Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes.
Rachel E. Ellsworth,D. Curtis Jamison,Jeffrey W. Touchman,Stephanie L. Chissoe,Valerie Maduro,Gerard G. Bouffard,Nicole Dietrich,Stephen M. Beckstrom-Sternberg,Leslie M. Iyer,Lauren A. Weintraub,Marc Cotton,Laura Courtney,Jennifer Edwards,Rachel Maupin,Philip Ozersky,Theresa Rohlfing,Patricia Wohldmann,Tracie L. Miner,Kimberley Kemp,Jason B. Kramer,Ian F Korf,Kimberlie Pepin,Lucinda Antonacci-Fulton,Robert S. Fulton,Patrick Minx,LaDeana W. Hillier,Richard K. Wilson,Robert H. Waterston,Webb Miller,Eric D. Green +29 more
TLDR
The generated sequence reveals the precise architecture of genes residing near CFTR/Cftr, including one known gene (WNT2/Wnt2) and two previously unknown genes that immediately flank CFTR or Cftr.Abstract:
The identification of the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 1989 represents a landmark accomplishment in human genetics. Since that time, there have been numerous advances in elucidating the function of the encoded protein and the physiological basis of cystic fibrosis. However, numerous areas of cystic fibrosis biology require additional investigation, some of which would be facilitated by information about the long-range sequence context of the CFTR gene. For example, the latter might provide clues about the sequence elements responsible for the temporal and spatial regulation of CFTR expression. We thus sought to establish the sequence of the chromosomal segments encompassing the human CFTR and mouse Cftr genes, with the hope of identifying conserved regions of biologic interest by sequence comparison. Bacterial clone-based physical maps of the relevant human and mouse genomic regions were constructed, and minimally overlapping sets of clones were selected and sequenced, eventually yielding ≈1.6 Mb and ≈358 kb of contiguous human and mouse sequence, respectively. These efforts have produced the complete sequence of the ≈189-kb and ≈152-kb segments containing the human CFTR and mouse Cftr genes, respectively, as well as significant amounts of flanking DNA. Analyses of the resulting data provide insights about the organization of the CFTR/Cftr genes and potential sequence elements regulating their expression. Furthermore, the generated sequence reveals the precise architecture of genes residing near CFTR/Cftr, including one known gene (WNT2/Wnt2) and two previously unknown genes that immediately flank CFTR/Cftr.read more
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Initial sequencing and comparative analysis of the mouse genome.
Robert H. Waterston,Kerstin Lindblad-Toh,Ewan Birney,Jane Rogers,Josep F. Abril,Pankaj K. Agarwal,Richa Agarwala,Rachel Ainscough,Marina Alexandersson,Peter An,Stylianos E. Antonarakis,John Attwood,Robert Baertsch,J Bailey,K F Barlow,Stephan Beck,Eric Berry,Bruce W. Birren,Toby Bloom,Peer Bork,Marc Botcherby,Nicolas Bray,Michael R. Brent,Daniel G. Brown,Daniel G. Brown,Stephen D. Brown,Carol J. Bult,John Burton,Jonathan Butler,R. D. Campbell,Piero Carninci,Simon Cawley,Francesca Chiaromonte,Asif T. Chinwalla,Deanna M. Church,Michele Clamp,C M Clee,Francis S. Collins,Lisa Cook,Richard R. Copley,Alan Coulson,Olivier Couronne,James Cuff,Val Curwen,Tim Cutts,Mark J. Daly,Robert David,Joy Davies,Kimberly D. Delehaunty,Justin Deri,Emmanouil T. Dermitzakis,Colin N. Dewey,Nicholas J. Dickens,Mark Diekhans,Sheila Dodge,Inna Dubchak,Diane M. Dunn,Sean R. Eddy,Laura Elnitski,Richard D. Emes,Pallavi Eswara,Eduardo Eyras,Adam Felsenfeld,Ginger A. Fewell,Paul Flicek,Karen Foley,Wayne N. Frankel,Lucinda Fulton,Robert S. Fulton,Terrence S. Furey,Diane Gage,Richard A. Gibbs,Gustavo Glusman,Sante Gnerre,Nick Goldman,Leo Goodstadt,Darren Grafham,Tina Graves,Eric D. Green,Simon G. Gregory,Roderic Guigó,Mark S. Guyer,Ross C. Hardison,David Haussler,Yoshihide Hayashizaki,Deana W. LaHillier,Angela S. Hinrichs,Wratko Hlavina,Timothy Holzer,Fan Hsu,Axin Hua,Tim Hubbard,Adrienne Hunt,Ian J. Jackson,David B. Jaffe,L. Steven Johnson,Matthew Jones,Thomas A. Jones,A Joy,Michael Kamal,Elinor K. Karlsson,Donna Karolchik,Arkadiusz Kasprzyk,Jun Kawai,Evan Keibler,Cristyn Kells,W. James Kent,Andrew Kirby,Diana L. Kolbe,Ian F Korf,Raju Kucherlapati,Edward J. Kulbokas,David Kulp,Tom Landers,J. P. Leger,Steven Leonard,Ivica Letunic,Rosie Levine,Jia Li,Ming Li,Christine Lloyd,Susan Lucas,Bin Ma,Donna Maglott,Elaine R. Mardis,Lucy Matthews,Evan Mauceli,John Mayer,Megan McCarthy,W. Richard McCombie,Stuart McLaren,Kirsten McLay,John Douglas Mcpherson,James Meldrim,Beverley Meredith,Jill P. Mesirov,Webb Miller,Tracie L. Miner,Emmanuel Mongin,Kate Montgomery,Michael J. Morgan,Richard Mott,James