BackgroundMTML-msBayes uses hierarchical approximate Bayesian computation (HABC) under a coalescent model to infer temporal patterns of divergence and gene flow across codistributed taxon-pairs. Under a model of multiple codistributed taxa that diverge into taxon-pairs with subsequent gene flow or isolation, one can estimate hyper-parameters that quantify the mean and variability in divergence times or test models of migration and isolation. The software uses multi-locus DNA sequence data collected from multiple taxon-pairs and allows variation across taxa in demographic parameters as well as heterogeneity in DNA mutation rates across loci. The method also allows a flexible sampling scheme: different numbers of loci of varying length can be sampled from different taxon-pairs.ResultsSimulation tests reveal increasing power with increasing numbers of loci when attempting to distinguish temporal congruence from incongruence in divergence times across taxon-pairs. These results are robust to DNA mutation rate heterogeneity. Estimating mean divergence times and testing simultaneous divergence was less accurate with migration, but improved if one specified the correct migration model. Simulation validation tests demonstrated that one can detect the correct migration or isolation model with high probability, and that this HABC model testing procedure was greatly improved by incorporating a summary statistic originally developed for this task (Wakeley's ΨW). The method is applied to an empirical data set of three Australian avian taxon-pairs and a result of simultaneous divergence with some subsequent gene flow is inferred.ConclusionsTo retain flexibility and compatibility with existing bioinformatics tools, MTML-msBayes is a pipeline software package consisting of Perl, C and R programs that are executed via the command line. Source code and binaries are available for download at http://msbayes.sourceforge.net/ under an open source license (GNU Public License).

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Blockade of the protein-protein interaction between the transmembrane protein programmed cell death protein 1 (PD-1) and its ligand PD-L1 has emerged as a promising immunotherapy for treating cancers. Using the technology of mirror-image phage display, we developed the first hydrolysis-resistant D-peptide antagonists to target the PD-1/PD-L1 pathway. The optimized compound (D) PPA-1 could bind PD-L1 at an affinity of 0.51 μM in vitro. A blockade assay at the cellular level and tumor-bearing mice experiments indicated that (D) PPA-1 could also effectively disrupt the PD-1/PD-L1 interaction in vivo. Thus D-peptide antagonists may provide novel low-molecular-weight drug candidates for cancer immunotherapy.

Histone acetylation and deacetylation are among the principal mechanisms by which chromatin is regulated during transcription, DNA silencing, and DNA repair. We analyzed patterns of genetic interactions uncovered during comprehensive genome-wide analyses in yeast to probe how histone acetyltransferase (HAT) and histone deacetylase (HDAC) protein complexes interact. The genetic interaction data unveil an underappreciated role of HDACs in maintaining cellular viability, and led us to show that deacetylation of the histone variant Htz1p at Lys 14 is mediated by Hda1p. Studies of the essential nucleosome acetyltransferase of H4 (NuA4) revealed acetylation-dependent protein stabilization of Yng2p, a potential nonhistone substrate of NuA4 and Rpd3C, and led to a new functional organization model for this critical complex. We also found that DNA double-stranded breaks (DSBs) result in local recruitment of the NuA4 complex, followed by an elaborate NuA4 remodeling process concomitant with Rpd3p recruitment and histone deacetylation. These new characterizations of the HDA and NuA4 complexes demonstrate how systematic analyses of genetic interactions may help illuminate the mechanisms of intricate cellular processes.[Keywords: Systems biology; histone; NuA4; acetylation; DNA repair] Supplemental material is available at http://www.genesdev.org. . These activities are coordinated in the cell, and comprise a system that dynamically regulates chromatin state. Systems with this many components are difficult to analyze using conventional genetics and biochemical methods, although some large-scale attempts have been made (Collins et al. 2007;Mitchell et al. 2008). Comprehensive assessment of this system is further complicated by the inclusion of essential genes (e.g., the essential acetyltransferase ESA1), requiring suitable conditional or hypomorphic query alleles. Moreover, recent studies in higher organisms have shown that HATs and HDACs have many substrates apart from histones (Glozak and Seto 2007;Xu et al. 2007), hinting that such substrates may exist in yeast as well.Several recent studies have demonstrated that comprehensive genetic interaction profiling can effectively resolve complex pathways into conceptually and experimentally tractable modules (Tong et al. 2004;Schuldiner et al. 2005;Pan et al. 2006;Collins et al. 2007). Intergenic interactions can be either aggravating (negative), such as synthetic fitness or lethality defects (SFL), or alleviating (positive) such as synthetic rescue (SR). The genes involved can function either in a common essential pathway or in distinct but compensatory pathways converging on the same essential function (Hartman et al. 2001).

Widespread changes to DNA methylation and chromatin are well documented in cancer, but the fate of higher-order chromosomal structure remains obscure. Here we integrated topological maps for colon tumors and normal colons with epigenetic, transcriptional, and imaging data to characterize alterations to chromatin loops, topologically associated domains, and large-scale compartments. We found that spatial partitioning of the open and closed genome compartments is profoundly compromised in tumors. This reorganization is accompanied by compartment-specific hypomethylation and chromatin changes. Additionally, we identify a compartment at the interface between the canonical A and B compartments that is reorganized in tumors. Remarkably, similar shifts were evident in non-malignant cells that have accumulated excess divisions. Our analyses suggest that these topological changes repress stemness and invasion programs while inducing anti-tumor immunity genes and may therefore restrain malignant progression. Our findings call into question the conventional view that tumor-associated epigenomic alterations are primarily oncogenic.

