Author Correction: Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals.

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

Global and specific responses of the histone acetylome to systematic perturbation.

Regulation of histone acetylation is fundamental to the utilization of eukaryotic genomes in chromatin. Aberrant acetylation contributes to disease and can be clinically combated by inhibiting the responsible enzymes. Our knowledge of the histone acetylation system is patchy because we so far lacked the methodology to describe acetylation patterns and their genesis by integrated enzyme activities. We devised a generally applicable, mass spectrometry-based strategy to precisely and accurately quantify combinatorial modification motifs. This was applied to generate a comprehensive inventory of acetylation motifs on histones H3 and H4 in Drosophila cells. Systematic depletion of known or suspected acetyltransferases and deacetylases revealed specific alterations of histone acetylation signatures, established enzyme-substrate relationships, and unveiled an extensive crosstalk between neighboring modifications. Unexpectedly, overall histone acetylation levels remained remarkably constant upon depletion of individual acetyltransferases. Conceivably, the acetylation level is adjusted to maintain the global charge neutralization of chromatin and the stability of nuclei.

Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals.

The functionality of stem cells declines during ageing, and this decline contributes to ageing-associated impairments in tissue regeneration and function. Alterations in developmental pathways have been associated with declines in stem-cell function during ageing, but the nature of this process remains poorly understood. Hox genes are key regulators of stem cells and tissue patterning during embryogenesis with an unknown role in ageing. Here we show that the epigenetic stress response in muscle stem cells (also known as satellite cells) differs between aged and young mice. The alteration includes aberrant global and site-specific induction of active chromatin marks in activated satellite cells from aged mice, resulting in the specific induction of Hoxa9 but not other Hox genes. Hoxa9 in turn activates several developmental pathways and represents a decisive factor that separates satellite cell gene expression in aged mice from that in young mice. The activated pathways include most of the currently known inhibitors of satellite cell function in ageing muscle, including Wnt, TGFß, JAK/STAT and senescence signalling. Inhibition of aberrant chromatin activation or deletion of Hoxa9 improves satellite cell function and muscle regeneration in aged mice, whereas overexpression of Hoxa9 mimics ageing-associated defects in satellite cells from young mice, which can be rescued by the inhibition of Hoxa9-targeted developmental pathways. Together, these data delineate an altered epigenetic stress response in activated satellite cells from aged mice, which limits satellite cell function and muscle regeneration by Hoxa9-dependent activation of developmental pathways.

The Metabolic Impact on Histone Acetylation and Transcription in Ageing.

Loss of cellular homeostasis during aging results in altered tissue functions and leads to a general decline in fitness and, ultimately, death. As animals age, the control of gene expression, which is orchestrated by multiple epigenetic factors, degenerates. In parallel, metabolic activity and mitochondrial protein acetylation levels also change. These two hallmarks of aging are effectively linked through the accumulating evidence that histone acetylation patterns are susceptible to alterations in key metabolites such as acetyl-CoA and NAD(+), allowing chromatin to function as a sensor of cellular metabolism. In this review we discuss experimental data supporting these connections and provide a context for the possible medical and physiological relevance.

Life span extension by targeting a link between metabolism and histone acetylation in Drosophila.

Old age is associated with a progressive decline of mitochondrial function and changes in nuclear chromatin. However, little is known about how metabolic activity and epigenetic modifications change as organisms reach their midlife. Here, we assessed how cellular metabolism and protein acetylation change during early aging in Drosophila melanogaster. Contrary to common assumptions, we find that flies increase oxygen consumption and become less sensitive to histone deacetylase inhibitors as they reach midlife. Further, midlife flies show changes in the metabolome, elevated acetyl-CoA levels, alterations in protein-notably histone-acetylation, as well as associated transcriptome changes. Based on these observations, we decreased the activity of the acetyl-CoA-synthesizing enzyme ATP citrate lyase (ATPCL) or the levels of the histone H4 K12-specific acetyltransferase Chameau. We find that these targeted interventions both alleviate the observed aging-associated changes and promote longevity. Our findings reveal a pathway that couples changes of intermediate metabolism during aging with the chromatin-mediated regulation of transcription and changes in the activity of associated enzymes that modulate organismal life span.