C. Mullikin,Donna M. Muzny,William E. Nash,Joanne O. Nelson,Michael N. Nhan,Robert Nicol,Zemin Ning,Chad Nusbaum,Michael J. O’Connor,Yasushi Okazaki,Karen Oliver,Emma Overton-Larty,Lior Pachter,Genís Parra,Kymberlie H. Pepin,Jane Peterson,Pavel A. Pevzner,Robert W. Plumb,Craig Pohl,Alex Poliakov,Tracy C. Ponce,Chris P. Ponting,Simon C. Potter,Michael A. Quail,Alexandre Reymond,Bruce A. Roe,Krishna M. Roskin,Edward M. Rubin,Alistair G. Rust,Ralph Santos,Victor Sapojnikov,Brian Schultz,Jörg Schultz,Matthias S. Schwartz,Scott Schwartz,Carol Scott,Steven Seaman,Steve Searle,Ted Sharpe,Andrew Sheridan,Ratna Shownkeen,Sarah Sims,Jonathan Singer,Guy Slater,Arian F.A. Smit,Douglas Smith,Brian Spencer,Arne Stabenau,Nicole Stange-Thomann,Charles W. Sugnet,Mikita Suyama,Glenn Tesler,Johanna Thompson,David Torrents,Evanne Trevaskis,John Tromp,Catherine Ucla,Abel Ureta-Vidal,Jade P. Vinson,Andrew von Niederhausern,Claire M. Wade,Melanie M. Wall,R. J. Weber,Robert B. Weiss,Michael C. Wendl,Anthony P. West,Kris A. Wetterstrand,Raymond Wheeler,Simon Whelan,Jamey Wierzbowski,David Willey,Sophie Williams,Richard K. Wilson,Eitan E. Winter,Kim C. Worley,Dudley Wyman,Shan Yang,Shiaw Pyng Yang,Evgeny M. Zdobnov,Michael C. Zody,Eric S. Lander +222 more
TL;DR: The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences.
Journal ArticleDOI
Conserved noncoding sequences are reliable guides to regulatory elements.
TL;DR: A 'working draft' of the human genome sequence is now available and Comparisons with the sequences of mouse and other species will be a powerful approach to identifying functional segments of the noncoding regions, such as gene regulatory elements.
Journal ArticleDOI
Meiotic arrest and aneuploidy in MLH3-deficient mice.
Steven M. Lipkin,Steven M. Lipkin,Peter B. Moens,Victoria Wang,Michelle L. Lenzi,Dakshine Shanmugarajah,Abigail Gilgeous,James W. Thomas,Jun Cheng,Jeffrey W. Touchman,Eric D. Green,Pam Schwartzberg,Francis S. Collins,Paula E. Cohen +13 more
TL;DR: The results show that Mlh3 has an essential and distinct role in mammalian meiosis, and it is shown that M lh3−/− mice are viable but sterile.
Journal ArticleDOI
The Phenotypic Consequences of CFTR Mutations
Rebecca Rowntree,Ann Harris +1 more
TL;DR: The current classification of CFTR mutation classes and resulting CF disease phenotypes are described and complex disease alleles and modifier genes are discussed along with alternative disorders, such as disseminated bronchiectasis and pancreatitis, which are also thought to result from CFTR mutations.
Journal ArticleDOI
EGASP: the human ENCODE Genome Annotation Assessment Project
Roderic Guigó,Paul Flicek,Josep F. Abril,Alexandre Reymond,Julien Lagarde,Stylianos E. Antonarakis,Michael Ashburner,Michael Ashburner,Vladimir B. Bajic,Vladimir B. Bajic,Ewan Birney,Robert Castelo,Eduardo Eyras,Catherine Ucla,Thomas R. Gingeras,Thomas R. Gingeras,Jennifer Harrow,Tim Hubbard,Suzanna E. Lewis,Suzanna E. Lewis,Martin G. Reese +20 more
TL;DR: The results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
Base-calling of automated sequencer traces using Phred. I. accuracy assessment
TL;DR: In this article, a base-calling program for automated sequencer traces, phred, with improved accuracy was proposed. But it was not shown to achieve a lower error rate than the ABI software, averaging 40%-50% fewer errors in the data sets examined independent of position in read, machine running conditions, or sequencing chemistry.
Journal ArticleDOI
Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA.
John R. Riordan,Johanna M. Rommens,Batsheva Kerem,Noa Alon,Richard Rozmahel,Zbyszko Grzelczak,Julian Zielenski,Si Lok,Natasa Plavsic,Jia Ling Chou,Mitchell L. Drumm,Michael C. Iannuzzi,Francis S. Collins,Lap-Chee Tsui +13 more
TL;DR: A deletion of three base pairs that results in the omission of a phenylalanine residue at the center of the first predicted nucleotide-binding domain was detected in CF patients.
Journal ArticleDOI
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Brent Ewing,Philip Green +1 more
TL;DR: The ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data, is developed and implemented in the base-calling program.
Journal ArticleDOI
Identification of the cystic fibrosis gene: genetic analysis.
Batsheva Kerem,Johanna M. Rommens,Janet A. Buchanan,Danuta Markiewicz,Tara K. Cox,Aravinda Chakravarti,Manuel Buchwald,Lap-Chee Tsui +7 more
TL;DR: Extended haplotype data based on DNA markers closely linked to the putative disease gene locus suggest that the remainder of the cystic fibrosis mutant gene pool consists of multiple, different mutations.
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