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Related Concept Videos

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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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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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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Related Experiment Video

Updated: Jul 11, 2025

Identification of Functional Protein Regions Through Chimeric Protein Construction
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Published on: January 8, 2019

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Pattern recognition in the landscape of seemingly random chimeric transcripts.

Aksheetha Sridhar1, Ankita S More2, Amruta R Jadhav2

  • 1Open Health Systems Laboratory, 9601 Medical Centre Drive, Rockville, MD 20850, US.

Computational and Structural Biotechnology Journal
|November 3, 2023
PubMed
Summary
This summary is machine-generated.

Chimeric transcripts (CTs) increase molecular diversity in ovarian cancer cells, contributing to tumor survival. Their formation involves complex genomic and spatial arrangements, suggesting non-random evolutionary mechanisms.

Keywords:
Chimera formationChimeric transcriptsChromatin architectureEvolutionInter- and intra-chromosomalMesenchymal signatureStructural annotationTransformation

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Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • Chimeric transcripts (CTs) derived from two genes contribute to tumor cell survival.
  • Existing research has gaps in understanding CT formation and diversity.

Purpose of the Study:

  • To systematically study the spectrum of CTs in ovarian cancer.
  • To elucidate the mechanisms and evolutionary aspects of CT generation.

Main Methods:

  • Analysis of RNA sequencing datasets from 160 ovarian cancer samples (The Cancer Genome Atlas).
  • Structural annotation of CTs, including partner gene localization and splicing.
  • Identification of phenotype-specific associations and evolutionary conservation.

Main Results:

  • Complexities in CTs arise from gene localization, splicing, and regulatory regions.
  • A mesenchymal signature was dynamically modulated during transformation.
  • Protein-coding CTs are conserved; non-coding CTs evolved more recently.
  • Genomically distanced genes can form CTs via 3D spatial proximity.

Conclusions:

  • CT formation is a non-random process enhancing molecular diversity in cancer cells.
  • Spatial gene arrangement is crucial for CT generation, even for distant genes.
  • CTs interact with regulatory networks, influencing tumor cell survival.