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Model organism redux, microRNA, Genaissance goes from SNPs to drugs

The cover story for Genome Technology’s March 2005 issue paid tribute to the field of plant and animal genomics by profiling scientists involved in compelling research on model organisms. Since then, many of the investigators we talked to then have continued fruitful research programs on their chosen species, while others have followed lines of inquiry that reach into the human genome.

Rick Wilson of Washington University’s Genome Sequencing Center spoke with us right after publishing a high-coverage physical map of the chicken genome; it looks like he’s had a busy year since then. He recently played a part in sequencing the human X chromosome, annotating sequences for chromosomes 2 and 4, and conducting a comparative analysis in human and chimp segmental duplications. And that’s just what he published in

Nature. Along with colleague Elaine Mardis, Wilson has been test-driving Solexa’s next-generation sequencer.

Last year’s cover story also featured Cold Spring Harbor Laboratory’s Robert Martienssen, who gave a brief history of his work on elucidating epigenetic mechanisms in maize and

Arabidopsis. Last summer, Martienssen co-chaired a workshop that resulted in a proposal for initiating a Human Epigenome Project, which may do much toward understanding human cancer initiation and progression. Andrew Feinberg, who presented at the AACR-sponsored workshop, tells us more about cancer research and epigenomics in this issue (see pg 29).

For a news piece in last year’s issue,

GT caught up with Elaine Ostrander after her move to NHGRI to take on the job of head of cancer genetics. Ostrander fit right in with the issue’s model organism motif, as she was a keynote speaker at last year’s Plant and Animal Genome Conference where she presented initial results on draft sequences for the canine genome. Less than one year later, Ostrander and others published a high-quality draft sequence, comparative analysis, and haplotype structure of the dog genome.

The feature in March 2005 was a story on microRNAs, which had just burst onto the scene as two separate research groups implicated the short RNA in the regulation of nearly a third of the human genome. One year later, researchers are reporting that the majority of mammalian genes appear to be influenced by small, non-coding RNAs, but are not directly regulated by microRNAs. That said, microRNAs continue to fascinate both researchers and vendors alike. The market for commercial microRNA microarrays is becoming increasingly competitive, with players like Ambion, CombiMatrix, Exiqon, and Invitrogen joining the mix.

But five years ago, the microRNA game was hardly an attention-getter. Instead, the siren song of pharmacogenomics had captured the imagination of moguls and MDs alike. It was in this environment that GT looked at Genaissance Pharmaceuticals’ growing SNP discovery business, which has since matured into a drug and diagnostic provider. Genaissance was acquired by Clinical Data last year, but not before inking deals with a couple of Japanese pharma companies. Early this year, Clinical Data split itself into two distinct subsidiaries: Clinical Data Molecular and Vital Diagnostics. Genaissance joins Icoria in comprising the molecular unit, which is slated to concentrate on pharmacogenomics and molecular diagnostics.            

 — Jen Crebs

Coming Up
Next Month in GT

Don’t miss these features in the April issue:

Bioimaging & systems biology
Researchers say that major bioimaging efforts, such as the proposed proteome imaging consortium, are gearing up to finally merge high-quality imaging data with other systems biology data in a meaningful way. We''ll look at the latest entries into the field, and explore how the foundation is being laid for bioimaging to make its mark in systems biology.

Evolution and function of microRNAs
A spate of papers has been published as researchers gain a greater understanding of how microRNAs came about and what exactly they do. GT looks in on this rapidly advancing field to let readers know about the latest findings and the people involved in this pioneering work.


The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.