In Nature this week, scientists led by HHMI's Raymond Deshaies describe the polyubiquitylation pathway, which is the conjugation of a series of ubiquitin molecules onto proteins as part of the degradation process. By employing "new theoretical and experimental methodologies," they were able to watch the process in milliseconds, and found that it actually proceeds sequentially. Specifically, they showed that the RING E3 enzymes SCFCdc4 and SCFbeta-TrCP work with the E2 Cdc34 to build chains on substrates by sequential transfer of single ubiquitins as opposed to doing it using en-bloc transfer, which a related News and Views piece discusses.
The Whitehead Institute's Rudolf Jaenisch led MIT scientists in work this week showing that iPS reprogramming of somatic cells is a "continuous stochastic process where almost all mouse donor cells eventually give rise to iPS cells on continued growth and transcription factor expression." By inhibiting the p53/p21 pathway or over-expressing Lin28, they were able to speed up iPS cell formation through increasing the cell division rate whereas over-expressing Nanog sped up the process independently of the rate of cell division. A review article touches on the research and therapeutic potential of lineage reprogramming, which involves using transcription factors to directly convert cells from one lineage to another.
Using a computational approach, Yale University scientists discovered new noncoding bacterial RNAs from metagenomic sequence data that are even bigger and more complex than what typically turns up from searches for new RNAs in these samples. Some of these new RNAs rival the known large ribozymes, they say in the abstract. "Our work reveals new classes of large RNAs exist, which would be akin to protein scientists finding new classes of enzymes," says lead author Ronald Breaker in a related story at GenomeWeb Daily News.
Massachusetts General Hospital's Brad Bernstein is senior author on a paper in Nature Methods this week that used Helicos' single molecule sequencing platform to directly sequence chromatin immunoprecipitated DNA "with minimal sample manipulation," they say in the abstract. It is the first time ChIP-seq has been performed from such a small amount (as little as 50 pg of DNA) of starting material and could lead to broader application of the technique to sample-poor areas of study like cancer and developmental biology.