William Etten - Academia.edu (original) (raw)

Papers by William Etten

Research paper thumbnail of A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat

Genome Research, 1999

The laboratory rat (Rattus norvegicus) is a key animal model for biomedical research. However, th... more The laboratory rat (Rattus norvegicus) is a key animal model for biomedical research. However, the genetic infrastructure required for connecting phenotype and genotype in the rat is currently incomplete. Here, we report the construction and integration of two genomic maps: a dense genetic linkage map of the rat and the first radiation hybrid (RH) map of the rat. The genetic map was constructed in two F 2 intercrosses (SHRSP × BN and FHH × ACI), containing a total of 4736 simple sequence length polymorphism (SSLP) markers. Allele sizes for 4328 of the genetic markers were characterized in 48 of the most commonly used inbred strains. The RH map is a lod Ն 3 framework map, including 983 SSLPs, thereby allowing integration with markers on various genetic maps and with markers mapped on the RH panel. Together, the maps provide an integrated reference to >3000 genes and ESTs and >8500 genetic markers (5211 of our SSLPs and >3500 SSLPs developed by other groups). ; James and Tanigami, RHdb (http://www.ebi.ac.uk/RHdb/index.html); Wilder (http://www.nih.gov/niams/scientific/ratgbase); ; RATMAP server (http://ratmap.gen.gu. se)] RH maps (v. 2.0) have been posted on our web sites at

Research paper thumbnail of Information translation communication protocol

Research paper thumbnail of Radiation hybrid map of the mouse genome

Nature genetics, 1999

Radiation hybrid (RH) maps are a useful tool for genome analysis, providing a direct method for l... more Radiation hybrid (RH) maps are a useful tool for genome analysis, providing a direct method for localizing genes and anchoring physical maps and genomic sequence along chromosomes. The construction of a comprehensive RH map for the human genome has resulted in gene maps reflecting the location of more than 30,000 human genes. Here we report the first comprehensive RH map of the mouse genome. The map contains 2,486 loci screened against an RH panel of 93 cell lines. Most loci (93%) are simple sequence length polymorphisms (SSLPs) taken from the mouse genetic map, thereby providing direct integration between these two key maps. We performed RH mapping by a new and efficient approach in which we replaced traditional gel- or hybridization-based assays by a homogeneous 5'-nuclease assays involving a single common probe for all genetic markers. The map provides essentially complete connectivity and coverage across the genome, and good resolution for ordering loci, with 1 centiRay (cR)...

Research paper thumbnail of A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat

Genome research, 1999

The laboratory rat (Rattus norvegicus) is a key animal model for biomedical research. However, th... more The laboratory rat (Rattus norvegicus) is a key animal model for biomedical research. However, the genetic infrastructure required for connecting phenotype and genotype in the rat is currently incomplete. Here, we report the construction and integration of two genomic maps: a dense genetic linkage map of the rat and the first radiation hybrid (RH) map of the rat. The genetic map was constructed in two F2 intercrosses (SHRSP x BN and FHH x ACI), containing a total of 4736 simple sequence length polymorphism (SSLP) markers. Allele sizes for 4328 of the genetic markers were characterized in 48 of the most commonly used inbred strains. The RH map is a lod >/= 3 framework map, including 983 SSLPs, thereby allowing integration with markers on various genetic maps and with markers mapped on the RH panel. Together, the maps provide an integrated reference to >3000 genes and ESTs and >8500 genetic markers (5211 of our SSLPs and >3500 SSLPs developed by other groups). [Bihoreau et...

Research paper thumbnail of A radiation hybrid map of mouse genes

Nature Genetics, 2001

A comprehensive gene-based map of a genome is a powerful tool for genetic studies and is especial... more A comprehensive gene-based map of a genome is a powerful tool for genetic studies and is especially useful for the positional cloning and positional candidate approaches. The availability of gene maps for multiple organisms provides the foundation for detailed conserved-orthology maps showing the correspondence between conserved genomic segments. These maps make it possible to use cross-species information in gene hunts and shed light on the evolutionary forces that shape the genome. Here we report a radiation hybrid map of mouse genes, a combined project of the Whitehead Institute/The map contains 11,109 genes, screened against the T31 RH panel 1 and positioned relative to a reference map containing 2,280 mouse genetic markers 2 . It includes 3,658 genes homologous to the human genome sequence 3 and provides a framework for overlaying the human genome sequence to the mouse and for sequencing the mouse genome. http://www.ncbi.nlm.nih.gov/UniGene/Mm.Home.html developmental ESTs from mouse embryo and neonate cDNA libraries http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html STS information, RH vectors, RH maps

