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Anne C Fergusonsmith - One of the best experts on this subject based on the ideXlab platform.
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high resolution map and imprinting analysis of the gtl2 dnchc1 domain on mouse Chromosome 12
Genomics, 2006Co-Authors: Sascha Tierling, Anne C Fergusonsmith, Martina Paulsen, Simone Dalbert, Sandra Schoppenhorst, Chenen Tsai, Sven Oliger, Jorn WalterAbstract:The imprinted Dlk1–Dio3 region on mouse Chromosome 12 contains six imprinted genes and a number of maternally expressed snoRNAs and miRNAs. Here we present a high-resolution sequence analysis of the 1.1-Mb segment telomeric to Gtl2 in mouse and a homology comparison to the human. Ppp2r5c and Dnchc1 at the telomeric end of the analyzed sequence are biallelically expressed, suggesting that the imprinted domain does not extend beyond the paternally expressed Dio3 gene. RT-PCR experiments support the predicted presence of a maternally expressed intergenic transcript(s) encompassing Gtl2, Rian, and Mirg. These maternally expressed genes, and also the intergenic transcript(s), show pronounced expression in the adult mouse brain, whereas the paternally transcribed Dio3 and the nonimprinted Ppp2r5c and Dnchc1 are expressed in different tissues. Hence, tissue-specific coregulation of maternally expressed genes might be an important feature of this domain.
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analysis of mouse conceptuses with uniparental duplication deficiency for distal Chromosome 12 comparison with Chromosome 12 uniparental disomy and implications for genomic imprinting
Cytogenetic and Genome Research, 2006Co-Authors: Maxine Tevendale, Marie Watkins, C Rasberry, Bruce M Cattanach, Anne C FergusonsmithAbstract:Distal mouse Chromosome 12 is imprinted. Phenotypic analysis of mouse embryos with maternal or paternal uniparental disomy for the whole of Chromosome 12 has characterized the developmental defects as
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analysis of mouse conceptuses with uniparental duplication deficiency for distal Chromosome 12 comparison with Chromosome 12 uniparental disomy and implications for genomic imprinting
Cytogenetic and Genome Research, 2006Co-Authors: Maxine Tevendale, Marie Watkins, C Rasberry, Bruce M Cattanach, Anne C FergusonsmithAbstract:Distal mouse Chromosome 12 is imprinted. Phenotypic analysis of mouse embryos with maternal or paternal uniparental disomy for the whole of Chromosome 12 has characterized the developmental defects associated with the altered dosage of imprinted genes on this Chromosome. Here we conduct a characterization of maternal and paternal Dp(dist12) mice using the reciprocal translocation T(4;12)47H. This limits the region analysed to the chromosomal domain distal to the T47H breakpoint in B3 on mouse Chromosome 12. Both MatDp(dist12)T47H and PatDp(dist12)T47H conceptuses are non-viable and the frequency of recovery of Dp(dist12) conceptuses by 10.5 days post coitum (dpc) was lower than expected after normal adjacent-1 disjunction. A subset of MatDp(dist12) embryos can survive up to one day post partum. In contrast to paternal uniparental disomy 12 embryos, no live PatDp (dist12) embryos were recovered after 16.5 days of gestation. Other phenotypes observed in maternal and paternal Chromosome 12 uniparental disomy mice are recapitulated in the Dp(dist12) mice and include placental, muscle and skeletal defects. Additional defects were also noted in the skin of both MatDp(dist12) and maternal uniparental disomy 12 embryos. This study shows that the developmental abnormalities associated with the altered parent of origin for mouse Chromosome 12 can be attributed to the genomic region distal to the T47H breakpoint.
