Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species

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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Genome-wide in silico identification and characterization of sodium-proton (Na+/H+) antiporters in Indica rice

Plant Gene ◽

10.1016/j.plgene.2021.100280 ◽

2021 ◽

pp. 100280

Author(s):

Tushar Khare ◽

Shrushti Joshi ◽

Kawaljeet Kaur ◽

Amrita Srivastav ◽

Varsha Shriram ◽

...

Keyword(s):

In Silico ◽

Indica Rice ◽

Genome Wide ◽

In Silico Identification ◽

Identification And Characterization

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Genome-wide in silico identification of GPI proteins in Mycosphaerella fijiensis and transcriptional analysis of two GPI-anchored β-1,3-glucanosyltransferases

Mycologia ◽

10.3852/12-103 ◽

2013 ◽

Vol 105 (2) ◽

pp. 285-296 ◽

Cited By ~ 7

Author(s):

Nuvia Kantún-Moreno ◽

Roberto Vázquez-Euán ◽

Miguel Tzec-Simá ◽

Leticia Peraza-Echeverría ◽

Rosa Grijalva-Arango ◽

...

Keyword(s):

In Silico ◽

Transcriptional Analysis ◽

Mycosphaerella Fijiensis ◽

Genome Wide ◽

In Silico Identification ◽

Gpi Proteins

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Peer Review #2 of "Genome-wide in silico identification of membrane-bound transcription factors in plant species (v0.1)"

10.7287/peerj.4051v0.1/reviews/2 ◽

2017 ◽

Keyword(s):

Transcription Factors ◽

Peer Review ◽

Plant Species ◽

In Silico ◽

Genome Wide ◽

Membrane Bound ◽

In Silico Identification

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In silico prediction and experimental validation of natural antisense transcripts in two cancer-associated regions of human chromosome 6

International Journal of Oncology ◽

10.3892/ijo_00000237 ◽

2009 ◽

Vol 34 (4) ◽

Author(s):

Acquati

Keyword(s):

Human Chromosome ◽

In Silico ◽

Experimental Validation ◽

Chromosome 6 ◽

In Silico Prediction ◽

Antisense Transcripts ◽

Natural Antisense Transcripts ◽

Human Chromosome 6

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

Nature Communications ◽

10.1038/s41467-020-19186-x ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Yajie Li ◽

Xiaorong Li ◽

Jun Yang ◽

Yuke He

Keyword(s):

Genetic Manipulation ◽

Biological Processes ◽

Sequencing Data ◽

Antisense Transcripts ◽

Natural Antisense Transcripts ◽

Genome Wide ◽

Eukaryotic Gene Expression ◽

Eukaryotic Gene ◽

Regulatory Loop ◽

Antisense Genes

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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