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Related Concept Videos

lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

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In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
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Multi-species Conserved Sequences02:51

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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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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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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RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
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Comparative genomics in the search for conserved long noncoding RNAs.

Michał Wojciech Szcześniak1, Magdalena Regina Kubiak1, Elżbieta Wanowska1

  • 1Adam Mickiewicz University in Poznań, Faculty of Biology, Institute of Human Biology and Evolution, Uniwersytetu Poznańskiego 6, Poznań 61-614, Poland.

Essays in Biochemistry
|April 22, 2021
PubMed
Summary

Identifying long noncoding RNA (lncRNA) orthologs is key to understanding gene regulation across species. Comparative genomics approaches are crucial due to lncRNA sequence plasticity, presenting unique challenges.

Keywords:
comparative genomicslong noncoding RNAsorthologssequence analysis

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Long noncoding RNAs (lncRNAs) are crucial regulators of eukaryotic gene expression.
  • Identifying orthologous lncRNAs is vital for comparative genomics and understanding conserved functions across species.
  • The sequence plasticity of lncRNAs complicates ortholog identification compared to protein-coding genes.

Purpose of the Study:

  • To review current advancements and challenges in identifying lncRNA orthologs.
  • To discuss the complexities of comparative genomics for lncRNAs.
  • To highlight key aspects of lncRNA conservation.

Main Methods:

  • Comparative genomics approaches.
  • Analysis of genomic sequence conservation.
  • Evaluation of splicing signal conservation.
  • Assessment of secondary structure conservation.
  • Examination of syntenic transcription patterns.

Main Results:

  • lncRNA ortholog identification is challenging due to high sequence plasticity.
  • Conservation can be assessed at multiple levels: sequence, splicing, structure, and synteny.
  • Specific and complex bioinformatic approaches are required for effective lncRNA comparative genomics.

Conclusions:

  • Comparative genomics of lncRNAs requires specialized methodologies.
  • Understanding lncRNA conservation across different levels is essential for functional inference.
  • Further development of computational tools is needed to overcome identification challenges.