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

F1000Research
Peng QinSheila McCormick

Abstract

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 model...Continue Reading

References

Oct 31, 2006·Proceedings of the National Academy of Sciences of the United States of America·Surekha Katiyar-AgarwalHailing Jin
May 15, 2007·Plant Physiology·Stefan R HenzMarkus Schmid
Jan 16, 2008·BMC Molecular Biology·Hailing JinJian-Kang Zhu
Aug 1, 2008·Plant Physiology·Filipe BorgesJörg D Becker
Mar 13, 2015·Plant Reproduction·Nicholas Rutley, David Twell
May 7, 2016·Bioinformatics·Nowlan H FreeseAnn E Loraine

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Datasets Mentioned

BETA
SRP022162

Methods Mentioned

BETA
RNA-seq

Software Mentioned

Excel
IGB Quickload
Integrated Genome Browser

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