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Research: Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types
- Akihiro Fujimoto,
- Masashi Fujita,
- Takanori Hasegawa,
- Jing Hao Wong,
- Kazuhiro Maejima,
- Aya Oku-Sasaki,
- Kaoru Nakano,
- Yuichi Shiraishi,
- Satoru Miyano,
- Go Yamamoto,
- Kiwamu Akagi,
- Seiya Imoto,
- and Hidewaki Nakagawa
Genome Res. March 2020 30: 334-346; Published in Advance March 24, 2020, doi:10.1101/gr.255026.119
...accessibility of DNA repair machinery, and DNA shape also influence the mutation rate. The effect of DNA damage against cell lineage–specific highly expressed genes is limited to microsatellites within specific genes in specific tissues (such as ALB gene in LI).The current study analyzed somatic indels...
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Research: Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers
- Kwiyeom Yoon,
- Sunghoon Lee,
- Tae-Su Han,
- So Yeon Moon,
- Sun Mi Yun,
- Seong-Ho Kong,
- Sungwoong Jho,
- Jinny Choe,
- Jieun Yu,
- Hyuk-Joon Lee,
- Ji Hyun Park,
- Hak-Min Kim,
- So Yeun Lee,
- Jongsun Park,
- Woo-Ho Kim,
- Jong Bhak,
- Han-Kwang Yang,
- and Seong-Jin Kim
Genome Res. July 2013 23: 1109-1117; Published in Advance June 4, 2013, doi:10.1101/gr.145706.112
...mixed with 25mg of tissue and 4 h incubation at 56°C in an upside-down position. Selected genes with MS mutations were amplified and sequenced in cell lines as well as MSI-H and MSS tissues genomic DNA.mRNA expressions for comparing to their transcript levels in FPKM to the transcriptomeswere verified...
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LETTER: Domain-Level Differences in Microsatellite Distribution and Content Result from Different Relative Rates of Insertion and Deletion Mutations
- David Metzgar,
- Li Liu,
- Christian Hansen,
- Kevin Dybvig,
- and Christopher Wills
Genome Res. March 1, 2002 12: 408-413; doi:10.1101/gr.198602
.... Immun. 68 : 871 – 876 . ↵ Metzgar D. , Bytof J. , Wills C. ( 2000 ) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res. 10 : 72 – 80 . ↵ Metzgar D. , Thomas E. , Davis C. , Field D. , Wills C. ( 2001 ) The microsatellites of Escherichia coli : An analysis...
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Research: DNA methylation at hepatitis B viral integrants is associated with methylation at flanking human genomic sequences
- Yoshiyuki Watanabe,
- Hiroyuki Yamamoto,
- Ritsuko Oikawa,
- Minoru Toyota,
- Masakazu Yamamoto,
- Norihiro Kokudo,
- Shinji Tanaka,
- Shigeki Arii,
- Hiroshi Yotsuyanagi,
- Kazuhiko Koike,
- and Fumio Itoh
Genome Res. March 2015 25: 328-337; Published in Advance February 4, 2015, doi:10.1101/gr.175240.114
...cluster into islands associated with transcriptional promoters, is an important mechanism for regulating gene expression. Additionally, host cells use methylation as a defense mechanism against foreign agents (e.g., viral DNA) (Doerfler 2008; Doerfler et al. 2001). DNA methylation suppresses...
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Research: Polymerase theta-mediated end joining of replication-associated DNA breaks in C. elegans
- Sophie F. Roerink,
- Robin van Schendel,
- and Marcel Tijsterman
Genome Res. June 2014 24: 954-962; Published in Advance March 10, 2014, doi:10.1101/gr.170431.113
...) polymerases. Emerging DNA double-strand breaks are repaired via an error-prone mechanism in which the outermost nucleotide of one end serves to prime DNA synthesis on the other end. This pathway critically depends on the A-family polymerase theta, which protects the genome against gross chromosomal...
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Method: Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair
- Thomas O. Auer,
- Karine Duroure,
- Anne De Cian,
- Jean-Paul Concordet,
- and Filippo Del Bene
Genome Res. January 2014 24: 142-153; Published in Advance October 31, 2013, doi:10.1101/gr.161638.113
...to be recruited to the target sequence by fusion to two separate zinc finger or TALE domains binding complementary sequences separated by a short DNA spacer. More recently, novel RNA-guided nucleases (RGNs) have been developed based on the CRISPR/Cas9 mechanism of bacterial defense against exogenousDNA (Jinek et...
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Method: Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
- Michael F. Lin,
- Pouya Kheradpour,
- Stefan Washietl,
- Brian J. Parker,
- Jakob S. Pedersen,
- and Manolis Kellis
Genome Res. November 2011 21: 1916-1928; Published in Advance October 12, 2011, doi:10.1101/gr.108753.110
...), as well as the possibility of selection on diffuse effects that can constrain all or most of an ORF, such as transcript structural stability or codon bias for translation efficiency (Chamary et al. 2006). To account for these, we evaluated each window against two models, one representing the average...
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Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V. Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...are often actionable, increased by >30% compared with the DNA-based repertoire provided by GDC. Truncation indels can also be important for designing cancer immunotherapy because frameshifts may create potent neoantigens containing amino acid sequences distinct from the self (Turajlic et al. 2017). Among...
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Research: A matter of life or death: How microsatellites emerge in and vanish from the human genome
- Yogeshwar D. Kelkar,
- Kristin A. Eckert,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. December 2011 21: 2038-2048; Published in Advance October 12, 2011, doi:10.1101/gr.122937.111
...of microsatellites in coding regions is likely due to selection against frameshift mutations (Li et al. 2004), the heterogeneity in microsatellite density among non-coding regions might be influenced by base composition (Bachtrog et al. 1999), distance to the telomere (Waterston et al. 2002), and recombination rates...
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Research: Genetic inhibitors of APOBEC3B-induced mutagenesis
- Tony M. Mertz,
- Elizabeth Rice-Reynolds,
- Ly Nguyen,
- Anna Wood,
- Cameron Cordero,
- Nicholas Bray,
- Victoria Harcy,
- Rudri K. Vyas,
- Debra Mitchell,
- Kirill Lobachev,
- and Steven A. Roberts
Genome Res. September 2023 33: 1568-1581; Published in Advance August 2, 2023, doi:10.1101/gr.277430.122
...by protecting against aberrant formation of single-stranded DNA (ssDNA). We found that the mutation spectra of A3B-induced mutations revealed genotype-specific patterns of strand-specific ssDNA formation and nucleotide incorporation across APOBEC-induced lesions. Combining these three metrics, we were able...
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