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In the October Issue

RNA Analysis
Thousands of Previously Unknown Transcription Factor Binding Sites Mapped Using Tiling Microarrays

New Bioinformatics Algorithm Predicts Forkhead Protein Plays a Role in Breast Cancer Estrogen Response

ChIP-on-chip Experiments Reveal Unique Mechanism Underlying Yeast Chromosome Segregation

Microarrays Detect Altered Expression of Mitochondria-Related Genes in Brains of Patients with Bipolar Disorder

DNA Analysis
Mitochondrial Genome Scan Finds Cancer Mutations in Saliva DNA Samples

New Microarray Improves Sensitivity of Cancer Detection by Pinpointing Small Changes in Mitochondrial DNA

Genome Scan Finds Mutations in at least a Quarter of Patients with Complex Mitochondrial Diseases

Microarrays Provide Fast and Sensitive Genetic Fingerprint for Forensic Investigations

Highest Resolution Study of Genome Replication Surprises Scientists with Unexpected Timing in S-phase

 

   
Thousands of Previously Unknown Transcription Factor Binding Sites Mapped Using Tiling Microarrays

Harvard's Kevin Struhl and Dana-Farber's Myles Brown discuss ChIP-on-chip as an unbiased method for transcription factor binding site identification

Scientists at the Dana-Farber Cancer Institute and Harvard Medical School are using chromatin immunoprecipitation (ChIP) combined with tiled microarrays, or ChIP-on-chip, to discover thousands of previously unknown transcription factor binding sites that regulate gene expression. Their findings reveal new information about the basic processes of transcription and potential regulatory targets for breast cancer treatments.

Myles Brown's research team in the Department of Medical Oncology at the Dana-Farber Cancer Institute is using ChIP-on-chip to define the gene expression pathways controlled by steroid hormones and their receptors, including the estrogen receptor in breast cancer and the androgen receptor in prostate cancer. Read more | Regulation

Mitochondrial Genome Scan Finds Cancer Mutations in Saliva DNA Samples

Johns Hopkins' Joseph Califano discusses the link between mitochondrial mutations and oral cancer with Duke's Amanda Parrish

Cancer researchers at Johns Hopkins Medical Institute have discovered a series of mitochondrial mutations linked to oral squamous cell carcinoma by analyzing the saliva from cancer patients with a new microarray, providing an initial step toward non-invasive early-detection screens.

Joseph Califano, associate professor of otolaryngology at Johns Hopkins, has studied the effects of carcinogens on the mitochondrial genome for the past four years. His team previously found that both tumors and saliva from head-neck cancer patients contained an increased amount of mitochondrial DNA content. Read more | Sequence Analysis

 
AMB Articles

• Regulation (4)
• Sequence Analysis (5)
• Expression Profiling (5)
• Translational Med. (3)
• Standardization (1)
• Bioinformatics (3)
• Transcriptome (1)
• Association Study (4)
• Copy Number (3)




Quarterly Issues
April 2005 (pdf, 715kb)
July 2005 (pdf, 1463kb)

Special Editions
Stem Cells

Trends in Tiling Arrays

Review recent studies using high-density tiled microarrays to explore different views of the genome at resolutions approaching the single nucleotide level. Topics covered include:

ChIP-on-chip assay development
Transcript mapping in regions of "junk DNA"
Transcription factor binding across the genome
The functional role of chromatin acetylation and methylation
The timing and initiation of DNA replication

 

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