Natural antisense transcripts of MIR398 genes suppress microR398 processing and attenuate plant thermotolerance

Abstract MicroRNAs (miRNAs) and natural antisense transcripts (NATs) control many biological processes and have been broadly applied for genetic manipulation of eukaryotic gene expression. Still unclear, however, are whether and how NATs regulate miRNA production. Here, we report that the cis-NATs of MIR398 genes repress the processing of their pri-miRNAs. Through genome-wide analysis of RNA sequencing data, we identify cis-NATs of MIRNA genes in Arabidopsis and Brassica. In Arabidopsis, MIR398b and MIR398c are coexpressed in vascular tissues with their antisense genes NAT398b and NAT398c, respectively. Knock down of NAT398b and NAT398c promotes miR398 processing, resulting in stronger plant thermotolerance owing to silencing of miR398-targeted genes; in contrast, their overexpression activates NAT398b and NAT398c, causing poorer thermotolerance due to the upregulation of miR398-targeted genes. Unexpectedly, overexpression of MIR398b and MIR398c activates NAT398b and NAT398c. Taken together, these results suggest that NAT398b/c repress miR398 biogenesis and attenuate plant thermotolerance via a regulatory loop.

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What are natural antisense transcripts good for?

Biochemical Society Transactions ◽

10.1042/bst0381144 ◽

2010 ◽

Vol 38 (4) ◽

pp. 1144-1149 ◽

Cited By ~ 30

Author(s):

Andreas Werner ◽

Daniel Swan

Keyword(s):

Gene Expression ◽

Gene Silencing ◽

Higher Order ◽

Transcriptional Gene Silencing ◽

Antisense Transcripts ◽

Natural Antisense Transcripts ◽

Protein Coding ◽

Eukaryotic Gene Expression ◽

Eukaryotic Gene

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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Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria

Nature Communications ◽

10.1038/s41467-021-21150-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Zhe Sun ◽

Alexander V. Yakhnin ◽

Peter C. FitzGerald ◽

Carl E. Mclntosh ◽

Mikhail Kashlev

Keyword(s):

Environmental Cues ◽

Start Site ◽

Transcription Start ◽

Genome Wide Analysis ◽

Genome Wide ◽

Eukaryotic Gene Expression ◽

Eukaryotic Gene ◽

Vitro Analysis ◽

In Vitro Analysis

AbstractPromoter-proximal pausing regulates eukaryotic gene expression and serves as checkpoints to assemble elongation/splicing machinery. Little is known how broadly this type of pausing regulates transcription in bacteria. We apply nascent elongating transcript sequencing combined with RNase I footprinting for genome-wide analysis of σ70-dependent transcription pauses in Escherichia coli. Retention of σ70 induces strong backtracked pauses at a 10−20-bp distance from many promoters. The pauses in the 10−15-bp register of the promoter are dictated by the canonical −10 element, 6−7 nt spacer and “YR+1Y” motif centered at the transcription start site. The promoters for the pauses in the 16−20-bp register contain an additional −10-like sequence recognized by σ70. Our in vitro analysis reveals that DNA scrunching is involved in these pauses relieved by Gre cleavage factors. The genes coding for transcription factors are enriched in these pauses, suggesting that σ70 and Gre proteins regulate transcription in response to changing environmental cues.

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A Novel H19 Antisense RNA Overexpressed in Breast Cancer Contributes to Paternal IGF2 Expression

Molecular and Cellular Biology ◽

10.1128/mcb.02103-07 ◽

2008 ◽

Vol 28 (22) ◽

pp. 6731-6745 ◽

Cited By ~ 103

Author(s):

Nathalie Berteaux ◽

Nathalie Aptel ◽

Guy Cathala ◽

Céline Genton ◽

Jean Coll ◽

...

Keyword(s):

Breast Cancer ◽

Antisense Rna ◽

Maternal Allele ◽

Human Breast ◽

Antisense Transcripts ◽

Distal Chromosome ◽

Eukaryotic Gene Expression ◽

Eukaryotic Gene ◽

Few Data ◽

Chromosome 11P15.5

ABSTRACT The H19/IGFf2 locus belongs to a large imprinted domain located on human chromosome 11p15.5 (homologue to mouse distal chromosome 7). The H19 gene is expressed from the maternal allele, while IGF2 is paternally expressed. Natural antisense transcripts and intergenic transcription have been involved in many aspects of eukaryotic gene expression, including genomic imprinting and RNA interference. However, apart from the identification of some IGF2 antisense transcripts, few data are available on that topic at the H19/IGF2 locus. We identify here a novel transcriptional activity at both the human and the mouse H19/IGF2 imprinted loci. This activity occurs antisense to the H19 gene and has the potential to produce a single 120-kb transcript that we called the 91H RNA. This nuclear and short-lived RNA is not imprinted in mouse but is expressed predominantly from the maternal allele in both mice and humans within the H19 gene region. Moreover, the transcript is stabilized in breast cancer cells and overexpressed in human breast tumors. Finally, knockdown experiments showed that, in humans, 91H, rather than affecting H19 expression, regulates IGF2 expression in trans.