The activation potential of MOF is constrained for dosage compensation.

The H4K16 acetyltransferase MOF plays a crucial role in dosage compensation in Drosophila but has additional, global functions. We compared the molecular context and effect of MOF in male and female flies, combining chromosome-wide mapping and transcriptome studies with analyses of defined reporter loci in transgenic flies. MOF distributes dynamically between two complexes, the dosage compensation complex and a complex containing MBD-R2, a global facilitator of transcription. These different targeting principles define the distribution of MOF between the X chromosome and autosomes and at transcription units with 5' or 3' enrichment. The male X chromosome differs from all other chromosomes in that H4K16 acetylation levels do not correlate with transcription output. The reconstitution of this phenomenon at a model locus revealed that the activation potential of MOF is constrained in male cells in the context of the DCC to arrive at the 2-fold activation of transcription characteristic of dosage compensation.

Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq.

Transcriptional enhancement of X-linked genes to compensate for the sex chromosome monosomy in Drosophila males is brought about by a ribonucleoprotein assembly called Male-Specific-Lethal or Dosage Compensation Complex (MSL-DCC). This machinery is formed in male flies and specifically associates with active genes on the X chromosome. After assembly at dedicated high-affinity "entry" sites (HAS) on the X chromosome, the complex distributes to the nearby active chromatin. High-resolution, genome-wide mapping of the MSL-DCC subunits by chromatin immunoprecipitation (ChIP) on oligonucleotide tiling arrays suggests a rather homogenous spreading of the intact complex onto transcribed chromatin. Coupling ChIP to deep sequencing (ChIP-seq) promises to map the chromosomal interactions of the DCC with improved resolution. We present ChIP-seq binding profiles for all complex subunits, including the first description of the RNA helicase MLE binding pattern. Exploiting the preferential representation of direct chromatin contacts upon high-energy shearing, we report a surprising functional and topological separation of MSL protein contacts at three classes of chromosomal binding sites. Furthermore, precise determination of DNA fragment lengths by paired-end ChIP-seq allows decrypting of the local complex architecture. Primary contacts of MSL-2 and MLE define HAS for the DCC. In contrast, association of the DCC with actively transcribed gene bodies is mediated by MSL-3 binding to nucleosomes. We identify robust MSL-1/MOF binding at a fraction of active promoters genome-wide. Correlation analyses suggest that this association reflects a function outside dosage compensation. Our comprehensive analysis provides a new level of information on different interaction modes of a multiprotein complex at distinct regions within the genome.

The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset.

The MOF (males absent on the first)-containing NSL (non-specific lethal) complex binds to a subset of active promoters in Drosophila melanogaster and is thought to contribute to proper gene expression. The determinants that target NSL to specific promoters and the circumstances in which the complex engages in regulating transcription are currently unknown. Here, we show that the NSL complex primarily targets active promoters and in particular housekeeping genes, at which it colocalizes with the chromatin remodeler NURF (nucleosome remodeling factor) and the histone methyltransferase Trithorax. However, only a subset of housekeeping genes associated with NSL are actually activated by it. Our analyses reveal that these NSL-activated promoters are depleted of certain insulator binding proteins and are enriched for the core promoter motif 'Ohler 5'. Based on these results, it is possible to predict whether the NSL complex is likely to regulate a particular promoter. We conclude that the regulatory capacity of the NSL complex is highly context-dependent. Activation by the NSL complex requires a particular promoter architecture defined by combinations of chromatin regulators and core promoter motifs.

Enzymatic nucleosome acetylation selectively affects activity of histone methyltransferases in vitro.

