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This Week in Cell: Sep 23, 2015

A pair of Cell studies explores the mechanisms by which protein kinase enzyme networks respond to environmental triggers in human cells. For the first of these, investigators from Denmark, Italy, and the US used a new computational method called KINspect to characterize the amino acid residues determining the peptide specificity of kinome targets under given conditions. Their analysis suggests determinant of specificity are interconnected, though peppered across distant sites in the kinome — patterns verified through direct testing on three suspected determinants of specificity.

Meanwhile, a group that included some of the same team members considers mutations in cancer that can upend typical kinome network signaling. With the help of a computational approach dubbed ReKINect, the researchers assessed hundreds of kinase enzyme domains and nearly 150,000 phosphorylation sites in the human proteome in an effort to identify so-called network-attacking mutations. In the process, they defined half of dozen network-attacking mutation types, using quantitative mass spec and existing exome data to verify the effects of such shifts with ovarian cancer cell lines and existing cancer genome data.

An international team led by investigators in the Netherlands describes the strategy it used to track genome-wide nuclear lamina interactions in individual human cells. Using a modified version of an in vivo mapping method called DamID, the researchers produced 395 single-cell maps from a human myeloid leukemia cell line. Coupled with Hi-C and imaging methods, the approach made it possible to pick out gene-poor parts of the genome that consistently make contact with the nuclear lamina during specific stages of the cell cycle as well as variable lamina-associated domains with more cell-type specific interactions.