The Experts below are selected from a list of 12 Experts worldwide ranked by ideXlab platform
Mariano Rocchi - One of the best experts on this subject based on the ideXlab platform.
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Evolutionary-new centromeres preferentially emerge within gene deserts
Genome Biology, 2008Co-Authors: Mariana Lomiento, Zhaoshi Jiang, Pietro D'addabbo, Evan E Eichler, Mariano RocchiAbstract:Background Evolutionary-new centromeres (ENCs) result from the seeding of a centromere at an ectopic location along the Chromosome during evolution. The novel centromere rapidly acquires the complex structure typical of eukaryote centromeres. This phenomenon has played an important role in shaping primate karyotypes. A recent study on the evolutionary-new centromere of macaque Chromosome 4 (Human 6) showed that the evolutionary-new centromere domain was deeply restructured, following the seeding, with respect to the corresponding Human region assumed as ancestral. It was also demonstrated that the region was devoid of genes. We hypothesized that these two observations were not merely coincidental and that the absence of genes in the seeding area constituted a crucial condition for the evolutionary-new centromere fixation in the population. Results To test our hypothesis, we characterized 14 evolutionary-new centromeres selected according to conservative criteria. Using different experimental approaches, we assessed the extent of genomic restructuring. We then determined the gene density in the ancestral domain where each evolutionary-new centromere was seeded. Conclusions Our study suggests that restructuring of the seeding regions is an intrinsic property of novel evolutionary centromeres that could be regarded as potentially detrimental to the normal functioning of genes embedded in the region. The absence of genes, which was found to be of high statistical significance, appeared as a unique favorable scenario permissive of evolutionary-new centromere fixation in the population.
Carolyn Y. Muller - One of the best experts on this subject based on the ideXlab platform.
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Chromosome 4 deletions are frequent in invasive cervical cancer and differ between histologic variants.
Gynecologic oncology, 2000Co-Authors: Jennifer B. Sherwood, Narayan Shivapurkar, W. Michael Lin, Raheela Ashfaq, David Miller, Adi F. Gazdar, Carolyn Y. MullerAbstract:Abstract Objective. Patterns of discontinuous deletion of Chromosome 4 have been described in histologic variants of lung carcinomas and may represent different "hotspot" targets for gene–environment interactions. Since similar environmental risks exist for cervical cancer, we investigated patterns of discontinuous deletion in two major histologic variants. Methods. Thirteen archival cases of squamous cell cancer (SCCA) and 11 cases of adenocarcinoma (AC) were precisely microdissected. Matched normal and tumor DNA were used for polymerase chain reaction (PCR) based loss of heterozygosity (LOH) analyses using 19 polymorphic markers spanning Chromosome 4. Human papillomavirus (HPV) detection was determined by PCR using general and type-specific primers (HPV 16, 18). Differences in LOH between histologic tumor types and chromosomal regions were determined using Fisher's exact test. Results. Loss at any Chromosome 4 locus occurred in 92% of all tumors studied, with the majority of deletions occurring on the long arm of the Chromosome. Four discrete minimal regions of discontinuous deletion (R) were identified. For these regions, LOH frequencies were 76% (R1, 4q34–q35), 48% (R2, 4q25–q26), 36% (R3, 4p15.1–p15.3), and 26% (R4, 4p16). Loss in SCCA predominated at 4q (4q34–q35; 83%) and in AC at 4p (4p15.3; 50%). Overall LOH on the p arm was significant in AC (82%) compared to SCCA (31%) ( P = 0.02). HPV detection was similar in SCCA (85%) and AC (73%), and HPV 16/18 subtypes were similarly represented in both histologies. Conclusions. Chromosome 4 deletions are frequent in cervical carcinomas. Different patterns of deletion between SCCA and AC may represent gene regions targeted by different gene–environment interactions in these tumor subtypes.
Mariana Lomiento - One of the best experts on this subject based on the ideXlab platform.
