RNA secondary structure analysis for abiotic stress resistant and housekeeping genes in Arabidopsis aliana and Oryza sativa

Shah, Syed Qasim

doi:10.19045/bspab.2016.50062

Cited by 4 publications

(2 citation statements)

References 9 publications

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“…Comparative genomics based research is a well-known approach for new interesting findings in various organisms [ 27 – 31 ]. Here, the comparative genomics-based homology search produced a total of 212 new conserved miRNAs from wheat ESTs ( S2 Table ).…”

Section: Resultsmentioning

confidence: 99%

Identification and annotation of newly conserved microRNAs and their targets in wheat (Triticum aestivum L.)

Achakzai¹,

Barozai²,

Din³

et al. 2018

PLoS ONE

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MicroRNAs (miRNAs) are small, non-coding and regulatory RNAs produce by cell endogenously. They are 18–26 nucleotides in length and play important roles at the post-transcriptional stage of gene regulation. Evolutionarily, miRNAs are conserved and their conservation plays an important role in the prediction of new miRNAs in different plants. Wheat (Triticum aestivum L.) is an important diet and consumed as second major crop in the world. This significant cereal crop was focused here through comparative genomics-based approach to identify new conserved miRNAs and their targeted genes. This resulted into a total of 212 new conserved precursor miRNAs (pre-miRNAs) belonging to 185 miRNA families. These newly profiled wheat’s miRNAs are also annotated for stem-loop secondary structures, length distribution, organ of expression, sense/antisense orientation and characterization from their expressed sequence tags (ESTs). Moreover, fifteen miRNAs along with housekeeping gene were randomly selected and subjected to RT-PCR expressional validation. A total of 32927 targets are also predicted and annotated for these newly profiled wheat miRNAs. These targets are found to involve in 50 gene ontology (GO) enrichment terms and significant processes. Some of the significant targets are RNA-dependent DNA replication (GO:0006278), RNA binding (GO:0003723), nucleic acid binding (GO:0003676), DNA-directed RNA polymerase activity (GO:0003899), magnesium ion transmembrane transporter activity (GO:0015095), antiporter activity (GO:0015297), solute:hydrogen antiporter activity (GO:0015299), protein kinase activity (GO:0004672), ATP binding (GO:0005524), regulation of Rab GTPase activity (GO:0032313) Rab GTPase activator activity (GO:0005097), regulation of signal transduction (GO:0009966) and phosphoprotein phosphatase inhibitor activity (GO:0004864). These findings will be helpful to manage this economically important grain plant for desirable traits through miRNAs regulation.

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Section: Resultsmentioning

confidence: 99%

Identification and annotation of newly conserved microRNAs and their targets in wheat (Triticum aestivum L.)

Achakzai¹,

Barozai²,

Din³

et al. 2018

PLoS ONE

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“…Comparative genome-based EST analysis is a wellestablished approach to find new interesting facts (Barozai and Husnain, 2011;Barozai et al, 2014;Shah et al, 2016) and identify conserved miRNAs in one species using already known miRNAs of another species (Barozai et al, 2011b(Barozai et al, , 2011c. Since it was developed, EST analysis has been widely used to identify conserved miRNAs in many plant species, including cotton, soybean, radish, tomato, chili, and potato.…”

Section: Detection Of Raw Sequences Of Mirnas From Estsmentioning

confidence: 99%

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

Bibi¹,

Barozai²,

Din³

2017

Turk J Agric For

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IntroductionMicroRNAs (miRNAs) are an extensive class of noncoding small endogenous RNAs of 18 to 26 nt in length that are derived from self-complementary fold-back structures of longer precursor sequences (pre-miRNAs) and are generated by Dicer-like 1 (DCL1) in plants (Bartel, 2004). Mature miRNAs inhibit gene expression at posttranscriptional levels by either targeting mRNAs for degradation or inhibiting protein translation. Both processes are accomplished by the complementary base pairing of miRNAs to their target mRNA sequences (Ambros, 2004). In plants, for a majority of cases, miRNAs interact with their targets through perfect or near-perfect base pairing and lead to target mRNA degradation (Jones-Rhoades et al., 2006). Increasing evidence has revealed that miRNAs play an important role in a wide range of development processes in plants, including cell proliferation, stress response, metabolism, inflammation, and signal transduction (Ambros, 2004;Jones-Rhoades et al., 2006;Zhang et al., 2007a;Ali et al., 2016) and crosskingdom gene regulation (Barozai and Din, 2017). To date, more than 28,645 miRNAs have been identified from 223 species of plants and animals and deposited in the publicly available database miRBase (Release 21) (Griffiths-Jones et al., 2008). The majority of plant miRNAs have been found in species with fully sequenced genomes including 713 from Oryza sativa, 401 from Populus trichocarpa, 384 from Arabidopsis thaliana, 343 from Solanum tuberosum, 321 from Zea mays, and 241 from Sorghum bicolor (Griffiths-Jones et al., 2008). miRNA-related research is continuously growing and miRNAs, along with their functions, are being identified and elucidated using a wide variety of computational tools and experimental methods including direct cloning, deep sequencing, and other approaches. Comparison of miRNAs across multiple plant species has demonstrated that some miRNAs are highly evolutionary conserved from species to species, such as from mosses to higher flowering eudicots in the plant kingdom (Floyd and Bowman, 2004;Zhang et al., 2006aZhang et al., , 2006b. Conservation of miRNA sequences has provided a powerful strategy for identifying miRNAs in other species. Currently, comparative genome-based homolog searches have been used to identify conserved miRNAs in many plant species, including cotton (

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Bioinformatics profiling and expressional studies of microRNAs in root, stem and leaf of the bioenergy plant switchgrass (Panicum virgatum L.) under drought stress

Barozai

Sangireddy

et al. 2018

Agri Gene

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RNA secondary structure analysis for abiotic stress resistant and housekeeping genes in Arabidopsis aliana and Oryza sativa

Cited by 4 publications

References 9 publications

Identification and annotation of newly conserved microRNAs and their targets in wheat (Triticum aestivum L.)

Identification and annotation of newly conserved microRNAs and their targets in wheat (Triticum aestivum L.)

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

Bioinformatics profiling and expressional studies of microRNAs in root, stem and leaf of the bioenergy plant switchgrass (Panicum virgatum L.) under drought stress

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