna-silencing-and-promotes-geminivirus-infection-by-degrading-sgs3-via-the-autophagy-pathway-in-nicotiana-benthamiana
#16
Fangfang Li, Nan Zhao, Zhenghe Li, Xiongbiao Xu, Yaqin Wang, Xiuling Yang, Shu-Sheng Liu, Aiming Wang, Xueping Zhou
A recently characterized calmodulin-like protein is an endogenous RNA silencing suppressor that suppresses sense-RNA induced post-transcriptional gene silencing (S-PTGS) and enhances virus infection, but the mechanism underlying calmodulin-like protein-mediated S-PTGS suppression is obscure. Here, we show that a calmodulin-like protein from Nicotiana benthamiana (NbCaM) interacts with Suppressor of Gene Silencing 3 (NbSGS3). Deletion analyses showed that domains essential for the interaction between NbSGS3 and NbCaM are also required for the subcellular localization of NbSGS3 and NbCaM suppressor activity...
February 17, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28212427/rbm46-regulates-mouse-embryonic-stem-cell-differentiation-by-targeting-%C3%AE-catenin-mrna-for-degradation
#17
Lei Zhai, Chenchen Wang, Yuanfan Chen, Shixin Zhou, Lingsong Li
Embryonic stem cells (ESCs) are pluripotent cells and have the capability for differentiation into any of the three embryonic germ layers. The Wnt/β-Catenin pathway has been shown to play an essential role in ESC differentiation regulation. Activation of β-Catenin by post-translational modification has been extensively studied. However, mechanism(s) of post-transcriptional regulation of β-Catenin are not well defined. In this study, we report an RNA recognition motif-containing protein (RNA binding motif protein 46, RBM46) which regulates the degradation of β-Catenin mRNA...
2017: PloS One
https://www.readbyqxmd.com/read/28212376/the-legionella-pneumophila-genome-evolved-to-accommodate-multiple-regulatory-mechanisms-controlled-by-the-csra-system
#18
Tobias Sahr, Christophe Rusniok, Francis Impens, Giulia Oliva, Odile Sismeiro, Jean-Yves Coppée, Carmen Buchrieser
The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. Here we identified and analyzed the direct targets of CsrA in the human pathogen Legionella pneumophila. Genome wide transcriptome, proteome and RNA-Co-immunoprecipitaion followed by deep sequencing of a wild type and a csrA mutant strain identified 479 RNAs with potential CsrA interaction sites located in the untranslated and/or coding regions of mRNAs or of known non-coding sRNAs...
February 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28208755/micrornas-new-insight-in-modulating-follicular-atresia-a-review
#19
REVIEW
Tesfaye Worku, Zia Ur Rehman, Hira Sajjad Talpur, Dinesh Bhattarai, Farman Ullah, Ngabu Malobi, Tesfaye Kebede, Liguo Yang
Our understanding of the post-transcriptional mechanisms involved in follicular atresia is limited; however, an important development has been made in understanding the biological regulatory networks responsible for mediating follicular atresia. MicroRNAs have come to be seen as a key regulatory actor in determining cell fate in a wide range of tissues in normal and pathological processes. Profiling studies of miRNAs during follicular atresia and development have identified several putative miRNAs enriched in apoptosis signaling pathways...
February 9, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28207953/sgs1-a-neomorphic-nac52-allele-impairing-ptgs-through-sgs3-down-regulation
#20
Nicolas Butel, Ivan Le Masson, Nathalie Bouteiller, Hervé Vaucheret, Taline Elmayan
Post-transcriptional gene silencing (PTGS) is a defense mechanism that targets invading nucleic acids from endogenous (transposons) or exogenous (pathogens, transgenes) origins. Genetic screens based on the reactivation of silenced transgenes have long been used to identify cellular PTGS components and regulators. Here we show that the first isolated PTGS-deficient mutant, sgs1, is impaired in the transcription factor NAC52. This mutant exhibits striking similarities with a mutant impaired in the H3K4me3 demethylase JMJ14 isolated from the same genetic screen...
February 16, 2017: Plant Journal: for Cell and Molecular Biology
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