On the cover of Science this week is a 3D map of the human genome. "While scientists have previously been able to resolve the three-dimensional structure of parts of the genome, a new study is the first to do so on a genome-wide scale," says a story at Technology Review. Using a method called Hi-C, which couples "proximity-based ligation with massively parallel sequencing," first authors Erez Lieberman-Aiden and Nynke van Berkum at MIT and the University of Massachusetts Medical School, respectively, created a map of all proximal and distal interactions to 1 MB resolution. Additionally, they found that chromosomes have two regions, "one for active genes and another for inactive genes, and the unentangled curvatures allow genes to be moved easily between them," says a Wired story. "At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus," they say in the abstract.
Bangor University's Peter Golyshin and Manuel Ferrer of Madrid's CSIC are senior authors on work that's built a metabolite array, otherwise called a reactome array. The array includes 1,676 dye-linked substrate compounds representing central metabolic pathways of all forms of life, they say, and can be used to study the functional workings of multiple metabolic pathways in mixed samples. To test, they applied three microbial communities from acidic volcanic pool, deep-sea brine lake, and hydrocarbon-polluted seawater to the array and were able reconstruct their global metabolisms.
Researchers led by MIT's Nir Hacohen and Aviv Regev studied the transcriptional response network behind pathogen infection in mouse dendritic cells. Using "an unbiased strategy," they discovered the function of 125 transcription factors, chromatin modifiers, and RNA binding proteins, from which they could build a network model of 24 core regulators and 76 fine-tuners.
In other work, Dennis Burton at Scripps led researchers that included those from the International AIDS Vaccine Initiative in a high-throughput screening effort to find new HIV-1 antibodies. Their screen identified two new broadly neutralizing antibodies from a clade A-infected donor in Africa. These antibodies recognize an epitope that is "preferentially expressed on trimeric Envelope protein and spans conserved regions of variable loops of the gp120 subunit," a possible new vaccine target, they say.
Two policy articles delve into the rippling effect of systems biology data. In one, scientists advocate data sharing and urge that good annotation practices be more frequently implemented. In another, researchers say that hardware advances should dictate better data collection standards for sequencing studies.