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https://www.readbyqxmd.com/read/28521416/a-proposed-method-for-the-relative-quantification-of-levels-of-circulating-micrornas-in-the-plasma-of-gastric-cancer-patients
#1
Mayra-Cecilia Suárez-Arriaga, Javier Torres, Margarita Camorlinga-Ponce, Alejandro Gómez-Delgado, Patricia Piña-Sánchez, Hilda-Alicia Valdez-Salazar, Rosa-María Ribas-Aparicio, Ezequiel M Fuentes-Pananá, Martha-Eugenia Ruiz-Tachiquín
Gastric cancer (GC) is the fifth most common type of malignancy and the third leading cause of cancer-associated mortality worldwide. It is necessary to identify novel methods aimed at improving the early diagnosis and treatment of GC. MicroRNA expression profiles in the plasma of patients with GC have demonstrated a potential use in the opportune diagnosis of this neoplasm. However, there are currently no standardized targets for use in the normalization of microRNA Cq values for different neoplasms. The present study tested two normalization approaches while analyzing plasma derived from patients with GC and non-atrophic gastritis...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28505386/c-d-box-snornas-form-methylating-and-non-methylating-ribonucleoprotein-complexes-old-dogs-show-new-tricks
#2
REVIEW
Marina Falaleeva, Justin R Welden, Marilyn J Duncan, Stefan Stamm
C/D box snoRNAs (SNORDs) are an abundantly expressed class of short, non-coding RNAs that have been long known to perform 2'-O-methylation of rRNAs. However, approximately half of human SNORDs have no predictable rRNA targets, and numerous SNORDs have been associated with diseases that show no defects in rRNAs, among them Prader-Willi syndrome, Duplication 15q syndrome and cancer. This apparent discrepancy has been addressed by recent studies showing that SNORDs can act to regulate pre-mRNA alternative splicing, mRNA abundance, activate enzymes, and be processed into shorter ncRNAs resembling miRNAs and piRNAs...
May 15, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28505348/implication-of-the-box-c-d-snornp-assembly-factor-rsa1p-in-u3-snornp-assembly
#3
Benjamin Rothé, Xavier Manival, Nicolas Rolland, Christophe Charron, Véronique Senty-Ségault, Christiane Branlant, Bruno Charpentier
The U3 box C/D snoRNA is one key element of 90S pre-ribosome. It contains a 5΄ domain pairing with pre-rRNA and the U3B/C and U3C΄/D motifs for U3 packaging into a unique small nucleolar ribonucleoprotein particle (snoRNP). The RNA-binding protein Snu13/SNU13 nucleates on U3B/C the assembly of box C/D proteins Nop1p/FBL and Nop56p/NOP56, and the U3-specific protein Rrp9p/U3-55K. Snu13p/SNU13 has a much lower affinity for U3C΄/D but nevertheless forms on this motif an RNP with box C/D proteins Nop1p/FBL and Nop58p/NOP58...
May 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28503414/adult-onset-deletion-of-the-prader-willi-syndrome-susceptibility-gene-snord116-in-mice-results-in-reduced-feeding-and-increased-fat-mass
#4
Louise Purtell, Yue Qi, Lesley Campbell, Amanda Sainsbury, Herbert Herzog
BACKGROUND: The imprinted small nucleolar RNA (snoRNA) Snord116 is implicated in the aetiology of Prader-Willi syndrome (PWS), a disease associated with hyperphagia and obesity. Germline deletion of Snord116 in mice has been found to lead to increased food intake but not to the development of obesity. To determine the role of Snord116 independent of potential compensatory developmental factors, we investigated the effects of conditional adult-onset deletion of Snord116 in mice. METHODS: Deletion of Snord116 was induced at 8 weeks of age by oral administration of tamoxifen to male Snord(lox/lox); ROSA(cre/+) mice, with vehicle-treated mice used as controls...
April 2017: Translational pediatrics
https://www.readbyqxmd.com/read/28485729/altered-expression-of-histamine-signaling-genes-in-autism-spectrum-disorder
#5
C Wright, J H Shin, A Rajpurohit, A Deep-Soboslay, L Collado-Torres, N J Brandon, T M Hyde, J E Kleinman, A E Jaffe, A J Cross, D R Weinberger
The histaminergic system (HS) has a critical role in cognition, sleep and other behaviors. Although not well studied in autism spectrum disorder (ASD), the HS is implicated in many neurological disorders, some of which share comorbidity with ASD, including Tourette syndrome (TS). Preliminary studies suggest that antagonism of histamine receptors 1-3 reduces symptoms and specific behaviors in ASD patients and relevant animal models. In addition, the HS mediates neuroinflammation, which may be heightened in ASD...
