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Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs

Markus Brameier, Astrid Herwig, Richard Reinhardt, Lutz Walter, Jens Gruber
2010 Nucleic Acids Research  
In particular, we demonstrate that several C/D box snoRNAs give rise to gene regulatory RNAs, named sno-miRNAs here.  ...  and C/D box snoRNAs.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkq776 pmid:20846955 pmcid:PMC3025573 fatcat:uiiuto2anjftrhnainv2imeira

Conservation of Archaeal C/D Box sRNA-Guided RNA Modifications

Ruth Breuer, Jose-Vicente Gomes-Filho, Lennart Randau
2021 Frontiers in Microbiology  
Each C/D box sRNA contains two guide sequences that can act in coordination to bridge rRNA sequences. Here, we will review the landscape of archaeal C/D box sRNA genes and their target sites.  ...  In archaea, these modification sites are determined by variable sets of C/D box sRNAs that guide the activity of the rRNA 2'-O-methyltransferase fibrillarin.  ...  Additionally, it was revealed that many snoRNAs are processed into shorter forms such as miRNA (called sno-miRNA) and efficiently exert gene regulatory functions (Brameier et al., 2011) .  ... 
doi:10.3389/fmicb.2021.654029 pmid:33776983 pmcid:PMC7994747 fatcat:yd4cr6fu3zbkzabcxrqbr3itl4

Emerging Functions for snoRNAs and snoRNA-Derived Fragments

Maliha Wajahat, Cameron Peter Bracken, Ayla Orang
2021 International Journal of Molecular Sciences  
This is in addition to a body of literature describing snoRNAs as an additional source of miRNA-like regulators.  ...  Whilst many of these are likely to be byproducts of degradation, there are nevertheless metabolically stable fragments derived from tRNAs, rRNAs, snoRNAs, and other non-coding RNA, with a number of examples  ...  Figure 1 . 1 The C/D box snoRNA structural features and associated protein cohort: (a) Stem-bulge-stem (K-turn) structure is a characteristic feature of the C/D box snoRNAs.  ... 
doi:10.3390/ijms221910193 pmid:34638533 fatcat:eupuqwro45hylo2qww4bv4evby

High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq [article]

Rafal Gumienny, Dominik Jedlinski, Georges Martin, Arnau Vina-Villaseca, Mihaela Zavolan
2016 bioRxiv   pre-print
However, to determine the targets of the many newly discovered regulatory RNAs in high-throughput remains a challenge.  ...  To globally assign guide small nucleolar RNAs to site of 2'-O-ribose methylation in human cells, we here developed novel computational methods for the analysis of data that was generated with protocols  ...  ACKNOWLEDGEMENTS R.G. and D.J. would like to thank the members of the Zavolan lab for input on the project.  ... 
doi:10.1101/037259 fatcat:zw7bex63frf4voyt2c76vl5jtq

RNomics: identification and function of small, non-messenger RNAs

Alexander Hüttenhofer, Jürgen Brosius, Jean-Pierre Bachellerie
2002 Current Opinion in Chemical Biology  
small nuclear RNA snoRNA small nucleolar RNA RNomics: identification and function of small, non-messenger RNAs  ...  Abbreviations dsRNA double-stranded RNA miRNAs microRNAs nmRNA non-messenger RNA RISC RNA-induced silencing complex RNAi RNA interference siRNA small interfering RNAs snmRNA small, non-messenger RNA snRNA  ...  Acknowledgements We thank all those colleagues who provided manuscripts before publication and apologize to those whose work could not be cited because of space limitations.  ... 
doi:10.1016/s1367-5931(02)00397-6 pmid:12470739 fatcat:46ha6vorxbdstfdhyucrccfhda

Small RNAs with big implications: new insights into H/ACA snoRNA function and their role in human disease

Mary McMahon, Adrian Contreras, Davide Ruggero
2014 Wiley Interdisciplinary Reviews - RNA  
Small nucleolar RNAs (snoRNAs), the most abundant group of intron-encoded ncRNAs, are classified into two families (box C/D snoRNAs and box H/ACA snoRNAs) and are required for post-transcriptional modifications  ...  may be regulated, and explore prospective expanding functions of H/ACA snoRNAs.  ...  This work was supported by the NIH (R01DK098057 and R01DK098057-07S1 to D.R.) and the Program for Breakthrough Biomedical Research, which is partially funded by the Sandler Foundation (M.M.).  ... 
doi:10.1002/wrna.1266 pmid:25363811 pmcid:PMC4390053 fatcat:mooznxjctbcffev7w53hrhv75i

Systematic Identification and Functional Validation of New snoRNAs in Human Muscle Progenitors

Baptiste Bogard, Claire Francastel, Florent Hubé
2021 Non-Coding RNA  
Small non-coding RNAs (sncRNAs) represent an important class of regulatory RNAs involved in the regulation of transcription, RNA splicing or translation.  ...  However, the characterization of the complete repertoire of sncRNAs in a given cellular context and the functional annotation of the human transcriptome are far from complete.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ncrna7030056 pmid:34564318 fatcat:wpqcfwalvnci7ackdlbxvrzwfa

Noncoding RNAs and RNA Editing in Brain Development, Functional Diversification, and Neurological Disease

Mark F. Mehler, John S. Mattick
2007 Physiological Reviews  
, modulated by the box C/D and box H/ACA snoRNAs, respectively (15, 174, 208) .  ...  In addition, a large number of tandemly repeated box C/D snoRNAs are located downstream from GLT2 (67).  ... 
doi:10.1152/physrev.00036.2006 pmid:17615389 fatcat:ihcler6mrzb2rce4vpff4igizi

