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Sifting Through the Rubble: miRNA “Degradome” Sequencing for miRNA Targets

January 26, 2009

The miRNA target prediction field has developed rapidly over the last few years. New entrants like miRanda, PicTar, DIANA, and RNA22 have acted as oracles to the target seeking research community, but have often left scientists with more questions than answers, so experimental validation is still required. Taking advantage of the fact that Arognaute-mediated mRNA […]

LCM to Data: Navigating the Small Sample Obstacle Course in DNA Methylation Profiling

January 25, 2009

Tissue heterogeneity has pestered researchers desiring a closer look at tissue-specific genomics and epigenomics. Sure, laser capture microdissection (LCM) platforms have been really helpful in isolating very small and specific regions of tissue, but that’s only half the battle. Working with minute amounts of LCM samples, particularly when they’re derived from the battered formalin-fixed paraffin-embedded […]

CHARMed I’m Shore: Meet the Latest Hotspots for DNA Methylation

January 19, 2009

Between reading Dilbert cartoons and refilling their Swingline staplers, many of corporate America’s finest day dream of holidays to distant islands, but they’re not alone. Researchers studying DNA methylation have made minimal attempts to hide their infatuation with CpG islands, after all, these regions tend to associate themselves with prestigious protein-coding regions of genes. An […]

CAGEd miRNAs: Taming Transcriptional Initiation

January 18, 2009

Most primary miRNA transcripts remain a mystery because they’re generally degraded by the time they leave the comfort of the nucleus. Where do the transcripts start? Do they have a single “peak” of initiation, or are there a variety of sites where they’re likely to begin? Limitations in the currently available molecular biology tool set […]

Summitting With PeakSeq.It’s About Mappability

January 10, 2009

ChIP-seq continues to assault bioinformatics teams with avalanches of data, but the upside of using this powerful approach brings some challenges along with it. Modeling background accurately requires a few tweaks, so before you get all excited about the double black diamond peaks that you’re seeing in regulatory motifs, you might want to factor in […]

Bisulfite Sequencing the “Other” Nucleic Acid: Methylated RNA

December 16, 2008

What’s good for the goose is good for the gander, so why shouldn’t bisulfite sequencing be used to study RNA cytosine methylation? Until recently, the harsh reaction conditions required for bisulfite deamination were considered detrimental to RNA stability. However, Matthias Schaefer and colleagues developed an RNA bisulfite sequencing procedure that reproducibly and quantitatively detected cytosine […]

To Code or Not to Code…Is that the Question?

December 10, 2008

In the past few years, ncRNAs have progressed from interesting anomalies to what some researchers think constitute the majority of the mammalian transcriptome. However, as reviewed by John Mattick and coworkers at the University of Queensland and the Ludwig Institute for Cancer Research (both in Australia), it’s increasingly difficult to distinguish coding from noncoding RNAs […]

Let It Sno

December 2, 2008

It’s December, the time of year when much of the States is blanketed in a frosty mantle of the white stuff. But as recently reported in Molecular Cell, the ACA45 RNA appears to have pulled the ultimate snow job. Nikolaus Rajewsky, Gunter Meister, and colleagues revealed that ACA45, which was previously thought to function exclusively […]

miRNA Fights Cancer-Promoting Histone Methyltransferase

November 23, 2008

What makes some tumors as gentle as purring kittens and others of the same cancer type as ferocious as saber-toothed tigers? A miRNA (miR-101) was recently shown to take a bite out of cancer by inhibiting the EZH2 histone methyltransferase. The study by Arul Chinnaiyan and co-workers at the University of Michigan Medical School, the […]

ncRNAs on the Brain

November 17, 2008

Do you remember the name of your fourth-grade teacher? How about what you had for lunch last Thursday? Highschool Prom date? Yeah, we went stag too, but if you’re having a hard time remebering key events, ncRNAs may be to blame! The human brain expresses high numbers of ncRNAs, and mounting evidence indicates important contributions […]

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