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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.
Applications of ribosome profiling
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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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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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An Integrated Approach for Microprotein Identification and Sequence Analysis
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FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs.

Mihnea P Dragomir1,2, Ganiraju C Manyam3, Leonie Florence Ott1,4

  • 1Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

Non-Coding RNA
|September 26, 2020
PubMed
Summary

Non-coding RNAs (ncRNAs) can encode small peptides (ncPEPs). The new FuncPEP database compiles 112 experimentally validated ncPEPs, aiding research into their cellular roles and disease involvement.

Keywords:
long non-coding RNAsmicropeptidesncRNA translationncRNA-encoded peptidesnon-coding RNAssmall open reading framessmall peptides

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Area of Science:

  • Molecular Biology
  • Genomics
  • Proteomics

Background:

  • Non-coding RNAs (ncRNAs) were traditionally defined as transcripts lacking protein-coding potential.
  • Emerging evidence indicates that some ncRNAs contain small open reading frames (smORFs) encoding functional small peptides (ncPEPs).
  • These ncPEPs are implicated in various cellular processes and disease pathogenesis.

Purpose of the Study:

  • To create a centralized, curated database of functional ncRNA-encoded peptides (ncPEPs).
  • To provide a comprehensive resource for researchers studying ncPEPs and their encoding ncRNAs.
  • To facilitate further investigation into the biological significance and therapeutic potential of ncPEPs.

Main Methods:

  • Literature review and data mining to identify experimentally validated ncPEPs.
  • Database development to store and annotate information on ncPEPs and their parent ncRNAs.
  • Annotation includes details on ncRNA transcripts, smORF characteristics, and functional validation.

Main Results:

  • Development of FuncPEP, a novel database for functional ncPEPs.
  • FuncPEP currently contains comprehensive annotations for 112 experimentally validated ncPEPs.
  • Detailed information is provided on the specific ncRNA transcripts encoding these peptides.

Conclusions:

  • FuncPEP serves as a valuable resource for the scientific community studying ncPEPs.
  • The database will aid in understanding the diverse biological roles of ncPEPs.
  • FuncPEP is expected to accelerate research into the medical applications of ncPEPs.