Biology Agriculture Aquaculture Horticulture Postharvest Forestry Geography Environment Health

Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

submitted by catisoya25 1 year and 11 months ago
Many eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, and yeasts. However, many questions remain regarding the features and biogenesis of nat-siRNAs. Results Through deep sequencing, we identified more than 17, unique siRNAs corresponding to cis-NATs from biotic and abiotic stress-challenged Arabidopsis thaliana and 56, from abiotic stress-treated rice. These siRNAs were enriched in the overlapping regions of NATs and exhibited either site-specific or distributed patterns, often with strand bias. Out of 1,439 and 767 cis-NAT pairs identified in Arabidopsis and rice, respectively, 84 and 119 could generate at least 1 siRNAs per million reads from the overlapping regions. Among them, 16 cis-NAT pairs from Arabidopsis and 34 from rice gave rise to nat-siRNAs exclusively in the overlap regions. Genetic analysis showed that the overlapping double-stranded RNAs could be processed by Dicer-like 1 (DCL1) and/or DCL3. The DCL3-dependent nat-siRNAs were also dependent on RNA-dependent RNA polymerase 2 (RDR2) and plant-specific RNA polymerase IV (PolIV), whereas only a fraction of DCL1-dependent nat-siRNAs was RDR- and PolIV-dependent. Furthermore, the levels of some nat-siRNAs were regulated by specific biotic or abiotic stress conditions in Arabidopsis and rice. Conclusions Our results suggest that nat-siRNAs display distinct distribution patterns and are generated by DCL1 and/or DCL3. Our analysis further supported the existence of nat-siRNAs in plants and advanced our understanding of their characteristics.

Topic: Biology

Add your comment

Please Login or Signup to leave a comment

Related stories

Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice
submitted by oleghell 1 year and 6 months ago - Topic: Biology
Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-NATs in various eukaryotic organisms. Genome-wide in silico analysis has identified a la...

Melanoma epigenetics: novel mechanisms, markers, and medicines
submitted by miow 20 days ago - Topic: Health
The incidence and mortality rates of cutaneous melanoma continue to increase worldwide, despite the deployment of targeted therapies. Recently, there has been rapid growth and development in our understanding of epigenetic mechanisms and their role in cancer pathobiology. Epigenetics—defined as the processes resulting in heritable changes in gene expression beyond those caused by altera...

Genome-wide Analysis of the Distribution of AP2/ERF Transcription Factors Reveals Duplication and Elucidates their Potential Function in Chinese Cabbage (Brassica rapa ssp. pekinensis)
submitted by vitvnhoa2 1 year and 4 months ago - Topic: Agriculture
The AP2/ERF family is one of the largest groups of transcription factors in plants. Members of this family are involved in various biological processes, such as plant development, pathogen defense and stress responses. Here, we identified a total of 289 AP2/ERF transcription factors from Chinese cabbage based on the genome sequence. According to sequence similarity and the number of AP2/ERF dom...

Chromatin modifiers and the promise of epigenetic therapy in acute leukemia
submitted by toareno 2 months ago - Topic: Health
Hematopoiesis is a tightly regulated process involving the control of gene expression that directs the transition from hematopoietic stem and progenitor cells to terminally differentiated blood cells. In leukemia, the processes directing self-renewal, differentiation and progenitor cell expansion are disrupted, leading to the accumulation of immature, non-functioning malignant cells. Insights i...

Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya
submitted by bioagri 3 months ago - Topic: Biology
The Kenyan East African zebu cattle are valuable and widely used genetic resources. Previous studies using microsatellite loci revealed the complex history of these populations with the presence of taurine and zebu genetic backgrounds. Here, we estimate at genome-wide level the genetic composition and population structure of the East African Shorthorn Zebu (EASZ) of western Kenya. A total of 54...

Genome-wide analysis of the distribution of AP2/ERF transcription factors reveals duplication and CBFs genes elucidate their potential function in Brassica oleracea
submitted by chorlis 1 month ago - Topic: Biology
Cabbage (Brassica oleracea) is one of the most important leaf vegetables grown worldwide. The entire cabbage genome sequence and more than fifty thousand proteins have been obtained to date. However a high degree of sequence similarity and conserved genome structure remain between cabbage and Arabidopsis; therefore, Arabidopsis is a viable reference species for comparative genomics studies. Tra...

Genomic insights of protein arginine methyltransferase Hmt1 binding reveals novel regulatory functions
submitted by lekicora 1 year and 6 months ago - Topic: Biology
Protein arginine methylation is a post-translational modification involved in important biological processes such as transcription and RNA processing. This modification is catalyzed by both type I and II protein arginine methyltransferases (PRMTs). One of the most conserved type I PRMTs is PRMT1, the homolog of which is Hmt1 in Saccharomyces cerevisiae. Hmt1 has been shown to play a role in var...

Elucidating the evolutionary history and expression patterns of nucleoside phosphorylase paralogs (vegetative storage proteins) in Populus and the plant kingdom
submitted by gseikmon 11 months ago - Topic: Agriculture
Nucleoside phosphorylases (NPs) have been extensively investigated in human and bacterial systems for their role in metabolic nucleotide salvaging and links to oncogenesis. In plants, NP-like proteins have not been comprehensively studied, likely because there is no evidence of a metabolic function in nucleoside salvage. However, in the forest trees genus Populus a family of NP-like proteins fu...

Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis
submitted by gorfeild2345 1 year and 9 months ago - Topic: Biology
The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four major groups namely, 1R-MYB, 2R-MYB, 3R-MYB and 4R-MYB based on the number and position of MYB repeats. MYB transcription factors are involved in plant development, secondary metabolis...

Structure, Evolution, and Expression of the β-Galactosidase Gene Family in Brassica campestris ssp. chinensis
submitted by vitvnhoa2 1 year and 2 months ago - Topic: Agriculture
Plant β-galactosidases (EC; BGAL) are associated with cell wall biogenesis and modification. β-Galactosidase isozymes are encoded by the BGAL multigene family in plants. In this study, 16 BcBGAL genes from the Brassica campestris ssp. chinensis (syn. Brassica rapa ssp. chinensis) genome were investigated and compared with those from Arabidopsis thaliana. A comprehensive genome-wide a...