Protein-Coding cis-Natural Antisense Transcripts Have High and Broad Expression in Arabidopsis

NATs (natural antisense transcripts) are important regulators of eukaryotic gene expression. Interference between the expression of protein-coding sense transcripts and the corresponding NAT is well documented. In the present review, we focus on an additional, higher-order role of NATs that is currently emerging. The recent discovery of endogenous siRNAs (short interfering RNAs), as well as NAT-induced transcriptional gene silencing, are key to the proposed novel function of NATs.

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Cell-specific cis-natural antisense transcripts (cis-NATs) in the sperm and the pollen vegetative cells of Arabidopsis thaliana

F1000Research ◽

10.12688/f1000research.13311.1 ◽

2018 ◽

Vol 7 ◽

pp. 93

Author(s):

Peng Qin ◽

Ann E. Loraine ◽

Sheila McCormick

Keyword(s):

Gene Expression ◽

Vegetative Cell ◽

Cell Types ◽

Antisense Transcripts ◽

Vegetative Cells ◽

Natural Antisense Transcripts ◽

Protein Coding ◽

Regulate Gene Expression ◽

Genome Wide ◽

Gene Models

Background: cis-NATs (cis-natural antisense transcripts) are transcribed from opposite strands of adjacent genes and have been shown to regulate gene expression by generating small RNAs from the overlapping region. cis-NATs are important for plant development and resistance to pathogens and stress. Several genome-wide investigations identified a number of cis-NAT pairs, but these investigations predicted cis-NATS using expression data from bulk samples that included lots of cell types. Some cis-NAT pairs identified from those investigations might not be functional, because both transcripts of cis-NAT pairs need to be co-expressed in the same cell. Pollen only contains two cell types, two sperm and one vegetative cell, which makes cell-specific investigation of cis-NATs possible. Methods: We investigated potential protein-coding cis-NATs in pollen and sperm using pollen RNA-seq data and TAIR10 gene models using the Integrated Genome Browser. We then used sperm microarray data and sRNAs in sperm and pollen to determine possibly functional cis-NATs in the sperm or vegetative cell, respectively. Results: We identified 1471 potential protein-coding cis-NAT pairs, including 131 novel pairs that were not present in TAIR10 gene models. In pollen, 872 possibly functional pairs were identified. 72 and 56 pairs were potentially functional in sperm and vegetative cells, respectively. sRNAs were detected at 794 genes, belonging to 739 pairs. Conclusion: These potential candidates in sperm and the vegetative cell are tools for understanding gene expression mechanisms in pollen.

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Genomic determinants for initiation and length of natural antisense transcripts in Entamoeba histolytica

Scientific Reports ◽

10.1038/s41598-020-77010-4 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Damien Mornico ◽

Chung-Chau Hon ◽

Mikael Koutero ◽

Christian Weber ◽

Jean-Yves Coppee ◽

...

Keyword(s):

Gene Expression ◽

Entamoeba Histolytica ◽

Regulatory System ◽

Antisense Transcripts ◽

Natural Antisense Transcripts ◽

Protein Coding ◽

Transcription Start Sites ◽

Spurious Transcription ◽

Intergenic Regions ◽

Opposite Strand

AbstractNatural antisense transcripts (NAT) have been reported in prokaryotes and eukaryotes. While the functions of most reported NATs remain unknown, their potentials in regulating the transcription of their counterparts have been speculated. Entamoeba histolytica, which is a unicellular eukaryotic parasite, has a compact protein-coding genome with very short intronic and intergenic regions. The regulatory mechanisms of gene expression in this compact genome are under-described. In this study, by genome-wide mapping of RNA-Seq data in the genome of E. histolytica, we show that a substantial fraction of its protein-coding genes (28%) has significant transcription on their opposite strand (i.e. NAT). Intriguingly, we found the location of transcription start sites or polyadenylation sites of NAT are determined by the specific motifs encoded on the opposite strand of the gene coding sequences, thereby providing a compact regulatory system for gene transcription. Moreover, we demonstrated that NATs are globally up-regulated under various environmental conditions including temperature stress and pathogenicity. While NATs do not appear to be consequences of spurious transcription, they may play a role in regulating gene expression in E. histolytica, a hypothesis which needs to be tested.

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Natural Antisense Transcripts at the Interface between Host Genome and Mobile Genetic Elements

Frontiers in Microbiology ◽

10.3389/fmicb.2017.02292 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 14

Author(s):

Hany S. Zinad ◽

Inas Natasya ◽

Andreas Werner

Keyword(s):

Mobile Genetic Elements ◽

Host Genome ◽

Antisense Transcripts ◽

Natural Antisense Transcripts ◽

Genetic Elements

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Natural antisense transcripts as therapeutic targets

Drug Discovery Today Therapeutic Strategies ◽

10.1016/j.ddstr.2013.03.001 ◽

2013 ◽

Vol 10 (3) ◽

pp. e119-e125 ◽

Cited By ~ 5

Author(s):

Paul Halley ◽

Olga Khorkova ◽

Claes Wahlestedt

Keyword(s):

Therapeutic Targets ◽

Antisense Transcripts ◽

Natural Antisense Transcripts

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Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

10.21203/rs.3.rs-280217/v1 ◽

2021 ◽

Author(s):

Yong-Chao Xu ◽

Jie Zhang ◽

Dong-Yan Zhang ◽

Ying-Hui Nan ◽

Song Ge ◽

...

Keyword(s):

Drought Stress ◽

Stress Response ◽

Wild Rice ◽

Oryza Rufipogon ◽

Cultivated Rice ◽

Antisense Transcripts ◽

High Genetic Diversity ◽

Natural Antisense Transcripts ◽

Form Complex ◽

Oryza Nivara

Abstract Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa L.), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although many rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa ssp. japonica) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1,246 lncRNAs were identified, including 1,091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1,091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes previously demonstrated to be involved in stress response; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare. Conclusion We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.

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