Posttranslational modification of histones plays a critical role in regulation of gene expression. These modifications include methylation and acetylation that work in combination to establish transcriptionally active or repressive chromatin states. Histone methyltransferases (HMTs) often have variable levels of activity in vitro depending on the form of substrate used. For example, certain HMTs prefer nucleosomes extracted from human or chicken cells as substrate compared to recombinant nucleosomes reconstituted from bacterially produced histones. We considered that pre-existing histone modifications in the extracted nucleosomes can affect the efficiency of catalysis by HMTs, suggesting functional cross-talk between histone-modifying enzymes within a complex network of interdependent activities. Here we systematically investigated the effect of nucleosome acetylation by EP300, GCN5L2 (KAT2A) and MYST1 (MOF) on histone 3 lysine 4 (H3K4), H3K9 and H4K20 methylation of nucleosomes by nine HMTs (MLL1, MLL3, SET1B, G9a, SETDB1, SUV39H1, SUV39H2, SUV420H1 and SUV420H2) in vitro. Our full kinetic characterization data indicate that site-specific acetylation of nucleosomal histones by specific acetyltransferases can create nucleosomes that are better substrates for specific HMTs. This includes significant increases in catalytic efficiencies of SETDB1, G9a and SUV420H2 after nucleosome acetylation in vitro.

ChromID identifies the protein interactome at chromatin marks.

Chromatin modifications regulate genome function by recruiting proteins to the genome. However, the protein composition at distinct chromatin modifications has yet to be fully characterized. In this study, we used natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for DNA methylation and histone tri-methylation at H3K4, H3K9 and H3K27 residues. We first demonstrated their utility as selective chromatin binders in living cells by stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localization, genomic distribution and histone-modification-binding preference. By fusing eCRs to the biotin ligase BASU, we established ChromID, a method for identifying the chromatin-dependent protein interactome on the basis of proximity biotinylation, and applied it to distinct chromatin modifications in mouse stem cells. Using a synthetic dual-modification reader, we also uncovered the protein composition at bivalently modified promoters marked by H3K4me3 and H3K27me3. These results highlight the ability of ChromID to obtain a detailed view of protein interaction networks on chromatin.

Publisher Correction: ChromID identifies the protein interactome at chromatin marks.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A Proteomic Connectivity Map.

Litichevskiy et al. describe the first large-scale use of targeted mass spectrometry to systematically investigate phospho-protein and histone modification networks across a panel of cell lines subjected to drug perturbations.

Anxiety modulation by the heart? Aerobic exercise and atrial natriuretic peptide.

Exercise has an anxiolytic activity and it increases the concentrations of atrial natriuretic peptide (ANP). Because ANP has an anxiolytic activity, this hormone might contribute to the anxiolytic effects of aerobic exercise. Cholecystokinin-tetrapeptide (CCK-4)-induced panic attacks were studied in 10 healthy subjects after "quiet rest" or 30 min of aerobic exercise. Plasma ANP concentrations were measured before and after exercise or quiet rest using a commercial IRMA kit. Compared to quiet rest, CCK-4-induced anxiety was reduced and plasma ANP concentrations were increased by prior exercise. This anxiolytic activity of exercise was correlated with the increase in plasma ANP concentrations. Our results suggest that besides other mechanisms, ANP might be a physiologically relevant humoral link between the heart and anxiety-related behavior contributing to the acute anxiolytic effects of exercise.

Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions.

Post-translational modifications (PTMs) are pivotal to cellular information processing, but how combinatorial PTM patterns ("motifs") are set remains elusive. We develop a computational framework, which we provide as open source code, to investigate the design principles generating the combinatorial acetylation patterns on histone H4 in Drosophila melanogaster. We find that models assuming purely unspecific or lysine site-specific acetylation rates were insufficient to explain the experimentally determined motif abundances. Rather, these abundances were best described by an ensemble of models with acetylation rates that were specific to motifs. The model ensemble converged upon four acetylation pathways; we validated three of these using independent data from a systematic enzyme depletion study. Our findings suggest that histone acetylation patterns originate through specific pathways involving motif-specific acetylation activity.

