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RNA biogenesis

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https://www.readbyqxmd.com/read/29146266/endophytism-or-saprophytism-decoding-the-lifestyle-transition-of-the-generalist-fungus-phomopsis-liquidambari
#1
Jun Zhou, Xin Li, Peng-Wei Huang, Chuan-Chao Dai
Filamentous ascomycete Phomopsis sp. are common inhabitants of natural ecosystems and, as saprophytes, are largely responsible for the destructive decay of litterfall, promoting the carbon and nitrogen cycles. Phomopsis liquidambari B3 can establish mutualistic symbiosis with a broad spectrum of crop plants. Colonizing dynamics observations and a growth promotion assay of rice and Arabidopsis thaliana revealed that the B3 colonization strategy is host-adapted and resulted in different growth promotions influenced by N availability...
January 2018: Microbiological Research
https://www.readbyqxmd.com/read/29144434/the-role-of-non-coding-rnas-in-cytoplasmic-male-sterility-in-flowering-plants
#2
REVIEW
Helena Štorchová
The interactions between mitochondria and nucleus substantially influence plant development, stress response and morphological features. The prominent example of a mitochondrial-nuclear interaction is cytoplasmic male sterility (CMS), when plants produce aborted anthers or inviable pollen. The genes responsible for CMS are located in mitochondrial genome, but their expression is controlled by nuclear genes, called fertility restorers. Recent explosion of high-throughput sequencing methods enabled to study transcriptomic alterations in the level of non-coding RNAs under CMS biogenesis...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29143818/visualization-of-chemical-modifications-in-the-human-80s-ribosome-structure
#3
S Kundhavai Natchiar, Alexander G Myasnikov, Hanna Kratzat, Isabelle Hazemann, Bruno P Klaholz
Chemical modifications of human ribosomal RNA (rRNA) are introduced during biogenesis and have been implicated in the dysregulation of protein synthesis, as is found in cancer and other diseases. However, their role in this phenomenon is unknown. Here we visualize more than 130 individual rRNA modifications in the three-dimensional structure of the human ribosome, explaining their structural and functional roles. In addition to a small number of universally conserved sites, we identify many eukaryote- or human-specific modifications and unique sites that form an extended shell in comparison to bacterial ribosomes, and which stabilize the RNA...
November 15, 2017: Nature
https://www.readbyqxmd.com/read/29143558/perturbation-of-rna-polymerase-i-transcription-machinery-by-ablation-of-heatr1-triggers-the-rpl5-rpl11-mdm2-p53-ribosome-biogenesis-stress-checkpoint-pathway-in-human-cells
#4
Zsofia Turi, Marketa Senkyrikova, Martin Mistrik, Jiri Bartek, Pavel Moudry
Ribosome biogenesis is an energy consuming process which takes place mainly in the nucleolus. By producing ribosomes to fuel protein synthesis, it is tightly connected with cell growth and cell cycle control. Perturbation of ribosome biogenesis leads to the activation of p53 tumor suppressor protein promoting processes like cell cycle arrest, apoptosis or senescence. This ribosome biogenesis stress pathway activates p53 through sequestration of MDM2 by a subset of ribosomal proteins (RPs), thereby stabilizing p53...
November 16, 2017: Cell Cycle
https://www.readbyqxmd.com/read/29139335/shprh-as-a-new-player-in-ribosomal-rna-transcription-and-its-potential-role-in-homeostasis-of-ribosomal-dna-repeats
#5
Deokjae Lee, Jun Hong Park, Shinseog Kim, Seon-Gyeong Lee, Kyungjae Myung
There are hundreds of copies of rDNA repeats in mammalian chromosomes and the ratio of active, poised, or inactive rDNA is regulated in epigenetic manners. Recent studies demonstrated that a post-DNA replication repair enzyme, SHPRH affects rRNA transcription by recognizing epigenetic markers on rDNA promoters and unveiled potential links between DNA repair and ribosome biogenesis (1) . This study suggests that SHPRH could be a link between mTOR-mediated epigenetic regulations and rRNA transcription, while concomitantly affecting genomic integrity...
