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RNA biogenesis

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https://www.readbyqxmd.com/read/28453394/expression-of-mir-23a-by-apoptotic-regulators-in-human-cancer-a-review
#1
Rabih Roufayel, Seifedine Kadry
MicroRNAs play fundamental roles in mammalian development, differentiation and cellular homeostasis by regulating essential processes such as proliferation, migration, metabolism, migration and cell death. These small non-coding RNAs are also responsible in RNA silencing, and in many developmental and pathological processes. Not surprisingly, miR-23a misexpression contributes to numerous diseases including cancer where certain miRNA genes have been classified as either oncogenes or tumor suppressor genes. Since a single microRNA is capable of targeting a large number of mRNA sequences, de-regulated miRNA expression has the ability to alter various transcripts and activate a wide range of cancer-related pathways...
April 28, 2017: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/28448529/a-genome-wide-analysis-of-the-rna-guided-silencing-pathway-in-coffee-reveals-insights-into-its-regulatory-mechanisms
#2
Christiane Noronha Fernandes-Brum, Pâmela Marinho Rezende, Thales Henrique Cherubino Ribeiro, Raphael Ricon de Oliveira, Thaís Cunha de Sousa Cardoso, Laurence Rodrigues do Amaral, Matheus de Souza Gomes, Antonio Chalfun-Junior
microRNAs (miRNAs) are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs) are derived from double-stranded RNA (dsRNA) or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL) in processing the smallRNAs (sRNAs) and ARGONAUTE (AGO) as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR), Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover...
2017: PloS One
https://www.readbyqxmd.com/read/28442996/structural-characteristics-of-simple-rna-repeats-associated-with-disease-and-their-deleterious-protein-interactions
#3
REVIEW
Adam Ciesiolka, Magdalena Jazurek, Karolina Drazkowska, Wlodzimierz J Krzyzosiak
Short Tandem Repeats (STRs) are frequent entities in many transcripts, however, in some cases, pathological events occur when a critical repeat length is reached. This phenomenon is observed in various neurological disorders, such as myotonic dystrophy type 1 (DM1), fragile X-associated tremor/ataxia syndrome, C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), and polyglutamine diseases, such as Huntington's disease (HD) and spinocerebellar ataxias (SCA). The pathological effects of these repeats are triggered by mutant RNA transcripts and/or encoded mutant proteins, which depend on the localization of the expanded repeats in non-coding or coding regions...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28441533/a-global-view-of-rna-protein-interactions-identifies-post-transcriptional-regulators-of-root-hair-cell-fate
#4
Shawn W Foley, Sager J Gosai, Dongxue Wang, Nur Selamoglu, Amelia C Sollitti, Tino Köster, Alexander Steffen, Eric Lyons, Fevzi Daldal, Benjamin A Garcia, Dorothee Staiger, Roger B Deal, Brian D Gregory
The Arabidopsis thaliana root epidermis is comprised of two cell types, hair and nonhair cells, which differentiate from the same precursor. Although the transcriptional programs regulating these events are well studied, post-transcriptional factors functioning in this cell fate decision are mostly unknown. Here, we globally identify RNA-protein interactions and RNA secondary structure in hair and nonhair cell nuclei. This analysis reveals distinct structural and protein binding patterns across both transcriptomes, allowing identification of differential RNA binding protein (RBP) recognition sites...
April 24, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28437065/a-macrocyclic-peptide-ligand-binds-the-oncogenic-microrna-21-precursor-and-suppresses-dicer-processing
#5
Matthew D Shortridge, Matthew J Walker, Tom Pavelitz, Yu Chen, Gabriele Varani
MicroRNAs (miRNAs) help orchestrate cellular growth and survival through post-transcriptional mechanisms. The dysregulation of miRNA biogenesis can lead to cellular growth defects, chemotherapeutic resistance and plays a direct role in the development of many chronic diseases. Among these RNAs, miR-21 is consistently overexpressed in most human cancers leading to the down regulation of key tumor suppressing and pro-apoptotic factors; suggesting that inhibition of miR-21 biogenesis could reverse these negative effects...