Research paper thumbnail of A 5'-terminal phosphate is required for stable ternary complex formation and translation of leaderless mRNA in Escherichia coli

RNA, 2012

The bacteriophage l's cI mRNA was utilized to examine the importance of the 59-terminal phosphate... more The bacteriophage l's cI mRNA was utilized to examine the importance of the 59-terminal phosphate on expression of leadered and leaderless mRNA in Escherichia coli. A hammerhead ribozyme was used to produce leadered and leaderless mRNAs, in vivo and in vitro, that contain a 59-hydroxyl. Although these mRNAs may not occur naturally in the bacterial cell, they allow for the study of the importance of the 59-phosphorylation state in ribosome binding and translation of leadered and leaderless mRNAs. Analyses with mRNAs containing either a 59-phosphate or a 59-hydroxyl indicate that leaderless cI mRNA requires a 59phosphate for stable ribosome binding in vitro as well as expression in vivo. Ribosome-binding assays show that 30S subunits and 70S ribosomes do not bind as strongly to 59-hydroxyl as they do to 59-phosphate containing leaderless mRNA and the tRNAdependent ternary complex is less stable. Additionally, filter-binding assays revealed that the 70S ternary complex formed with a leaderless mRNA containing a 59-hydroxyl has a dissociation rate (k off ) that is 4.5-fold higher compared with the complex formed with a 59-phosphate leaderless mRNA. Fusion to a lacZ reporter gene revealed that leaderless cI mRNA expression with a 59-hydroxyl was >100-fold lower than the equivalent mRNA with a 59-phosphate. These data indicate that a 59-phosphate is an important feature of leaderless mRNA for stable ribosome binding and expression.

Research paper thumbnail of An AUG initiation codon, not codon-anticodon complementarity, is required for the translation of unleadered mRNA in Escherichia coli

Molecular Microbiology, 1998

We determined the in vivo translational efficiency of 'unleadered' lacZ compared with a conventio... more We determined the in vivo translational efficiency of 'unleadered' lacZ compared with a conventionally leadered lacZ with and without a Shine-Dalgarno (SD) sequence in Escherichia coli and found that changing the SD sequence of leadered lacZ from the consensus 5Ј-AGGA-3Ј to 5Ј-UUUU-3Ј results in a 15-fold reduction in translational efficiency; however, removing the leader altogether results in only a twofold reduction. An increase in translation coincident with the removal of the leader lacking a SD sequence suggests the existence of stronger or novel translational signals within the coding sequence in the absence of the leader. We examined, therefore, a change in the translational signals provided by altering the AUG initiation codon to other naturally occurring initiation codons (GUG, UUG, CUG) in the presence and absence of a leader and find that mRNAs lacking leader sequences are dependent upon an AUG initiation codon, whereas leadered mRNAs are not. This suggests that mRNAs lacking leader sequences are either more dependent on perfect codon-anticodon complementarity or require an AUG initiation codon in a sequence-specific manner to form productive initiation complexes. A mutant initiator tRNA with compensating anticodon mutations restored expression of leadered, but not unleadered, mRNAs with UAG start codons, indicating that codon-anticodon complementarity was insufficient for the translation of mRNA lacking leader sequences. These data suggest that a cognate AUG initiation codon specifically serves as a stronger and different translational signal in the absence of an untranslated leader.

Research paper thumbnail of Proximity of the Start Codon to a Leaderless mRNA's 5 ' Terminus Is a Strong Positive Determinant of Ribosome Binding and Expression in Escherichia coli

Research paper thumbnail of A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

Nature, 2001

We describe a map of 1.42 million single nucleotide polymorphisms (SNPs) distributed throughout t... more We describe a map of 1.42 million single nucleotide polymorphisms (SNPs) distributed throughout the human genome, providing an average density on available sequence of one SNP every 1.9 kilobases. These SNPs were primarily discovered by two projects: The SNP Consortium and the analysis of clone overlaps by the International Human Genome Sequencing Consortium. The map integrates all publicly available SNPs with described genes and other genomic features. We estimate that 60,000 SNPs fall within exon (coding and untranslated regions), and 85% of exons are within 5 kb of the nearest SNP. Nucleotide diversity varies greatly across the genome, in a manner broadly consistent with a standard population genetic model of human history. This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.