Differentiation and activation of lymphocytes are documented to result in changes in glycosylation associated with biologically important consequences. In this report, we have systematically examined global changes in N-linked glycosylation following activation of murine CD4 T cells, CD8 T cells, and B cells by MALDI-TOF mass spectrometry profiling, and investigated the molecular basis for those changes by assessing alterations in the expression of glycan transferase genes. Surprisingly, the major change observed in activated CD4 and CD8 T cells was a dramatic reduction of sialylated biantennary N-glycans carrying the terminal NeuGcα2-6Gal sequence, and a corresponding increase in glycans carrying the Galα1-3Gal sequence. This change was accounted for by a decrease in the expression of the sialyltransferase ST6Gal I, and an increase in the expression of the galactosyltransferase, α1-3GalT. Conversely, in B cells no change in terminal sialylation of N-linked glycans was evident, and the expression of the same two glycosyltransferases was increased and decreased, respectively. The results have implications for differential recognition of activated and unactivated T cells by dendritic cells and B cells expressing glycan-binding proteins that recognize terminal sequences of N-linked glycans.

The yeast synthetic lethal genetic interaction network contains rich information about underlying pathways and protein complexes as well as new genetic interactions yet to be discovered. We have developed a graph diffusion kernel as a unified framework for inferring complex/pathway membership analogous to "friends" and genetic interactions analogous to "enemies" from the genetic interaction network. When applied to the Saccharomyces cerevisiae synthetic lethal genetic interaction network, we can achieve a precision around 50% with 20% to 50% recall in the genome-wide prediction of new genetic interactions, supported by experimental validation. The kernels show significant improvement over previous best methods for predicting genetic interactions and protein co-complex membership from genetic interaction data.[Supplemental material is available online at www.genome.org.]Genetics establishes links between genotype and phenotype. Many genes are pleiotropic, carrying out multiple functions in different pathways under different environmental conditions and can have partially redundant function with other genes. Genetic buffering can be evolutionarily stable (Nowak et al. 1997). While individual gene perturbations may have little or no effect, combined perturbations can generate a phenotype. This is the rationale of genetic interaction screens, which test for phenotypes from two-gene perturbations that differ from the singlegene effects. Pairwise genetic interaction screens have been valuable in understanding functional relationships between genes and assigning functions to genes in a pathway-dependent manner.With the completion of the Yeast Knockout deletion collection (Giaever et al. 2002), high-throughput studies of pairwise lethal or growth defect interactions between null or hypomorph alleles of Saccharomyces cerevisiae (budding yeast) have made vast progress in the past few years. "Synthetic growth defect" or "synthetic sickness" describes a genetic interaction between two genes whose individual deletion mutants have minimal growth defects, while the double knockout results in a significant growth defect under a given condition. A subset of those pairs whose double knockouts lead to diminished growth or death are called "synthetic lethal" (Dobzhansky 1946). We will refer to the union of "synthetic sickness" and "synthetic lethal" as a "synthetic fitness or lethal interaction," or SFL. Multiple studies have screened a subset of deletions or hypomorph alleles against the entire set of viable yeast deletion mutants using methods including synthetic genetic array (SGA) (Tong et al. 2001, synthetic lethality analyzed by microarray (SLAM), and diploid-based SLAM (dSLAM) (Ooi et al. 2003;Pan et al. 2004Pan et al. , 2006. A second approach, termed an epistatic miniarray profile, searches for both positive and negative interactions among a subset of genes (Collins et al. 2007).Large . To achieve these goals, especially prediction of pathway membership, algorithms have progressed from counting the number of shared neighbo...

In the yeast, Saccharomyces cerevisiae, oligosaccharyl transferase (OT) is composed of nine different transmembrane proteins. Using a glycosylatable peptide containing a photoprobe, we previously found that only one essential subunit, Ost1p, was specifically labeled by the photoprobe and recently have shown that it does not contain the recognition domain for the glycosylatable sequence Asn-Xaa-Thr/Ser. In this study we utilized additional glycosylatable peptides containing two photoreactive groups and found that these were linked to Stt3p and Ost3p. Stt3p is the most conserved subunit in the OT complex, and therefore 21 block mutants in the lumenal region were prepared. Of the 14 lethal mutant proteins only two, as well as one temperature-sensitive mutant protein, were incorporated into the OT complex. However, using microsomes prepared from these three strains, the labeling of Ost1p was markedly decreased upon photoactivation with the Asn-Bpa-Thr photoprobe. Based on the block mutants single amino acid mutations were prepared and analyzed. From all of these results, we conclude that the sequence from residues 516 to 520, WWDYG in Stt3p, plays a central role in glycosylatable peptide recognition and/or the catalytic glycosylation process.