Insilco Prediction and Characterization of microRNAs from Oncopeltus fasciatus (Hemiptera: Lygaeidae) Genome

Ellango, R.; Asokan, R.; Ramamurthy, V. V.

doi:10.1007/s12010-016-2072-1

Cited by 7 publications

(5 citation statements)

References 30 publications

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“…All previous reported mature animal miRNA and precursor sequences were obtained from miRBase (version 21 released in June 2014; available at http://www.mirbase.org/). This miRNA dataset was used as query sequences for BLAST based homology search against tick genome and was carried out in BioEdit version 7.2.5 with an E value �0.01 and default value for the other parameters as described [46]. All the selected pre-miRNA sequences were then submitted to Mfold online software (http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form) to predict secondary structure (hairpin) and calculate free energy (ΔG).…”

Section: Microrna Prediction From Tick Genomementioning

confidence: 99%

“…The minimal folding free energy index (MFEI) was calculated to avoid designating other RNAs as miRNAs. Identification of I. scapularis miR-133 targets was accomplished using MiRanda version 3.3a (http://www.microrna.org/ ) and RNAhybrid version 2.1.2 (http://bibiserv.techfak.unibielefeld.de/rnahybrid/) with the parameters described in the previous study [46].…”

Section: Microrna Prediction From Tick Genomementioning

confidence: 99%

“…The miRNAs are first synthesized as long primary pri-miRNA by RNA polymerase II [45,46]. The pri-miRNA is then cleaved into approximately 70-100 base pairs short precursor pre-miRNA by drosha and then exported into cytoplasm and processed by dicer into 20-26 bp miRNA duplex consisting of guide strand and a passenger strand [46,47]. The passenger strand gets degraded leaving guide strand to become matured miRNA [47].…”

Section: Introductionmentioning

confidence: 99%

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Repression of tick microRNA-133 induces organic anion transporting polypeptide expression critical for Anaplasma phagocytophilum survival in the vector and transmission to the vertebrate host

et al. 2020

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The microRNAs (miRNAs) are important regulators of gene expression. In this study, we provide evidence for the first time to show that rickettsial pathogen Anaplasma phagocytophilum infection results in the down-regulation of tick microRNA-133 (miR-133), to induce Ixodes scapularis organic anion transporting polypeptide (isoatp4056) gene expression critical for this bacterial survival in the vector and for its transmission to the vertebrate host. Transfection studies with recombinant constructs containing transcriptional fusions confirmed binding of miR-133 to isoatp4056 mRNA. Treatment with miR-133 inhibitor resulted in increased bacterial burden and isoatp4056 expression in ticks and tick cells. In contrast, treatment with miR-133 mimic or pre-mir-133 resulted in dramatic reduction in isoatp4056 expression and bacterial burden in ticks and tick cells. Moreover, treatment of ticks with pre-mir-133 affected vector-mediated A. phagocytophilum infection of murine host. These results provide novel insights to understand impact of modulation of tick miRNAs on pathogen colonization in the vector and their transmission to infect the vertebrate host.

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Section: Microrna Prediction From Tick Genomementioning

confidence: 99%

Section: Microrna Prediction From Tick Genomementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Repression of tick microRNA-133 induces organic anion transporting polypeptide expression critical for Anaplasma phagocytophilum survival in the vector and transmission to the vertebrate host

et al. 2020

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“…However, most of the data are available and are already being used for comparative work. The miRNA content of Oncopeltus has been analyzed and six of the identified miRNAs were found in insects for the first time (Ellango, Asokan, & Ramamurthy, ), providing a key datapoint for following the evolution of insect miRNAs. An embryonic RNAseq project using the genome as a reference (Ginzburg et al, this issue), is providing new candidate genes for future developmental work not relying on data from Drosophila .…”