April 24, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28431265/nucleolar-reorganization-in-response-to-rdna-damage
#6
REVIEW
Marjolein van Sluis, Brian McStay
Nucleoli, sites of ribosome biogenesis, form around nucleolar organizer regions (NORs) comprising rDNA arrays, located on human acrocentric chromosome p-arms. NORs provide an opportunity to investigate the DNA double strand break (DSB) response at highly transcribed, repetitive, essential loci. Targeted introduction of DSBs into rDNA results in ATM-dependent inhibition of RNA-polymerase I transcription, coupled with movement of rDNA from the nucleolar interior to anchoring points at the periphery. Reorganization renders rDNA accessible to repair factors, normally excluded from nucleoli...
April 18, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28431233/a-compendium-of-rna-binding-proteins-that-regulate-microrna-biogenesis
#7
Thomas Treiber, Nora Treiber, Uwe Plessmann, Simone Harlander, Julia-Lisa Daiß, Norbert Eichner, Gerhard Lehmann, Kevin Schall, Henning Urlaub, Gunter Meister
During microRNA (miRNA) biogenesis, two endonucleolytic reactions convert stem-loop-structured precursors into mature miRNAs. These processing steps can be posttranscriptionally regulated by RNA-binding proteins (RBPs). Here, we have used a proteomics-based pull-down approach to map and characterize the interactome of a multitude of pre-miRNAs. We identify ∼180 RBPs that interact specifically with distinct pre-miRNAs. For functional validation, we combined RNAi and CRISPR/Cas-mediated knockout experiments to analyze RBP-dependent changes in miRNA levels...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28430077/host-pathogen-interactions-modulated-by-small-rnas
#8
Waqar Islam, Zujian Wu, Saif Ul Islam
Biological processes such as defense mechanisms and microbial offence strategies are regulated through RNA induced interference in eukaryotes. Genetic mutations are modulated through biogenesis of small RNAs which directly impacts upon host development. Plant defense mechanisms are regulated and supported by a diversified group of small RNAs which are involved in streamlining several RNA interference pathways leading towards the initiation of pathogen gene silencing mechanisms. In the similar context, pathogens also utilize the support of small RNAs to launch their offensive attacks...
April 21, 2017: RNA Biology
https://www.readbyqxmd.com/read/28429085/the-role-of-rna-alternative-splicing-in-regulating-cancer-metabolism
#9
REVIEW
Itamar Kozlovski, Zahava Siegfried, Adi Amar-Schwartz, Rotem Karni
Tumor cells alter their metabolism by a wide array of mechanisms to promote growth and proliferation. Dysregulated expression and/or somatic mutations of key components of the glycolytic pathway/TCA cycle as well as other metabolic pathways allow tumor cells to improve their ability to survive harsh conditions such as hypoxia and the presence of reactive oxygen species, as well as the ability to obtain nutrients to increase lipids, protein, and nucleic acids biogenesis. Approximately 95% of the human protein encoding genes undergo alternative splicing (AS), a regulated process of gene expression that greatly diversifies the proteome by creating multiple proteins from a single gene...
April 20, 2017: Human Genetics
https://www.readbyqxmd.com/read/28425468/transcriptome-analysis-of-mango-mangifera-indica-l-fruit-epidermal-peel-to-identify-putative-cuticle-associated-genes
#10
Julio C Tafolla-Arellano, Yi Zheng, Honghe Sun, Chen Jiao, Eliel Ruiz-May, Miguel A Hernández-Oñate, Alberto González-León, Reginaldo Báez-Sañudo, Zhangjun Fei, David Domozych, Jocelyn K C Rose, Martín E Tiznado-Hernández
Mango fruit (Mangifera indica L.) are highly perishable and have a limited shelf life, due to postharvest desiccation and senescence, which limits their global distribution. Recent studies of tomato fruit suggest that these traits are influenced by the expression of genes that are associated with cuticle metabolism. However, studies of these phenomena in mango fruit are limited by the lack of genome-scale data. In order to gain insight into the mango cuticle biogenesis and identify putative cuticle-associated genes, we analyzed the transcriptomes of peels from ripe and overripe mango fruit using RNA-Seq...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28420675/integrative-analysis-unveils-new-functions-for-the-drosophila-cutoff-protein-in-non-coding-rna-biogenesis-and-gene-regulation
#11
Yuri Pritykin, Tarcisio Brito, Trudi Schupbach, Mona Singh, Attilio Pane
Piwi-Interacting RNAs (piRNAs) are central components of the piRNA pathway, which directs transposon silencing and guarantees genome integrity in the germ cells of several metazoans. In Drosophila, piRNAs are produced from discrete regions of the genome termed piRNA clusters, whose expression relies on the RDC complex comprised of the core proteins Rhino, Deadlock and Cutoff. To date, the RDC complex has been exclusively implicated in the regulation of the piRNA loci. Here we further elucidate the function of Cutoff and the RDC complex by performing genome-wide ChIP-seq and RNA-seq assays in the Drosophila germline and analyzing these data together with other publicly available data sets...
