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This Week in Genome Biology: Jul 28, 2010

In Genome Biology, Swedish researchers aimed to identify transcribed regions of the chimpanzee transcriptome, and found a large number of novel exons and 3' UTRs. The researchers say they identified 12,843 expressed genes, and 9,826 novel transcribed regions that don't overlap with annotated exons, mRNAs, or ESTs. They also described and experimentally validated a "putative novel multi-exon gene that belongs to the ATP-cassette transporter gene family. ... In addition to novel exons and UTRs, novel transcribed regions may also stem from different types of noncoding transcripts." The team also notes that the data supports the view that mammalian gene annotations are incomplete.

Researchers from Germany and California suggest that active DNA demethylation is a precisely targeted event that is connected to the modification of histones. The team writes it has identified some novel examples of active DNA demethylation using a global, comparative CpG methylation profiling approach, and has characterized the accompanying transcriptional and epigenetic events during monocytic differentiation. "We show that active DNA demethylation is not restricted to proximal promoters and that the time-course of demethylation varies for individual CpGs," the researchers write. "Irrespective of their location, the removal of methylated cytosines always coincided with the appearance of activating histone marks."

Also, an international team of researchers report the extent to which a dosage imbalance of specific genes from human chromosome 21 perturb certain molecular pathways and lead to disease. The team developed the first mouse embryonic stem cell bank of human chromosome 21 genes, and compared mouse ES cells containing the whole chromosome and mouse ES cells overexpressing single genes from the chromosome. "We determined that only a subset of genes produces a strong transcriptional response when overexpressed in mouse ES cells and that this effect can be predicted taking into account the basal gene expression level and the protein secondary structure," the researchers write, concluding that human chromosome 21-mouse ES cell banks are an important resource in the study of human aneuploidy disorders.

And finally in Genome Biology this week, researchers from Harvard, Stanford, and Israel suggest that the composition and regulation of maternal and zygotic transcriptomes shows that reproduction is species-specific. Using genomic data to identify and compare maternal and zygotic expressed genes from six different animals, the researchers write that they found that mammalian maternal genes are enriched for complex regulatory regions and that egg-laying animals are enriched for maternal genes that lack transcriptional specificity. "We propose that this lack of specificity for maternal expression in egg-laying animals indicates that a large fraction of maternal genes are expressed non-functionally, providing only supplemental nutritional content to the developing embryo," the team writes.

The Scan

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.

Duke University Team Develops Programmable RNA Tool for Cell Editing

Researchers have developed an RNA-based editing tool that can target specific cells, as they describe in Nature.

Novel Gene Editing Approach for Treating Cystic Fibrosis

Researchers in Science Advances report on their development of a non-nuclease-based gene editing approach they hope to apply to treat cystic fibrosis.

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.