CENTROIDFOLD: a web server for RNA secondary structure prediction

Sato, Kengo; Hamada, Michiaki; Asai, Kiyoshi; Mituyama, Toutai

doi:10.1093/nar/gkp367

Cited by 281 publications

(249 citation statements)

References 11 publications

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“…Any common secondary structure in the E and M regions was not predicted by Mfold or CentroidFold computer tools (Sato et al 2009). These results suggest that these two regions of MALAT-1 have distinct sequence or secondary structure that directs localization to nuclear speckles.…”

Section: Malat-1 Is Stably Retained In the Nucleusmentioning

confidence: 99%

Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles

Miyagawa

Tano

Mizuno

et al. 2012

RNA

216

192

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MALAT-1 noncoding RNA is localized to nuclear speckles despite its mRNA-like characteristics. Here, we report the identification of several key factors that promote the localization of MALAT-1 to nuclear speckles and also provide evidence that MALAT-1 is involved in the regulation of gene expression. Heterokaryon assays revealed that MALAT-1 does not shuttle between the nucleus and cytoplasm. RNAi-mediated repression of the nuclear speckle proteins, RNPS1, SRm160, or IBP160, which are well-known mRNA processing factors, resulted in the diffusion of MALAT-1 to the nucleoplasm. We demonstrated that MALAT-1 contains two distinct elements directing transcripts to nuclear speckles, which were also capable of binding to RNPS1 in vitro. Depletion of MALAT-1 represses the expression of several genes. Taken together, our results suggest that RNPS1, SRm160, and IBP160 contribute to the localization of MALAT-1 to nuclear speckles, where MALAT-1 could be involved in regulating gene expression.

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Section: Malat-1 Is Stably Retained In the Nucleusmentioning

confidence: 99%

Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles

Miyagawa

Tano

Mizuno

et al. 2012

RNA

216

192

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“…We further predicted the secondary structures of the sRNAs using RNAfold (Hofacker 2003) and CentroidFold (Sato et al 2009). As illustrated in Figure 4 and Supplemental Figure S1, most of the sRNAs contained a typical I-shaped terminator or a stem-loop for mycobacteria RNA without a long poly(U) stretch (Gardner et al 2011).…”

Section: Identification Of Transcription Start Sites (Tss) By 59 Racementioning

confidence: 99%

Identification of small RNAs in Mycobacterium smegmatis using heterologous Hfq

Qin

et al. 2012

RNA

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Gene regulation by small RNAs (sRNAs) has been extensively studied in various bacteria. However, the presence and roles of sRNAs in mycobacteria remain largely unclear. Immunoprecipitation of RNA chaperone Hfq to enrich for sRNAs is one of the effective methods to isolate sRNAs. However, the lack of an identified mycobacterial hfq restricts the feasibility of this approach. We developed a novel method that takes advantage of the conserved inherent sRNAs-binding capability of heterologous Hfq from Escherichia coli to enrich sRNAs from Mycobacterium smegmatis, a model organism for studying Mycobacterium tuberculosis. We validated 12 trans-encoded and 12 cis-encoded novel sRNAs in M. smegmatis. Many of these sRNAs are differentially expressed at exponential phase compared with stationary phase, suggesting that sRNAs are involved in the growth of mycobacteria. Intriguingly, five of the cis-encoded novel sRNAs target known transposases. Phylogenetic conservation analysis shows that these sRNAs are pathogenicity dependent. We believe that our findings will serve as an important reference for future analysis of sRNAs regulation in mycobacteria and will contribute significantly to the development of sRNAs prediction programs. Moreover, this novel method of using heterologous Hfq for sRNAs enrichment can be of general use for the discovery of bacterial sRNAs in which no endogenous Hfq is identified.

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“…We used two modeling programs-CentroidFold (Sato et al 2009) and the SRNA program of Sfold (Ding et al 2004)-to predict secondary structures for a 500-nt and a 200-nt region, respectively, surrounding the U-motif that is recognized by Vas. Both programs predicted that the U residues were mostly in a double-stranded basepaired region that was interrupted by several unpaired residues (Supplemental Fig.…”

Section: Vas Activates Mei-p26 Translationmentioning

confidence: 99%

Vasa promotes Drosophila germline stem cell differentiation by activating mei-P26 translation by directly interacting with a (U)-rich motif in its 3′ UTR

Liu

Han²,

Lasko³

2009

Genes Dev.

106

105

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Vasa (Vas) is a DEAD-box RNA-binding protein required in Drosophila at several steps of oogenesis and for primordial germ cell (PGC) specification. Vas associates with eukaryotic initiation factor 5B (eIF5B), and this interaction has been implicated in translational activation of gurken mRNA in the oocyte. Vas is expressed in all ovarian germline cells, and aspects of the vas-null phenotype suggest a function in regulating the balance between germline stem cells (GSCs) and their fate-restricted descendants. We used a biochemical approach to recover Vas-associated mRNAs and obtained mei-P26, whose product represses microRNA activity and promotes GSC differentiation. We found that vas and mei-P26 mutants interact, and that mei-P26 translation is substantially reduced in vas mutant cells. In vitro, Vas protein bound specifically to a (U)-rich motif in the mei-P26 39 untranslated region (UTR), and Vas-dependent regulation of GFP-mei-P26 transgenes in vivo was dependent on the same (U)-rich 39 UTR domain. The ability of Vas to activate mei-P26 expression in vivo was abrogated by a mutation that greatly reduces its interaction with eIF5B. Taken together, our data support the conclusion that Vas promotes germ cell differentiation by directly activating mei-P26 translation in early-stage committed cells.[Keywords: Oogenesis; RNA-binding protein; DEAD-box; patterning; development] Supplemental material is available at http://www.genesdev.org.

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CENTROIDFOLD: a web server for RNA secondary structure prediction

Cited by 281 publications

References 11 publications

Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles

Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles

Identification of small RNAs in Mycobacterium smegmatis using heterologous Hfq

Vasa promotes Drosophila germline stem cell differentiation by activating mei-P26 translation by directly interacting with a (U)-rich motif in its 3′ UTR

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