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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
.... pneumophila provides an amenable model to investigate how an intracellular bacterial infection may affect the regulation of chromosome folding, and its consequences, in a eukaryotic host.The investigation of organization and regulation of A. castellanii in response to infection requires a highly contiguous...
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ARTICLE: Functional expression of yeast artificial chromosome-human multidrug resistance genes in mouse cells.
- H Kusaba,
- K Kohno,
- K Asakuno,
- M Kuwano,
- K Okumura,
- E D Green,
- D Schlessinger,
- and M Wada
Genome Res. October 1995 5: 245-258; doi:10.1101/gr.5.3.245
...genes, PGY1 and PGY3, are located on human chromosome 7, and three relevant mouse genes, mdr1a, mdr1b, and mdr2, are located on mouse chromosome 5. An LMD1 cell line was established after the transfer of a 580-kb yeast artificial chromosome (YAC) clone carrying the human MDR locus into mouse L cells...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
.... 2020) or Strainy for bacterial strain phasing (Table 1; Kazantseva et al. 2024). However, specialized methods for phasing multiple cancer clones are yet to be developed.De novo assembly, showcased by many recent germline long-read studies, could also reveal somatic variation in cryptic and difficult...
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ARTICLE: A YAC-based contig of 1.5 Mb spanning the human multidrug resistance gene region and delineating the amplification unit in three human multidrug-resistant cell lines.
- K Torigoe,
- S Sato,
- H Kusaba,
- K Kohno,
- M Kuwano,
- K Okumura,
- E D Green,
- L C Tsui,
- S W Scherer,
- and D Schlessinger
Genome Res. October 1995 5: 233-244; doi:10.1101/gr.5.3.233
....A. , Little, R.D. , Burke, D.T. , Korsmeyer, S.J. , Schlessinger, D. , Olson. M.V. Brownstein, B.H., Silverman, G.A. Little, R.D. Burke, D.T. Korsmeyer, S.J. Schlessinger, D. and Olson. M.V. 1989 . Isolation of single-copy human genes from a library of yeast artificial chromosome clones. Science 244 : 1348...
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ARTICLE: The Small Chromosomes of Trypanosoma brucei Involved in Antigenic Variation Are Constructed Around Repetitive Palindromes
- Bill Wickstead,
- Klaus Ersfeld,
- and Keith Gull
Genome Res. June 2004 14: 1014-1024; doi:10.1101/gr.2227704
...satellite regions in other species. RESULTS Small Chromosome-Derived BACs The bacterial artificial chromosome (BAC) library RPCI-93 ( http://bacpac.chori.org/tbrucei93.htm ) provides 84-fold haploid T. brucei coverage at an insert size of 50–200 kb. It was generated from non-chromosome-specific genomic DNA...
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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
...et al. 2004 ), and gene expression arrays ( Neve et al. 2006 ). More recently, bacterial artificial chromosome (BAC)-based end sequence profiling (ESP) ( Volik et al. 2003 , 2006 ; Raphael et al. 2008 ) has been applied to study genomic rearrangements in cancer s. Volik and colleagues sequenced...
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LETTER: Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution
- Graham R. Bignell,
- Thomas Santarius,
- Jessica C.M. Pole,
- Adam P. Butler,
- Janet Perry,
- Erin Pleasance,
- Chris Greenman,
- Andrew Menzies,
- Sheila Taylor,
- Sarah Edkins,
- Peter Campbell,
- Michael Quail,
- Bob Plumb,
- Lucy Matthews,
- Kirsten McLay,
- Paul A.W. Edwards,
- Jane Rogers,
- Richard Wooster,
- P. Andrew Futreal,
- and Michael R. Stratton
Genome Res. September 2007 17: 1296-1303; Published in Advance August 3, 2007, doi:10.1101/gr.6522707
...to identify those with potential rearrangements, and subsequent shotgun sequencing of rearranged clones. In an analysis of the breast cancer cell line, MCF7, end sequencing revealed many rearranged bacterial artificial chromosomes (BACs) connecting multiple amplified genomic regions ( Volik et al. 2003 , 2006...
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ARTICLE: Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host
- Hidehiro Toh,
- Brian L. Weiss,
- Sarah A.H. Perkin,
- Atsushi Yamashita,
- Kenshiro Oshima,
- Masahira Hattori,
- and Serap Aksoy
Genome Res. February 2006 16: 149-156; Published in Advance December 19, 2005, doi:10.1101/gr.4106106
...of the complete sequence of Sodalis ' chromosome (4,171,146 bp, encoding 2,432 protein coding sequences) indicates a reduced coding capacity of 51%. Furthermore, the chromosome contains 972 pseudogenes, an inordinately high number compared with that of other bacterial species. A high proportion...
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ARTICLE: 4.5-Mb YAC STS contig at 50-kb resolution, spanning Xq25 deletions in two patients with lymphoproliferative syndrome.
- G Porta,
- S MacMillan,
- R Nagaraja,
- S Mumm,
- I Zucchi,
- G Pilia,
- S Maio,
- T Featherstone,
- and D Schlessinger
Genome Res. January 1997 7: 27-36; doi:10.1101/gr.7.1.27
.... and Huxley. C. 1993 . Extrachromosomal maintenance and amplification of yeast artificial chromosome DNA in mouse cells. Genomics 17 : 267 – 278 . Freije, D. , Schlessinger. D. Freije, D. and Schlessinger. D. 1992 . A 1.6-Mb contig of yeast artificial chromosomes around the human factor VIII gene reveals...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...to it is the trans-element. The biological relevance of these elements must be evaluated individually. Analyzed DNA can be a synthetic, naked DNA sequence of in vitro origin; an artificial chromosome introduced into a cell (exogenous DNA); or endogenous DNA within the cell's . Exogenous DNA loses characteristics...
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