Want to catch up on some of the latest methods, new technologies, and expert technical tricks? You’re in the right place. Here’s a list of our favorite emerging Technology and Methods articles from the last year or so to really jump-start your 2011. Check ‘em out!
DNA Methylation Analysis
Methylome Analysis Snapshot
February 11, 2010. State of Methylome Analysis – Genome-Wide Methylation Techniques Review: New to the field, or just want to make sure you’ve still got a hold of the technology landscape. This review article gives you the ins and outs on the latest techniques for methylation analysis…as of last winter anyways.
RRBS- Reduced Representation Bisulfite Sequencing Evolves
January 13, 2010. More DNAm Data, Less Sample – Reduced Representation is No BS: For the cost/sample conscious researcher looking at genomic methylation, the RRBS continues to evolve and is a great weapon.
Bead It: Methylation Analysis On Beads
April 6, 2010. Single Tube DNAm Analysis. Better Than Sliced Bread?: MOB, or methylation on beads, speeds up the bisulfite conversion process by combining multiple steps into one tube, and at the same time gets better results.
SMRTer DNA Methylation Sequencing
May 10, 2010. Getting SMRT with Direct DNA Methylation Detection: Single Molecule, Real-Time (SMRT) sequencing from PacBio raises the bar for Next-gen DNA methylation sequencing by allowing direct single molecule analysis of the 5th base.
Directed DNA Methylation
July 8, 2010. Triplex Oligos Enable Targeted DNA Methylation: Read, aim, methylate. Interested in what functional consequences comes with DNA methylation at a locus of your choice? You might be interested in this method that uses oligos to target a methyltransferase enzyme right where you want it, so you can control what’s methylated or not.
Since 5-hmC has been such a hot topic, it’s not surprising to see a few new methods pop up to fill that analysis void. Look them over and find your favorite.
- October 26, 2010. That’s Sweet: Tracking Down 5-hmC with Sugar: This method from Zymo uses a glucosyltransferase to tack on glucose to any 5hmCs it finds. You can then use differential cleavage from restriction enzymes to decipher which sites have 5-hmC instead of the standard 5-mC.
- December 15, 2010. Enriching 5-hmC Detection with Sugar: In a twist on the previous glucose-tagging approach, this technique uses the glucose, after it gets linked to biotin, as a way to pull down genomic fragments containing 5-hmC. Once enriched, your sample is ready for qPCR, ChIP or sequencing.
- December 16, 2010. Small Pores Provide Smoother 5-hmC Experience: Sending DNA molecules through a nanopore gives this setup the ability to figure out the proportions of cytosine, methylcytosine and 5-hmC in a given strand based on current changes.
SCAN Chromatin Analysis Device
March 2, 2010. SCAN-ing For Chromatin Gold: The SCAN platform can ID several histone marks or modifications on a single chromatin molecule, all at one time.
Getting into the Specifics of Chromatin Antibodies
Researchers around the world rolled up their lab coats and put antibodies to the test in using some hand new tools.
- December 24, 2010. Combinatorial Histone Interactions Put Antibodies’ Specificity in a Bind: Peptide arrays containing a library of combinatorially modified histone peptides were put to work in more crowded working environments where multiple histone marks were present to see how they performed.
- October 13th, 2010. A Matter of Specificity: Peptide arrays comprising 382 peptides from 8 different regions within N-terminal tails of histones, Bock et al. studied the specificity of 36 widely used commercial antibodies from various commercial suppliers.
- December 9, 2010. Naughty and Nice ChIP Antibodies: A consortium of chromatin researchers put commercial ChIP antibodies through the lab bench ringer and created a nice resource for the research community in the process.
Histone Structure Database
September 15, 2010. Grabbing Histones by the Tail: The Structural Genomics Consortium created The Structural Genomics of Histone Tails webserver to house all of the known data about histone structure, including a 3D interface. Just try not to spend days on end playing with the interactive histone models.
CATCH-IT Nucleosome Anaylsis
June 9, 2010. Nucleosome dynamics: CATCH-IT if you can: The CATCH-IT technique uses metabolic labeling of histones to give a snapshot of nucleosome dynamics and measure turnover.
NCBI Epigenomics Sample Database
October 26, 2010. Take a Look: NCBI Epigenomics Sample Browser: This resource contains tons of public epigenomics data sets, and lets you browse, search and align them however you like with a user friendly browser. Best of all, you can take advantage of all this data for free…well, except for your tax dollars that is.
miRNA Analysis Methods
miRNA Microarray Lineup
April 6, 2010. Breaking Down miRNA Microarrays: Ignore the marketing rhetoric, this review provides data that can help you choose the miRNA array setup that suits your lab best.
January 6, 2010. RIP-Chip Tears Into miRNP Complex Analysis: Using AGO antibodies to pull down entire microribonucleoprotein complexes opens the door to more in depth study of miRNA::mRNA interactions.