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epigenetic analysis of the dlk1 gtl2 imprinted domain on mouse Chromosome 12 implications for imprinting control from comparison with igf2 h19
Human Molecular Genetics, 2002Co-Authors: Shuji Takada, Maxine Tevendale, Bruce M Cattanach, Martina Paulsen, Chenen Tsai, Gavin Kelsey, Anne C FergusonsmithAbstract:Abstract Dlk1 and Gtl2 are reciprocally imprinted genes located 80 kb apart on mouse Chromosome 12. Similarities between this domain and that of the well characterized Igf2-H19 locus have been previously noted. Comparative genomic and epigenetic analysis of these two domains might help identify allele-specific epigenetic regulatory elements and common features involved in aspects of imprinting control. Here we describe a detailed methylation analysis of the Dlk1-Gtl2 domain on both parental alleles in the mouse. Like the Igf2-H19 domain, areas of differential methylation are hypermethylated on the paternal allele and hypomethylated on the maternal allele. Three differentially methylated regions (DMRs), each with different epigenetic characteristics, have been identified. One DMR is intergenic, contains tandem repeats and is the only region that inherits a paternal methylation mark from the germline. An intronic DMR contains a conserved putative CTCF-binding domain. All three DMRs have both unique and common features compared to those identified in the Igf2-H19 domain.
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parental origin specific developmental defects in mice with uniparental disomy for Chromosome 12
Development, 2000Co-Authors: Pantelis Georgiades, Marie Watkins, M A Surani, Anne C FergusonsmithAbstract:Genetic analysis has shown that the distal portion of mouse Chromosome 12 is imprinted; however, the developmental roles of imprinted genes in this region are not known. We have therefore generated conceptuses with uniparental disomy for Chromosome 12, in which both copies of Chromosome 12 are either paternally or maternally derived (pUPD12 and mUPD12, respectively). Both types of UPD12 result in embryos that are non-viable and that exhibit distinct developmental abnormalities. Embryos with pUPD12 die late in gestation, whereas embryos with mUPD12 can survive to term but die perinatally. The mUPD12 conceptuses are invariably growth-retarded while pUPD12 conceptuses exhibit placentomegaly. Skeletal muscle maturation defects are evident in both types of UPD12. In addition, embryos with paternal UPD12 have costal cartilage defects and hypo-ossification of mesoderm-derived bones. In embryos with mUPD12, the development of the neural crest-derived middle ear ossicles is defective. Some of these anomalies are consistent with those seen with uniparental disomies of the orthologous Chromosome 14 region in humans. Thus, imprinted genes on Chromosome 12 are essential for viability, the regulation of prenatal growth, and the development of mesodermal and neural crest-derived lineages.
K F Schertz - One of the best experts on this subject based on the ideXlab platform.
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fertility restorer locus rf1 of sorghum sorghum bicolor l encodes a pentatricopeptide repeat protein not present in the colinear region of rice Chromosome 12
Theoretical and Applied Genetics, 2005Co-Authors: Robert R Klein, Patricia E Klein, John E Mullet, P Minx, William L Rooney, K F SchertzAbstract:With an aim to clone the sorghum fertility restorer gene Rf1, a high-resolution genetic and physical map of the locus was constructed. The Rf1 locus was resolved to a 32-kb region spanning four open reading frames: a plasma membrane Ca2+-ATPase, a cyclin D-1, an unknown protein, and a pentatricopeptide repeat (PPR13) gene family member. An ~19-kb region spanning the cyclin D-1 and unknown protein genes was completely conserved between sterile and fertile plants as was the sequence spanning the coding region of the Ca2+-ATPase. In contrast, 19 sequence polymorphisms were located in an ~7-kb region spanning PPR13, and all markers cosegregated with the fertility restoration phenotype. PPR13 was predicted to encode a mitochondrial-targeted protein containing a single exon with 14 PPR repeats, and the protein is classified as an E-type PPR subfamily member. To permit sequence-based comparison of the sorghum and rice genomes in the Rf1 region, 0.53 Mb of sorghum Chromosome 8 was sequenced and compared to the colinear region of rice Chromosome 12. Genome comparison revealed a mosaic pattern of colinearity with an ~275-kb gene-poor region with little gene conservation and an adjacent, ~245-kb gene-rice region that is more highly conserved between rice and sorghum. Despite being located in a region of high gene conservation, sorghum PPR13 was not located in a colinear position on rice Chromosome 12. The present results suggest that sorghum PPR13 represents a potential candidate for the sorghum Rf1 gene, and its presence in the sorghum genome indicates a single gene transposition event subsequent to the divergence of rice and sorghum ancestors.
