In vitro FRAP reveals the ATP-dependent nuclear mobilization of the exon junction complex protein SRm160

We present a new in vitro system for characterizing the binding and mobility of enhanced green fluorescent protein (EGFP)-labeled nuclear proteins by fluorescence recovery after photobleaching in digitonin-permeabilized cells. This assay reveals that SRm160, a splicing coactivator and component of the exon junction complex (EJC) involved in RNA export, has an adenosine triphosphate (ATP)-dependent mobility. Endogenous SRm160, lacking the EGFP moiety, could also be released from sites at splicing speckled domains by an ATP-dependent mechanism. A second EJC protein, RNPS1, also has an ATP-dependent mobility, but SRm300, a protein that binds to SRm160 and participates with it in RNA splicing, remains immobile after ATP supplementation. This finding suggests that SRm160-containing RNA export, but not splicing, complexes have an ATP-dependent mobility. We propose that RNA export complexes have an ATP-regulated mechanism for release from binding sites at splicing speckled domains. In vitro fluorescence recovery after photobleaching is a powerful tool for identifying cofactors required for nuclear binding and mobility

Geometric combinatorial algebras: cyclohedron and simplex

In this paper we report on results of our investigation into the algebraic structure supported by the combinatorial geometry of the cyclohedron. Our new graded algebra structures lie between two well known Hopf algebras: the Malvenuto-Reutenauer algebra of permutations and the Loday-Ronco algebra of binary trees. Connecting algebra maps arise from a new generalization of the Tonks projection from the permutohedron to the associahedron, which we discover via the viewpoint of the graph associahedra of Carr and Devadoss. At the same time that viewpoint allows exciting geometrical insights into the multiplicative structure of the algebras involved. Extending the Tonks projection also reveals a new graded algebra structure on the simplices. Finally this latter is extended to a new graded Hopf algebra (one-sided) with basis all the faces of the simplices.Comment: 23 figures, new expanded section about Hopf algebra of simplices, with journal correction