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This Week in Genome Research: Feb 3, 2010

In the early, online edition of Genome Research this week, MD Anderson Cancer Center researcher Jean-Pierre Issa and his team found DNA methylation levels shifts at some genes in aging mouse tissues. When they compared DNA methylation profiles at more than 3,600 genes in intestinal tissue from three-month-old and 35-month-old mice, the researchers found 774 genes with more methylation in the older mice and 466 with less methylation. "Our findings demonstrate a surprisingly high rate of hyper- and hypomethylation as a function of age in normal mouse small intestine tissues and a strong tissue-specificity to the process," they write. "We conclude that epigenetic deregulation is a common feature of aging in mammals."

French, British, and Swiss researchers explore how replication timing affects neutral substitution patterns in mammalian genomes. The team did sequencing experiments with labeled DNA to follow replication across the human genome and looked at data on substitution patterns in human, chimpanzee, and other mammalian genomes. Their results suggest replication timing can influence non-CpG substitution rates and contribute to mammalian evolution.

Researchers from the University of California, San Francisco, and Kaiser Permanente Northern California demonstrate that they could find functional elements in non-coding DNA using genetic variation patterns. By sifting through polymorphism data in sequences from three public databases, the team showed that genetic variants within non-coding sequences can be used to find a range of functional elements — from splice sites to potential slice site enhancers.

Australian researchers show that a protein called ATRX contributes to telomere structure. Although past research has shown that ATRX mutations can cause X-linked mental retardation, little was known about its function. Now, researchers show that the ATRX protein is found at the telomeres of mouse embryonic stem cells during interphase, where it acts with the histone H3.3 to help localize another protein, CBX5. "These findings suggest a novel function of ATRX," they write, "working in conjunction with H3.3 and CBX5, as a key regulator of [embryonic stem] cell telomere chromatin."

The Scan

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.

Study Highlights Pitfall of Large Gene Panels in Clinical Genomic Analysis

An analysis in Genetics in Medicine finds that as gene panels get larger, there is an increased chance of uncovering benign candidate variants.

Single-Cell Atlas of Drosophila Embryogenesis

A new paper in Science presents a single-cell atlas of fruit fly embryonic development over time.

Phage Cocktail Holds Promise for IBD

Researchers uncovered a combination phage therapy that targets Klebsiella pneumonia strains among individuals experiencing inflammatory bowel disease flare ups, as they report in Cell.