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https://www.readbyqxmd.com/read/28629949/the-diversity-of-long-noncoding-rnas-and-their-generation
#1
REVIEW
Huang Wu, Li Yang, Ling-Ling Chen
Long noncoding RNAs (lncRNAs) are emerging as potential key regulators in gene expression networks and exhibit a surprising range of shapes and sizes. Several distinct classes of lncRNAs are transcribed from different DNA elements, including promoters, enhancers, and intergenic regions in eukaryotic genomes. Additionally, others are derived from long primary transcripts with noncanonical RNA processing pathways, generating new RNA species with unexpected formats. These lncRNAs can be processed by several mechanisms, including ribonuclease P (RNase P) cleavage to generate mature 3' ends, capping by small nucleolar RNA (snoRNA)-protein (snoRNP) complexes at their ends, or the formation of circular structures...
June 16, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28623187/control-of-box-c-d-snornp-assembly-by-n-6-methylation-of-adenine
#2
Lin Huang, Saira Ashraf, Jia Wang, David Mj Lilley
N(6)-methyladenine is the most widespread mRNA modification. A subset of human box C/D snoRNA species have target GAC sequences that lead to formation of N(6)-methyladenine at a key trans Hoogsteen-sugar A·G base pair, of which half are methylated in vivo The GAC target is conserved only in those that are methylated. Methylation prevents binding of the 15.5-kDa protein and the induced folding of the RNA Thus, the assembly of the box C/D snoRNP could in principle be regulated by RNA methylation at its critical first stage...
June 16, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28601222/synthesis-function-and-heterogeneity-of-snorna-guided-posttranscriptional-nucleoside-modifications-in-eukaryotic-ribosomal-rnas
#3
Anthony K Henras, Célia Plisson-Chastang, Odile Humbert, Yves Romeo, Yves Henry
Ribosomal RNAs contain numerous 2'-O-methylated nucleosides and pseudouridines. Methylation of the 2' oxygen of ribose moieties and isomerization of uridines into pseudouridines are catalyzed by C/D and H/ACA small nucleolar ribonucleoprotein particles, respectively. We review the composition, structure, and mode of action of archaeal and eukaryotic C/D and H/ACA particles. Most rRNA modifications cluster in functionally crucial regions of the rRNAs, suggesting they play important roles in translation. Some of these modifications promote global translation efficiency or modulate translation fidelity...
2017: Enzymes
https://www.readbyqxmd.com/read/28578939/clinical-significance-of-c-d-box-small-nucleolar-rna-u76-as-an-oncogene-and-a-prognostic-biomarker-in-hepatocellular-carcinoma
#4
Long Wu, Lei Chang, Haitao Wang, Weijie Ma, Qin Peng, Yufeng Yuan
BACKGROUND: Recent evidence has suggested novel roles of small nucleolar RNAs (snoRNAs) in tumorigenicity. However, the roles of C/D box snoRNA U76 (SNORD76) in the development of hepatocellular carcinoma (HCC) remain unknown. Herein, we systematically evaluated dysregulation of snoRNAs in HCC and clarified the biomarker potential and biological significance of SNORD76 in HCC. METHODS: We performed quantitative analyses of the expression of SNORD76 in 66 HCC specimens to compare its expression pattern between tumor tissue and matched non-tumor tissue...
May 31, 2017: Clinics and Research in Hepatology and Gastroenterology
https://www.readbyqxmd.com/read/28575120/structural-basis-for-5-ets-recognition-by-utp4-at-the-early-stages-of-ribosome-biogenesis
#5
Fabiola R Calviño, Markus Kornprobst, Géza Schermann, Fabienne Birkle, Klemens Wild, Tamas Fischer, Ed Hurt, Yasar Luqman Ahmed, Irmgard Sinning
Eukaryotic ribosome biogenesis begins with the co-transcriptional assembly of the 90S pre-ribosome. The 'U three protein' (UTP) complexes and snoRNP particles arrange around the nascent pre-ribosomal RNA chaperoning its folding and further maturation. The earliest event in this hierarchical process is the binding of the UTP-A complex to the 5'-end of the pre-ribosomal RNA (5'-ETS). This oligomeric complex predominantly consists of β-propeller and α-solenoidal proteins. Here we present the structure of the Utp4 subunit from the thermophilic fungus Chaetomium thermophilum at 2...
2017: PloS One
https://www.readbyqxmd.com/read/28566452/correction-for-zhu-et-al-utp14-recruits-and-activates-the-rna-helicase-dhr1-to-undock-u3-snorna-from-the-preribosome
#6
Jieyi Zhu, Xin Liu, Margarida Anjos, Carl C Correll, Arlen W Johnson
No abstract text is available yet for this article.
June 15, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28554868/a-novel-deletion-of-snurf-snrpn-exon-1-in-a-patient-with-prader-willi-like-phenotype
#7
Yang Cao, Susan S AlHumaidi, Eissa A Faqeih, Beth A Pitel, Patrick Lundquist, Umut Aypar
Here we report the smallest deletion involving SNURF/SNRPN that causes major symptoms of Prader-Willi syndrome (PWS), including hypotonia, dysmorphic features, intellectual disability, and obesity. A female patient with the aforementioned and additional features was referred to the Mayo Clinic Cytogenetics laboratory for genetic testing. Chromosomal microarray analysis and subsequent Sanger sequencing identified a de novo 6.4 kb deletion at 15q11.2, containing exon 1 of the SNURF gene and exon 1 of the shortest isoform of the SNRPN gene...
May 26, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28542199/specialized-box-c-d-snornps-act-as-antisense-guides-to-target-rna-base-acetylation
#8
Sunny Sharma, Jun Yang, Rob van Nues, Peter Watzinger, Peter Kötter, Denis L J Lafontaine, Sander Granneman, Karl-Dieter Entian
Box C/D snoRNAs are known to guide site-specific ribose methylation of ribosomal RNA. Here, we demonstrate a novel and unexpected role for box C/D snoRNAs in guiding 18S rRNA acetylation in yeast. Our results demonstrate, for the first time, that the acetylation of two cytosine residues in 18S rRNA catalyzed by Kre33 is guided by two orphan box C/D snoRNAs-snR4 and snR45 -not known to be involved in methylation in yeast. We identified Kre33 binding sites on these snoRNAs as well as on the 18S rRNA, and demonstrate that both snR4 and snR45 establish extended bipartite complementarity around the cytosines targeted for acetylation, similar to pseudouridylation pocket formation by the H/ACA snoRNPs...
May 2017: PLoS Genetics
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
#9
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
#10
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...
June 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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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 16, 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
#19
Vaibhav Chikne, Sachin Kumar Gupta, Tirza Doniger, Shanmugha Rajan K, 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 that are common to all the kinetoplastidea including Leishmania and Trypanosoma cruzi. Trypanosomes possess two canonical RNA poly (A) polymerases (PAPs) 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, and 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
#20
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
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