Research paper thumbnail of A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat

Genome Research, 1999

The laboratory rat (Rattus norvegicus) is a key animal model for biomedical research. However, th... more The laboratory rat (Rattus norvegicus) is a key animal model for biomedical research. However, the genetic infrastructure required for connecting phenotype and genotype in the rat is currently incomplete. Here, we report the construction and integration of two genomic maps: a dense genetic linkage map of the rat and the first radiation hybrid (RH) map of the rat. The genetic map was constructed in two F 2 intercrosses (SHRSP × BN and FHH × ACI), containing a total of 4736 simple sequence length polymorphism (SSLP) markers. Allele sizes for 4328 of the genetic markers were characterized in 48 of the most commonly used inbred strains. The RH map is a lod Ն 3 framework map, including 983 SSLPs, thereby allowing integration with markers on various genetic maps and with markers mapped on the RH panel. Together, the maps provide an integrated reference to >3000 genes and ESTs and >8500 genetic markers (5211 of our SSLPs and >3500 SSLPs developed by other groups). ; James and Tanigami, RHdb (http://www.ebi.ac.uk/RHdb/index.html); Wilder (http://www.nih.gov/niams/scientific/ratgbase); ; RATMAP server (http://ratmap.gen.gu. se)] RH maps (v. 2.0) have been posted on our web sites at

Research paper thumbnail of Information translation communication protocol

Research paper thumbnail of Radiation hybrid map of the mouse genome

Nature genetics, 1999

Radiation hybrid (RH) maps are a useful tool for genome analysis, providing a direct method for l... more Radiation hybrid (RH) maps are a useful tool for genome analysis, providing a direct method for localizing genes and anchoring physical maps and genomic sequence along chromosomes. The construction of a comprehensive RH map for the human genome has resulted in gene maps reflecting the location of more than 30,000 human genes. Here we report the first comprehensive RH map of the mouse genome. The map contains 2,486 loci screened against an RH panel of 93 cell lines. Most loci (93%) are simple sequence length polymorphisms (SSLPs) taken from the mouse genetic map, thereby providing direct integration between these two key maps. We performed RH mapping by a new and efficient approach in which we replaced traditional gel- or hybridization-based assays by a homogeneous 5'-nuclease assays involving a single common probe for all genetic markers. The map provides essentially complete connectivity and coverage across the genome, and good resolution for ordering loci, with 1 centiRay (cR)...

Research paper thumbnail of A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat

Genome research, 1999

The laboratory rat (Rattus norvegicus) is a key animal model for biomedical research. However, th... more The laboratory rat (Rattus norvegicus) is a key animal model for biomedical research. However, the genetic infrastructure required for connecting phenotype and genotype in the rat is currently incomplete. Here, we report the construction and integration of two genomic maps: a dense genetic linkage map of the rat and the first radiation hybrid (RH) map of the rat. The genetic map was constructed in two F2 intercrosses (SHRSP x BN and FHH x ACI), containing a total of 4736 simple sequence length polymorphism (SSLP) markers. Allele sizes for 4328 of the genetic markers were characterized in 48 of the most commonly used inbred strains. The RH map is a lod >/= 3 framework map, including 983 SSLPs, thereby allowing integration with markers on various genetic maps and with markers mapped on the RH panel. Together, the maps provide an integrated reference to >3000 genes and ESTs and >8500 genetic markers (5211 of our SSLPs and >3500 SSLPs developed by other groups). [Bihoreau et...

Research paper thumbnail of A radiation hybrid map of mouse genes

Nature Genetics, 2001

A comprehensive gene-based map of a genome is a powerful tool for genetic studies and is especial... more A comprehensive gene-based map of a genome is a powerful tool for genetic studies and is especially useful for the positional cloning and positional candidate approaches. The availability of gene maps for multiple organisms provides the foundation for detailed conserved-orthology maps showing the correspondence between conserved genomic segments. These maps make it possible to use cross-species information in gene hunts and shed light on the evolutionary forces that shape the genome. Here we report a radiation hybrid map of mouse genes, a combined project of the Whitehead Institute/The map contains 11,109 genes, screened against the T31 RH panel 1 and positioned relative to a reference map containing 2,280 mouse genetic markers 2 . It includes 3,658 genes homologous to the human genome sequence 3 and provides a framework for overlaying the human genome sequence to the mouse and for sequencing the mouse genome. http://www.ncbi.nlm.nih.gov/UniGene/Mm.Home.html developmental ESTs from mouse embryo and neonate cDNA libraries http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html STS information, RH vectors, RH maps

