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LETTER: Similar compositional biases are caused by very different mutational effects
- Eduardo P.C. Rocha,
- Marie Touchon,
- and Edward J. Feil
Genome Res. December 2006 16: 1537-1547; Published in Advance October 26, 2006, doi:10.1101/gr.5525106
...in dsDNA, and speculating that U is inefficiently repaired, this seems a very small mutational cause for such a large compositional effect. Many hypotheses have been put forward to explain replication-associated compositional strand bias. They have been extensively reviewed ( Francino and Ochman 1997...
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Research: The frequent evolutionary birth and death of functional promoters in mouse and human
- Robert S. Young,
- Yoshihide Hayashizaki,
- Robin Andersson,
- Albin Sandelin,
- Hideya Kawaji,
- Masayoshi Itoh,
- Timo Lassmann,
- Piero Carninci,
- The FANTOM Consortium,
- Wendy A. Bickmore,
- Alistair R. Forrest,
- and Martin S. Taylor
Genome Res. October 2015 25: 1546-1557; Published in Advance July 30, 2015, doi:10.1101/gr.190546.115
...of housekeeping and testis promoters but high levels of constraint measured by DAF tests are all consistent with the suggestion that promoter regions active in the germline have elevated nucleotide substitution mutation rates (Taylor et al. 2006, 2008), an observation that may relate to elevated replication-associated...
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Method: Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method
- Zhi-Xiong Zhou,
- Mei-Jun Zhang,
- Xu Peng,
- Yuko Takayama,
- Xing-Ya Xu,
- Ling-Zhi Huang,
- and Li-Lin Du
Genome Res. April 2013 23: 705-715; Published in Advance December 17, 2012, doi:10.1101/gr.146357.112
...rather than the act of transcription (Ivessa et al. 2003). Replication-associated Rad52 enrichment patterns in the hst4 mutant Acetylation at histone H3 lysine 56 (H3K56Ac) preferentially occurs during S phase and in response to DNA damage in yeasts and human (Costelloe and Lowndes 2010). In S. pombe, H3...
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Research: Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia
- Tyrone Ryba,
- Dana Battaglia,
- Bill H. Chang,
- James W. Shirley,
- Quinton Buckley,
- Benjamin D. Pope,
- Meenakshi Devidas,
- Brian J. Druker,
- and David M. Gilbert
Genome Res. October 2012 22: 1833-1844; Published in Advance May 24, 2012, doi:10.1101/gr.138511.112
...is a 170-amino acid globular domain found at the C terminus of proteins for which there is evidence of involvement in inflammatory response (Compte et al. 2004). The histone gene cluster contains a total of six genes, HIST1H4H, HIST1H2BI, HIST1H3G, HIST1H2BH, HIST1H3F, and HIST1H4G. Interestingly...
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Letter: The consequences of genetic drift for bacterial genome complexity
- Chih-Horng Kuo,
- Nancy A. Moran,
- and Howard Ochman
Genome Res. August 2009 19: 1450-1454; Published in Advance June 5, 2009, doi:10.1101/gr.091785.109
...in protein-coding sequences (Yang and Bielawski 2000; Daubin and Moran 2004; Novichkov et al. 2009). Because point mutations causing amino acid replacements are often deleterious, the rate of nonsynonymous substitution per site (Ka) is usually much less than the rate of synonymous substitution per site (Ks...
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Letter: HBEGF, SRA1, and IK: Three cosegregating genes as determinants of cardiomyopathy
- Frauke Friedrichs,
- Christian Zugck,
- Gerd-Jörg Rauch,
- Boris Ivandic,
- Dieter Weichenhan,
- Margit Müller-Bardorff,
- Benjamin Meder,
- Nour Eddine El Mokhtari,
- Vera Regitz-Zagrosek,
- Roland Hetzer,
- Arne Schäfer,
- Stefan Schreiber,
- Jian Chen,
- Isaac Neuhaus,
- Ruiru Ji,
- Nathan O. Siemers,
- Norbert Frey,
- Wolfgang Rottbauer,
- Hugo A. Katus,
- and Monika Stoll
Genome Res. March 2009 19: 395-403; Published in Advance December 8, 2008, doi:10.1101/gr.076653.108
...), and mutations in &gt;20 genes have been found to cause DCM ( Franz et al. 2001 ; Ahmad et al. 2005 ). Almost half of these DCM causing mutations are located in genes that encode sarcomere proteins. The main sarcomeric filament proteins, actin (ACTC), myosin (MYH7), and titin (TTN) have been reported to harbor...
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LETTER: Reconstructing the ancestor of Mycobacterium leprae: The dynamics of gene loss and genome reduction
- Laura Gómez-Valero,
- Eduardo P.C. Rocha,
- Amparo Latorre,
- and Francisco J. Silva
Genome Res. August 2007 17: 1178-1185; Published in Advance July 10, 2007, doi:10.1101/gr.6360207
...diptheriae NCTC13129 (Cdi). The sequence data for Mma were produced by a collaborative project of the Sanger Institute and can be obtained from ftp://ftp.sanger.ac.uk/pub/pathogens/mm/ . Phylogenetic analysis A concatenated amino acid sequence alignment of 12 proteins involved in informative processes...
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LETTER: Human gene organization driven by the coordination of replication and transcription
- Maxime Huvet,
- Samuel Nicolay,
- Marie Touchon,
- Benjamin Audit,
- Yves d'Aubenton-Carafa,
- Alain Arneodo,
- and Claude Thermes
Genome Res. September 2007 17: 1278-1285; Published in Advance August 3, 2007, doi:10.1101/gr.6533407
...model of the factory-roof pattern of the S profile. We propose that this pattern results from the superimposition, in germ-line cells, of strand asymmetries associated with replication and transcription. ( B ) Model of the replication-associated skew profiles corresponding to two fixed putative adjacent...
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LETTER: A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
- Oliver A. Hampton,
- Petra Den Hollander,
- Christopher A. Miller,
- David A. Delgado,
- Jian Li,
- Cristian Coarfa,
- Ronald A. Harris,
- Stephen Richards,
- Steven E. Scherer,
- Donna M. Muzny,
- Richard A. Gibbs,
- Adrian V. Lee,
- and Aleksandar Milosavljevic
Genome Res. February 2009 19: 167-177; Published in Advance December 3, 2008, doi:10.1101/gr.080259.108
...—those containing LCRs—by converting simple replication-associated breaks into detectable rearrangements. An analogy here exists between LCRs and DSB repair on one hand and microsatellites and mismatch repair on the other ( Lengauer et al. 1998 ): By presenting challenges to DNA replication, LCRs...
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Methods: Genome-wide comparisons of variation in linkage disequilibrium
- Yik Y. Teo,
- Andrew E. Fry,
- Kanishka Bhattacharya,
- Kerrin S. Small,
- Dominic P. Kwiatkowski,
- and Taane G. Clark
Genome Res. October 2009 19: 1849-1860; Published in Advance June 18, 2009, doi:10.1101/gr.092189.109
...with large sample sizes leading to low statistical power, as the associated polymorphism is simply not in sufficiently strong LD with the functional polymorphism in a different population to present any evidence of replicated association (Teo et al. 2009). Knowledge of the extent of LD differences around...

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