November 15, 2017: Transcription
https://www.readbyqxmd.com/read/29138420/expression-of-both-poly-r-c-binding-protein-1-pcbp1-and-mirna-3978-is-suppressed-in-peritoneal-gastric-cancer-metastasis
#6
Fu-Jian Ji, Yuan-Yu Wu, Zhe An, Xue-Song Liu, Jun-Nan Jiang, Fang-Fang Chen, Xue-Dong Fang
The expression of legumain which has been shown overexpressed in patients with metastatic gastric cancer is positively correlated to both disease progression and outcome, and negatively correlated to microRNA (miR)-3978 expression. The RNA-binding protein, poly r(C) binding protein 1 (PCBP1) was the most downregulated protein in the metastatic tissue specimens. Quantitative real-time PCR showed that PCBP1 expression is transcriptionally downregulated in peritoneal metastasis tissues. RNA immunoprecipitation experiments showed that PCBP1 and miR-3978 are sequestered in normal peritoneal tissue, but the complex is disrupted following metastatic progression...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29134494/expression-of-telomere-associated-proteins-is-interdependent-to-stabilize-native-telomere-structure-and-telomere-dysfunction-by-g-quadruplex-ligand-causes-terra-upregulation
#7
Ratan Sadhukhan, Priyanka Chowdhury, Sourav Ghosh, Utpal Ghosh
Telomere DNA can form specialized nucleoprotein structure with telomere-associated proteins to hide free DNA ends or G-quadruplex structures under certain conditions especially in presence of G-quadruplex ligand. Telomere DNA is transcribed to form non-coding telomere repeat-containing RNA (TERRA) whose biogenesis and function is poorly understood. Our aim was to find the role of telomere-associated proteins and telomere structures in TERRA transcription. We silenced four [two shelterin (TRF1, TRF2) and two non-shelterin (PARP-1, SLX4)] telomere-associated genes using siRNA and verified depletion in protein level...
November 13, 2017: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29130960/piwi-proteins-and-piwi-interacting-rna-emerging-roles-in-cancer
#8
Yi-Neng Han, Yuan Li, Sheng-Qiang Xia, Yuan-Yuan Zhang, Jun-Hua Zheng, Wei Li
P-Element induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a type of noncoding RNAs (ncRNAs) and interact with PIWI proteins. piRNAs were primarily described in the germline, but emerging evidence revealed that piRNAs are expressed in a tissue-specific manner among multiple human somatic tissue types as well and play important roles in transposon silencing, epigenetic regulation, gene and protein regulation, genome rearrangement, spermatogenesis and germ stem-cell maintenance. PIWI proteins were first discovered in Drosophila and they play roles in spermatogenesis, germline stem-cell maintenance, self-renewal, retrotransposons silencing and the male germline mobility control...
November 3, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29130210/imaging-newly-transcribed-rna-in-cells-by-using-a-clickable-azide-modified-utp-analog
#9
Anupam A Sawant, Sanjeev Galande, Seergazhi G Srivatsan
Robust RNA labeling and imaging methods that enable the understanding of cellular RNA biogenesis and function are highly desired. In this context, we describe a practical chemical labeling method based on a bioorthogonal reaction, namely, azide-alkyne cycloaddition reaction, which facilitates the fluorescence imaging of newly transcribed RNA in both fixed and live cells. This strategy involves the transfection of an azide-modified UTP analog (AMUTP) into mammalian cells, which gets specifically incorporated into RNA transcripts by RNA polymerases present inside the cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29127290/ksrp-specifies-monocytic-and-granulocytic-differentiation-through-regulating-mir-129-biogenesis-and-runx1-expression
#10
Hongmei Zhao, Xiaoshuang Wang, Ping Yi, Yanmin Si, Puwen Tan, Jinrong He, Shan Yu, Yue Ren, Yanni Ma, Junwu Zhang, Dong Wang, Fang Wang, Jia Yu
RNA-binding proteins (RBPs) integrate the processing of RNAs into post-transcriptional gene regulation, but the direct contribution of them to myeloid cell specification is poorly understood. Here, we report the first global RBP transcriptomic analysis of myeloid differentiation by combining RNA-seq analysis with myeloid induction in CD34(+) hematopoietic progenitor cells. The downregulated expression of the KH-Type Splicing Regulatory Protein (KSRP) during monocytopoiesis and up-regulated expression during granulopoiesis suggests that KSRP has divergent roles during monocytic and granulocytic differentiation...