April 18, 2017: RNA
https://www.readbyqxmd.com/read/28419777/micrornas-as-biomarkers-for-psychiatric-disorders-with-a-focus-on-autism-spectrum-disorder-current-progress-in-genetic-association-studies-expression-profiling-and-translational-research
#12
REVIEW
Yubin Hu, Erik A Ehli, Dorret I Boomsma
MicroRNAs (miRNAs) are a group of small noncoding RNA molecules, 18-25 nucleotides in length, which can negatively regulate gene expression at the post-transcriptional level by binding to messenger RNAs. About half of all identified miRNAs in humans are expressed in the brain and display regulatory functions important for many biological processes related to the development of the central nervous system (CNS). Disruptions in miRNA biogenesis and miRNA-target interaction have been related to CNS diseases, including psychiatric disorders...
April 17, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28416566/structure-of-deah-rha-atpase-prp43p-bound-to-rna-implicates-a-pair-of-hairpins-and-motif-va-in-translocation-along-rna
#13
Yangzi He, Jonathan P Staley, Gregers Rom Andersen, Klaus H Nielsen
Three families of nucleic acid-dependent ATPases (DEAH/RHA, Ski2-like and NS3/NPH-II), termed the DExH ATPases, are thought to execute myriad functions by processive, ATP-dependent, 3' to 5' translocation along single-stranded nucleic acid. While the mechanism of translocation of the viral NS3/NPH-II family has been studied extensively, it has not been clear if or how the principles that have emerged for this family extend to the other two families. Here we report the crystal structure of the yeast DEAH/RHA family ATPase Prp43p, which functions in splicing and ribosome biogenesis, in complex with poly-uracil and a non-hydrolysable ATP analogue...
April 17, 2017: RNA
https://www.readbyqxmd.com/read/28416533/capturing-in-vivo-rna-transcriptional-dynamics-from-the-malaria-parasite-plasmodium-falciparum
#14
Heather J Painter, Manuela Carrasquilla, Manuel Llinás
To capture the transcriptional dynamics within proliferating cells, methods to differentiate nascent transcription from pre-existing mRNAs are desired. One approach is to label newly synthesized mRNA transcripts in vivo through the incorporation of modified pyrimidines. However, the human malaria parasite, Plasmodium falciparum, is incapable of pyrimidine salvage for mRNA biogenesis. To capture cellular mRNA dynamics during Plasmodium development, we engineered parasites that can salvage pyrimidines through the expression of a single bifunctional yeast fusion gene, cytosine deaminase/uracil phosphoribosyltransferase (FCU)...
April 17, 2017: Genome Research
https://www.readbyqxmd.com/read/28415970/drosophila-melanogaster-retrotransposon-and-inverted-repeat-derived-endogenous-sirnas-are-differentially-processed-in-distinct-cellular-locations
#15
Andrew W Harrington, Michael R McKain, Daniel Michalski, Kaylyn M Bauer, Joshua M Daugherty, Mindy Steiniger
BACKGROUND: Endogenous small interfering (esi)RNAs repress mRNA levels and retrotransposon mobility in Drosophila somatic cells by poorly understood mechanisms. 21 nucleotide esiRNAs are primarily generated from retrotransposons and two inverted repeat (hairpin) loci in Drosophila culture cells in a Dicer2 dependent manner. Additionally, proteins involved in 3' end processing, such as Symplekin, CPSF73 and CPSR100, have been recently implicated in the esiRNA pathway. RESULTS: Here we present evidence of overlap between two essential RNA metabolic pathways: esiRNA biogenesis and mRNA 3' end processing...
