Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq.

BackgroundThe robustness of ChIP-seq datasets is highly dependent upon the antibodies used. Currently, polyclonal antibodies are the standard despite several limitations: They are non-renewable, vary in performance between lots and need to be validated with each new lot. In contrast, monoclonal antibody lots are renewable and provide consistent performance. To increase ChIP-seq standardization, we investigated whether monoclonal antibodies could replace polyclonal antibodies. We compared monoclonal antibodies that target five key histone modifications (H3K4me1, H3K4me3, H3K9me3, H3K27ac and H3K27me3) to their polyclonal counterparts in both human and mouse cells.ResultsOverall performance was highly similar for four monoclonal/polyclonal pairs, including when we used two distinct lots of the same monoclonal antibody. In contrast, the binding patterns for H3K27ac differed substantially between polyclonal and monoclonal antibodies. However, this was most likely due to the distinct immunogen used rather than the clonality of the antibody.ConclusionsAltogether, we found that monoclonal antibodies as a class perform equivalently to polyclonal antibodies for the detection of histone post-translational modifications in both human and mouse. Accordingly, we recommend the use of monoclonal antibodies in ChIP-seq experiments

Structural basis for DNMT3A-mediated de novo DNA methylation.

DNA methylation by de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) at cytosines is essential for genome regulation and development. Dysregulation of this process is implicated in various diseases, notably cancer. However, the mechanisms underlying DNMT3 substrate recognition and enzymatic specificity remain elusive. Here we report a 2.65-ångström crystal structure of the DNMT3A-DNMT3L-DNA complex in which two DNMT3A monomers simultaneously attack two cytosine-phosphate-guanine (CpG) dinucleotides, with the target sites separated by 14 base pairs within the same DNA duplex. The DNMT3A-DNA interaction involves a target recognition domain, a catalytic loop, and DNMT3A homodimeric interface. Arg836 of the target recognition domain makes crucial contacts with CpG, ensuring DNMT3A enzymatic preference towards CpG sites in cells. Haematological cancer-associated somatic mutations of the substrate-binding residues decrease DNMT3A activity, induce CpG hypomethylation, and promote transformation of haematopoietic cells. Together, our study reveals the mechanistic basis for DNMT3A-mediated DNA methylation and establishes its aetiological link to human disease

The roles of motivation and ability in controlling the consequences of stereotype suppression

Two experiments investigated the conditions under which previously suppressed stereotypes are applied in impression formation. In Experiment 1, the extent to which a previously suppressed racial stereotype influenced subsequent impressions depended on the race of the target who was subsequently encountered. Whereas impressions of race-unspecified targets were assimilated to the stereotype following its suppression, no such effects were observed when the target belonged to the racial group whose stereotype had been initially suppressed. These results demonstrate that when perceivers are motivated to avoid stereo-typing individuals, the influence of a stereotype that has been previously activated through suppression is minimized. Experiment 2 demonstrated that these processing goals effectively reduce the impact of suppression-activated stereotypes only when perceivers have sufficient capacity to enact the goals. These results suggest that both sufficient motivation and capacity are necessary to prevent heightened stereotyping following stereotype suppression

LCAA, a Novel Factor Required for Magnesium Protoporphyrin Monomethylester Cyclase Accumulation and Feedback Control of Aminolevulinic Acid Biosynthesis in Tobacco

Low Chlorophyll Accumulation A (LCAA) antisense plants were obtained from a screen for genes whose partial down-regulation results in a strong chlorophyll deficiency in tobacco (Nicotiana tabacum). The LCAA mutants are affected in a plastid-localized protein of unknown function, which is conserved in cyanobacteria and all photosynthetic eukaryotes. They suffer from drastically reduced light-harvesting complex (LHC) contents, while the accumulation of all other photosynthetic complexes per leaf area is less affected. As the disturbed accumulation of LHC proteins could be either attributable to a defect in LHC biogenesis itself or to a bottleneck in chlorophyll biosynthesis, chlorophyll synthesis rates and chlorophyll synthesis intermediates were measured. LCAA antisense plants accumulate magnesium (Mg) protoporphyrin monomethylester and contain reduced protochlorophyllide levels and a reduced content of CHL27, a subunit of the Mg protoporphyrin monomethylester cyclase. Bimolecular fluorescence complementation assays confirm a direct interaction between LCAA and CHL27. 5-Aminolevulinic acid synthesis rates are increased and correlate with an increased content of glutamyl-transfer RNA reductase. We suggest that LCAA encodes an additional subunit of the Mg protoporphyrin monomethylester cyclase, is required for the stability of CHL27, and contributes to feedback-control of 5-aminolevulinic acid biosynthesis, the rate-limiting step of chlorophyll biosynthesis

Histone peptide microarray screen of chromo and Tudor domains defines new histone lysine methylation interactions

Additional file 6: Figure S4. CHD7 chromodomain histone peptide microarray. A) Representative array images of CHD7 chromodomain showing peptide binding indicated in red (right panel). The peptide tracer is shown in green (left panel). Positive antibody controls are outlined in white. B) Scatter plot of the relative binding of CHD7 chromodomain from two independent peptide arrays. All modified and unmodified H4 (1–23) peptides are shown in red. All other peptides are shown in black. C) Relative binding to the indicated histone peptides from one representative array. Data were normalized to the most intense binding and the average and standard deviation of triplicate spots is shown