The acute antipanic activity of aerobic exercise.

OBJECTIVE: Regular physical activity is anxiolytic for both healthy subjects and patients with panic disorder. However, the acute antipanic activity of exercise has not yet been studied systematically. METHOD: The effects of quiet rest or aerobic treadmill exercise (30 minutes at 70% of maximum oxygen consumption) on cholecystokinin tetrapeptide (CCK-4)-induced panic attacks were studied in a crossover design in 15 healthy subjects. The effects were measured with the Acute Panic Inventory. RESULTS: Panic attacks occurred in 12 subjects after rest but in only six subjects after exercise. In both conditions, CCK-4 administration was followed by a significant increase in Acute Panic Inventory scores; however, prior exercise resulted in significantly lower scores than quiet rest. CONCLUSIONS: Aerobic exercise has an acute antipanic activity in healthy subjects. If the authors' results are confirmed in patients, the optimum intensity and duration of acute exercise for achieving antipanic effects will have to be characterized.

Low-latency system for evaluation of image-enhancement-algorithms on patients using subretinal implants.

In this paper, a real-time system consisting of a camera device, computational unit and head mounted display, adjusted to the needs of patients using subretinal implants, is presented. Retinal implants demonstrated to partially restore useful vision to patients suffering from hereditary retinal degeneration diseases. Even though various implant-mediated visual perceptions in daily-life were reported, perceived vision could be enhanced using algorithms well known from image-processing. Due to strict area limitations subretinal implants can only cover well-chosen and carefully examined functionality within the silicon device. To gain flexibility in testing different kinds of image enhancement algorithms, a software solution allowing quick changes is desired. The system presented here, allows recording and displaying reality on a head mounted display with low latency, while maintaining true to scale representation. Additionally different types of pixel-based image-enhancement-algorithms can be applied on the captured content to modify the perceived image.

Dosage compensation and the global re-balancing of aneuploid genomes.

Diploid genomes are exquisitely balanced systems of gene expression. The dosage-compensation systems that evolved along with monosomic sex chromosomes exemplify the intricacies of compensating for differences in gene copy number by transcriptional regulation.

Blockade of TTX-resistant and TTX-sensitive Na+ currents in cultured dorsal root ganglion neurons by fomocaine and the fomocaine derivative Oe 9000.

Fomocaine and its new derivative Oe 9000 are local anesthetics in which the inner aromatic moiety carries a phenoxymethyl substituent and is linked to the tertiary amine by an alkylene chain, rendering these compounds considerably lipophilic and increasing their chemical and metabolic stability. Although fomocaine was used for surface anesthesia, the presumed mode of action of fomocaine and Oe 9000, the blockade of voltage-gated Na(+) currents in neurons, has not been investigated. In the present experiments we used the whole-cell mode of the patch-clamp technique and studied the effect of both drugs on voltage-gated Na(+) currents in isolated and cultured dorsal root ganglion (DRG) neurons from adult rats. Both drugs reversibly reduced slowly activating and inactivating tetrodotoxin-resistant (TTX-R) Na(+) currents as well as rapidly activating and inactivating TTX-sensitive (TTX-S) Na(+) currents at low micromolar concentrations. For the reduction of TTX-R Na(+) currents the IC(50) of fomocaine was 10.3µM, and the IC(50) for the more hydrophilic Oe 9000 was 4.5µM. These IC(50) values are more than one order of magnitude lower than the corresponding IC(50) of other local anesthetics such as lidocaine. Similar as for other local anesthetics, the effects showed a frequency dependence indicating that the compounds preferentially bind to the open and/or inactivated state of the channel. These data establish for the first time the functional suppression of TTX-R and TTX-S Na(+) currents by fomocaine and Oe 9000 in neurons. They support the further research into the use of Oe 9000 as a novel local anesthetic.

