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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...
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RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA
09:36

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Published on: April 10, 2018

LncATLAS database for subcellular localization of long noncoding RNAs.

David Mas-Ponte1,2, Joana Carlevaro-Fita3,4, Emilio Palumbo1

  • 1Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.

RNA (New York, N.Y.)
|April 8, 2017
PubMed
Summary
This summary is machine-generated.

lncATLAS is a new web resource that maps the subcellular localization of thousands of long noncoding RNAs (lncRNAs) in human cells. This tool simplifies understanding lncRNA function by providing accessible localization data, overcoming experimental limitations.

Keywords:
chromatincytoplasmlncRNAlong noncoding RNAnucleussubcellular localization

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Subcellular localization of long noncoding RNAs (lncRNAs) is crucial for understanding their molecular functions.
  • Experimental determination of lncRNA localization is often time-consuming and resource-intensive.
  • A centralized, accessible resource for lncRNA localization data is needed.

Purpose of the Study:

  • To develop a comprehensive resource, lncATLAS, for mapping the subcellular localization of human lncRNAs.
  • To provide a user-friendly webserver for accessing and analyzing lncRNA localization data.
  • To facilitate research into lncRNA function by making localization information widely available.

Main Methods:

  • Utilized RNA-sequencing data from 15 human cell lines.
  • Applied the relative concentration index (RCI) to quantify lncRNA localization across cellular compartments.
  • Developed a webserver (lncatlas.crg.eu) for data visualization and retrieval.

Main Results:

  • lncATLAS includes localization data for 6768 GENCODE-annotated lncRNAs.
  • Localization is presented across various cellular compartments and 15 cell types.
  • The resource allows comparison of lncRNA distribution with other genes and generates publication-quality figures.

Conclusions:

  • lncATLAS significantly enhances the accessibility of lncRNA subcellular localization data.
  • The resource empowers researchers to investigate lncRNA functions more efficiently.
  • lncATLAS democratizes access to critical lncRNA localization information for the scientific community.