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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Nuclear Localization Signals and Import01:46

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Proteins targeted to the nucleus carry short stretches of amino acid sequences called the nuclear localization signal or NLS. Classical nuclear localization signals are of two types: monopartite and bipartite NLS. Monopartite classical NLS (cNLS) consists of a single cluster of 4-8 amino acids. Bipartite cNLS consists of two clusters of  2-3 amino acids and a 9-12 residue long proline-rich linker bridging the two clusters. Signal clusters are rich in positively charged amino acids such as...
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Regulated mRNA Transport02:22

Regulated mRNA Transport

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In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing...
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Nuclear Protein Sorting01:34

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Nuclear protein sorting is the selective trafficking of histones, polymerases, gene regulatory proteins into the nucleus and exporting RNAs and ribosomes to the cytosol. It is a tightly controlled process that regulates gene expression within a cell.
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Ribosome Profiling02:24

Ribosome Profiling

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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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A sizable fraction of proteins destined for ER are first synthesized in the cell cytosol and then transported across the ER membrane–a process called post-translational translocation. Similar to cotranslationally translocated proteins, these proteins also use the Sec translocon complex to enter the ER lumen.
Targeting proteins to the ER
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RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation.

Tianyu Cui1, Yiying Dou1, Puwen Tan1

  • 1Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.

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Summary

RNALocate v2.0 enhances understanding of cellular biology by providing an updated resource for RNA subcellular localization analysis. This comprehensive tool aids researchers in exploring biological functions and molecular mechanisms within the cell.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Understanding the spatial distribution of the transcriptome at the subcellular level is crucial for advancing biological and disease research.
  • The precise localization of RNA molecules within a cell dictates their function and influences cellular processes.

Purpose of the Study:

  • To update and enhance RNALocate, a freely accessible resource for RNA subcellular localization analysis.
  • To provide researchers with an improved tool for studying biological functions and molecular mechanisms related to RNA localization.

Main Methods:

  • Expansion of data sources and species coverage in RNALocate v2.0.
  • Integration of RNA-sequencing (RNA-seq) datasets with subcellular localization information.
  • Addition and reorganization of RNA information, including localization conditions, homology, interactions, and disease associations.
  • Incorporation of three new prediction tools: DM3Loc, iLoc-lncRNA, and iLoc-mRNA.

Main Results:

  • RNALocate v2.0 offers expanded data coverage and new analytical tools for RNA subcellular localization.
  • The updated resource integrates diverse RNA information, facilitating deeper insights into cellular architecture.
  • New prediction tools enhance the capability to analyze RNA localization for different RNA types.

Conclusions:

  • RNALocate v2.0 serves as a comprehensive resource for researchers investigating RNA subcellular localization.
  • The updated platform aids in deconvoluting the complex cellular architecture and understanding RNA's role in biological functions and diseases.