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lncRNA - Long Non-coding RNAs02:39

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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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Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
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Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
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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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Annotation of nuclear lncRNAs based on chromatin interactions.

Saumya Agrawal1, Andrey Buyan2,3, Jessica Severin1

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Long non-coding RNAs (lncRNAs) are abundant in human cells. This study used Hi-C data to show that lncRNAs can recruit regulatory proteins to target genes, influencing gene expression through 3D genome organization.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • The human genome extensively transcribes long non-coding RNAs (lncRNAs), which are prevalent in various cell types.
  • Nuclear lncRNAs function as local regulatory elements within the cell nucleus.

Purpose of the Study:

  • To investigate the role of nuclear lncRNAs in gene regulation.
  • To identify potential target genes of lncRNAs using chromatin interaction data.

Main Methods:

  • Utilized Hi-C data to analyze chromatin 3D conformation and RNA-chromatin interactions.
  • Integrated RNA-protein interaction data to understand lncRNA function.
  • Developed an interactive web portal for data visualization.

Main Results:

  • Demonstrated that chromatin interactions of nuclear lncRNAs are dictated by local 3D chromatin conformation.
  • Showed that nuclear lncRNAs act as scaffolds, recruiting regulatory proteins to target gene promoters and enhancers.
  • Identified a mechanism where lncRNAs direct regulatory factors to spatially proximate locations.

Conclusions:

  • Nuclear lncRNAs play a significant role in directing regulatory factors to specific genomic locations.
  • The 3D genome organization influences the function of lncRNAs in gene regulation.
  • Findings provide insights into the regulatory mechanisms of lncRNAs in human cells.