Reactive and Regulative Temperament in Youths: Psychometric Evaluation of the Early Adolescent Temperament Questionnaire-Revised

The present study examined the psychometric properties of the self-report version of the Early Adolescent Temperament Questionnaire-Revised (EATQ-R), which is a scale for measuring reactive and regulative temperament traits, in a large sample of children and adolescents (N = 1,055). The results indicated that the internal consistency was acceptable for most EATQ-R temperament scales. Further, principal components analysis of the instrument yielded a structure with nine components, which generally reflected the temperament scales of the EATQ-R. The test–retest stability of the scale was moderate to good, whereas the parent–child agreement was rather low. Finally, the scale correlated in a theoretically meaningful way with children’s self-reports of personality and psychopathology. It can be concluded that the EATQ-R is a useful scale for measuring aspects of reactive and regulative temperament in children and adolescents, although there is certainly room for improving the instrument

Mindfulness-based interventions for young offenders: a scoping review

Youth offending is a problem worldwide. Young people in the criminal justice system have frequently experienced adverse childhood circumstances, mental health problems, difficulties regulating emotions and poor quality of life. Mindfulness-based interventions can help people manage problems resulting from these experiences, but their usefulness for youth offending populations is not clear. This review evaluated existing evidence for mindfulness-based interventions among such populations. To be included, each study used an intervention with at least one of the three core components of mindfulness-based stress reduction (breath awareness, body awareness, mindful movement) that was delivered to young people in prison or community rehabilitation programs. No restrictions were placed on methods used. Thirteen studies were included: three randomized controlled trials, one controlled trial, three pre-post study designs, three mixed-methods approaches and three qualitative studies. Pooled numbers (n = 842) comprised 99% males aged between 14 and 23. Interventions varied so it was not possible to identify an optimal approach in terms of content, dose or intensity. Studies found some improvement in various measures of mental health, self-regulation, problematic behaviour, substance use, quality of life and criminal propensity. In those studies measuring mindfulness, changes did not reach statistical significance. Qualitative studies reported participants feeling less stressed, better able to concentrate, manage emotions and behaviour, improved social skills and that the interventions were acceptable. Generally low study quality limits the generalizability of these findings. Greater clarity on intervention components and robust mixed-methods evaluation would improve clarity of reporting and better guide future youth offending prevention programs

Civilian casualties and public support for military action: Experimental evidence

In contrast to the expansive literature on military casualties and support for war, we know very little about public reactions to foreign civilian casualties. This article, based on representative sample surveys in the US and Britain, reports four survey experiments weaving information about civilian casualties into vignettes about Western military action. These produce consistent evidence of civilian casualty aversion: where death tolls were higher, support for force was invariably and significantly lower. Casualty effects were moderate in size but robust across our two cases and across different scenarios. They were also strikingly resistant to moderation by other factors manipulated in the experiments, such as the framing of casualties or their religious affiliation. The importance of numbers over even strongly humanizing frames points towards a utilitarian rather than a social-psychological model of casualty aversion. Either way, civilian casualties deserve a more prominent place in the literature on public support for war

Defending the genome from the enemy within:mechanisms of retrotransposon suppression in the mouse germline

The viability of any species requires that the genome is kept stable as it is transmitted from generation to generation by the germ cells. One of the challenges to transgenerational genome stability is the potential mutagenic activity of transposable genetic elements, particularly retrotransposons. There are many different types of retrotransposon in mammalian genomes, and these target different points in germline development to amplify and integrate into new genomic locations. Germ cells, and their pluripotent developmental precursors, have evolved a variety of genome defence mechanisms that suppress retrotransposon activity and maintain genome stability across the generations. Here, we review recent advances in understanding how retrotransposon activity is suppressed in the mammalian germline, how genes involved in germline genome defence mechanisms are regulated, and the consequences of mutating these genome defence genes for the developing germline

Children’s Moral Emotion Attribution in the Happy Victimizer Task: The Role of Response Format

Previous research in the happy victimizer tradition indicated that preschool and early elementary-school children attribute positive emotions to the violator of a moral norm, whereas older children attribute negative moral emotions. Cognitive and motivational processes have been suggested as underlying this developmental shift. The current research investigated whether making the happy victimizer task less cognitively demanding, by providing children with alternative response formats, would increase children’s attribution of moral emotions and moral motivation. In Study 1, 93 4- to 7-year-old British children responded to the happy victimizer questions either in a normal condition (where they spontaneously pointed with a finger), a wait condition (where they had to wait before giving their answers), or an arrow condition (where they had to point with a paper arrow). In Study 2, 40 Spanish 4-year-old children responded in the happy victimizer task either in a normal or a wait condition. In both studies, participants’ attribution of moral emotions and moral motivation was significantly higher in the conditions with alternative response formats (wait, arrow) than in the normal condition. The role of cognitive abilities for emotion attribution in the happy victimizer task is discussed