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Your search keyword '"Connolly, Charles M."' showing total 3 results
Start Over Author "Connolly, Charles M." Publisher escholarship, university of california
3 results on '"Connolly, Charles M."'

1. Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival.

Author

Zaidi, Syed H, Harrison, Tabitha A, Phipps, Amanda I, Steinfelder, Robert, Trinh, Quang M, Qu, Conghui, Banbury, Barbara L, Georgeson, Peter, Grasso, Catherine S, Giannakis, Marios, Adams, Jeremy B, Alwers, Elizabeth, Amitay, Efrat L, Barfield, Richard T, Berndt, Sonja I, Borozan, Ivan, Brenner, Hermann, Brezina, Stefanie, Buchanan, Daniel D, Cao, Yin, Chan, Andrew T, Chang-Claude, Jenny, Connolly, Charles M, Drew, David A, Farris, Alton Brad, Figueiredo, Jane C, French, Amy J, Fuchs, Charles S, Garraway, Levi A, Gruber, Steve, Guinter, Mark A, Hamilton, Stanley R, Harlid, Sophia, Heisler, Lawrence E, Hidaka, Akihisa, Hopper, John L, Huang, Wen-Yi, Huyghe, Jeroen R, Jenkins, Mark A, Krzyzanowski, Paul M, Lemire, Mathieu, Lin, Yi, Luo, Xuemei, Mardis, Elaine R, McPherson, John D, Miller, Jessica K, Moreno, Victor, Mu, Xinmeng Jasmine, Nishihara, Reiko, Papadopoulos, Nickolas, Pasternack, Danielle, Quist, Michael J, Rafikova, Adilya, Reid, Emma EG, Shinbrot, Eve, Shirts, Brian H, Stein, Lincoln D, Teney, Cherie D, Timms, Lee, Um, Caroline Y, Van Guelpen, Bethany, Van Tassel, Megan, Wang, Xiaolong, Wheeler, David A, Yung, Christina K, Hsu, Li, Ogino, Shuji, Gsur, Andrea, Newcomb, Polly A, Gallinger, Steven, Hoffmeister, Michael, Campbell, Peter T, Thibodeau, Stephen N, Sun, Wei, Hudson, Thomas J, and Peters, Ulrike

Abstract

Colorectal cancer (CRC) is a biologically heterogeneous disease. To characterize its mutational profile, we conduct targeted sequencing of 205 genes for 2,105 CRC cases with survival data. Our data shows several findings in addition to enhancing the existing knowledge of CRC. We identify PRKCI, SPZ1, MUTYH, MAP2K4, FETUB, and TGFBR2 as additional genes significantly mutated in CRC. We find that among hypermutated tumors, an increased mutation burden is associated with improved CRC-specific survival (HR = 0.42, 95% CI: 0.21-0.82). Mutations in TP53 are associated with poorer CRC-specific survival, which is most pronounced in cases carrying TP53 mutations with predicted 0% transcriptional activity (HR = 1.53, 95% CI: 1.21-1.94). Furthermore, we observe differences in mutational frequency of several genes and pathways by tumor location, stage, and sex. Overall, this large study provides deep insights into somatic mutations in CRC, and their potential relationships with survival and tumor features.

Published
2020

2. RNA polymerase III interferes with Ty3 integration

Author

Connolly, Charles M and Sandmeyer, Suzanne B

Subjects
Genetics, RNA Polymerase III, RNA, Transfer, RNA-Binding Proteins, Retroelements, Saccharomyces cerevisiae, Transcription, Genetic, Virus Integration, integration, retrovirus, RNA polymerase III, transposable element, tRNA gene, Ty3, Medicinal and Biomolecular Chemistry, Biochemistry and Cell Biology, Evolutionary Biology, Biochemistry & Molecular Biology
Abstract

Ty3, a gypsylike retrotransposon of budding yeast, integrates at the transcription initiation site of genes transcribed by RNA polymerase III (pol III). It was previously shown that integration in vitro requires intact promoter elements and the pol III transcription factors TFIIIB and TFIIIC. In order to test the effect of pol III on integration, increasing amounts of a pol III-containing fraction were added to Ty3 in vitro integration reactions. The pol III-containing fraction was inhibitory to integration. These results are consistent with a model where the Ty3 integration complex and pol III recognize similar features of the stable transcription complex and compete with each other for access to the transcription initiation site.

Published
1997

3. Requirement of RNA Polymerase III Transcription Factors for in Vitro Position-Specific Integration of a Retroviruslike Element

Author

Kirchner, Jacqueline, Connolly, Charles M, and Sandmeyer, Suzanne B

Subjects
Biotechnology, Genetics, DNA Nucleotidyltransferases, Integrases, Models, Genetic, Mutagenesis, Site-Directed, RNA Polymerase III, RNA, Transfer, Tyr, Recombination, Genetic, Retroelements, Saccharomyces cerevisiae, Transcription Factor TFIIIB, Transcription Factors, Transcription Factors, TFIII, Transcription, Genetic, Virus Integration, General Science & Technology
Abstract

The yeast retroviruslike element Ty3 inserts at the transcription initiation sites of genes transcribed by RNA polymerase III (Pol III). An in vitro integration assay was developed with the use of Ty3 viruslike particles and a modified SUP2 tyrosine transfer RNA (tRNA(Tyr)) gene target. Integration was position-specific and required Ty3 integrase, Pol III transcription factor (TF) IIIB-, TFIIIC-, and Pol III-containing fractions showed that TFIIIB and TFIIIC, together, were sufficient for position-specific Ty3 integration, but not for transcription. This report demonstrates that in vitro integration of a retroelement can be targeted by cellular proteins.

Published
1995

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