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Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- Jonathan M. Mudge,
- Irwin Jungreis,
- Toby Hunt,
- Jose Manuel Gonzalez,
- James C. Wright,
- Mike Kay,
- Claire Davidson,
- Stephen Fitzgerald,
- Ruth Seal,
- Susan Tweedie,
- Liang He,
- Robert M. Waterhouse,
- Yue Li,
- Elspeth Bruford,
- Jyoti S. Choudhary,
- Adam Frankish,
- and Manolis Kellis
Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
...by a cytosine residue, both of which are known correlates of readthrough. (C) A large cluster of PCCRs on the “−” strand of C. elegans Chromosome I suggests there is a 1271-amino-acid single-exon gene with ORF at positions 2054512–2058327. There is no alignment for a few codons on each end of the Phylo...
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LETTER: A High-Resolution Physical Map of Human Chromosome 21p Using Yeast Artificial Chromosomes
- Sheng-Yue Wang,
- Marc Cruts,
- Jurgen Del-Favero,
- Yi Zhang,
- Fadel Tissir,
- Marie-Claude Potier,
- David Patterson,
- Dean Nizetic,
- Assumpció Bosch,
- Haiming Chen,
- Lynda Bennett,
- Xavier Estivill,
- Anna Kessling,
- Stylianos E. Antonarakis,
- and Christine van Broeckhoven
Genome Res. November 1, 1999 9: 1059-1073; doi:10.1101/gr.9.11.1059
...A High-Resolution Physical Map of Human Chromosome 21p Using Yeast Artificial Chromosomes Sheng-Yue Wang 1 , Marc Cruts 1 , Jurgen Del-Favero 1 , Yi Zhang 1 , Fadel Tissir 1 , Marie-Claude Potier 2 , David Patterson 3...
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REVIEW: Protocols for trapping internal and 3'-terminal exons.
- P E Nisson,
- A Ally,
- and P C Watkins
Genome Res. August 1994 4: S24-S39
.... , Buckler, A.J. , Brown, S.D.M. , North. M.A. Gibson, F., Lehrach, H. Buckler, A.J. Brown, S.D.M. and North. M.A. 1994 . Isolation conserved sequnces from yeast artificial chromosomes by exon amplification. BioTechniques 16 : 453 – 459 . 21.. Nisson, P.E., , Rashtian, A. , Watkins. P.C. Nisson, P...
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Method: A high-coverage artificial chromosome library for the genome-wide screening of drug-resistance genes in malaria parasites
- Shiroh Iwanaga,
- Izumi Kaneko,
- and Masao Yuda
Genome Res. May 2012 22: 985-992; Published in Advance March 16, 2012, doi:10.1101/gr.124164.111
.... The artificial chromosome—which consists of three essential elements, the centromere, the telomere, and the replication origin—is an attractive genetic tool for molecular biology–based studies in eukaryotes. The first eukaryotic artificial chromosome was developed in the budding yeast Saccharomyces cerevisiae...
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ARTICLE: Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
- France Denoeud,
- Philipp Kapranov,
- Catherine Ucla,
- Adam Frankish,
- Robert Castelo,
- Jorg Drenkow,
- Julien Lagarde,
- Tyler Alioto,
- Caroline Manzano,
- Jacqueline Chrast,
- Sujit Dike,
- Carine Wyss,
- Charlotte N. Henrichsen,
- Nancy Holroyd,
- Mark C. Dickson,
- Ruth Taylor,
- Zahra Hance,
- Sylvain Foissac,
- Richard M. Myers,
- Jane Rogers,
- Tim Hubbard,
- Jennifer Harrow,
- Roderic Guigó,
- Thomas R. Gingeras,
- Stylianos E. Antonarakis,
- and Alexandre Reymond
Genome Res. June 2007 17: 746-759; doi:10.1101/gr.5660607
...alternative explanation for this result is methodological, as we sometimes had to artificially extend RACEfrags on their 3′ end to be able to design the 25mer oligonucleotides with sufficient specificities (see Methods). Hence, we may have sometimes designed oligonucleotides that do not map to exons. View...
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ARTICLE: Cloning of 559 potential exons of genes of human chromosome 21 by exon trapping.
- H Chen,
- R Chrast,
- C Rossier,
- M A Morris,
- M D Lalioti,
- and S E Antonarakis
Genome Res. August 1996 6: 747-760; doi:10.1101/gr.6.8.747
.... A dense linkage map and almost complete physical maps based on yeast artificial chromosomes (YACs) and cosmids have been developed. We have used exon trapping to identify portions of genes from randomly picked chromosome 21-specific cosmids, to contribute to the creation of the transcription (genic) map...
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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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METHODS: Linker-Mediated Recombinational Subcloning of Large DNA Fragments Using Yeast
- Christopher K. Raymond,
- Elizabeth H. Sims,
- and Maynard V. Olson
Genome Res. January 1, 2002 12: 190-197; doi:10.1101/gr.205201
.... ↵ Frengen E. , Weichenhan D. , Zhao B. , Osoegawa K. , van Geel M. , de Jong P. ( 1999 ) A modular, positive selection bacterial artificial chromosome vector with multiple cloning sites. Genomics 58 : 250 – 253 . ↵ Geitz R. , Woods R. ( 2001 ) Genetic transformation of yeast. BioTechniques 30 : 816 – 831...
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RESOURCE: Bacterial Artificial Chromosome Libraries for Mouse Sequencing and Functional Analysis
- Kazutoyo Osoegawa,
- Minako Tateno,
- Peng Yeong Woon,
- Eirik Frengen,
- Aaron G. Mammoser,
- Joseph J. Catanese,
- Yoshihide Hayashizaki,
- and Pieter J. de Jong
Genome Res. January 1, 2000 10: 116-128; doi:10.1101/gr.10.1.116
...with acceptable genomic fidelity as compared with yeast artificial chromosome (YAC) cloning systems. In addition to the increased clone fidelity and low levels of cloning artifacts, BACs and PACs can more easily be separated from host DNA than YACs. Consequently, BACs and PACs provide excellent templates...
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LETTER: Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae
- Michaël Bekaert,
- Hugues Richard,
- Bernard Prum,
- and Jean-Pierre Rousset
Genome Res. October 2005 15: 1411-1420; doi:10.1101/gr.4258005
...identification strategy. We first download and parse the nucleic acid sequences, the intron/exon data, and their position on chromosomes. We stock them in a local database for more reliability. Our system seeks genomic configurations compatible with a -1 ribosomal frameshifting event using the following criteria...

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