November 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/29126230/a-survey-of-software-tools-for-microrna-discovery-and-characterization-using-rna-seq
#11
Michele Bortolomeazzi, Enrico Gaffo, Stefania Bortoluzzi
Since the small RNA-sequencing (sRNA-seq) technology became available, it allowed the discovery of thousands new microRNAs (miRNAs) in humans and many other species, providing new data on these small RNAs (sRNAs) of high biological and translational relevance. MiRNA discovery has not yet reached saturation, even in the most studied model organisms, and many researchers are using sRNA-seq in studies with different aims in biomedicine, fundamental research and in applied animal sciences. We review several miRNA discovery and characterization software tools that implement different strategies, providing a useful guide for researchers to select the programs best suiting their study objectives and data...
November 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29124426/molecular-chaperones-involved-in-mitochondrial-iron-sulfur-protein-biogenesis
#12
REVIEW
Rafal Dutkiewicz, Malgorzata Nowak
Iron-sulfur (FeS) clusters are prosthetic groups critical for the function of many proteins in all domains of life. FeS proteins function in processes ranging from oxidative phosphorylation and cofactor biosyntheses to DNA/RNA metabolism and regulation of gene expression. In eukaryotic cells, mitochondria play a central role in the process of FeS biogenesis and support maturation of FeS proteins localized within mitochondria and in other cellular compartments. In humans, defects in mitochondrial FeS cluster biogenesis lead to numerous pathologies, which are often fatal...
November 9, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/29118118/n-myc-downstream-regulated-gene-1-restricts-hepatitis-c-virus-propagation-by-regulating-lipid-droplet-biogenesis-and-viral-assembly
#13
Cameron J Schweitzer, Fang Zhang, Audrey Boyer, Kristin Valdez, Maggie Cam, T Jake Liang
Host cells harbor various intrinsic mechanisms to restrict viral infections as a first line of antiviral defense. Viruses have evolved various countermeasures against these antiviral mechanisms. Here we show that N-Myc Downstream-Reguated Gene 1 (NDRG1) limits productive HCV infection by inhibiting viral assembly. Interestingly, HCV infection down-regulates NDRG1 protein and mRNA expression. Loss of NDRG1 increases the size and number of lipid droplets, which are the sites of HCV assembly. HCV suppresses NDRG1 expression by up-regulating MYC, which directly inhibits the transcription of NDRG1 Up-regulation of MYC also leads to reduced expression of NDRG1-specific kinase SGK1, resulting in markedly diminished phosphorylation of NDRG1...
November 8, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29115582/passenger-strand-of-mir-145-3p-acts-as-a-tumor-suppressor-by-targeting-myo1b-in-head-and-neck-squamous-cell-carcinoma
#14
Yasutaka Yamada, Keiichi Koshizuka, Toyoyuki Hanazawa, Naoko Kikkawa, Atsushi Okato, Tetsuya Idichi, Takayuki Arai, Sho Sugawara, Koji Katada, Yoshitaka Okamoto, Naohiko Seki
Analysis of the microRNA (miRNA) expression signature of head and neck squamous cell carcinoma (HNSCC) based on RNA sequencing showed that dual strands of pre‑miR‑145 (miR‑145‑5p, guide strand; and miR‑145‑3p, passenger strand) were significantly reduced in cancer tissues. In miRNA biogenesis, passenger strands of miRNAs are degraded and have no biological activities in cells. The aims of this study were to investigate the functional significance of the passenger strand of miR‑145 and to identify miR‑145‑3p‑regulated oncogenic genes in HNSCC cells...
November 6, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/29113304/significant-association-of-yap1-and-hspc111-proteins-with-poor-prognosis-in-chinese-gastric-cancer-patients
#15
Shanshan Huang, Lingling Zhu, Yuan Cao, Li Li, Yongtao Xie, Jun Deng, Jianping Xiong
Hippo-YAP1 is a tumor-suppressor signaling pathway that inhibits cell proliferation and accelerates apoptosis. However, the role of YAP1 in gastric cancer (GC) is still in dispute. Ribosomal biogenesis is closely correlated with human malignancies. HBV pre-S2 trans-regulated protein 3 (HSPC111) is a portion of an RNA-dependent complex and plays a crucial role in ribosome biosynthesis. Nevertheless, little is known about the expression and function of this factor in GC. In the present study, we evaluated the significance of YAP1 together with HSPC111 in gastric cancer...
