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Related Concept Videos

Nuclear Fusion02:45

Nuclear Fusion

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The process of converting very light nuclei into heavier nuclei is also accompanied by the conversion of mass into large amounts of energy, a process called fusion. The principal source of energy in the sun is a net fusion reaction in which four hydrogen nuclei fuse and ultimately produce one helium nucleus and two positrons.
A helium nucleus has a mass that is 0.7% less than that of four hydrogen nuclei; this lost mass is converted into energy during the fusion. This reaction produces about...
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Nuclear Export of mRNA02:31

Nuclear Export of mRNA

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Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in...
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RNA Splicing01:32

RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Nuclear Stability03:18

Nuclear Stability

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Protons and neutrons, collectively called nucleons, are packed together tightly in a nucleus. With a radius of about 10−15 meters, a nucleus is quite small compared to the radius of the entire atom, which is about 10−10 meters. Nuclei are extremely dense compared to bulk matter, averaging 1.8 × 1014 grams per cubic centimeter. If the earth’s density were equal to the average nuclear density, the earth’s radius would be only about 200 meters.
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Non-nuclear Inheritance01:29

Non-nuclear Inheritance

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Most DNA resides in the nucleus of a cell. However, some organelles in the cell cytoplasm⁠—such as chloroplasts and mitochondria⁠—also have their own DNA. These organelles replicate their DNA independently of the nuclear DNA of the cell in which they reside. Non-nuclear inheritance describes the inheritance of genes from structures other than the nucleus.
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RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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Related Experiment Video

Updated: Feb 15, 2026

Identification of Circular RNAs using RNA Sequencing
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High-throughput identification of RNA nuclear enrichment sequences.

Chinmay J Shukla1,2,3,4, Alexandra L McCorkindale1,5, Chiara Gerhardinger1,2

  • 1Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.

The EMBO Journal
|January 17, 2018
PubMed
Summary

Researchers developed a new assay to test RNA functionality, identifying 109 nuclear localization domains in long noncoding RNAs (lncRNAs). This method enables large-scale functional screening of RNA elements.

Keywords:
RNAde novo inference of regionshigh‐throughput reporter assaylncRNAnuclear localization

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Identification of Circular RNAs using RNA Sequencing
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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
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Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing
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Highly Efficient Ligation of Small RNA Molecules for MicroRNA Quantitation by High-Throughput Sequencing

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Area of Science:

  • Molecular Biology
  • Genomics
  • RNA Biology

Background:

  • The post-genomic era has revealed numerous noncoding regulatory regions, necessitating scalable functional assays.
  • Existing methods like massively parallel reporter assays are effective for DNA elements but less so for RNA functionality.
  • Understanding the functional roles of long noncoding RNAs (lncRNAs) is a key challenge.

Purpose of the Study:

  • To introduce a novel high-throughput assay, Massively Parallel RNA Assay (MPRNA), for assessing RNA functionality at scale.
  • To utilize MPRNA to identify RNA regions responsible for nuclear localization within lncRNAs.
  • To explore the potential of MPRNA for investigating diverse RNA-based functions.

Main Methods:

  • Developed and applied Massively Parallel RNA Assay (MPRNA) to analyze over 10,000 RNA segments.
  • Fused 11,969 oligos tiling 38 human lncRNAs to a cytosolic transcript.
  • Utilized cell fractionation and barcode sequencing to identify nuclear enrichment sequences.

Main Results:

  • Identified 109 unique RNA regions that significantly drive nuclear enrichment of the fused transcript.
  • Discovered a cytosine-rich motif within these nuclear localization regions.
  • Confirmed high conservation and over-representation of these sequences in global nuclear fractionation data.
  • Validated findings for many regions using single-molecule RNA fluorescence in situ hybridization.

Conclusions:

  • MPRNA is a powerful high-throughput tool for assaying RNA functionality.
  • Successfully identified novel RNA-based nuclear localization domains within lncRNAs.
  • Demonstrated the utility of MPRNA for future large-scale functional investigations of RNA elements.