Unstated Rules of the Academia

"What they didn't teach you in Grad School" by Paul Gray and David E Drew is a valuable book for anyone considering a career in academia. The authors who are long-term academics themselves, give very  concise and to-the-point collection of hints to help you survive in academia. 

  It is reminiscent of "How to Get a PhD" ( a book which helped me go through the painful years of gradschool) with a wider scope including any part of an academic career from  job search, teaching, research and tenure process to academic publishing and writing. 

What is most prominent about the book is the funny, witty and frank style which makes it a very easy read. I have not finished the book yet but one can finish it in a couple of sittings however the best might be to digest the material. As the authors say about academia,  "It is a good life and it is a lifestyle for which you even get paid" however to the people who think it is also not an easy career path, this book should be really helpful.

ChIP-Exo: An exonuclease based improvement to the accuracy of CHIP-Seq technique

On: Rhee and Pugh, 2011 in Cell.

When DNA microarray techniques were combined with Chromatin Immunoprecipitation (ChIP) method, the protein-DNA interaction analyses promoted to the genome-wide level: ChIP-on-chip. Although microarrays have intrinsic shortcomings such as nonspecific noise and limited genome covering, ChIP-on-chip was the state-of-the art technique (for DNA-protein interaction research) at the beginnings of the 2000s. In the second half of the decade, genome-wide analyses have jumped up several steps with next generation sequencing technology: ChIP-seq. In the latest issue of Cell, Rhee and Pugh further improved the accuracy of ChIP-seq.

ChIP-Exo uses 5'-3' (lambda) exonuclease to chop up 5' ends of the immunoprecipitated DNA protein complexes. The exonuclease stops however, because of the DNA binding protein hindrance. Since the enzyme does not cut 3' ends, the protruding ends are still available to map the DNA to the genome but the technique adds accuracy by gaining the almost exact location of the protein on DNA. The theoretical drawback is the presence of other crosslinked proteins on DNA. In this direction, the authors confirmed that the presence of nucleosomes does not prevent nuclease activity. The de novo motif search revealed recognition sites of a number of transcription factors very accurately.

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution
Rhee, HoSung; Pugh, B.Franklin
Cell doi:10.1016/j.cell.2011.11.013 (volume 147 issue 6 pp.1408 - 1419)