Su(H)-Mediated Repression Positions Gene Boundaries along the Dorsal-Ventral Axis of Drosophila Embryos

In Drosophila embryos, a nuclear gradient of the Dorsal (Dl) transcription factor directs differential gene expression along the dorsoventral (DV) axis, translating it into distinct domains that specify future mesodermal, neural, and ectodermal territories. However, the mechanisms used to differentially position gene expression boundaries along this axis are not fully understood. Here, using a combination of approaches, including mutant phenotype analyses and chromatin immunoprecipitation, we show that the transcription factor Suppressor of Hairless, Su(H), helps define dorsal boundaries for many genes expressed along the DV axis. Synthetic reporter constructs also provide molecular evidence that Su(H) binding sites support repression and act to counterbalance activation through Dl and the ubiquitous activator Zelda. Our study highlights a role for broadly expressed repressors, like Su(H), and organization of transcription factor binding sites within cis-regulatory modules as important elements controlling spatial domains of gene expression to facilitate flexible positioning of boundaries across the entire DV axis

Divergent Transcriptional Regulatory Logic at the Intersection of Tissue Growth and Developmental Patterning

The Yorkie/Yap transcriptional coactivator is a well-known regulator of cellular proliferation in both invertebrates and mammals. As a coactivator, Yorkie (Yki) lacks a DNA binding domain and must partner with sequence-specific DNA binding proteins in the nucleus to regulate gene expression; in Drosophila, the developmental regulators Scalloped (Sd) and Homothorax (Hth) are two such partners. To determine the range of target genes regulated by these three transcription factors, we performed genome-wide chromatin immunoprecipitation experiments for each factor in both the wing and eye-antenna imaginal discs. Strong, tissue-specific binding patterns are observed for Sd and Hth, while Yki binding is remarkably similar across both tissues. Binding events common to the eye and wing are also present for Sd and Hth; these are associated with genes regulating cell proliferation and “housekeeping” functions, and account for the majority of Yki binding. In contrast, tissue-specific binding events for Sd and Hth significantly overlap enhancers that are active in the given tissue, are enriched in Sd and Hth DNA binding sites, respectively, and are associated with genes that are consistent with each factor's previously established tissue-specific functions. Tissue-specific binding events are also significantly associated with Polycomb targeted chromatin domains. To provide mechanistic insights into tissue-specific regulation, we identify and characterize eye and wing enhancers of the Yki-targeted bantam microRNA gene and demonstrate that they are dependent on direct binding by Hth and Sd, respectively. Overall these results suggest that both Sd and Hth use distinct strategies – one shared between tissues and associated with Yki, the other tissue-specific, generally Yki-independent and associated with developmental patterning – to regulate distinct gene sets during development

Yorkie Promotes Transcription by Recruiting a Histone Methyltransferase Complex

SummaryHippo signaling limits organ growth by inhibiting the transcriptional coactivator Yorkie. Despite the key role of Yorkie in both normal and oncogenic growth, the mechanism by which it activates transcription has not been defined. We report that Yorkie binding to chromatin correlates with histone H3K4 methylation and is sufficient to locally increase it. We show that Yorkie can recruit a histone methyltransferase complex through binding between WW domains of Yorkie and PPxY sequence motifs of NcoA6, a subunit of the Trithorax-related (Trr) methyltransferase complex. Cell culture and in vivo assays establish that this recruitment of NcoA6 contributes to Yorkie’s ability to activate transcription. Mammalian NcoA6, a subunit of Trr-homologous methyltransferase complexes, can similarly interact with Yorkie’s mammalian homolog YAP. Our results implicate direct recruitment of a histone methyltransferase complex as central to transcriptional activation by Yorkie, linking the control of cell proliferation by Hippo signaling to chromatin modification

Quantitative analysis of multi-components by single marker method combined with UPLC-PAD fingerprint analysis based on saikosaponin for discrimination of Bupleuri Radix according to geographical origin

Background: Saikosaponins are regarded as one of the most likely antipyretic constituents of Bupleuri Radix, establishing a comprehensive method that can reflect both the proportion of all constituents and the content of each saikosaponin is critical for its quality evaluation.Methods: In this study, the combination method of quantitative analysis of multiple components with a single marker (QAMS) and fingerprint was firstly established for simultaneous determination of 7 kinds of saikosaponins in Bupleuri Radix by ultra-high performance liquid chromatography (UPLC).Results: The results showed that saikosaponin d was identified as the optimum IR by evaluating the fluctuations and stability of the relative calibration factors (RCFs) under four different conditions. The new QAMS method has been confirmed to accurately quantify the 7 kinds of saikosaponins by comparing the obtained results with those obtained from external standard method and successfully classify the 20 batches of Bupleuri Radix from 8 provinces of China. The experimental time of fingerprint was significantly reduced to approximate 0.5 h through UPLC-PAD method, a total of 17 common peaks were identified.Conclusion: The QAMS-fingerprint method is feasible and reliable for the quality evaluation of Bupleuri Radix. This method could be considered to be spread in the production enterprises of Bupleuri Radix