October 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/29110746/lead-promotes-abnormal-angiogenesis-induced-by-ccm3-gene-defects-via-mitochondrial-pathway
#16
Y Sun, H Zhang, X Xing, Z Zhao, J He, J Li, J Chen, M Wang, Y He
Lead is one of the environmental pollutants with cardiovascular toxicity. The embryos are particularly sensitive to lead exposure, because it can move through the blood-placental barrier and the blood-brain barrier easily during embryonic development. Cerebral cavernous malformations 3 (CCM3) gene plays an important role in cardiovascular development, mainly affecting cell proliferation, differentiation and apoptosis. In this study, we established a blood vessel development model of mouse embryos in order to imitate human people with CCM3 genes defects and exposing to environment toxin Pb in utero...
November 7, 2017: Journal of Developmental Origins of Health and Disease
https://www.readbyqxmd.com/read/29109185/genome-wide-screens-reveal-new-gene-products-that-influence-genetic-competence-in-streptococcus-mutans
#17
Robert C Shields, Greg O'Brien, Natalie Maricic, Alexandria Kesterson, Megan Grace, Stephen J Hagen, Robert A Burne
A network of genes and at least two peptide signaling molecules tightly control when Streptococcus mutans becomes competent to take up DNA from its environment. Widespread changes in the expression of genes occur when S. mutans is presented with competence signal peptides in vitro, including increased production of the alternative sigma factor, ComX, which activates late competence genes. Still, the way that gene products that are regulated by competence peptides influence DNA uptake and cellular physiology are not well understood...
November 6, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/29109067/the-insertion-in-the-double-stranded-rna-binding-domain-of-human-drosha-is-important-for-its-function
#18
Xiaoxiao Zhang, Peng Li, Jian Lin, Haochu Huang, Bin Yin, Yan Zeng
microRNAs (miRNAs) are first transcribed as long, primary transcripts, which are then processed by multiple enzymes and proteins to generate the single-stranded, approximately 22-nucleotide (nt)-long mature miRNAs. A critical step in animal miRNA biogenesis is the cleavage of primary miRNA transcripts (pri-miRNAs) to produce precursor miRNAs (pre-miRNAs) by the enzyme Drosha. How Drosha recognizes its substrates remains incompletely understood. In this study we constructed a series of human Drosha mutants and examined their enzymatic activities and interaction with RNAs...
November 3, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29107738/extracellular-vesicles-released-from-mesenchymal-stromal-cells-stimulate-bone-growth-in-osteogenesis-imperfecta
#19
Satoru Otsuru, Laura Desbourdes, Adam J Guess, Ted J Hofmann, Theresa Relation, Takashi Kaito, Massimo Dominici, Masahiro Iwamoto, Edwin M Horwitz
BACKGROUND: Systemic infusion of mesenchymal stromal cells (MSCs) has been shown to induce acute acceleration of growth velocity in children with osteogenesis imperfecta (OI) despite minimal engraftment of infused MSCs in bones. Using an animal model of OI we have previously shown that MSC infusion stimulates chondrocyte proliferation in the growth plate and that this enhanced proliferation is also observed with infusion of MSC conditioned medium in lieu of MSCs, suggesting that bone growth is due to trophic effects of MSCs...
October 26, 2017: Cytotherapy
https://www.readbyqxmd.com/read/29107693/wdr74-participates-in-an-early-cleavage-of-the-pre-rrna-processing-pathway-in-cooperation-with-the-nucleolar-aaa-atpase-nvl2
#20
Nobuhiro Hiraishi, Yo-Ichi Ishida, Haruka Sudo, Masami Nagahama
WD repeat-containing protein 74 (WDR74), a nucleolar-localized protein, is the mammalian ortholog of Nsa1, a 60S ribosome assembly factor in yeast. We previously showed that WDR74 associates with MTR4, the nuclear exosome-assisting RNA helicase, whose dissociation is prohibited by an ATPase-deficient mutant of the AAA-type chaperone NVL2. However, the functions and regulation of WDR74 during ribosome biogenesis in cooperation with NVL2 remains unknown. Here, we demonstrated that knockdown of WDR74 leads to significant defects in the pre-rRNA cleavage within the internal transcribed spacer 1 (ITS1), occurring in an early stage of the processing pathway...
October 28, 2017: Biochemical and Biophysical Research Communications
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