Gout JF, Li W, Fritsch C, Li A, Haroon S, Singh L, Hua D, Fazelinia H, Smith Z, Seeholzer S, Thomas K, Lynch M, Vermulst M.
The landscape of transcription errors in eukaryotic cells.
Sci Adv. 2017 Oct;3(10):e1701484. Epub 2017 Oct 20
PubMed.
Progress in understanding the crucial mechanisms underlying Alzheimer’s disease has been hampered by technical barriers. However, in the past few years many promising technical improvements have appeared, such as iPSC technology and gene-editing approaches (CRISPR/Cas9).
Very recently, new techniques to look at transcriptional mutagenesis, i.e., the occurrence of errors in the conversion of DNA to RNA, have been described (Reid-Bayliss and Loeb, 2017). These assays eliminate errors introduced during RNA library preparation, amongst others, and have enabled detailed analysis of the landscape of transcription errors in eukaryotic cells.
UBB+1 in neurofibrillary tangles in AD hippocampus. [Courtesy of Science/AAAS 1998.]
In one of these studies, a modified version of the “circle-sequencing” assay was used to provide a particularly detailed analysis of erroneous transcription in yeast. Originally, this assay was used to study the mutation rate of RNA viruses, but with a few adaptations, the authors were able to use this approach to probe the fidelity of transcription in eukaryotic cells. Excitingly, the authors were also able to show that these errors can cause various phenotypic changes in the cells, such as an increase in proteotoxic stress, and widespread metabolic alterations (Vermulst et al., 2015; Wang et al., 2016). Previous studies have indicated that mammalian cells also contain DNA-RNA differences. Increased error rates during aging have been shown to occur in human cells in a process dubbed “molecular misreading” (van Leeuwen et al., 1998; Apr 1999 news).
Usually, aberrant RNAs are detected and degraded by the non-sense mediated decay (NMD) pathway. NMD requires a downstream intron that is remarkably absent in a molecular misreading-derived Ubiquitin B mRNA (Gentier and Van Leeuwen, 2015). The result is that dinucleotide deletions (Δ GU) in Ubiquitin B transcripts survive and are translated into misframed Ubiquitin B (UBB+1) that cannot be efficiently degraded by the ubiquitin-proteasome system (UPS). Consequently UBB+1 accumulates in neurofibrillary tangles and neuritic plaques of cortical neurons in AD patients. Subsequently, UBB+1 impairs not only protein quality control but may also promote seeding of misfolded proteins.
Intriguingly, high-fidelity RNA-seq in yeast now indicates that there is an intrinsic limit to the capacity of NMD (Oct 2017 news). In conclusion, we think that now is the right time for the AD field to include transcriptional infidelity in the cellular phase of AD (De Strooper and Karran, 2016; Mar 2016 webinar) with proteotoxic stress and metabolic changes as one of the leading mechanisms.
The technology described here by Gout et al. could be instrumental in this effort. For example, by probing the fidelity of transcription in WT and AD brains throughout the genome, the circle-sequencing assay could reveal novel hot spots for transcription errors in AD patients. By analyzing these hot spots in greater detail, these observations could reveal the molecular mechanisms that drive error-prone transcription, and provide important clues about their contribution to disease progression.
References:
Reid-Bayliss KS, Loeb LA.
Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations.
Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):9415-9420. Epub 2017 Aug 10
PubMed.
Vermulst M, Denney AS, Lang MJ, Hung CW, Moore S, Moseley MA, Mosely AM, Thompson JW, Thompson WJ, Madden V, Gauer J, Wolfe KJ, Summers DW, Schleit J, Sutphin GL, Haroon S, Holczbauer A, Caine J, Jorgenson J, Cyr D, Kaeberlein M, Strathern JN, Duncan MC, Erie DA.
Transcription errors induce proteotoxic stress and shorten cellular lifespan.
Nat Commun. 2015 Aug 25;6:8065.
PubMed.
van Leeuwen FW, de Kleijn DP, van den Hurk HH, Neubauer A, Sonnemans MA, Sluijs JA, Köycü S, Ramdjielal RD, Salehi A, Martens GJ, Grosveld FG, Peter J, Burbach H, Hol EM.
Frameshift mutants of beta amyloid precursor protein and ubiquitin-B in Alzheimer's and Down patients.
Science. 1998 Jan 9;279(5348):242-7.
PubMed.
Gentier RJ, van Leeuwen FW.
Misframed ubiquitin and impaired protein quality control: an early event in Alzheimer's disease.
Front Mol Neurosci. 2015;8:47. Epub 2015 Sep 2
PubMed.
De Strooper B, Karran E.
The Cellular Phase of Alzheimer's Disease.
Cell. 2016 Feb 11;164(4):603-15.
PubMed.