May 9, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28475895/slert-regulates-ddx21-rings-associated-with-pol-i-transcription
#6
Yu-Hang Xing, Run-Wen Yao, Yang Zhang, Chun-Jie Guo, Shan Jiang, Guang Xu, Rui Dong, Li Yang, Ling-Ling Chen
Dysregulated rRNA synthesis by RNA polymerase I (Pol I) is associated with uncontrolled cell proliferation. Here, we report a box H/ACA small nucleolar RNA (snoRNA)-ended long noncoding RNA (lncRNA) that enhances pre-rRNA transcription (SLERT). SLERT requires box H/ACA snoRNAs at both ends for its biogenesis and translocation to the nucleolus. Deletion of SLERT impairs pre-rRNA transcription and rRNA production, leading to decreased tumorigenesis. Mechanistically, SLERT interacts with DEAD-box RNA helicase DDX21 via a 143-nt non-snoRNA sequence...
May 4, 2017: Cell
https://www.readbyqxmd.com/read/28468917/the-circadian-dynamics-of-small-nucleolar-rna-in-the-mouse-liver
#7
Stuart Aitken, Colin A Semple
The circadian regulation of gene expression allows plants and animals to anticipate predictable environmental changes. While the influence of the circadian clock has recently been shown to extend to ribosome biogenesis, the dynamics and regulation of the many small nucleolar RNA that are required in pre-ribosomal RNA folding and modification are unknown. Using a novel computational method, we show that 18S and 28S pre-rRNA are subject to circadian regulation in a nuclear RNA sequencing time course. A population of snoRNA with circadian expression is identified that is functionally associated with rRNA modification...
May 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28468764/a-resource-for-functional-profiling-of-noncoding-rna-in-the-yeast-saccharomyces-cerevisiae
#8
Steven Parker, Marcin Fraczek, Jian Wu, Sara Shamsah, Alkisti Manousaki, Kobchai Dungrattanalert, Rogerio Alves de Almeida, Diego Estrada-Rivadeneyra, Walid Omara, Daniela Delneri, Raymond T O'Keefe
Eukaryotic genomes are extensively transcribed generating many different RNAs with no known function. We have constructed 1502 molecular barcoded ncRNA gene deletion strains encompassing 443 ncRNAs in the yeast Saccharomyces cerevisiae as tools for ncRNA functional analysis. This resource includes deletions of small nuclear RNAs (snRNAs), transfer RNAs (tRNAs), small nucleolar RNAs (snoRNAs) and other annotated ncRNAs as well as the more recently identified stable unannotated transcripts (SUTs) and cryptic unstable transcripts (CUTs) whose functions are largely unknown...
May 3, 2017: RNA
https://www.readbyqxmd.com/read/28466632/small-nucleolar-rna-47-promotes-tumorigenesis-by-regulating-emt-markers-in-hepatocellular-carcinoma
#9
Guangcai Li, Yuan He, Xiaoqing Liu, Zhen Zheng, Ming Zhang, Faxiang Qin, Xiong Lan
BACKGROUND: Hepatocellular carcinoma (HCC) is third leading cause of cancer-related death globally. Evidence suggest that small nucleolar RNAs (snoRNAs) have emerged as key regulators of tumor development and progression in HCC. However, the biological significance of snoRNAs in HCC remains unclear. METHODS: We investigated the role of snoRA47 in a total of 60 paired HCC samples and six different human HCC cell lines by using qRT-PCR. Besides, snoRA47 was silenced through the siRNA transfection to determine whether snoRA47-siRNA is able to affect cell proliferation, invasion and metastasis by regulating the expressions of "epithelial-mesenchymal transition'' (EMT) markers...
May 2, 2017: Minerva Medica
https://www.readbyqxmd.com/read/28465432/different-phosphoisoforms-of-rna-polymerase-ii-engage-the-rtt103-termination-factor-in-a-structurally-analogous-manner
#10
Corey M Nemec, Fan Yang, Joshua M Gilmore, Corinna Hintermair, Yi-Hsuan Ho, Sandra C Tseng, Martin Heidemann, Ying Zhang, Laurence Florens, Audrey P Gasch, Dirk Eick, Michael P Washburn, Gabriele Varani, Aseem Z Ansari
The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcription. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific "readers." Whereas phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. Here, we identify a role for phospho-Thr4 in transcription termination at noncoding small nucleolar RNA (snoRNA) genes...
