Abstract/Details

Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors


2007 2007

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Abstract (summary)

The availability of genomic resources makes possible the study of liver cancer by innovative approaches allowing an efficient characterization of the differences between tumor and normal samples. This study presents an effective, combinatorial methodology for genome-scale characterization of tumors. First, changes in gene expression, as monitored on RNA expression arrays, were identified as the HCC transcriptome. Then, I optimized a new method of chromatin immunoprecipitation (ChIP) experiments to permit the analysis of liver biopsies and cell populations in numbers as low as 10,000 cells. Using the modified ChIP protocol, I characterized the chromatin modifications and defined active and inactive gene promoters on a genome-wide scale. Next, I employed a novel method named “virtual comparative genomic hybridization” (vCGH) to study copy number changes. Finally, through comparison of RNA Polymerase II binding, chromatin structure, and copy number changes, I determined that the major contributor to the creation of the liver tumor transcriptome was changes in gene copy number.

Indexing (details)


Subject
Molecular biology;
Cellular biology;
Oncology
Classification
0307: Molecular biology
0379: Cellular biology
0992: Oncology
Identifier / keyword
Health and environmental sciences; Biological sciences; Chromatin immunoprecipitation; Gene expression; Hepatocellular carcinoma; Liver tumors
Title
Analysis of the mechanisms mediating tumor-specific changes in gene expression in human liver tumors
Author
Acevedo, Luis G.
Number of pages
181
Publication year
2007
Degree date
2007
School code
0262
Source
DAI-B 68/12, Dissertation Abstracts International
Place of publication
Ann Arbor
Country of publication
United States
ISBN
9780549377153
Advisor
Farnham, Peggy J.; Bresnick, Emery H.
University/institution
The University of Wisconsin - Madison
University location
United States -- Wisconsin
Degree
Ph.D.
Source type
Dissertations & Theses
Language
English
Document type
Dissertation/Thesis
Dissertation/thesis number
3294027
ProQuest document ID
304815724
Copyright
Database copyright ProQuest LLC; ProQuest does not claim copyright in the individual underlying works.
Document URL
http://search.proquest.com/docview/304815724
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