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fertility restorer locus rf1 of sorghum sorghum bicolor l encodes a pentatricopeptide repeat protein not present in the colinear region of rice Chromosome 12
Theoretical and Applied Genetics, 2005Co-Authors: Robert R Klein, Patricia E Klein, John E Mullet, P Minx, William L Rooney, K F SchertzAbstract:With an aim to clone the sorghum fertility restorer gene Rf1, a high-resolution genetic and physical map of the locus was constructed. The Rf1 locus was resolved to a 32-kb region spanning four open reading frames: a plasma membrane Ca(2+)-ATPase, a cyclin D-1, an unknown protein, and a pentatricopeptide repeat (PPR13) gene family member. An approximately 19-kb region spanning the cyclin D-1 and unknown protein genes was completely conserved between sterile and fertile plants as was the sequence spanning the coding region of the Ca(2+)-ATPase. In contrast, 19 sequence polymorphisms were located in an approximately 7-kb region spanning PPR13, and all markers cosegregated with the fertility restoration phenotype. PPR13 was predicted to encode a mitochondrial-targeted protein containing a single exon with 14 PPR repeats, and the protein is classified as an E-type PPR subfamily member. To permit sequence-based comparison of the sorghum and rice genomes in the Rf1 region, 0.53 Mb of sorghum Chromosome 8 was sequenced and compared to the colinear region of rice Chromosome 12. Genome comparison revealed a mosaic pattern of colinearity with an approximately 275-kb gene-poor region with little gene conservation and an adjacent, approximately 245-kb gene-rice region that is more highly conserved between rice and sorghum. Despite being located in a region of high gene conservation, sorghum PPR13 was not located in a colinear position on rice Chromosome 12. The present results suggest that sorghum PPR13 represents a potential candidate for the sorghum Rf1 gene, and its presence in the sorghum genome indicates a single gene transposition event subsequent to the divergence of rice and sorghum ancestors.
Pieter J. Jong - One of the best experts on this subject based on the ideXlab platform.
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isolation of a cosmid sublibrary for a region of Chromosome 12 frequently amplified in human cancers using a complex Chromosome microdissection probe
Genomics, 1996Co-Authors: Abdel G Elkahloun, Jennifer S Mcninch, Xin Yuan Guan, Paul S. Meltzer, Jeffrey M. Trent, Pieter J. JongAbstract:Chromosome-specific cosmid libraries are an extremely useful resource for positional cloning projects. Once a particular region of interest has been identified, it would be of value to have an approach for isolating Chromosome band-specific cosmids that could be assembled into a sublibrary for rapid screening. We constructed a region-specific sublibrary of 700 cosmids by screening a Chromosome 12-specific cosmid library with a complex probe generated by degenerate oligonucleotide-primed PCR of a microdissected homogeneously staining region containing sequences amplified from Chromosome 12q13-q15. Based on fluorescence in situ hybridization, approximately 60% of the cosmids in the sublibrary were derived from the microdissected region. To demonstrate further the utility of this sublibrary, a 150-kb contig containing the SAS and CDK4 genes was constructed, as well as several additional contigs between CDK4 and MDM2. This study demonstrates the possibility of utilizing probes generated by microdissection for assembling band-specific sublibraries that are amenable to rapid screening with multiple markers.
