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 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.
Highlights
Natural antisense transcripts (NATs) are endogenous transcripts that contain sequences complementary to each other
We loaded TAIR10 gene models s and pollen RNA-seq into IGB, manually scanned for cisNATs in each chromosome, based on the following parameters: 1) the orientation of two adjacent genes in TAIR10 was reverse and complementary; 2) the length of transcripts mapping to the overlap of two adjacent genes was larger than 21nt, because the size of sRNA generated by cis-NATs is normally larger than 21 nt; and 3) both adjacent genes encoded proteins
Potential cis-NATs with one expressed gene in pollen RNA-seq data might still be functional in pollen
Summary
Natural antisense transcripts (NATs) are endogenous transcripts that contain sequences complementary to each other. NATs have been shown to regulate gene expression by generating small RNAs from the overlapping region (Zhang et al, 2013). Based on the relative orientation and overlap degree of two transcripts, cis-NATs can be categorized into three types: head-to-head (5′ to 5′), tail-to-tail (3′ to 3′) and fully overlapping (Jin et al, 2008). Cis-NATs are widely present in plants, animals and fungi (Zhang et al, 2013). Cis-NATs are important for pathogen resistance (Katiyar-Agarwal et al, 2006), stress tolerance (Borsani et al, 2005), successful fertilization (Ron et al, 2010), and phosphate homeostasis and plant fitness (Jabnoune et al, 2013)
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