Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa

Yu, Xiang; Yang, Jun; Li, Xiaorong; Liu, Xuxin; Sun, Chongyang; Wu, Feijie; He, Yuqing

doi:10.1186/1471-2229-13-208

Cited by 70 publications

(52 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the past decade, many lncRNAs have been identified by high‐throughput sequencing of Arabidopsis (Liu et al ., ; Di et al ., ; Wang et al ., ), rice (Lu et al ., ; Zhang et al ., ), maize (Li et al ., ; Zhang et al ., ), Brassica rapa . (Yu et al ., ), populus (Shuai et al ., ), Triticum aestivum (wheat; Xin et al ., ), Gossypium spp . (cotton; Wang et al ., ) Gossypium arboreum (cotton; Zou et al ., ), Solanum lycopersicum (tomato; Wang et al ., ; Zhu et al ., ; Wang et al ., ), Cucumis sativus (cucumber; Hao et al ., ) and other plants.…”

Section: Introductionmentioning

confidence: 99%

Stress‐responsive regulation of long non‐coding RNA polyadenylation in Oryza sativa

Yuan

Yang

et al. 2018

The Plant Journal

View full text Add to dashboard Cite

Recently, long non-coding RNAs (lncRNAs) have been demonstrated to be involved in many biological processes of plants; however, a systematic study on transcriptional and, in particular, post-transcriptional regulation of stress-responsive lncRNAs in Oryza sativa (rice) is lacking. We sequenced three types of RNA libraries (poly(A)+, poly(A)- and nuclear RNAs) under four abiotic stresses (cold, heat, drought and salt). Based on an integrative bioinformatics approach and ~200 high-throughput data sets, ~170 of which have been published, we revealed over 7000 lncRNAs, nearly half of which were identified for the first time. Notably, we found that the majority of the ~500 poly(A) lncRNAs that were differentially expressed under stress were significantly downregulated, but approximately 25% were found to have upregulated non-poly(A) forms. Moreover, hundreds of lncRNAs with downregulated polyadenylation (DPA) tend to be highly conserved, show significant nuclear retention and are co-expressed with protein-coding genes that function under stress. Remarkably, these DPA lncRNAs are significantly enriched in quantitative trait loci (QTLs) for stress tolerance or development, suggesting their potential important roles in rice growth under various stresses. In particular, we observed substantially accumulated DPA lncRNAs in plants exposed to drought and salt, which is consistent with the severe reduction of RNA 3'-end processing factors under these conditions. Taken together, the results of this study reveal that polyadenylation and subcellular localization of many rice lncRNAs are likely to be regulated at the post-transcriptional level. Our findings strongly suggest that many upregulated/downregulated lncRNAs previously identified by traditional RNA-seq analyses need to be carefully reviewed to assess the influence of post-transcriptional modification.

show abstract

Section: Introductionmentioning

confidence: 99%

Stress‐responsive regulation of long non‐coding RNA polyadenylation in Oryza sativa

Yuan

Yang

et al. 2018

The Plant Journal

View full text Add to dashboard Cite

show abstract

“…Genome-wide cis-NAT characterization in Solanaceae and cis-NAT evolution cis-NAT genes have been actively studied in recent years due to their interesting regulatory mechanisms and important functions . Genome-wide cis-NAT identification has been performed in several species, such as Arabidopsis, rice, soybean and Brassica rapa (Wang et al, 2005(Wang et al, , 2006Hu et al, 2013;Yu et al, 2013;Yuan et al, 2015). However, genome-wide NAT identification relies on well-annotated transcriptome data.…”