RNA degradome--its biogenesis and functions

P. Jackowiak, M. Nowacka, P. M. Strozycki, M. Figlerowicz
2011 Nucleic Acids Research  
The continuous decay of RNA molecules is associated not only with nucleotide turnover, but also with transcript maturation and quality control.  ...  Others preferentially digest mature, functional RNAs to yield a variety of molecules that together constitute the RNA degradome.  ...  Most (90%) of the snoRNA degradation products identified came from a 34-nt-long fragment located in the 3 0 -end of a single C/D box type molecule (18) .  ... 
doi:10.1093/nar/gkr450 pmid:21653558 pmcid:PMC3177198 fatcat:astztd345vbl7mokym5pabdetq

Functional diversity of small nucleolar RNAs

2019 Nucleic Acids Research  
Small nucleolar RNAs (snoRNAs) are short non-protein-coding RNAs with a long-recognized role in tuning ribosomal and spliceosomal function by guiding ribose methylation and pseudouridylation at targeted  ...  Here, we discuss the new and unforeseen roles attributed to snoRNAs, focusing on the presumed mechanisms of action.  ...  A subgroup of C/D-box snoRNAs (e.g.  ... 
doi:10.1093/nar/gkz1140 pmid:31828325 pmcid:PMC7038934 fatcat:tb2srl263vg3ll2uvslrr2cx24

Linking RNA Processing and Function

Run-Wen Yao, Chu-Xiao Liu, Ling-Ling Chen
2020 Cold Spring Harbor Symposia on Quantitative Biology  
movement of nascent precursor ribosomal RNA (pre-rRNA) in the human nucleolus as an example.  ...  Here we summarize the recent progress in linking the processing and function of these unconventionally processed lncRNAs; we also discuss how directional RNA movement is achieved using the radial flux  ...  (D) Subtypes of snoRNA-ended lncRNAs. sno-lncRNAs, and SPAs can be ended with either box C/D or box H/ACA snoRNAs at their ends. Figure 3 .Figure 4 . 34 The biogenesis and function of SLERT.  ... 
doi:10.1101/sqb.2019.84.039495 pmid:32019863 fatcat:xa6ehrm6kvhqfik6eawblsb6xy

Diversity and functional convergence of small noncoding RNAs in male germ cell differentiation and fertilization

Jesús García-López, Lola Alonso, David B. Cárdenas, Haydeé Artaza-Alvarez, Juan de Dios Hourcade, Sergio Martínez, Miguel A. Brieño-Enríquez, Jesús del Mazo
2015 RNA: A publication of the RNA Society  
In addition to microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), other sncRNAs generated from small nucleolar RNAs (snoRNAs), tRNAs, or rRNAs processing may also play important regulatory roles in  ...  RNAs-derived from tRNAs and rRNAs interacting with PIWI proteins are not generated by the ping-pong pathway and could be a source of primary piRNAs.  ...  Growing evidence supports the hypothesis that snoRNAs molecules can serve as source of small RNAs with miRNA-like functions.  ... 
doi:10.1261/rna.048215.114 pmid:25805854 pmcid:PMC4408801 fatcat:2ta7tphup5fqhpt4vyknwce6ru

Processing of snoRNAs as a new source of regulatory non-coding RNAs

Marina Falaleeva, Stefan Stamm
2012 Bioessays  
C/D box snoRNA fragmentation patterns are conserved across multiple cell types, suggesting a processing event, rather than degradation.  ...  The initially made transcripts undergo further processing generating shorter, metabolically stable RNAs with diverse functions.  ...  Figure 3 . 3 Schematic alignment of psnoRNAs to a generic C/D box snoRNA On the top is a hypothetical, generic C/D box snoRNA.  ... 
doi:10.1002/bies.201200117 pmid:23180440 pmcid:PMC3732821 fatcat:nf4yvgymknfypkxl5nohzw7z3u

Identification and functional characterization of intermediate-size non-coding RNAs in maize

Dandan Li, Huili Qiao, Wujie Qiu, Xin Xu, Tiemei Liu, Qianling Jiang, Renyi Liu, Zhujin Jiao, Kun Zhang, Lijun Bi, Runsheng Chen, Yunchao Kan
2018 BMC Genomics  
Conclusions: We provided a genome-wide identification and functional analysis of ncRNAs with a size range of 50-500 nt in maize. 111 novel ncRNAs were cloned and 40 ncRNAs were determined to be specific  ...  The majority of eukaryote genomes can be actively transcribed into non-coding RNAs (ncRNAs), which are functionally important in development and evolution.  ...  Seventy of them (63%) were annotated as snoRNA-like transcripts, including 42 C/D box, 27 H/ ACA box snoRNAs, and one U3 snoRNA. Twenty-seven ncRNAs (24%) were classified as snRNAs and one as tRNA.  ... 
doi:10.1186/s12864-018-5103-1 fatcat:kbqupuaz5bek5a6nq4yiy4iqjq

Small nucleolar RNAs in cancer

Kaiissar Mannoor, Jipei Liao, Feng Jiang
2012 Biochimica et Biophysica Acta. CR. Reviews on Cancer  
We are beginning to comprehend the functional repercussions of snoRNAs in the development and progression of malignancy.  ...  In this review, we will describe current studies that have shed new light on the functions of snoRNAs in carcinogenesis and the potential applications for cancer diagnosis and diagnosis.  ...  Acknowledgments The authors' work cited in this review was funded by grants from National Cancer Institute (NCI) grants CA161837, CA135382, CA137742, and CA133956), American Cancer Society Research Scholar  ... 
doi:10.1016/j.bbcan.2012.03.005 pmid:22498252 pmcid:PMC3842010 fatcat:uu6ll33wtfbbrmjsxco2u3viha
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