Section: Oncopeltus In the Genomic Agementioning

confidence: 99%

Oncopeltus fasciatus as an evo‐devo research organism

Chipman

2017

Genesis

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The large milkweed bug Oncopeltus fasciatus was one of the main study insects for a range of biological questions throughout much of the 20 century. Its importance waned with the introduction of Drosophila melanogaster as a genetic model organism. The evo-devo revolution of the turn of the century re-introduced Oncopeltus into the scientific community, and it has proved increasingly useful, mostly within a comparative context for evolution driven research. The last few years have seen a number of significant contributions to our understanding of the evolution of developmental processes in insects, and in arthropods in general, arise from work on Oncopeltus. This review presents some of the key studies and shows how they have provided new insights into evolutionary questions. The advent of whole genome sequencing and genome editing techniques is reducing the gap between Drosophila and (re-)emerging systems such as Oncopeltus. We expect that the ease of work on Oncopeltus and its pivotal phylogenetic position will contribute to the expansion of its use within the evo-devo community and more broadly in arthropod research.

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“…In this study, we employed an EST based homology search to identify miRNAs in jute using currently available 826 expressed sequence tags (ESTs) from the NCBI Genbank database. To avoid the difficulties of searching from genomic sequence surveys or unavailability of whole genome sequences, EST based miRNA identification by using specialized software has already been accepted successfully over the other approaches [34,35,36,37,38]. The present study was employed with the Identification and Characterization of conserved microRNAs in the genome of fibre biogenesis crop jute by using EST based comparative genomics approach.…”

Section: Introductionmentioning

confidence: 99%

In silicoIdentification and Functional Characterization of Conserved miRNAs in Fibre Biogenesis CropCorchorus capsularis

Hasan

Ahmed

et al. 2020

Preprint

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Corchorus capsularis, commonly known as jute occupies the leading position in the production of natural fibre and fibre based products alongside lower environmental threat. Nowadays, the study of lignin biosynthesis pathways with other molecular basis of fibres formation are being more focused for its economic perspective. Small noncoding ~21 to 24 nt nucleotides long microRNAs play significant roles in regulating the gene expression as well as different functions in cellular growth and development. Here, the study adopted a comprehensive in silico approach to identify and characterize the conserved miRNAs in the genome of C. capsularis including specific gene targets involved in the crucial cellular process. Expressed Sequence Tags (ESTs) based homology search of 3350 known miRNAs of dicotyledons were allowed against 763 nonredundant ESTs of jute genome resulted in the prediction of 5 potential miRNA candidates belonging five different miRNA families (miR1536, miR9567-3p, miR4391, miR11300, and miR8689). The putative miRNAs were 18 nucleotide length, within a range of -0.49 to -1.56 MFEI values and 55% to 61% of (A+U) content of their correspondence pre-miRNAs. A total of 1052 gene targets of putative miRNAs were identified and their functions were extensively analyzed. Most of the gene targets were involved in plant growth, cell cycle regulation, organelle synthesis, developmental process and environmental responses. The five gene targets, namely, NAC Domain Containing Protein, WRKY DNA binding protein, 3-dehydroquinate synthase, Sadenosyl-L-Met-dependent methyl transferase and Vascular-related NAC-Domain were found to be involved in the lignin biosynthesis, phenylpropanoid pathways and secondary wall formation which could play significant roles in the overall fibre biogenesis. The characterization of conserved miRNAs and their functional annotation of specific gene targets might enhance the more miRNA discovery, strengthening the complete understanding of miRNAs association in the cellular basis of lignin biosynthesis towards the production of high standard jute products.

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Insilco Prediction and Characterization of microRNAs from Oncopeltus fasciatus (Hemiptera: Lygaeidae) Genome

Cited by 7 publications

References 30 publications

Repression of tick microRNA-133 induces organic anion transporting polypeptide expression critical for Anaplasma phagocytophilum survival in the vector and transmission to the vertebrate host

Repression of tick microRNA-133 induces organic anion transporting polypeptide expression critical for Anaplasma phagocytophilum survival in the vector and transmission to the vertebrate host

Oncopeltus fasciatus as an evo‐devo research organism

In silicoIdentification and Functional Characterization of Conserved miRNAs in Fibre Biogenesis CropCorchorus capsularis

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