The acute antipanic and anxiolytic activity of aerobic exercise in patients with panic disorder and healthy control subjects.

Regular physical activity is anxiolytic in both healthy subjects and patients with panic disorder. In contrast, acute exercise may induce acute panic attacks or increase subjective anxiety in patients with panic disorder more than in other people. The effects of quiet rest or an aerobic treadmill exercise (30 min at an intensity of 70% of the maximal oxygen uptake, VO2max) on cholecystokinin tetrapeptide (CCK-4) induced panic attacks were studied in a crossover design in 12 patients with panic disorder and 12 matched healthy subjects. The effects of CCK-4 (25 microg in patients and 50 microg in control subjects) were measured with the Acute Panic Inventory (API) score, comparing panic attack frequencies, total score, and subscores for anxiety and somatic symptoms. CCK-4-induced panic attacks were less frequent after prior exercise: they occurred in 15 (62.5%) subjects after rest (9 patients and 6 control subjects), but only 5 (20.8%) subjects after exercise (4 patients and 1 control subject). In both conditions, CCK-4 administration induced a significant increase in the total API score and the anxiety and somatic symptoms subsores. However, compared to prior rest, exercise resulted in a significantly reduced CCK-4-induced increase of the total API score and the anxiety subscore. In patients with panic disorder exercise increased the total API score and the somatic symptoms subscale but not the anxiety subscore. Patients with panic disorder showed increased somatic but not anxiety symptoms after an acute bout of exercise. Severity of CCK-4-induced panic and anxiety, on the other hand was reduced by exercise. These findings suggest that in addition to exercise training an acute bout of exercise may be used to reduce anxiety and panic attack frequency and intensity in panic disorder patients.

Efeito do manejo do solo e da matéria orgânica solúvel em água quente na estabilidade de agregados de um latossolo argiloso / Effect of orchard soil management and hot water soluble organic matter on aggregate stability of a clayey oxisol

Estudou-se a estabilidade de agregados de um latossolo vermelho distroférrico submetido às seguintes situações: vegetação nativa de floresta; culturas anuais por 20 anos; pomar cítrico manejado com cobertura verde permanente com a leguminosa Arachis prostrata Bong. ex Benth.; pomar com cobertura de vegetação espontânea (predomínio de gramíneas) controlada com roçadora (3-4 vezes no período de chuvas) e uma gradagem a disco ao ano (no período seco); pomar sem vegetação por meio de capina manual. Os tratamentos no pomar foram mantidos durante 9 anos. A estabilidade de agregados foi determinada em amostras submetidas ou não a tratamento para retirada da matéria orgânica solúvel em água quente. O solo sob vegetação de floresta teve maior quantidade de agregados estáveis, seguido do solo sob pomar com cobertura permanente de leguminosas ou gramíneas. A estabilidade dos agregados não foi afetada pela extração do carbono solúvel em água quente, embora tenha havido correlação positiva entre o teor de carbono solúvel em água quente e a agregação do solo.

It was studied the aggregate stability of an oxisol maintained with vegetation of native forest; annual crops for 20 years; a citrus orchard mantained during 9 years with permanent ground cover of Arachis prostrata Bong. Ex Benth.; or permanent spontaneous vegetation (mainly gramineous) controlled by mowing (3-4 times in the rain period of rains) and tillage (once a year in the dry period); or bare soil maintained by manual weeding. The aggregate stability was determined in samples submitted or not to treatment to remove hot water soluble organic matter. The forest vegetation provided larger stability followed by the orchard submitted to the permanent covering with leguminous or gramineous plants. Extraction of hot-water soluble carbon did not cause significant differences in aggregate stability, although there has been a significant correlation between hot water soluble carbon and soil aggregation.