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characterization of two Chromosome 12 cosmid libraries and development of stss from cosmids mapped by fish
Genomics, 1993Co-Authors: Kate Montgomery, Janine M Leblanc, Jennifer S Mcninch, Peter Tsai, David C. Ward, Raju Kucherlapati, Pieter J. Jong, Kenneth S KrauterAbstract:The authors have constructed and characterized two related human Chromosome 12-specific cosmid libraries. DNA from flow-sorted Chromosomes from a somatic cell hybrid was cloned into a cosmid vector. Approximately 61% of the cosmids in the nearly 26,200 member arrayed libraries (LL12NC01 and LL12NC02) contain human DNA inserts, and 31% of the cosmids derived from human DNA contain CA repeats. One hundred and fifty-two cosmids isolated from the libraries have been mapped by fluorescence in situ hybridization (FISH). Cosmids containing human DNA inserts were localized by FISH exclusively to Chromosome 12, confirming the chromosomal specificity of the libraries. The cosmids have been localized to all parts of this Chromosome, although some regions are more highly represented than others. Partial sequence information was obtained from 44 mapped cosmids, and oligonucleotide primer pairs were synthesized that define unique sequence tagged sites (STSs). These mapped cosmids, and unique STSs derived from them, provide a set of useful clones and primer pairs for screening YAC libraries and developing contigs centered on regions of interest within Chromosome 12. In addition, 120 of the mapped cosmids contain CA repeats, and thus they also provide a useful resource for defining highly polymorphic simple tandem repeat elements that servemore » as genetic markers for linkage analysis and disease gene localization. 56 refs., 4 figs., 2 tabs.« less
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Characterization of two Chromosome 12 cosmid libraries and development of STSs from cosmids mapped by FISH.
Genomics, 1993Co-Authors: Kate Montgomery, Janine M Leblanc, Jennifer S Mcninch, Peter Tsai, David C. Ward, Raju Kucherlapati, Pieter J. Jong, Kenneth S KrauterAbstract:We have constructed and characterized two related human Chromosome 12-specific cosmid libraries. DNA from flow-sorted Chromosomes from a somatic cell hybrid was cloned into a cosmid vector. Approximately 61% of the cosmids in the nearly 26,200 member arrayed libraries (LL12NC01 and LL12NC02) contain human DNA inserts, and 31% of the cosmids derived from human DNA contain CA repeats. One hundred and fifty-two cosmids isolated from the libraries have been mapped by fluorescence in situ hybridization (FISH). Cosmids containing human DNA inserts were localized by FISH exclusively to Chromosome 12, confirming the chromosomal specificity of the libraries. The cosmids have been localized to all parts of this Chromosome, although some regions are more highly represented than others. Partial sequence information was obtained from 44 mapped cosmids, and oligonucleotide primer pairs were synthesized that define unique sequence tagged sites (STSs). These mapped cosmids, and unique STSs derived from them, provide a set of useful clones and primer pairs for screening YAC libraries and developing contigs centered on regions of interest within Chromosome 12. In addition, 120 of the mapped cosmids contain CA repeats, and thus they also provide a useful resource for defining highly polymorphic simple tandem repeat elements that serve as genetic markers for linkage analysis and disease gene localization.
Robert R Klein - One of the best experts on this subject based on the ideXlab platform.
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fertility restorer locus rf1 of sorghum sorghum bicolor l encodes a pentatricopeptide repeat protein not present in the colinear region of rice Chromosome 12
Theoretical and Applied Genetics, 2005Co-Authors: Robert R Klein, Patricia E Klein, John E Mullet, P Minx, William L Rooney, K F SchertzAbstract:With an aim to clone the sorghum fertility restorer gene Rf1, a high-resolution genetic and physical map of the locus was constructed. The Rf1 locus was resolved to a 32-kb region spanning four open reading frames: a plasma membrane Ca2+-ATPase, a cyclin D-1, an unknown protein, and a pentatricopeptide repeat (PPR13) gene family member. An ~19-kb region spanning the cyclin D-1 and unknown protein genes was completely conserved between sterile and fertile plants as was the sequence spanning the coding region of the Ca2+-ATPase. In contrast, 19 sequence polymorphisms were located in an ~7-kb region spanning PPR13, and all markers cosegregated with the fertility restoration phenotype. PPR13 was predicted to encode a mitochondrial-targeted protein containing a single exon with 14 PPR repeats, and the protein is classified as an E-type PPR subfamily member. To permit sequence-based comparison of the sorghum and rice genomes in the Rf1 region, 0.53 Mb of sorghum Chromosome 8 was sequenced and compared to the colinear region of rice Chromosome 12. Genome comparison revealed a mosaic pattern of colinearity with an ~275-kb gene-poor region with little gene conservation and an adjacent, ~245-kb gene-rice region that is more highly conserved between rice and sorghum. Despite being located in a region of high gene conservation, sorghum PPR13 was not located in a colinear position on rice Chromosome 12. The present results suggest that sorghum PPR13 represents a potential candidate for the sorghum Rf1 gene, and its presence in the sorghum genome indicates a single gene transposition event subsequent to the divergence of rice and sorghum ancestors.
