Abstract-We present MUSE (MUtation-baSEd fault localization technique), a new fault localization technique based on mutation analysis. A key idea of MUSE is to identify a faulty statement by utilizing different characteristics of two groups of mutants-one that mutates a faulty statement and the other that mutates a correct statement. We also propose a new evaluation metric for fault localization techniques based on information theory, called Locality Information Loss (LIL): it can measure the aptitude of a localization technique for automated fault repair systems as well as human debuggers. The empirical evaluation using 14 faulty versions of the five real-world programs shows that MUSE localizes a fault after reviewing 7.4 statements on average, which is about 25 times more precise than the state-of-the-art SBFL technique Op2.

Hypoxia-inducible factor-1α (HIF-1α) mediates hypoxic responses and regulates gene expression involved in angiogenesis, invasion and metabolism. Among the various HIF-1α posttranslational modifications, HIF-1α methylation and its physiological role have not yet been elucidated. Here we show that HIF-1α is methylated by SET7/9 methyltransferase, and that lysine-specific demethylase 1 reverses its methylation. The functional consequence of HIF-1α methylation is the modulation of HIF-1α stability primarily in the nucleus, independent of its proline hydroxylation, during long-term hypoxic and normoxic conditions. Knock-in mice bearing a methylation-defective Hif1aKA/KA allele exhibit enhanced retinal angiogenesis and tumour vascularization via HIF-1α stabilization. Importantly, S28Y and R30Q mutations of HIF-1α, found in human cancers, are involved in the altered HIF-1α stability. Together, these results demonstrate a role for HIF-1α methylation in regulating protein stability, thereby modulating biological output including retinal and tumour angiogenesis, with therapeutic implications in human cancer.

SUMMARY Lysine methylation within histones is crucial for transcriptional regulation and thus links chromatin states to biological outcomes. Although recent studies have extended lysine methylation to nonhistone proteins, underlying molecular mechanisms such as the upstream signaling cascade that induces lysine methylation and downstream target genes modulated by this modification have not been elucidated. Here, we show that Reptin, a chromatin-remodeling factor, is methylated at lysine 67 in hypoxic conditions by the methyltransferase G9a. Methylated Reptin binds to the promoters of a subset of hypoxia-responsive genes and negatively regulates transcription of these genes to modulate cellular responses to hypoxia.

Pontin is a chromatin remodeling factor that possesses both ATPase and DNA helicase activities. Although Pontin is frequently overexpressed in human cancers of various types and implicated in oncogenic functions, the upstream signaling network leading to the regulation of Pontin that in turn affects transcription of downstream target genes has not been extensively studied. Here, we identify Pontin is methylated by G9a/GLP methyltransferases in hypoxic condition and potentiates HIF-1α-mediated activation by increasing the recruitment of p300 coactivator to a subset of HIF-1α target promoters. Intriguingly, Pontin methylation results in the increased invasive and migratory properties by activating downstream target gene, Ets1. In contrast, inhibition of Pontin methylation results in the suppression of tumorigenic and metastatic properties. Together, our data provide new approaches by targeting Pontin methylation and its downstream targets for the development of therapeutic agents for human cancers.epigenetics | transcriptional regulation | covalent nonhistone modification

A smectic liquid crystal (LC) containing a rigid biphenyl group and semifluorinated chains exhibits a high density of toric focal conic domains (TFCDs) arranged in an ordered array when confined within a microchannel. The formation of the TFCDs is strongly influenced by the width (W) and depth (h) of the confined microchannels, most importantly, by the channel depth. We studied a broad variety of microchannels, with varying width in the range of 3-200 mum and depth in the range of 2-10 mum. The radius of the TFCDs increases with increases in the width until the saturated radius is achieved, which is determined by the depth of the channel. We used the elastic-anchoring model of TFCD formation to explain the experimental observations. The model allows one to trace the dependence of the TFCD radius on the channel depth h, to explain why the TFCDs do not form in channels that are too shallow or too narrow.