Comments
University Maastricht
UMC Utrecht
Transcription errors in Alzheimer’s disease
Progress in understanding the crucial mechanisms underlying Alzheimer’s disease has been hampered by technical barriers. However, in the past few years many promising technical improvements have appeared, such as iPSC technology and gene-editing approaches (CRISPR/Cas9).
Very recently, new techniques to look at transcriptional mutagenesis, i.e., the occurrence of errors in the conversion of DNA to RNA, have been described (Reid-Bayliss and Loeb, 2017). These assays eliminate errors introduced during RNA library preparation, amongst others, and have enabled detailed analysis of the landscape of transcription errors in eukaryotic cells.
UBB+1 in neurofibrillary tangles in AD hippocampus. [Courtesy of Science/AAAS 1998.]
In one of these studies, a modified version of the “circle-sequencing” assay was used to provide a particularly detailed analysis of erroneous transcription in yeast. Originally, this assay was used to study the mutation rate of RNA viruses, but with a few adaptations, the authors were able to use this approach to probe the fidelity of transcription in eukaryotic cells. Excitingly, the authors were also able to show that these errors can cause various phenotypic changes in the cells, such as an increase in proteotoxic stress, and widespread metabolic alterations (Vermulst et al., 2015; Wang et al., 2016). Previous studies have indicated that mammalian cells also contain DNA-RNA differences. Increased error rates during aging have been shown to occur in human cells in a process dubbed “molecular misreading” (van Leeuwen et al., 1998; Apr 1999 news).
Usually, aberrant RNAs are detected and degraded by the non-sense mediated decay (NMD) pathway. NMD requires a downstream intron that is remarkably absent in a molecular misreading-derived Ubiquitin B mRNA (Gentier and Van Leeuwen, 2015). The result is that dinucleotide deletions (Δ GU) in Ubiquitin B transcripts survive and are translated into misframed Ubiquitin B (UBB+1) that cannot be efficiently degraded by the ubiquitin-proteasome system (UPS). Consequently UBB+1 accumulates in neurofibrillary tangles and neuritic plaques of cortical neurons in AD patients. Subsequently, UBB+1 impairs not only protein quality control but may also promote seeding of misfolded proteins.
Intriguingly, high-fidelity RNA-seq in yeast now indicates that there is an intrinsic limit to the capacity of NMD (Oct 2017 news). In conclusion, we think that now is the right time for the AD field to include transcriptional infidelity in the cellular phase of AD (De Strooper and Karran, 2016; Mar 2016 webinar) with proteotoxic stress and metabolic changes as one of the leading mechanisms.
The technology described here by Gout et al. could be instrumental in this effort. For example, by probing the fidelity of transcription in WT and AD brains throughout the genome, the circle-sequencing assay could reveal novel hot spots for transcription errors in AD patients. By analyzing these hot spots in greater detail, these observations could reveal the molecular mechanisms that drive error-prone transcription, and provide important clues about their contribution to disease progression.
References:
Reid-Bayliss KS, Loeb LA. Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations. Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):9415-9420. Epub 2017 Aug 10 PubMed.
Vermulst M, Denney AS, Lang MJ, Hung CW, Moore S, Moseley MA, Mosely AM, Thompson JW, Thompson WJ, Madden V, Gauer J, Wolfe KJ, Summers DW, Schleit J, Sutphin GL, Haroon S, Holczbauer A, Caine J, Jorgenson J, Cyr D, Kaeberlein M, Strathern JN, Duncan MC, Erie DA. Transcription errors induce proteotoxic stress and shorten cellular lifespan. Nat Commun. 2015 Aug 25;6:8065. PubMed.
Wang IX, Grunseich C, Chung YG, Kwak H, Ramrattan G, Zhu Z, Cheung VG. RNA-DNA sequence differences in Saccharomyces cerevisiae. Genome Res. 2016 Nov;26(11):1544-1554. Epub 2016 Sep 16 PubMed.
van Leeuwen FW, de Kleijn DP, van den Hurk HH, Neubauer A, Sonnemans MA, Sluijs JA, Köycü S, Ramdjielal RD, Salehi A, Martens GJ, Grosveld FG, Peter J, Burbach H, Hol EM. Frameshift mutants of beta amyloid precursor protein and ubiquitin-B in Alzheimer's and Down patients. Science. 1998 Jan 9;279(5348):242-7. PubMed.
Gentier RJ, van Leeuwen FW. Misframed ubiquitin and impaired protein quality control: an early event in Alzheimer's disease. Front Mol Neurosci. 2015;8:47. Epub 2015 Sep 2 PubMed.
De Strooper B, Karran E. The Cellular Phase of Alzheimer's Disease. Cell. 2016 Feb 11;164(4):603-15. PubMed.
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