May 2, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28456523/the-canonical-poly-a-polymerase-pap1-polyadenylates-non-coding-rnas-and-is-essential-for-snorna-biogenesis-in-trypanosoma-brucei
#11
Vaibhav Chikne, Sachin Kumar Gupta, Tirza Doniger, K Shanmugha Rajan, Smadar Cohen-Chalamish, Hiba Waldman Ben-Asher, Liat Kolet, Nasreen Hag Yahia, Ron Unger, Elisabetta Ullu, Nikolay G Kolev, Christian Tschudi, Shulamit Michaeli
The parasite Trypanosoma brucei is the causative agent of African sleeping sickness and is known for its unique RNA processing mechanisms which are common to all the kinetoplastidea including Leishmania and Trypanosoma cruzi. Trypanosomes possess two canonical RNA poly (A) polymerases termed PAP1 and PAP2. PAP1 is encoded by one of the only two genes harboring cis-spliced introns in this organism and its function is currently unknown. In trypanosomes all mRNAs, as well as non-coding RNAs such as small nucleolar RNAs (snoRNAs) and long non-coding RNAs (lncRNAs), undergo trans-splicing and polyadenylation...
April 26, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28449079/small-non-coding-rna-and-cancer
#12
Giulia Romano, Dario Veneziano, Mario Acunzo, Carlo M Croce
The ENCODE project has reported that at least 80% of the human genome is biologically active, yet only a small part of human DNA encodes for protein. The massive amount of RNA transcribed but not translated into protein can be classified as housekeeping RNA (such as rRNA, tRNA) and regulatory RNA (such as miRNA, piRNA, lncRNA). Small non-coding RNAs, in particular, have been the focus of many studies in the last 20 years and their fundamental role in many human diseases is currently well established. Inter alia, their role in cancer development and progression, as well as in drug resistance, is being increasingly investigated...
May 1, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28448962/progressive-changes-in-non-coding-rna-profile-in-leucocytes-with-age
#13
Maider Muñoz-Culla, Haritz Irizar, Ana Gorostidi, Ainhoa Alberro, Iñaki Osorio-Querejeta, Javier Ruiz-Martínez, Javier Olascoaga, Adolfo López de Munain, David Otaegui
It has been observed that immune cell deterioration occurs in the elderly, as well as a chronic low-grade inflammation called inflammaging. These cellular changes must be driven by numerous changes in gene expression and in fact, both protein-coding and non-coding RNA expression alterations have been observed in peripheral blood mononuclear cells from elder people. In the present work we have studied the expression of small non-coding RNA (microRNA and small nucleolar RNA -snoRNA-) from healthy individuals from 24 to 79 years old...
April 2017: Aging
https://www.readbyqxmd.com/read/28429321/euglena-transcript-processing
#14
David C McWatters, Anthony G Russell
RNA transcript processing is an important stage in the gene expression pathway of all organisms and is subject to various mechanisms of control that influence the final levels of gene products. RNA processing involves events such as nuclease-mediated cleavage, removal of intervening sequences referred to as introns and modifications to RNA structure (nucleoside modification and editing). In Euglena, RNA transcript processing was initially examined in chloroplasts because of historical interest in the secondary endosymbiotic origin of this organelle in this organism...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28426094/sirt7-dependent-deacetylation-of-cdk9-activates-rna-polymerase-ii-transcription
#15
Maximilian F Blank, Sifan Chen, Fabian Poetz, Martina Schnölzer, Renate Voit, Ingrid Grummt
SIRT7 is an NAD+-dependent protein deacetylase that regulates cell growth and proliferation. Previous studies have shown that SIRT7 is required for RNA polymerase I (Pol I) transcription and pre-rRNA processing. Here, we took a proteomic approach to identify novel molecular targets and characterize the role of SIRT7 in non-nucleolar processes. We show that SIRT7 interacts with numerous proteins involved in transcriptional regulation and RNA metabolism, the majority of interactions requiring ongoing transcription...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28420675/integrative-analysis-unveils-new-functions-for-the-drosophila-cutoff-protein-in-non-coding-rna-biogenesis-and-gene-regulation
#16
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/28419966/small-nucleolar-rna-aca11-promotes-proliferation-migration-and-invasion-in-hepatocellular-carcinoma-by-targeting-the-pi3k-akt-signaling-pathway
#17
Long Wu, Junying Zheng, Ping Chen, Quanyan Liu, Yufeng Yuan
Emerging evidence suggests that tumorigenesis involves dysregulation of small nucleolar RNAs (snoRNAs). However, the role of small nucleolar RNA ACA11 (ACA11) in the development of hepatocellular carcinoma (HCC) remains unknown. Expression of ACA11 was measured using quantitative RT-PCR in 92 HCC specimens and 7 HCC cell lines. We found that ACA11 expression was significantly upregulated in HCC tissues and hepatoma cell lines. This upregulation of ACA11 in HCC tumors was significantly associated with histological grade, HBV infection, Barcelona Clinic Liver Cancer stage, portal vein tumor thrombus and poorer patient survival...
