Discovering non-coding RNA elements in Drosophila 3' untranslated regions

Zhong, Cuncong; Andrews, Justen; Zhang, Shaojie

doi:10.1504/ijbra.2014.062996

Cited by 3 publications

(4 citation statements)

References 54 publications

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“…For example, thousands of long ncRNAs (lncRNAs) were found using deep sequencing [ 25 – 27 ]. A study focusing on 3’-untranslated regions (UTRs) found 184 ncRNA clusters [ 28 ]. A quarter of the genomic regions that currently lack annotated genes, i.e., that are currently considered “intergenic”, show transcriptional activity (according to the intersection of the current annotation [ 29 ] and a genome-wide tiling array study [ 30 ]).…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of novel conserved RNA structures in Drosophila

et al. 2018

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BackgroundComparative genomics approaches have facilitated the discovery of many novel non-coding and structured RNAs (ncRNAs). The increasing availability of related genomes now makes it possible to systematically search for compensatory base changes – and thus for conserved secondary structures – even in genomic regions that are poorly alignable in the primary sequence. The wealth of available transcriptome data can add valuable insight into expression and possible function for new ncRNA candidates. Earlier work identifying ncRNAs in Drosophila melanogaster made use of sequence-based alignments and employed a sliding window approach, inevitably biasing identification toward RNAs encoded in the more conserved parts of the genome.ResultsTo search for conserved RNA structures (CRSs) that may not be highly conserved in sequence and to assess the expression of CRSs, we conducted a genome-wide structural alignment screen of 27 insect genomes including D. melanogaster and integrated this with an extensive set of tiling array data. The structural alignment screen revealed ∼30,000 novel candidate CRSs at an estimated false discovery rate of less than 10%. With more than one quarter of all individual CRS motifs showing sequence identities below 60%, the predicted CRSs largely complement the findings of sliding window approaches applied previously. While a sixth of the CRSs were ubiquitously expressed, we found that most were expressed in specific developmental stages or cell lines. Notably, most statistically significant enrichment of CRSs were observed in pupae, mainly in exons of untranslated regions, promotors, enhancers, and long ncRNAs. Interestingly, cell lines were found to express a different set of CRSs than were found in vivo. Only a small fraction of intergenic CRSs were co-expressed with the adjacent protein coding genes, which suggests that most intergenic CRSs are independent genetic units.ConclusionsThis study provides a more comprehensive view of the ncRNA transcriptome in fly as well as evidence for differential expression of CRSs during development and in cell lines.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5234-4) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Identification and characterization of novel conserved RNA structures in Drosophila

et al. 2018

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“…However, in recent years, it has been found that these regions contain functionally important elements ( Cai, 2016 ) and independent transcription of miRNAs with their own promoters ( Hess et al, 2006 ). Intergenic regions may also contain unidentified functional elements, such as non-coding RNA ( Zhong et al, 2014 ; Fariha and Changrui, 2019 ). It is currently believed that intergenic regions can control gene expression and inhibition, and help RNA to identify genes with low conservation and diversity ( Ingvarsson et al, 2016 ; Bakhtiarizadeh and Salehi, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Screening and Verification of Molecular Markers and Genes Related to Salt-Alkali Tolerance in Portunus trituberculatus

Zhang

Xiao

et al. 2022

Front. Genet.

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Salt-alkali tolerance is one of the important breeding traits of Portunus trituberculatus. Identification of molecular markers linked to salt-alkali tolerance is prerequisite to develop such molecular marker-assisted breeding. In this study, Bulked Segregant Analysis (BSA) was used to screen molecular markers associated with salt-alkali tolerance trait in P. trituberculatus. Two DNA mixing pools with significant difference in salt-alkali tolerance were prepared and 94.83G of high-quality sequencing data was obtained. 855 SNPs and 1051 Indels were firstly selected as candidate markers by BSA analysis, out of which, 20 markers were further selected via △index value (close to 0 or 1) and eight of those were successfully verified. In addition, based on the located information of the markers in genome, eight candidate genes related to salt-alkali tolerance were anchored including ubiquitin-conjugating enzyme, aspartate–tRNA ligase, vesicle-trafficking protein, and so on. qPCR results showed that the expression patterns of all these genes changed significantly after salt-alkali stress, suggesting that they play certain roles in salt-alkali adaptation. Our results will provide applicable markers for molecular marker-assisted breeding and help to clarify the mechanisms of salt-alkali adaptation of P. trituberculatus.

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“…can be used to perform all-against-all alignments on these RNA transcripts, which will then be subsequently summarized as the distance matrix for clustering purposes. Various clustering algorithms [ 8 , 39 ] can then be applied to identify ncRNA families with similar secondary structures and infer their amazing cellular and molecular functionalities.…”

Section: Methodsmentioning

confidence: 99%

“…Recently, genome-wide RNA structurome analysis has led to many interesting discoveries regarding novel regulatory mechanisms. For example, analysis of the RNA structural elements in Drosophila melanogaster 3’-UTR suggests a cluster of ncRNA elements that can direct the localization of their upstream genes within the spermatids [ 8 ]. Similar studies have also been applied to the Ciona intestinalis genome for novel ncRNA family discovery [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

Efficient alignment of RNA secondary structures using sparse dynamic programming

Zhong

Zhang

2013

BMC Bioinformatics

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BackgroundCurrent advances of the next-generation sequencing technology have revealed a large number of un-annotated RNA transcripts. Comparative study of the RNA structurome is an important approach to assess their biological functionalities. Due to the large sizes and abundance of the RNA transcripts, an efficient and accurate RNA structure-structure alignment algorithm is in urgent need to facilitate the comparative study. Despite the importance of the RNA secondary structure alignment problem, there are no computational tools available that provide high computational efficiency and accuracy. In this case, designing and implementing such an efficient and accurate RNA secondary structure alignment algorithm is highly desirable.ResultsIn this work, through incorporating the sparse dynamic programming technique, we implemented an algorithm that has an O(n3) expected time complexity, where n is the average number of base pairs in the RNA structures. This complexity, which can be shown assuming the polymer-zeta property, is confirmed by our experiments. The resulting new RNA secondary structure alignment tool is called . Benchmark results indicate that can significantly speedup RNA structure-structure alignments compared to other state-of-the-art RNA alignment tools, while maintaining high alignment accuracy.ConclusionsUsing the sparse dynamic programming technique, we are able to develop a new RNA secondary structure alignment tool that is both efficient and accurate. We anticipate that the new alignment algorithm will significantly promote comparative RNA structure studies. The program, , is freely available at http://genome.ucf.edu/ERA.

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Discovering non-coding RNA elements in Drosophila 3' untranslated regions

Cited by 3 publications

References 54 publications

Identification and characterization of novel conserved RNA structures in Drosophila

Identification and characterization of novel conserved RNA structures in Drosophila

Screening and Verification of Molecular Markers and Genes Related to Salt-Alkali Tolerance in Portunus trituberculatus

Efficient alignment of RNA secondary structures using sparse dynamic programming

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