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Related Concept Videos

Pre-mRNA Processing: Modification of pre-mRNA Ends01:35

Pre-mRNA Processing: Modification of pre-mRNA Ends

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a cap to the 5' end of the growing transcript. In this process, a 5' phosphate is replaced by modified guanosine that has a methyl group attached (7-methyl guanosine). This 5' cap helps the cell...
RNA Splicing01:32

RNA Splicing

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...
RNA Editing02:23

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
Leaky Scanning02:28

Leaky Scanning

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 stands for...

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

A multispecies polyadenylation site model.

Eric S Ho1, Samuel I Gunderson, Siobain Duffy

  • 1Department of Molecular Genetics, Microbiology and Immunology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA. eric.ho@umdnj.edu

BMC Bioinformatics
|February 2, 2013
PubMed
Summary
This summary is machine-generated.

A new polyadenylation site model uses minimal features for accurate prediction across species. This approach improves poly(A) site recognition, overcoming challenges in diverse genomic structures.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Polyadenylation is a highly conserved post-transcriptional process across all life domains.
  • Existing poly(A) site prediction models face challenges due to variations in genomic structure across species.
  • Previous methods often rely on numerous features, leading to high dimensionality and limited cross-genome validation.

Purpose of the Study:

  • To develop a more general and accurate poly(A) site recognition model.
  • To simplify poly(A) site prediction by using a minimal set of essential features.
  • To improve prediction accuracy across diverse species, including plants and animals.

Main Methods:

  • Surveyed nine existing poly(A) site prediction methods (1999-2011).
  • Developed a novel model using three di-trinucleotide profiles and predicted nucleosome occupancy.
  • Employed principle component analysis for feature identification and validated using logistic regression and linear discriminant analysis.

Main Results:

  • The proposed model achieved high prediction accuracy: 85-92% sensitivity and 85-96% specificity in seven animal and plant species.
  • The model demonstrated effectiveness across diverse species, overcoming limitations of previous methods.
  • Cross-species prediction accuracy correlated with phylogenetic distances, suggesting evolutionary conservation.

Conclusions:

  • A minimal four-feature model is sufficient for accurate poly(A) site learning and prediction in eukaryotes.
  • The developed model offers improved accuracy and broader applicability compared to existing methods.
  • This approach simplifies poly(A) site recognition, facilitating research across different eukaryotic organisms.