Searching journal content for articles similar to Shinbrot et al. 24 (11): 1740.

Displaying results 1-9 of 9

For checked items

view abstracts
download to citation manager

Select this article
Research: APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication
- Vladimir B. Seplyarskiy,
- Ruslan A. Soldatov,
- Konstantin Y. Popadin,
- Stylianos E. Antonarakis,
- Georgii A. Bazykin,
- and Sergey I. Nikolaev
Genome Res. February 2016 26: 174-182; Published in Advance January 11, 2016, doi:10.1101/gr.197046.115
...–770. Shinbrot E, Henninger EE, Weinhold N, Covington KR, Göksenin AY, Schultz N, Chao H, Doddapaneni H, Muzny DM, Gibbs RA, et al. 2014. Exonucleasemutations in DNA polymerase epsilon reveal replication strand specificmutation patterns and human origins of replication. Genome Res 24: 1740–1750. Smith HC...
Select this article
Research: Human mismatch repair system balances mutation rates between strands by removing more mismatches from the lagging strand
- Maria A. Andrianova,
- Georgii A. Bazykin,
- Sergey I. Nikolaev,
- and Vladimir B. Seplyarskiy
Genome Res. August 2017 27: 1336-1343; Published in Advance May 16, 2017, doi:10.1101/gr.219915.116
..., Weinhold N, Covington KR, Goksenin AY, Schultz N, Chao H, Doddapaneni H, Muzny DM, Gibbs RA, et al. 2014. Exonuclease mutations in DNA polymerase ɛ reveal replication strand specific mutation patterns and human origins of replication. Genome Res 24: 1740–1750. Shlien A, Campbell BB, de Borja R, Alexandrov...
Select this article
Method: Quantification of somatic mutation flow across individual cell division events by lineage sequencing
- Yehuda Brody,
- Robert J. Kimmerling,
- Yosef E. Maruvka,
- David Benjamin,
- Juniper J. Elacqua,
- Nicholas J. Haradhvala,
- Jaegil Kim,
- Kent W. Mouw,
- Kristjana Frangaj,
- Amnon Koren,
- Gad Getz,
- Scott R. Manalis,
- and Paul C. Blainey
Genome Res. December 2018 28: 1901-1918; Published in Advance November 20, 2018, doi:10.1101/gr.238543.118
...colon carcinoma cell line HT115 possesses a missense mutation in one copy of the DNA polymerase epsilon (POLE) gene, specifically a V411L mutation in the exonuclease domain which has been associated with hypermutated cancer phenotypes (Barretina et al. 2012; Forbes et al. 2015). POLE exonuclease...
OPEN ACCESS ARTICLE
Select this article
Research: Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition
- Scott A. Lujan,
- Anders R. Clausen,
- Alan B. Clark,
- Heather K. MacAlpine,
- David M. MacAlpine,
- Ewa P. Malc,
- Piotr A. Mieczkowski,
- Adam B. Burkholder,
- David C. Fargo,
- Dmitry A. Gordenin,
- and Thomas A. Kunkel
Genome Res. November 2014 24: 1751-1764; Published in Advance September 12, 2014, doi:10.1101/gr.178335.114
...state, nucleosome proximity, and sequence context. Further, error rates and DNA mismatch repair efficiency both vary by mismatch type, responsible polymerase, replication time, and replication origin proximity. Mutation patterns implicate replication infidelity as one driver of variation in somatic...
Select this article
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...
OPEN ACCESS ARTICLE
Select this article
Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
...′-GCTGGTGG-3′, RecBCD nicks the strand with that sequence and loads RecA onto the newly generated 3′-end. Polymerization of RecA then forms a single-stranded DNA–protein filament, which can engage homologous duplex DNA to form a D-loop. Replication can be initiated at the invading 3′-end in the D...
OPEN ACCESS ARTICLE
Select this article
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
...in their DNA MMR machinery, this result would reflect the pattern of mutation without DNA MMR. In early replication, template strands may exist as single strands for a longer period, facilitating the occurrence of deletions.In addition to replication timing, DNA shape parameters were also associated...
OPEN ACCESS ARTICLE
Select this article
LETTER: A Transcript Map for the 2.8-Mb Region Containing the Multiple Endocrine Neoplasia Type 1 Locus
- Siradanahalli C. Guru,
- Sunita K. Agarwal,
- Pachiappan Manickam,
- Shodimu-Emmanuel Olufemi,
- Judy S. Crabtree,
- Jane M. Weisemann,
- Mary Beth Kester,
- Young S. Kim,
- Yingping Wang,
- Michael R. Emmert-Buck,
- Lance A. Liotta,
- Allen M. Spiegel,
- Mark S. Boguski,
- Bruce A. Roe,
- Francis S. Collins,
- Stephen J. Marx,
- Lee Burns,
- and Settara C. Chandrasekharappa
Genome Res. July 1, 1997 7: 725-735; doi:10.1101/gr.7.7.725
...was biotinylated using biotin-14-dCTP and terminal deoxynucleotidyl transferase (TdT). A complex population of double-stranded phagemid DNA containing cDNA inserts was converted to single-stranded DNA using Gene II and Exonuclease III. Hybrids between the biotinylated oligonucleotide and single-stranded DNA formed...
Select this article
LETTER: The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403
- Alexander Bolotin,
- Patrick Wincker,
- Stéphane Mauger,
- Olivier Jaillon,
- Karine Malarme,
- Jean Weissenbach,
- S. Dusko Ehrlich,
- and Alexei Sorokin
Genome Res. May 1, 2001 11: 731-753; Published in Advance April 11, 2001, doi:10.1101/gr.169701
...is greater than that of the terminus, as there are conserved elements ( dnaA and dnaN genes, DnaA boxes) in the vicinity of the former but not of the latter ( rtp gene was not found). We choose as the coordinate 1 of the the middle of a Hin dIII site localized near the replication origin (Fig 1 ). View...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Shinbrot et al. 24 (11): 1740.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: