Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs

Xie, Jun; Zhang, Ming; Zhou, Tao; Hua, Xia; Tang, Long; Wang, Weilin

doi:10.1093/nar/gkl873

Cited by 61 publications

(52 citation statements)

References 29 publications

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“…Eighteen up-regulated transcripts and 388 down-regulated transcripts met these strict criteria and are presented in Dataset S1 and Dataset S2. No matches to small RNAs in snoRNAbase (27) and miRBase (28) were found. The 10 highest ranked up-regulated and 20 highest ranked down-regulated transcripts are listed in Table 2.…”

Section: Resultsmentioning

confidence: 98%

Changes in prostate gene expression in men undergoing an intensive nutrition and lifestyle intervention

Ornish

Magbanua

Weidner

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

267

152

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Epidemiological and prospective studies indicate that comprehensive lifestyle changes may modify the progression of prostate cancer. However, the molecular mechanisms by which improvements in diet and lifestyle might affect the prostate microenvironment are poorly understood. We conducted a pilot study to examine changes in prostate gene expression in a unique population of men with low-risk prostate cancer who declined immediate surgery, hormonal therapy, or radiation and participated in an intensive nutrition and lifestyle intervention while undergoing careful surveillance for tumor progression. Consistent with previous studies, significant improvements in weight, abdominal obesity, blood pressure, and lipid profile were observed (all P < 0.05), and surveillance of low-risk patients was safe. Gene expression profiles were obtained from 30 participants, pairing RNA samples from control prostate needle biopsy taken before intervention to RNA from the same patient's 3-month postintervention biopsy. Quantitative real-time PCR was used to validate array observations for selected transcripts. Two-class paired analysis of global gene expression using significance analysis of microarrays detected 48 up-regulated and 453 down-regulated transcripts after the intervention. Pathway analysis identified significant modulation of biological processes that have critical roles in tumorigenesis, including protein metabolism and modification, intracellular protein traffic, and protein phosphorylation (all P < 0.05). Intensive nutrition and lifestyle changes may modulate gene expression in the prostate. Understanding the prostate molecular response to comprehensive lifestyle changes may strengthen efforts to develop effective prevention and treatment. Larger clinical trials are warranted to confirm the results of this pilot study.exercise ͉ lifestyle changes ͉ prostate cancer ͉ SHOC2 ͉ stress management E pidemiological evidence (1, 2) and migrant studies (3) indicate that the incidence of clinically significant prostate cancer is much lower in parts of the world where people eat a predominantly low-fat, plant-based diet. We (4, 5) and others (6) have shown previously that diet and lifestyle interventions in men with earlystage prostate cancer decrease prostate-specific antigen (PSA) and decrease the rate of PSA increase. These studies provided some evidence that comprehensive lifestyle changes may have therapeutic potential in early prostate cancers. However, although these interventions are associated with decreased circulating insulin-like growth factor 1 (IGF1) (7), and although serum from men after intervention has reduced the ability to stimulate prostate cell-line growth in vitro (4), the actual molecular effects of these interventions in prostate tissue have not been previously examined.Many men with indolent prostate cancers detected by PSA screening will not exhibit disease progression during their lifetime; their treatment and associated side effects are unnecessary (8). We report here the results of the Gene Expressio...

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Section: Resultsmentioning

confidence: 98%

Changes in prostate gene expression in men undergoing an intensive nutrition and lifestyle intervention

Ornish

Magbanua

Weidner

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

267

152

View full text Add to dashboard Cite

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“…The nc transcript annotations were collected from public databases and literature sources (for sources and filtering steps, see Materials and Methods). Briefly, the set includes lncRNAs (n = 4740) from UCSC (Pruitt et al 2009b) and RefSeq (Hsu et al 2006) and intergenic lncRNAs (Cabili et al 2011); antisense RNAs (n = 625) (Chen et al 2004;Engström et al 2006;Ge et al 2008); structural RNAs (n = 131) (Griffiths-Jones et al 2003;Schattner et al 2005;Xie et al 2007); regions with consistent expression evidence in ENCODE RNAseq data sets (n = 4340) (Birney et al 2007); nonexonic ultra conserved elements (n = 331) (Bejerano et al 2004); and long (>60 nt) EvoFold predictions of regions with evolutionarily conserved RNA secondary structure (n = 1599) (Pedersen et al 2006). Given that the array would also be applied in a cancer setting, we included transcripts of cancer-associated pc genes (n = 6856), primarily from the Cancer Gene Index (Suh et al 2010).…”

