Related Experiment Video
Updated: Jul 28, 2026
10:36
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
Published on: August 3, 2018
Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing
Terrence S Furey1, Mark Diekhans, Yontao Lu
1Center for Biomolecular Science and Engineering, Department of Computer Science, University of California, Santa Cruz, Santa Cruz, California 95064, USA. booch@cse.ucsc.edu
Genome Research
|October 19, 2004
Summary
Human genome sequencing reveals thousands of discrepancies with existing mRNA collections. The genome sequence appears more accurate, suggesting potential errors in mRNA data that require reconciliation.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- The NCBI Reference Sequence (RefSeq) and NIH Mammalian Gene Collection (MGC) provide human mRNA sequences.
- These sequences are widely accepted as accurate gene representations.
Purpose of the Study:
- To computationally compare human mRNA sequences with the human genome sequence.
- To identify and analyze discrepancies between these two critical resources.
Main Methods:
- Comparative analysis of mRNA sequences against the human genome sequence.
- Verification of discrepancies using additional mRNA and EST data.
- Screening against a human genomic DNA diversity panel.
Main Results:
- Several thousand discrepancies (substitutions, frame shifts) were found between mRNA and genome sequences.
- Genome sequence variants had stronger supporting evidence than mRNA variants.
- 60% of potential SNPs were verified, and evidence for RNA editing was found.
Conclusions:
- The human genome sequence appears more accurate than current mRNA collections.
- Discrepancies may represent polymorphisms, RNA editing, or somatic variations.
- Future mRNA collections should reconcile all genome sequence variations to ensure accuracy.
Related Concept Videos
02:07Improving Translational Accuracy
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
02:27Nonsense-mediated mRNA Decay
The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
02:18Alternative RNA Splicing
Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
02:23RNA 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...
02:28Leaky 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...
02:46Genome Copying Errors
DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.