In early online work in Science this week led by Harvard's Martha Bulyk and University of Toronto's Timothy Hughes, they used microarrays of all 10-base-pair sequences to look at binding specificities of 104 mouse DNA-binding proteins. Their results, they say, show a "complex landscape of binding, with virtually every protein analyzed possessing unique preferences," and with half of the proteins binding to more than one sequence.
While an editorial looks at how careers in translational medicine can be advanced through better exchange of knowledge between scientists and clinicians, several news stories check in on President Obama's 2010 budget proposal. In one, the authors identify possible problem areas between Obama and the research community, including "compromising on greenhouse gas reductions, overselling new energy technologies, succumbing to disease politics, leading NIH over a cliff again, and ignoring his scientific advisers," they write.
Scientists at the Waksman Institute at Rutgers University have detected abortive transcription in bacterial cells in vivo. Using hybridization with locked nucleic acid probes to detect microRNAs, not only did they observe abortive transcripts, but they also found that abortive initiation increased when interactions between RNA polymerase and the promoter were strengthened or when transcription was prevented.
Two papers explore methylated cytosines. In one, HHMI scientists used thin-layer chromatography, high-pressure liquid chromatography, and mass spec to identify an "unusual DNA nucleotide," in the DNA of Purkinje neurons, 5-hydroxymethyl-2'-deoxycytidine (hmdC). In another paper, scientists used a computational search to find TET1, a fusion partner of the MLL gene in acute myeloid leukemia, and then showed that TET1 is an enzyme that can convert methylated C bases to 5-hydroxymethylcytosine both in vitro and in vivo.