Section: Expression Platform and Transcript Definitionmentioning

confidence: 99%

“…4. 829 nc transcripts from the Rfam, snoBase, and tRNAscan databases that were at least 60 nucleotides long (Griffiths-Jones et al 2003;Schattner et al 2005;Xie et al 2007). 5.…”

Section: Expression and Conservation Of Noncoding Rnasmentioning

confidence: 99%

Identification of expressed and conserved human noncoding RNAs

Nielsen

Tehler

Vang

et al. 2013

RNA

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The past decade has shown mammalian genomes to be pervasively transcribed and identified thousands of noncoding (nc) transcripts. It is currently unclear to what extent these transcripts are of functional importance, as experimental functional evidence exists for only a small fraction. Here, we characterize the expression and evolutionary conservation properties of 12,115 known and novel nc transcripts, including structural RNAs, long nc RNAs (lncRNAs), antisense RNAs, EvoFold predictions, ultraconserved elements, and expressed nc regions. Expression levels are evaluated across 12 human tissues using a custom-designed microarray, supplemented with RNAseq. Conservation levels are evaluated at both the base level and at the syntenic level. We combine these measures with epigenetic mark annotations to identify subsets of novel nc transcripts that show characteristics similar to known functional ncRNAs. Few novel nc transcripts show both high expression and conservation levels. However, overall, we observe a positive correlation between expression and both conservation and epigenetic annotations, suggesting that a subset of the expressed transcripts are under purifying selection and likely functional. The identified subsets of expressed and conserved novel nc transcripts may form the basis for further functional characterization.

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“…Methylation and pseudouridylation (C/D and H/ACA box) guide snoRNAs C/D box and H/ACA box snoRNA families guide the 29-Oribose methylations and pseudouridylations, respectively, on rRNAs and spliceosomal snRNAs in vertebrates (Kiss 2001), tRNAs in Archaea (Xie et al 2007), and even probably eukaryotic mRNAs (Cavaille et al 2000;Kishore and Stamm 2006). Among the 31 candidate snoRNAs we identified, 27 were C/D box type and 4 were H/ACA type snoRNAs ( Table 1).…”

Section: Telomerase Rnamentioning

confidence: 99%

Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis

Chakrabarti¹,

Pearson²,

Grate³

et al. 2007

RNA

115

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As the genomes of more eukaryotic pathogens are sequenced, understanding how molecular differences between parasite and host might be exploited to provide new therapies has become a major focus. Central to cell function are RNA-containing complexes involved in gene expression, such as the ribosome, the spliceosome, snoRNAs, RNase P, and telomerase, among others. In this article we identify by comparative genomics and validate by RNA analysis numerous previously unknown structural RNAs encoded by the Plasmodium falciparum genome, including the telomerase RNA, U3, 31 snoRNAs, as well as previously predicted spliceosomal snRNAs, SRP RNA, MRP RNA, and RNAse P RNA. Furthermore, we identify six new RNA coding genes of unknown function. To investigate the relationships of the RNA coding genes to other genomic features in related parasites, we developed a genome browser for P. falciparum (http://areslab.ucsc.edu/cgi-bin/hgGateway). Additional experiments provide evidence supporting the prediction that snoRNAs guide methylation of a specific position on U4 snRNA, as well as predicting an snRNA promoter element particular to Plasmodium sp. These findings should allow detailed structural comparisons between the RNA components of the gene expression machinery of the parasite and its vertebrate hosts.

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Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs

Cited by 61 publications

References 29 publications

Changes in prostate gene expression in men undergoing an intensive nutrition and lifestyle intervention

Changes in prostate gene expression in men undergoing an intensive nutrition and lifestyle intervention

Identification of expressed and conserved human noncoding RNAs

Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis

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