Section: Improving Pepper Genome Annotation By Pacbio Fulllength Cdnamentioning

confidence: 99%

Full‐length mRNA sequencing and gene expression profiling reveal broad involvement of natural antisense transcript gene pairs in pepper development and response to stresses

et al. 2019

View full text Add to dashboard Cite

Summary Pepper is an important vegetable with great economic value and unique biological features. In the past few years, significant development has been made toward understanding the huge complex pepper genome; however, pepper functional genomics has not been well studied. To better understand the pepper gene structure and pepper gene regulation, we conducted full‐length mRNA sequencing by PacBio sequencing and obtained 57 862 high‐quality full‐length mRNA sequences derived from 18 362 previously annotated and 5769 newly detected genes. New gene models were built that combined the full‐length mRNA sequences and corrected approximately 500 fragmented gene models from previous annotations. Based on the full‐length mRNA, we identified 4114 and 5880 pepper genes forming natural antisense transcript (NAT) genes in‐cis and in‐trans, respectively. Most of these genes accumulate small RNAs in their overlapping regions. By analyzing these NAT gene expression patterns in our transcriptome data, we identified many NAT pairs responsive to a variety of biological processes in pepper. Pepper formate dehydrogenase 1 (FDH1), which is required for R‐gene‐mediated disease resistance, may be regulated by nat‐siRNAs and participate in a positive feedback loop in salicylic acid biosynthesis during resistance responses. Several cis‐NAT pairs and subgroups of trans‐NAT genes were responsive to pepper pericarp and placenta development, which may play roles in capsanthin and capsaicin biosynthesis. Using a comparative genomics approach, the evolutionary mechanisms of cis‐NATs were investigated, and we found that an increase in intergenic sequences accounted for the loss of most cis‐NATs, while transposon insertion contributed to the formation of most new cis‐NATs. Open Research Badges This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at http://bigd.big.ac.cn/gsa Accession number, CRA001412

show abstract

“…A global analysis of the heat‐responsive chloroplast small RNAs (csRNAs) and cis‐NATs‐derived small interfering RNAs (nat‐siRNAs) was also conducted in Chinese cabbage (Wang et al ; Yu et al ). Many csRNAs and nat‐siRNAs derived from 12 cis‐NATs were responsive to heat stress, suggesting their potential roles in transcriptional or post‐transcriptional regulation under heat stress in plants (Wang et al ; Yu et al ).…”

Section: The Associations Between Sirnas Other Small Rnas and Tempermentioning

confidence: 99%

Small RNAs in regulating temperature stress response in plants

Liu

Yan

Yang

et al. 2017

JIPB

View full text Add to dashboard Cite

These authors contributed equally to this work. doi: 10.1111/jipb.12571 Yue-Qin ChenBin Liu *Correspondences: Yue-Qin Chen (lsscyq@mail.sysu.edu.cn); Bin Liu (lbgz1009@163.com, Dr. Liu is fully responsible for the distribution of all materials associated with this article).Abstract Due to global climate change, temperature stress has become one of the primary causes of crop losses worldwide. Much progress has been made in unraveling the complex stress response mechanisms in plants, particularly in the identification of temperature stress responsive protein-coding genes. Recently discovered microRNAs (miRNAs) and endogenous small-interfering RNAs (siRNAs) have also been demonstrated as important players in plant temperature stress response. Using high-throughput sequencing, many small RNAs, especially miRNAs, have been identified to be triggered by cold or heat. Subsequently, several studies have shown an important functional role for these small RNAs in cold or heat tolerance. These findings greatly broaden our understanding of endogenous small RNAs in plant stress response control. Here, we highlight new findings regarding the roles of miRNAs and siRNAs in plant temperature stress response and acclimation. We also review the current understanding of the regulatory mechanisms of small RNAs in temperature stress response, and explore the outlook for the use of these small RNAs in molecular breeding for improvement of temperature stress tolerance in plants.

show abstract

Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa

Cited by 70 publications

References 40 publications

Stress‐responsive regulation of long non‐coding RNA polyadenylation in Oryza sativa

Stress‐responsive regulation of long non‐coding RNA polyadenylation in Oryza sativa

Full‐length mRNA sequencing and gene expression profiling reveal broad involvement of natural antisense transcript gene pairs in pepper development and response to stresses

Small RNAs in regulating temperature stress response in plants

Contact Info

Product

Resources

About