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fertility restorer locus rf1 of sorghum sorghum bicolor l encodes a pentatricopeptide repeat protein not present in the colinear region of rice Chromosome 12
Theoretical and Applied Genetics, 2005Co-Authors: Robert R Klein, Patricia E Klein, John E Mullet, P Minx, William L Rooney, K F SchertzAbstract:With an aim to clone the sorghum fertility restorer gene Rf1, a high-resolution genetic and physical map of the locus was constructed. The Rf1 locus was resolved to a 32-kb region spanning four open reading frames: a plasma membrane Ca(2+)-ATPase, a cyclin D-1, an unknown protein, and a pentatricopeptide repeat (PPR13) gene family member. An approximately 19-kb region spanning the cyclin D-1 and unknown protein genes was completely conserved between sterile and fertile plants as was the sequence spanning the coding region of the Ca(2+)-ATPase. In contrast, 19 sequence polymorphisms were located in an approximately 7-kb region spanning PPR13, and all markers cosegregated with the fertility restoration phenotype. PPR13 was predicted to encode a mitochondrial-targeted protein containing a single exon with 14 PPR repeats, and the protein is classified as an E-type PPR subfamily member. To permit sequence-based comparison of the sorghum and rice genomes in the Rf1 region, 0.53 Mb of sorghum Chromosome 8 was sequenced and compared to the colinear region of rice Chromosome 12. Genome comparison revealed a mosaic pattern of colinearity with an approximately 275-kb gene-poor region with little gene conservation and an adjacent, approximately 245-kb gene-rice region that is more highly conserved between rice and sorghum. Despite being located in a region of high gene conservation, sorghum PPR13 was not located in a colinear position on rice Chromosome 12. The present results suggest that sorghum PPR13 represents a potential candidate for the sorghum Rf1 gene, and its presence in the sorghum genome indicates a single gene transposition event subsequent to the divergence of rice and sorghum ancestors.
W G Kearns - One of the best experts on this subject based on the ideXlab platform.
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assignment of the hypoxia inducible factor 1α gene to a region of conserved synteny on mouse Chromosome 12 and human Chromosome 14q
Genomics, 1996Co-Authors: Gregg L Semenza, Narayan V Iyer, Myunggeol Pang, W G KearnsAbstract:Hypoxia-inducible factor 1 (HIF-1) is a basic helix-loop-helix transcription factor that mediates homeostatic responses to hypoxia. HIF-1 is a heterodimer consisting of HIF-1{alpha} which is encoded by the HIF1A gene, complexes with HIF-1{beta}, which is encoded by the ARNT gene. In this paper we report the assignment of Hif1a and HIF1A to mouse Chromosome 12 and human Chromosome 14, respectively. HIF1A was assigned to human Chromosome 14q21-q24 by analysis of somatic cell hybrids and by fluorescence in situ hybridization. Hif1a was localized by interspecific backcross analysis within a region of mouse Chromosome 12 encompassing >30 cM that demonstrates conservation of synteny with a region of human Chromosome 14 extending from PAX9 at 14q12-q13 to IGHC at 14q32.33. 12 refs., 2 figs.