Research paper thumbnail of A 5'-terminal phosphate is required for stable ternary complex formation and translation of leaderless mRNA in Escherichia coli

RNA, 2012

The bacteriophage l's cI mRNA was utilized to examine the importance of the 59-terminal phosphate... more The bacteriophage l's cI mRNA was utilized to examine the importance of the 59-terminal phosphate on expression of leadered and leaderless mRNA in Escherichia coli. A hammerhead ribozyme was used to produce leadered and leaderless mRNAs, in vivo and in vitro, that contain a 59-hydroxyl. Although these mRNAs may not occur naturally in the bacterial cell, they allow for the study of the importance of the 59-phosphorylation state in ribosome binding and translation of leadered and leaderless mRNAs. Analyses with mRNAs containing either a 59-phosphate or a 59-hydroxyl indicate that leaderless cI mRNA requires a 59phosphate for stable ribosome binding in vitro as well as expression in vivo. Ribosome-binding assays show that 30S subunits and 70S ribosomes do not bind as strongly to 59-hydroxyl as they do to 59-phosphate containing leaderless mRNA and the tRNAdependent ternary complex is less stable. Additionally, filter-binding assays revealed that the 70S ternary complex formed with a leaderless mRNA containing a 59-hydroxyl has a dissociation rate (k off ) that is 4.5-fold higher compared with the complex formed with a 59-phosphate leaderless mRNA. Fusion to a lacZ reporter gene revealed that leaderless cI mRNA expression with a 59-hydroxyl was >100-fold lower than the equivalent mRNA with a 59-phosphate. These data indicate that a 59-phosphate is an important feature of leaderless mRNA for stable ribosome binding and expression.

Research paper thumbnail of An AUG initiation codon, not codon-anticodon complementarity, is required for the translation of unleadered mRNA in Escherichia coli

Molecular Microbiology, 1998

We determined the in vivo translational efficiency of 'unleadered' lacZ compared with a conventio... more We determined the in vivo translational efficiency of 'unleadered' lacZ compared with a conventionally leadered lacZ with and without a Shine-Dalgarno (SD) sequence in Escherichia coli and found that changing the SD sequence of leadered lacZ from the consensus 5Ј-AGGA-3Ј to 5Ј-UUUU-3Ј results in a 15-fold reduction in translational efficiency; however, removing the leader altogether results in only a twofold reduction. An increase in translation coincident with the removal of the leader lacking a SD sequence suggests the existence of stronger or novel translational signals within the coding sequence in the absence of the leader. We examined, therefore, a change in the translational signals provided by altering the AUG initiation codon to other naturally occurring initiation codons (GUG, UUG, CUG) in the presence and absence of a leader and find that mRNAs lacking leader sequences are dependent upon an AUG initiation codon, whereas leadered mRNAs are not. This suggests that mRNAs lacking leader sequences are either more dependent on perfect codon-anticodon complementarity or require an AUG initiation codon in a sequence-specific manner to form productive initiation complexes. A mutant initiator tRNA with compensating anticodon mutations restored expression of leadered, but not unleadered, mRNAs with UAG start codons, indicating that codon-anticodon complementarity was insufficient for the translation of mRNA lacking leader sequences. These data suggest that a cognate AUG initiation codon specifically serves as a stronger and different translational signal in the absence of an untranslated leader.

Research paper thumbnail of Proximity of the Start Codon to a Leaderless mRNA's 5 ' Terminus Is a Strong Positive Determinant of Ribosome Binding and Expression in Escherichia coli

Research paper thumbnail of A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

Nature, 2001

We describe a map of 1.42 million single nucleotide polymorphisms (SNPs) distributed throughout t... more We describe a map of 1.42 million single nucleotide polymorphisms (SNPs) distributed throughout the human genome, providing an average density on available sequence of one SNP every 1.9 kilobases. These SNPs were primarily discovered by two projects: The SNP Consortium and the analysis of clone overlaps by the International Human Genome Sequencing Consortium. The map integrates all publicly available SNPs with described genes and other genomic features. We estimate that 60,000 SNPs fall within exon (coding and untranslated regions), and 85% of exons are within 5 kb of the nearest SNP. Nucleotide diversity varies greatly across the genome, in a manner broadly consistent with a standard population genetic model of human history. This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.