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

Genome Research ◽

10.1101/gr.149310.112 ◽

2013 ◽

Vol 23 (10) ◽

pp. 1730-1739 ◽

Cited By ~ 35

Author(s):

S. Li ◽

L. M. Liberman ◽

N. Mukherjee ◽

P. N. Benfey ◽

U. Ohler

Keyword(s):

Rna Sequencing ◽

Sequencing Data ◽

Antisense Transcripts ◽

Natural Antisense Transcripts ◽

Integrated Detection

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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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Workflow for Genome-Wide Determination of Pre-mRNA Splicing Efficiency from Yeast RNA-seq Data

BioMed Research International ◽

10.1155/2016/4783841 ◽

2016 ◽

Vol 2016 ◽

pp. 1-9 ◽

Cited By ~ 5

Author(s):

Martin Převorovský ◽

Martina Hálová ◽

Kateřina Abrhámová ◽

Jiří Libus ◽

Petr Folk

Keyword(s):

Growth Conditions ◽

Mrna Splicing ◽

Rna Seq ◽

Fastq Format ◽

Genome Wide ◽

Eukaryotic Gene Expression ◽

Eukaryotic Gene ◽

Splicing Efficiency ◽

Splice Junctions

Pre-mRNA splicing represents an important regulatory layer of eukaryotic gene expression. In the simple budding yeast Saccharomyces cerevisiae, about one-third of all mRNA molecules undergo splicing, and splicing efficiency is tightly regulated, for example, during meiotic differentiation. S. cerevisiae features a streamlined, evolutionarily highly conserved splicing machinery and serves as a favourite model for studies of various aspects of splicing. RNA-seq represents a robust, versatile, and affordable technique for transcriptome interrogation, which can also be used to study splicing efficiency. However, convenient bioinformatics tools for the analysis of splicing efficiency from yeast RNA-seq data are lacking. We present a complete workflow for the calculation of genome-wide splicing efficiency in S. cerevisiae using strand-specific RNA-seq data. Our pipeline takes sequencing reads in the FASTQ format and provides splicing efficiency values for the 5′ and 3′ splice junctions of each intron. The pipeline is based on up-to-date open-source software tools and requires very limited input from the user. We provide all relevant scripts in a ready-to-use form. We demonstrate the functionality of the workflow using RNA-seq datasets from three spliceosome mutants. The workflow should prove useful for studies of yeast splicing mutants or of regulated splicing, for example, under specific growth conditions.

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The Closely Related RNA helicases, UAP56 and URH49, Preferentially Form Distinct mRNA Export Machineries and Coordinately Regulate Mitotic Progression

Molecular Biology of the Cell ◽

10.1091/mbc.e09-10-0913 ◽

2010 ◽

Vol 21 (16) ◽

pp. 2953-2965 ◽

Cited By ~ 67

Author(s):

Tomohiro Yamazaki ◽

Naoko Fujiwara ◽

Hiroko Yukinaga ◽

Miki Ebisuya ◽

Takuya Shiki ◽

...

Keyword(s):

Gene Expression ◽

Nuclear Export ◽

Mrna Export ◽

Mitotic Progression ◽

Rna Helicases ◽

Target Mrnas ◽

Genome Wide ◽

Chromatid Cohesion ◽

Eukaryotic Gene Expression ◽

Eukaryotic Gene

Nuclear export of mRNA is an essential process for eukaryotic gene expression. The TREX complex couples gene expression from transcription and splicing to mRNA export. Sub2, a core component of the TREX complex in yeast, has diversified in humans to two closely related RNA helicases, UAP56 and URH49. Here, we show that URH49 forms a novel URH49–CIP29 complex, termed the AREX (alternative mRNA export) complex, whereas UAP56 forms the human TREX complex. The mRNAs regulated by these helicases are different at the genome-wide level. The two sets of target mRNAs contain distinct subsets of key mitotic regulators. Consistent with their target mRNAs, depletion of UAP56 causes mitotic delay and sister chromatid cohesion defects, whereas depletion of URH49 causes chromosome arm resolution defects and failure of cytokinesis. In addition, depletion of the other human TREX components or CIP29 causes mitotic defects similar to those observed in UAP56- or URH49-depleted cells, respectively. Taken together, the two closely related RNA helicases have evolved to form distinct mRNA export machineries, which regulate mitosis at different steps.

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