Denisovan archaic hominins and modern humans went through at least two rounds of mixing, according to University of Washington and Princeton University researchers. Using a new reference-free strategy to boost the power of the S* statistic method, the team searched for signs of archaic admixture in genome sequences for 5,639 Eurasian or Oceanic individuals enrolled through the 1000 Genomes Project, UK10K study, and Simons Genome Diversity project. Based on archaic allele patterns in these contemporary individuals, compared with Altai Denisovan and Altai Neanderthal sequences, the study's authors detected two distinct stretches of Denisovan ancestry in Asian and Papuan populations. "The component closely related to the Altai Denisovan is primarily present in East Asians," they write, "whereas the component more distantly related to the Altai Denisovan forms the major part of the Denisovan ancestry in Papuans and South Asians." GenomeWeb has more on the study, here.
A team from China takes a look at open chromatin accessibility patterns in early human embryogenesis for another Cell study. The researchers used DNase I hypersensitive site sequencing to map chromatin accessibility in two-, four- and eight-cell embryos, as well as slightly more advanced embryos from the morula and blastocyst stages of development and primary tissue samples. Their comparisons with developing mouse embryos indicate that human embryos seem to express evolutionarily older genes at earlier stages of development, while relying on the Oct4 transcription factor during a zygotic genome activation stage that happens earlier in the human embryos than in mice.
Finally, researchers from Germany, Australia, and the UK describe a multiplexed, quantitative liquid chromatography-tandem mass spectrometry-based method for following protein production and degradation dynamics. The approach — known as multiplexed proteome dynamics profiling, or mPDP — brings together the stable isotope labeling with amino acids in cell culture (SILAC) labeling method and isobaric mass tagging to track proteome dynamics by mass spec. For the study, the team applied mPDP in three cellular contexts, following the proteomic dynamics of BET transcription factor family degradation, estrogen receptor degradation, and heat shock protein 90 chaperone inhibition.