PlantNATsDB: a comprehensive database of plant natural antisense transcripts

Chen, Dijun; Yuan, Chunhui; Zhang, Jian; Zhang, Zhao; Bai, Lin; Meng, Yijun; Chen, Lingling; Chen, Ming

doi:10.1093/nar/gkr823

Cited by 77 publications

(73 citation statements)

References 35 publications

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“…The rRNA, tRNA, snRNA, and snoRNA were annotated by aligning them against the Rfam database (Rfam:http://www.sanger.ac.uk/software/Rfam) and the NCBI GenBank databases (GenBank:http://www.ncbi.nlm.nih.gov/blast/Blast.cgi). Natural antisense transcripts and trans-acting small interfering RNAs were identified by using the PlantNATsDB (http://bis.zju.edu.cn/pnatdb/) and UEA sRNA tools, respectively (Moxon et al, 2008; Chen et al, 2011). The repeat sequences were annotated by aligning them to the Repbase database by RepeatMasker (Bao et al, 2015; Smit et al, 2013-2015).…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification of MicroRNAs and Their Targets in the Leaves and Fruits of Eucommia ulmoides Using High-Throughput Sequencing

Wang

Wuyun

2016

Front. Plant Sci.

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MicroRNAs (miRNAs), a group of endogenous small non-coding RNAs, play important roles in plant growth, development, and stress response processes. Eucommia ulmoides Oliver (hardy rubber tree) is one of the few woody plants capable of producing trans-1, 4-polyisoprene (TPI), also known as Eu-rubber, which has been utilized as an industrial raw material and is extensively cultivated in China. However, the mechanism of TPI biosynthesis has not been identified in E. ulmoides. To characterize small RNAs and their targets with potential biological roles involved in the TPI biosynthesis in E. ulmoides, in the present study, eight small RNA libraries were constructed and sequenced from young and mature leaves and fruits of E. ulmoides. Further analysis identified 34 conserved miRNAs belonging to 20 families (two unclassified families), and 115 novel miRNAs seemed to be specific to E. ulmoides. Among these miRNAs, fourteen conserved miRNAs and 49 novel miRNAs were significantly differentially expressed and identified as Eu-rubber accumulation related miRNAs. Based on the E. ulmoides genomic data, 202 and 306 potential target genes were predicted for 33 conserved and 92 novel miRNAs, respectively; the predicted targets are mostly transcription factors and functional genes, which were enriched in metabolic pathways and biosynthesis of secondary metabolites. Noticeably, based on the expression patterns of miRNAs and their target genes in combination with the Eu-rubber accumulation, the negative correlation of expression of six miRNAs (Eu-miR14, Eu-miR91, miR162a, miR166a, miR172c, and miR396a) and their predicted targets serving as potential regulators in Eu-rubber accumulation. This study is the first to detect conserved and novel miRNAs and their potential targets in E. ulmoides and identify several candidate genes potentially controlling rubber accumulation, and thus provide molecular evidence for understanding the roles of miRNAs in regulating the TPI biosynthesis in E. ulmoides.

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Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification of MicroRNAs and Their Targets in the Leaves and Fruits of Eucommia ulmoides Using High-Throughput Sequencing

Wang

Wuyun

2016

Front. Plant Sci.

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“…2 The predicted lncRNAs were complementary to annotated genes in TAIR10 was used as reference of genes. If two transcripts overlap in the genome, they will be selected as putative cis -NAT pairs.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide view of natural antisense transcripts in Arabidopsis thaliana

et al. 2015

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Natural antisense transcripts (NATs) are endogenous transcripts that can form double-stranded RNA structures. Many protein-coding genes (PCs) and non-protein-coding genes (NPCs) tend to form cis-NATs and trans-NATs, respectively. In this work, we identified 4,080 cis-NATs and 2,491 trans-NATs genome-widely in Arabidopsis. Of these, 5,385 NAT-siRNAs were detected from the small RNA sequencing data. NAT-siRNAs are typically 21nt, and are processed by Dicer-like 1 (DCL1)/DCL2 and RDR6 and function in epigenetically activated situations, or 24nt, suggesting these are processed by DCL3 and RDR2 and function in environment stress. NAT-siRNAs are significantly derived from PC/PC pairs of trans-NATs and NPC/NPC pairs of cis-NATs. Furthermore, NAT pair genes typically have similar pattern of epigenetic status. Cis-NATs tend to be marked by euchromatic modifications, whereas trans-NATs tend to be marked by heterochromatic modifications.

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“…Although sequencing of cDNA/EST libraries ( Jen et al 2005;Wang et al 2005) and microarray experiments (Ge et al 2008;Morrissy et al 2011) have provided preliminary genome-wide assessments of cis-NATs (Henz et al 2007;Jin et al 2008;Chen et al 2012), results from these early studies are less than ideal (Weber et al 2007). In recent years, the advent of high-throughput sequencing has provided the opportunity to systematically characterize the transcriptome at higher coverage and better accuracy than conventional approaches (Mortazavi et al 2008).…”

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confidence: 99%

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

Liberman

Mukherjee

et al. 2013

Genome Res.

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Pairs of RNA molecules transcribed from partially or entirely complementary loci are called cis-natural antisense transcripts (cis-NATs), and they play key roles in the regulation of gene expression in many organisms. A promising experimental tool for profiling sense and antisense transcription is strand-specific RNA sequencing (ssRNA-seq). To identify cisNATs using ssRNA-seq, we developed a new computational method based on a model comparison framework that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries. Applying the method to new ssRNA-seq data from whole-root and cell-type-specific Arabidopsis libraries confirmed most of the known cis-NAT pairs and identified 918 additional cis-NAT pairs. Newly identified cis-NAT pairs are supported by polyadenylation data, alternative splicing patterns, and RT-PCR validation. We found 209 cis-NAT pairs that have opposite expression levels in neighboring cell types, implying cell-type-specific roles for cis-NATs. By integrating a genome-wide epigenetic profile of Arabidopsis, we identified a unique chromatin signature of cis-NATs, suggesting a connection between cis-NAT transcription and chromatin modification in plants. An analysis of small-RNA sequencing data showed that~4% of cis-NAT pairs produce putative cis-NAT-induced siRNAs. Taken together, our data and analyses illustrate the potential for multifaceted regulatory roles of plant cis-NATs.

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PlantNATsDB: a comprehensive database of plant natural antisense transcripts

Cited by 77 publications

References 35 publications

Genome-Wide Identification of MicroRNAs and Their Targets in the Leaves and Fruits of Eucommia ulmoides Using High-Throughput Sequencing

Genome-Wide Identification of MicroRNAs and Their Targets in the Leaves and Fruits of Eucommia ulmoides Using High-Throughput Sequencing

Genome-wide view of natural antisense transcripts in Arabidopsis thaliana

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

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