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Evolutionary-new centromeres preferentially emerge within gene deserts
Genome Biology, 2008Co-Authors: Mariana Lomiento, Zhaoshi Jiang, Pietro D'addabbo, Evan E Eichler, Mariano RocchiAbstract:Background Evolutionary-new centromeres (ENCs) result from the seeding of a centromere at an ectopic location along the Chromosome during evolution. The novel centromere rapidly acquires the complex structure typical of eukaryote centromeres. This phenomenon has played an important role in shaping primate karyotypes. A recent study on the evolutionary-new centromere of macaque Chromosome 4 (Human 6) showed that the evolutionary-new centromere domain was deeply restructured, following the seeding, with respect to the corresponding Human region assumed as ancestral. It was also demonstrated that the region was devoid of genes. We hypothesized that these two observations were not merely coincidental and that the absence of genes in the seeding area constituted a crucial condition for the evolutionary-new centromere fixation in the population. Results To test our hypothesis, we characterized 14 evolutionary-new centromeres selected according to conservative criteria. Using different experimental approaches, we assessed the extent of genomic restructuring. We then determined the gene density in the ancestral domain where each evolutionary-new centromere was seeded. Conclusions Our study suggests that restructuring of the seeding regions is an intrinsic property of novel evolutionary centromeres that could be regarded as potentially detrimental to the normal functioning of genes embedded in the region. The absence of genes, which was found to be of high statistical significance, appeared as a unique favorable scenario permissive of evolutionary-new centromere fixation in the population.
Jennifer B. Sherwood - One of the best experts on this subject based on the ideXlab platform.
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Chromosome 4 deletions are frequent in invasive cervical cancer and differ between histologic variants.
Gynecologic oncology, 2000Co-Authors: Jennifer B. Sherwood, Narayan Shivapurkar, W. Michael Lin, Raheela Ashfaq, David Miller, Adi F. Gazdar, Carolyn Y. MullerAbstract:Abstract Objective. Patterns of discontinuous deletion of Chromosome 4 have been described in histologic variants of lung carcinomas and may represent different "hotspot" targets for gene–environment interactions. Since similar environmental risks exist for cervical cancer, we investigated patterns of discontinuous deletion in two major histologic variants. Methods. Thirteen archival cases of squamous cell cancer (SCCA) and 11 cases of adenocarcinoma (AC) were precisely microdissected. Matched normal and tumor DNA were used for polymerase chain reaction (PCR) based loss of heterozygosity (LOH) analyses using 19 polymorphic markers spanning Chromosome 4. Human papillomavirus (HPV) detection was determined by PCR using general and type-specific primers (HPV 16, 18). Differences in LOH between histologic tumor types and chromosomal regions were determined using Fisher's exact test. Results. Loss at any Chromosome 4 locus occurred in 92% of all tumors studied, with the majority of deletions occurring on the long arm of the Chromosome. Four discrete minimal regions of discontinuous deletion (R) were identified. For these regions, LOH frequencies were 76% (R1, 4q34–q35), 48% (R2, 4q25–q26), 36% (R3, 4p15.1–p15.3), and 26% (R4, 4p16). Loss in SCCA predominated at 4q (4q34–q35; 83%) and in AC at 4p (4p15.3; 50%). Overall LOH on the p arm was significant in AC (82%) compared to SCCA (31%) ( P = 0.02). HPV detection was similar in SCCA (85%) and AC (73%), and HPV 16/18 subtypes were similarly represented in both histologies. Conclusions. Chromosome 4 deletions are frequent in cervical carcinomas. Different patterns of deletion between SCCA and AC may represent gene regions targeted by different gene–environment interactions in these tumor subtypes.
Zhaoshi Jiang - One of the best experts on this subject based on the ideXlab platform.
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Evolutionary-new centromeres preferentially emerge within gene deserts
Genome Biology, 2008Co-Authors: Mariana Lomiento, Zhaoshi Jiang, Pietro D'addabbo, Evan E Eichler, Mariano RocchiAbstract:Background Evolutionary-new centromeres (ENCs) result from the seeding of a centromere at an ectopic location along the Chromosome during evolution. The novel centromere rapidly acquires the complex structure typical of eukaryote centromeres. This phenomenon has played an important role in shaping primate karyotypes. A recent study on the evolutionary-new centromere of macaque Chromosome 4 (Human 6) showed that the evolutionary-new centromere domain was deeply restructured, following the seeding, with respect to the corresponding Human region assumed as ancestral. It was also demonstrated that the region was devoid of genes. We hypothesized that these two observations were not merely coincidental and that the absence of genes in the seeding area constituted a crucial condition for the evolutionary-new centromere fixation in the population. Results To test our hypothesis, we characterized 14 evolutionary-new centromeres selected according to conservative criteria. Using different experimental approaches, we assessed the extent of genomic restructuring. We then determined the gene density in the ancestral domain where each evolutionary-new centromere was seeded. Conclusions Our study suggests that restructuring of the seeding regions is an intrinsic property of novel evolutionary centromeres that could be regarded as potentially detrimental to the normal functioning of genes embedded in the region. The absence of genes, which was found to be of high statistical significance, appeared as a unique favorable scenario permissive of evolutionary-new centromere fixation in the population.