June 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28415578/high-expression-of-mir-125b-2-and-snord116-noncoding-rna-clusters-characterize-erg-related-b-cell-precursor-acute-lymphoblastic-leukemia
#18
Elena Vendramini, Marco Giordan, Emanuela Giarin, Barbara Michielotto, Grazia Fazio, Gianni Cazzaniga, Andrea Biondi, Daniela Silvestri, Maria Grazia Valsecchi, Martina U Muckenthaler, Andreas E Kulozik, Valter Gattei, Shai Izraeli, Giuseppe Basso, Geertruy Te Kronnie
ERG-related leukemia is a B cell precursor acute lymphoblastic leukemia (BCP ALL) subtype characterized by aberrant expression of DUX4 and ERG transcription factors, and highly recurrent ERG intragenic deletions. ERG-related patients have remarkably favorable outcome despite a high incidence of inauspicious IKZF1 aberrations.We describe clinical and genomic features of the ERG-related cases in an unselected cohort of B-other BCP ALL pediatric patients enrolled in the AIEOP ALL 2000 therapeutic protocol. We report a small noncoding RNA signature specific of ERG-related group, with up-regulation of miR-125b-2 cluster on chromosome 21 and several snoRNAs in the Prader-Willi locus at 15q11...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28410200/snord47-a-box-c-d-snorna-suppresses-tumorigenesis-in-glioblastoma
#19
Bin Xu, Min-Hua Ye, Shi-Gang Lv, Qi-Xue Wang, Miao-Jing Wu, Bing Xiao, Chun-Sheng Kang, Xin-Gen Zhu
SNORD47 is a member of the C/D box small nucleolar RNAs, which have been implicated in cancer development. We intended to investigate the therapeutic potential of SNORD47 in glioma. We found that the expression of SNORD47 was downregulated in glioma tissues samples and inversely associated with advanced tumor stage (WHO grade IV). Kaplan-Meier survival analysis revealed that glioma patients with high SNORD47 expression had longer overall survival than those with low SNORD47 expression. SNORD47 suppressed the proliferation of glioma cells and induced G2 phase arrest...
March 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28390868/small-nucleolar-noncoding-rna-snora23-upregulated-in-human-pancreatic-ductal-adenocarcinoma-regulates-expression-of-syne2-to-promote-growth-and-metastasis-of-xenograft-tumors-in-mice
#20
Lin Cui, Kenji Nakano, Sumalee Obchoei, Kiyoko Setoguchi, Masaki Matsumoto, Tsuyoshi Yamamoto, Satoshi Obika, Kazuaki Shimada, Nobuyoshi Hiraoka
BACKGROUND & AIMS: Small nucleolar noncoding RNAs (snoRNAs) regulate function of ribosomes, and specific snoRNAs are dysregulated in some cancer cells. We investigated dysregulation of snoRNAs in pancreatic ductal adenocarcinoma (PDAC) cells. METHODS: We investigated snoRNA expression in PDAC cell lines by cDNA microarray and quantitative reverse transcription (qRT)-PCR. In PDAC (n=133), intraductal papillary mucinous neoplasm (IPMN, n=16), mucinous cystic neoplasm-associated PDAC (n=1), and non-tumor pancreas (n=8) and liver (n=3) tissues from subjects who underwent surgical resection, levels of snoRNA were measured by qRT-PCR and compared with clinicopathological parameters and survival times determined by Kaplan Meier analysis...
April 5, 2017: Gastroenterology
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