April 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28414550/expression-of-long-noncoding-rna-urothelial-cancer-associated-1-promotes-cisplatin-resistance-in-cervical-cancer
#16
Bi Wang, Zhi Huang, Rui Gao, Zhu Zeng, Weiming Yang, Yuan Sun, Wei Wei, Zhongqing Wu, Lei Yu, Qinshan Li, Shuai Zhang, Fenghu Li, Guoli Liu, Bingjie Liu, Li Leng, Wei Zhan, Yanlong Yu, Guozhen Yang, Shi Zhou
Cisplatin resistance is still one of the main reasons for failure of clinical therapy for cervical cancer. But the underlying molecular mechanisms involved in cisplatin resistance of cervical cancer have still remained unclear. Recent studies reported that long noncoding RNAs (lncRNAs) are novel nonprotein-coding transcripts, which might play a key role in cancer biogenesis and prognosis. One of the lncRNAs, urothelial cancer associated 1 (UCA1), has been shown to promote different types of cancer cell proliferation, migration, and invasion...
April 2017: Cancer Biotherapy & Radiopharmaceuticals
https://www.readbyqxmd.com/read/28409453/sirna-mediated-silencing-of-peroxisomal-genes-in-mammalian-cells
#17
Tina A Schrader, Michael Schrader
RNAi technologies are a valuable tool in the identification and investigation of proteins that are involved in peroxisome biogenesis and function. Small interfering RNA (siRNA) has developed into the most commonly used RNAi tool for the induction of transient, short-term silencing of protein coding genes. Although siRNA can induce gene knockdown in a variety of mammalian cell lines, their utility is limited by efficient uptake of synthetic oligonucleotides into the cells. Here, we describe different transfection methods that have been successfully used by us to silence peroxisomal genes in a variety of cell lines, including primary human skin fibroblasts, which are usually difficult to transfect...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28407097/mircat2-accurate-prediction-of-plant-and-animal-micrornas-from-next-generation-sequencing-datasets
#18
Claudia Paicu, Irina Mohorianu, Matthew Stocks, Ping Xu, Aurore Coince, Martina Billmeier, Tamas Dalmay, Vincent Moulton, Simon Moxon
Motivation: MicroRNAs are a class of _21-22 nucleotide small RNAs which are excised from a stable hairpin-like secondary structure. They have important gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in eukaryotes. There are several computational tools for miRNA detection from next-generation sequencing (NGS) datasets. However, many of these tools suffer from high false positive and false negative rates. Here we present a novel miRNA prediction algorithm, miRCat2...
April 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28405745/lethal-albinic-seedling-encoding-a-threonyl-trna-synthetase-is-involved-in-development-of-plastid-protein-synthesis-system-in-rice
#19
Yuan-Yan Zhang, Yuan-Yuan Hao, Yi-Hua Wang, Chun-Ming Wang, Yun-Long Wang, Wu-Hua Long, Di Wang, Xi Liu, Ling Jiang, Jian-Min Wan
An albinic rice is caused by mutation of threonyl-tRNA synthetase, which is essential for plant development by stabilizing of NEP and PEP gene expressions and chloroplast protein synthesis. Chloroplast biogenesis and development depend on complex genetic mechanisms. Apart from their function in translation, aminoacyl-tRNA synthetases (aaRSs) play additional role in gene expression regulation, RNA splicing, and cytokine activity. However, their detailed functions in plant development are still poorly understood...
April 12, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28402503/poly-a-specific-ribonuclease-is-a-nuclear-ribosome-biogenesis-factor-involved-in-human-18s-rrna-maturation
#20
Christian Montellese, Nathalie Montel-Lehry, Anthony K Henras, Ulrike Kutay, Pierre-Emmanuel Gleizes, Marie-Françoise O'Donohue
The poly-A specific ribonuclease (PARN), initially characterized for its role in mRNA catabolism, supports the processing of different types of non-coding RNAs including telomerase RNA. Mutations in PARN are linked to dyskeratosis congenita and pulmonary fibrosis. Here, we show that PARN is part of the enzymatic machinery that matures the human 18S ribosomal RNA (rRNA). Consistent with its nucleolar steady-state localization, PARN is required for 40S ribosomal subunit production and co-purifies with 40S subunit precursors...
April 10, 2017: Nucleic Acids Research
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