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Genomics In The Journals: Sep 20, 2012

NEW YORK (GenomeWeb News) – In PLoS ONE, a team from Ohio and California describes findings from its transcriptional and epigenetic analyses of autism brain samples.

The team assessed post-mortem brain samples from nine males with idiopathic autism and nine unaffected, age-matched male controls, focusing on two brain regions: the cerebellar hemisphere cortex and the Brodmann area 19 occipital cortex. While their array- and bisulfite sequencing-based assessments of these samples did not uncover any notable DNA methylation differences in individuals with autism, the researchers did see a dip in the expression of certain genes in the autistic brain samples. These included genes implicated in brain-related processes in the past, along with representatives from mitochondrial oxidative phosphorylation and protein production pathways. In addition, their results hint that some of the gene expression variability found in brain samples from those with autism may coincide with differences in behavioral symptoms reported for the individuals.

"[O]ur data suggest that there are particular biological pathways associated with different symptom domains in autism," Cleveland Clinic researcher Marvin Natowicz, the study's senior author, and his colleagues noted. "Perhaps clinical heterogeneity in autism is the result of differences in these specific pathways which act to control domain severities semi-independently."

An American and Norwegian team looks at epigenetic features that foretell a honeybee's behavioral fate in Nature Neuroscience.

Using whole-genome bisulfite sequencing and a method called "comprehensive high-throughput arrays for relative methylation," or CHARM, the researchers looked at DNA methylation profiles in genetically identical bees belonging to different castes (i.e., queens versus worker bees) and sub-castes (forager versus nurse workers).

The analyses didn't uncover any clear methylation differences at the caste level. But study authors did detect DNA methylation distinctions in worker bees from the forager and nurse sub-castes: 155 regions of the genome were differentially methylated in nurses and foragers. In bees from the forager sub-caste that were coerced into taking over the role of nurse bees, meanwhile, the team saw shifts in DNA methylation at 107 sites in the genome, including 57 of the sites identified in the initial nurse-forager comparison.

"We found that DNA methylation was able to revert, concomitant with experimental reversion of foragers back to nurses," the study's authors wrote. "This suggests a sub-caste-specific methylation signature that assists in forming sub-caste phenotypes."

"Our results are, to the best of our knowledge, the first to show reversible DNA methylation corresponding to a reversible behavioral phenotype in any species," they added.

An international team has outlined its efforts to chart gene expression across anatomically defined regions of the human brain in Nature.

Researchers from the Allen Institute for Brain Science and elsewhere did array-based gene expression profiling on the various cell types found in around 900 carefully defined regions of the brain, using post-mortem samples from two healthy male individuals. Data for a third brain was also incorporated into the map, as was histological information on the samples. The resulting transcriptional map of the human brain — dubbed the Allen Human Brain Atlas — is available online.

The study authors' preliminary analyses indicated that the majority of known human genes are active in at least one of the brain regions tested. While expression profiles in the brains of different individuals appear fairly similar overall, they noted, the atlas offers the chance to peek at finer scale gene activity profiles between individuals, across brain regions, and within different cell types.

"This study demonstrates the value of a global analysis of gene expression throughout the entire brain and has implications for understanding brain function, development, evolution, and disease," co-first author Ed Lein, a researcher with the Allen Institute for Brain Science, said in a statement. "These results only scratch the surface of what can be learned from this immense data set."

Last year, a team from the Allen Institute for Brain Science announced that it was releasing data generated through the Allen Human Brain Atlas effort and discussed initial findings on the first two brains assessed through the project.

The same gene that contributes to coat patterning in domestic tabby cats also spells out the shape of a cheetah's spots, according to a study in Science.

In an effort to untangle the genetics behind dark and light color patterns in cats, an international research team started by comparing striped mackeral tabby cats with blotched tabby cats. By genotyping tissue samples from dozens of feral cats in California — and consulting data from the domestic cat genome sequence — the team determined that blotched tabby cats carry a mutation affecting both copies of an enzyme-coding gene called Taqpep. The same mutation occurs in at least one wild cat, too, they found: the king cheetah, a blotchy-spotted African cheetah with stripes running down its back.

Using an EcoP151-tagged Digital Gene Expression method, nicknamed EDGE, they went on to compare gene expression patterns in cheetah skin samples collected at sites where black and yellow fur neighbored one another. That analysis indicated that the king cheetah's singular coat pattern stems from Taqpep alterations that ultimately affect which hair cells will have higher or lower expression of a second gene, endothelin3 (Endn3), which is found at enhanced levels in dark hair cells.

"Mutation of a single gene causes stripes to become blotches, and spots to become stripes," co-corresponding author Gregory Barsh, a researcher affiliated with the HudsonAlpha Institute and Stanford University, said in a statement. "This is very strong evidence that Edn3 is a critical regulator of black versus yellow hair in animals."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

The Scan

Suicidal Ideation-Linked Loci Identified Using Million Veteran Program Data

Researchers in PLOS Genetics identify risk variants within and across ancestry groups with a genome-wide association study involving veterans with or without a history of suicidal ideation.

Algorithm Teases Out Genetic Ancestry in Individuals at Biobank Scale

Researchers develop an algorithm known as Rye to tease apart ancestry fractions in admixed individuals at a biobank-scale, applying it to 488,221 UK Biobank participants in Nucleic Acids Research.

Multi-Ancestry Analysis Highlights Comparable Common Variants at Complex Trait-Linked Loci

Researchers in Nature Genetics examine common variants implicated in more than three dozen conditions, estimating genetic effect similarities across ancestry tracts in admixed individuals.

Sick Newborns Selected for WGS With Automated Pipeline

Researchers successfully prioritized infants with potential Mendelian conditions for whole-genome sequencing or rapid whole-genome sequencing, as they report in Genome Medicine.