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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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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...
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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
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RACE - Rapid Amplification of cDNA Ends02:35

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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Ribosome Profiling02:24

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Identification of Circular RNAs using RNA Sequencing
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Identification of Circular RNAs using RNA Sequencing

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CircCode: A Powerful Tool for Identifying circRNA Coding Ability.

Peisen Sun1,2, Guanglin Li1,2

  • 1Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China.

Frontiers in Genetics
|October 26, 2019
PubMed
Summary
This summary is machine-generated.

Researchers developed CircCode, a tool to identify translated circular RNAs (circRNAs). This tool analyzed human and Arabidopsis thaliana ribosome profiles, identifying thousands of translated circRNAs with high sensitivity and low false discovery rates.

Keywords:
bioinformaticscircular RNAsclassificationcoding potentialribosome profiling datatranslation

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Circular RNAs (circRNAs) are prevalent in eukaryotes and involved in regulatory pathways, but their functions, including translation, are not fully understood.
  • Identifying the translation potential of circRNAs is crucial for understanding their biological roles, yet few computational tools exist for this purpose.
  • Advancements in high-throughput sequencing and ribosome profiling enable sensitive detection of RNA coding potential.

Purpose of the Study:

  • To develop a computational tool, CircCode, for identifying the translation potential of circRNAs.
  • To investigate the translation potential of circRNAs in humans and *Arabidopsis thaliana* using the developed tool.
  • To evaluate the performance of CircCode in terms of sensitivity and accuracy.

Main Methods:

  • Development of CircCode, a Python 3-based command-line framework for identifying circRNA coding ability.
  • Utilizing ribosome profiling databases from NCBI to analyze circRNA translation.
  • Application of CircCode to human and *Arabidopsis thaliana* datasets.

Main Results:

  • Identification of 3,610 translated circRNAs in humans and 1,569 in *A. thaliana* based on ribosome profiling data.
  • CircCode demonstrated high sensitivity and a low false discovery rate in identifying translated circRNAs.
  • The CircCode tool provides a simple and powerful method for investigating circRNA translation potential.

Conclusions:

  • CircCode is an effective and sensitive tool for identifying translated circRNAs.
  • The study identified a significant number of translated circRNAs in humans and *A. thaliana*, expanding the understanding of circRNA functions.
  • CircCode is freely available, facilitating further research into circRNA translation and function.