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In an effort by several research groups, a genome-wide RNAi-based screen presents a list of validated genes involved in cilia assembly and maintenance, and reveals previously unidentified ciliopathy factors.
Groth and colleagues identify proteins associated with newly synthesized DNA — isolated by nascent chromatin capture — as well as proteins associated with mature DNA, and find factors not previously linked to replication or nascent chromatin.
Zon and colleagues have performed a reverse genetic screen to target orthologues of 425 human chromatin factors in zebrafish. This allowed them to delineate chromatin regulators that function at distinct stages of primitive and definitive blood formation.
Plath and colleagues survey the global histone modification changes linked to reprogramming. They delineate that the H3K9-methylation-associated protein Cbx3 restricts late events of reprogramming and, in particular, prevents the expression of the pluripotent gene Nanog.
Bakal, Wong and colleagues performed an RNAi screen in Drosophila cells, as well as imaging and systems-level analyses, to identify genes regulating morphological complexity in heterogeneous cell populations. They report that rather than generating novel shapes, most genes control a switch-like transition between distinct morphologies. The authors also extend their findings to mouse and human melanoma cells.
Human embryonic stem cells contain 5-hydroxymethylcytosine (5hmC) generated by the TET enzyme. Jin and colleagues show that TET1 increases 5hmC levels during reprogramming to human inducible pluripotent stem cells, and although this change is critical for optimal epigenetic reprogramming, it does not compromise primed pluripotency.
Maliga and colleagues have produced a library of bacterial artificial chromosome (BAC) transgenes encoding tagged human kinesin and myosin motors, and have generated a collection of BAC-expressing human and mouse cell lines for the study of motor function.
Cell polarity is important for the function of many animal cells, and several aspects of its establishment are conserved across species, from worm to human. Ahringer and colleagues have performed large-scale genetic interaction screens in Caenorhabditis elegans to identify a network of polarity regulators that includes genes not previously associated with polarity, such as the nuclear pore protein NPP-2.
Clark and colleagues have characterized the stages during which global epigenetic reprogramming occurs in human primordial germ cells, and delineate the appearance of these changes at 16 days of differentiation.
Brown and colleagues take a systems-level approach to the DNA damage response by analysing the changes in localization and abundance of proteins in response to replication stress, using a budding yeast GFP fusion library and high-throughput microscopy.
Watt and colleagues carried out an RNAi screen to identify epigenetic modifiers involved in the control of epidermal differentiation. They delineate a network of genetic interactions using a Bayesian mixture model approach, and uncover two complexes of modifiers that differentially affect self-renewal and differentiation of epidermal stem cells.
Pepperkok, Simpson and colleagues performed genome-wide RNAi screens in human cells to uncover regulators of the secretory pathway. They also identify protein networks with previously unappreciated roles in secretory pathway regulation.
Wedlich-Söldner and colleagues characterize the localization of plasma membrane proteins in Saccharomyces cerevisiae by total internal reflection microscopy and deconvolution. Their data reveal a self-organization of proteins into patterns and demonstrate that association of the arginine transporter Can1 with its membrane domain is important for its function.
Elledge and colleagues performed siRNA (short interfering RNA) screens in human cells to identify regulators of homologous recombination (HR), a mechanism for the repair of double-strand breaks in DNA. Validation of screen data reveals the susceptibility of HR siRNA screens to off-target effects but defines the heterogeneous ribonucloprotein RBMX as a regulator of HR.
Cowan and colleagues have developed a method to efficiently differentiate human pluripotent stem cells into functional white or brown adipocytes, through the transient expression of PPARG2 alone or in combination with CEBP and PRDM16. The programmed cells are able to give rise to ectopic fat pads with white or brown adipose tissue characteristics.
Improperly folded proteins are targeted for destruction through the endoplasmic-reticulum-associated degradation pathway (ERAD). Kopito and colleagues present a high-resolution interaction analysis of the ERAD system in combination with functional genomics, and identify new ERAD components.
Bershadsky and colleagues show that fibroblast polarization depends on matrix rigidity and focal adhesion mechanosensing. They target protein tyrosine kinases through RNAi to identify signalling molecules that regulate traction force generation, focal adhesion assembly and mechanosensitivity.