Related Experiment Video
Updated: Oct 31, 2025
06:34
A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
Published on: January 21, 2020
8.6K
Computational Analysis of Transposable Elements and CircRNAs in Plants
Liliane Santana Oliveira1,2, Andressa Caroline Patera3, Douglas Silva Domingues3,4
1Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil. liliane.sntn@gmail.com.
Methods in Molecular Biology (Clifton, N.J.)
|July 1, 2021
Summary
This study introduces computational tools for analyzing plant transposable elements (TEs) and circular RNAs (circRNAs). It also presents data analysis on their features and associations in Arabidopsis thaliana.
Area of Science:
- Plant genomics
- Bioinformatics
- Molecular biology
Background:
- Transposable elements (TEs) and circular RNAs (circRNAs) are crucial genetic components in plants.
- Understanding their interplay is vital for plant genome evolution and gene regulation.
- Existing literature provides a foundation, but comprehensive analysis tools and integrated data are needed.
Purpose of the Study:
- To describe computational tools and databases for identifying and analyzing plant TEs and circRNAs.
- To perform data analysis on publicly available TE and circRNA datasets.
- To investigate the association between circRNAs and TEs in plants, focusing on Arabidopsis thaliana.
Main Methods:
- Utilized computational tools and databases for TE and circRNA identification and analysis.
- Performed exploratory data analysis on public circRNA and TE datasets.
- Investigated sequence features and the circRNA:TE association in Arabidopsis thaliana.
Main Results:
- Detailed description of available computational resources for plant TE and circRNA research.
- Exploratory analysis revealed key sequence features of circRNAs and TEs.
- Identified associations between circRNAs and TEs in the model plant Arabidopsis thaliana.
Conclusions:
- The study provides valuable computational resources for plant TE and circRNA research.
- The analysis highlights important sequence features and interactions between TEs and circRNAs.
- Findings contribute to understanding the role of TEs and circRNAs in plant genome dynamics.
Related Concept Videos
02:13Overview of Transposition and Recombination
17.0K
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
17.0K
02:57DNA-only Transposons
15.1K
DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
The donor site from where the transposon is excised is either degraded or...
15.1K
03:18Non-LTR Retrotransposons
12.2K
As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
12.2K
01:24Transposons
435
Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
435
02:02Cis-regulatory Sequences
11.0K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
11.0K
02:57piRNA - Piwi-interacting RNAs
7.1K
PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
7.1K