DNA and Chromosomes
- ChIP-Seq is a widespread experimental method for determining the global enrichment of chromatin modifications and genome-associated factors. Whereas it is straightforward to compare the relative genomic distribution of these epigenetic features, researchers have also made efforts to compare their signal strength using external references for normalization. New work now suggests that these “spike-ins” could lead to inaccurate conclusions due to intrinsic issues of the methodology and instead calls for new criteria of experimental reporting that may permit internal standardization when certain parameters are fulfilled.
- Integration of spacers into CRISPR loci requires the Cas1/Cas2 integrase complex, frequently in combination with Cas4 exonuclease. However, several CRISPR-Cas systems lack Cas4. Whether Cas4-like activity is dispensable in these systems or provided by an unidentified actor was not known. In this issue of the Journal of Biological Chemistry, Ramachandran et al. show that in subtype I-E systems, Cas4-like activity is supplied by DnaQ-superfamily exonucleases, providing a beautiful example of cellular machinery moonlighting in support of CRISPR-Cas adaptive immunity.
- DNA double-strand break repair by homologous recombination is initiated by the Ctp1 protein together with the Mre11–Rad50–Nbs1 nuclease complex in Schizosaccharomyces pombe, but the mechanism by which Ctp1 promotes this process has remained unknown. Andres et al. now use atomic force microscopy to image Ctp1–DNA complexes, demonstrating a striking capacity of Ctp1 filaments to bridge DNA molecules. This unanticipated role of Ctp1 might help explain how the processing of DNA ends is coordinated to facilitate DNA break repair.
- The distinctive profile of the double-helix DNA molecule is today, along with Rutherford’s depiction of the atom as a miniature planetary system, a worldwide-recognized symbol of twentieth-century science. The complex story of how DNA’s tertiary structure was determined is also well-known. Surprisingly, however, far less is commonly known about how the structural subunits of the nucleic acids—i.e. nucleotides, nucleosides, and the specific carbohydrates that distinguish DNA and RNA—were first identified and their connectivity ascertained.