Identification and characterization of novel amphioxus microRNAs by Solexa sequencing

An analysis of amphioxus miRNAs suggests an expansion of miRNAs played a key role in the evolution of chordates to vertebrate

Ground beetle assemblages in Beijing’s new mountain forests

Mature forests have been almost completely destroyed in China’s northern regions, but this has been followed by large-scale reforestation in the wake of environmental degradation. Although future forest plantations are expected to expand over millions of hectares, knowledge about the ecology and biodiversity of China’s replanted forests remains very limited. Addressing these knowledge gaps, we recorded ground beetle (Coleoptera: Carabidae) communities in five secondary forest types: plantations of Chinese Pine (Pinus tabulaeformis) and Prince Rupprecht’s Larch (Larix principis-rupprechtii), Oak (Quercus wutaishanica) and Asian White Birch (Betula platyphylla) woodlands, and naturally regenerated mixed forest. Species richness peaked in mixed forests, while pine and oak woodlands harboured discrete communities of intermediate species richness. Oak, pine and mixed forest habitats also showed high levels of species turnover between plots. Canopy closure was an important factor influencing ground beetle assemblages and diversity, and a number of forest specialist species only occurred in pine or oak forests. We believe that some forest specialists have survived earlier deforestation and appear to be supported by new plantation forests, but maintenance of secondary native oak and mixed forests is crucial to safeguard the overall species pool

Snap: an integrated SNP annotation platform

Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical research. Using a user-friendly web interface, genes can be searched by name, description, position, SNP ID or clone name. Several public databases are integrated, including gene information from Ensembl, protein features from Uniprot/SWISS-PROT, Pfam and DAS-CBS. Gene relationships are fetched from BIND, MINT, KEGG and are integrated with ortholog data from TreeFam to extend the current interaction networks. Integrated tools for primer-design and mis-splicing analysis have been developed to facilitate experimental analysis of individual genes with focus on their variation. Snap is available at and at

Regulation of Orai1/STIM1 mediated ICRAC by intracellular pH

Ca²⁺ release activated Ca²⁺-(CRAC) channels composed of two cellular proteins, Ca²⁺-sensing stromal interaction molecule 1 (STIM1) and pore-forming Orai1, are the main mediators of the Ca²⁺ entry pathway activated in response to depletion of intracellular Ca²⁺ stores. Previously it has been shown that the amplitude of CRAC current (ICRAC) strongly depends on extracellular and intracellular pH. Here we investigate the intracellular pH (pHi) dependence of ICRAC mediated by Orai1 and STIM1ectopically expressed in HEK293 cells. The results indicate that pHi affects not only the amplitude of the current, but also Ca²⁺ dependent gating of CRAC channels. Intracellular acidification changes the kinetics of ICRAC, introducing prominent re-activation component in the currents recorded in response to voltage steps to strongly negative potentials. ICRAC with similar kinetics can be observed at normal pHi if the expression levels of Orai1 are increased, relative to the expression levels of STIM1. Mutations in the STIM1 inactivation domain significantly diminish the dependence of ICRAC kinetics on pHi, but have no effect on pHi dependence of ICRAC amplitude, implying that more than one mechanism is involved in CRAC channel regulation by intracellular pH.D. Gavriliouk, N.R. Scrimgeour, S. Grigoryev, L. Ma, F.H. Zhou, G.J. Barritt, G.Y. Rychko

Community Detection in Multiplex Networks

A multiplex network models different modes of interaction among same-type entities. In this article we provide a taxonomy of community detection algorithms in multiplex networks. We characterize the different algorithms based on various properties and we discuss the type of communities detected by each method. We then provide an extensive experimental evaluation of the reviewed methods to answer three main questions: to what extent the evaluated methods are able to detect ground-truth communities, to what extent different methods produce similar community structures and to what extent the evaluated methods are scalable. One goal of this survey is to help scholars and practitioners to choose the right methods for the data and the task at hand, while also emphasizing when such choice is problematic.Comment: 55 pages. Accepted for publication on ACM Computing Surveys in a shorter versio