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Behavioural experiences activate the FOS transcription factor in sparse populations of neurons that are critical for encoding and recalling specific events 1 – 3 . However, there is limited understanding of the mechanisms by which experience drives circuit reorganization to establish a network of Fos -activated cells. It is also not known whether FOS is required in this process beyond serving as a marker of recent neural activity and, if so, which of its many gene targets underlie circuit reorganization. Here we demonstrate that when mice engage in spatial exploration of novel environments, perisomatic inhibition of Fos -activated hippocampal CA1 pyramidal neurons by parvalbumin-expressing interneurons is enhanced, whereas perisomatic inhibition by cholecystokinin-expressing interneurons is weakened. This bidirectional modulation of inhibition is abolished when the function of the FOS transcription factor complex is disrupted. Single-cell RNA-sequencing, ribosome-associated mRNA profiling and chromatin analyses, combined with electrophysiology, reveal that FOS activates the transcription of Scg2 , a gene that encodes multiple distinct neuropeptides, to coordinate these changes in inhibition. As parvalbumin- and cholecystokinin-expressing interneurons mediate distinct features of pyramidal cell activity 4 – 6 , the SCG2-dependent reorganization of inhibitory synaptic input might be predicted to affect network function in vivo. Consistent with this prediction, hippocampal gamma rhythms and pyramidal cell coupling to theta phase are significantly altered in the absence of Scg2 . These findings reveal an instructive role for FOS and SCG2 in establishing a network of Fos -activated neurons via the rewiring of local inhibition to form a selectively modulated state. The opposing plasticity mechanisms acting on distinct inhibitory pathways may support the consolidation of memories over time. Novel experiences in mice lead to opposing effects on inhibition of Fos -activated hippocampal CA1 pyramidal neurons by parvalbumin- and cholecystokinin-expressing interneurons, revealing the roles of FOS and SCG2 in neural plasticity and consolidation of memories.

Neuronal activity is crucial for adaptive circuit remodelling but poses an inherent risk to the stability of the genome across the long lifespan of postmitotic neurons 1 – 5 . Whether neurons have acquired specialized genome protection mechanisms that enable them to withstand decades of potentially damaging stimuli during periods of heightened activity is unknown. Here we identify an activity-dependent DNA repair mechanism in which a new form of the NuA4–TIP60 chromatin modifier assembles in activated neurons around the inducible, neuronal-specific transcription factor NPAS4. We purify this complex from the brain and demonstrate its functions in eliciting activity-dependent changes to neuronal transcriptomes and circuitry. By characterizing the landscape of activity-induced DNA double-strand breaks in the brain, we show that NPAS4–NuA4 binds to recurrently damaged regulatory elements and recruits additional DNA repair machinery to stimulate their repair. Gene regulatory elements bound by NPAS4–NuA4 are partially protected against age-dependent accumulation of somatic mutations. Impaired NPAS4–NuA4 signalling leads to a cascade of cellular defects, including dysregulated activity-dependent transcriptional responses, loss of control over neuronal inhibition and genome instability, which all culminate to reduce organismal lifespan. In addition, mutations in several components of the NuA4 complex are reported to lead to neurodevelopmental and autism spectrum disorders. Together, these findings identify a neuronal-specific complex that couples neuronal activity directly to genome preservation, the disruption of which may contribute to developmental disorders, neurodegeneration and ageing. A neuron-specific activity-dependent DNA repair mechanism is identified, the impairment of which may lead to neurodevelopmental disorders, neurodegeneration and ageing.

Histone modifications regulate transcription by RNA polymerase II and maintain a balance between active and repressed chromatin states. The conserved Paf1 complex (Paf1C) promotes specific histone modifications during transcription elongation, but the mechanisms by which it facilitates these marks are undefined. We previously identified a 90-amino acid region within the Rtf1 subunit of Paf1C that is necessary for Paf1C-dependent histone modifications in Saccharomyces cerevisiae . Here we show that this histone modification domain (HMD), when expressed as the only source of Rtf1, can promote H3 K4 and K79 methylation and H2B K123 ubiquitylation in yeast. The HMD can restore histone modifications in rtf1Δ cells whether or not it is directed to DNA by a fusion to a DNA binding domain. The HMD can facilitate histone modifications independently of other Paf1C subunits and does not bypass the requirement for Rad6–Bre1. The isolated HMD localizes to chromatin, and this interaction requires residues important for histone modification. When expressed outside the context of full-length Rtf1, the HMD associates with and causes Paf1C-dependent histone modifications to appear at transcriptionally inactive loci, suggesting that its function has become deregulated. Finally, the Rtf1 HMDs from other species can function in yeast. Our findings suggest a direct and conserved role for Paf1C in coupling histone modifications to transcription elongation.

The conserved eukaryotic Paf1 complex regulates RNA synthesis by RNA polymerase II at multiple levels, including transcript elongation, transcript termination, and chromatin modifications. To better understand the contributions of the Paf1 complex to transcriptional regulation, we generated mutations that alter conserved residues within the Rtf1 subunit of the Saccharomyces cerevisiae Paf1 complex. Importantly, single amino acid substitutions within a region of Rtf1 that is conserved from yeast to humans, which we termed the histone modification domain, resulted in the loss of histone H2B ubiquitylation and impaired histone H3 methylation. Phenotypic analysis of these mutations revealed additional defects in telomeric silencing, transcription elongation, and prevention of cryptic initiation. We also demonstrated that amino acid substitutions within the Rtf1 histone modification domain disrupt 3′-end formation of snoRNA transcripts and identify a previously uncharacterized regulatory role for the histone H2B K123 ubiquitylation mark in this process. Cumulatively, our results reveal functionally important residues in Rtf1, better define the roles of Rtf1 in transcription and histone modification, and provide strong genetic support for the participation of histone modification marks in the termination of noncoding RNAs.

The ambitious goals of precision cosmology with wide-field optical surveys such as the Dark Energy Survey (DES) and the Large Synoptic Survey Telescope (LSST) demand precision CCD astronomy as their foundation. This in turn requires an understanding of previously uncharacterized sources of systematic error in CCD sensors, many of which manifest themselves as static effective variations in pixel area. Such variation renders a critical assumption behind the traditional procedure of flat fielding-that a sensor's pixels comprise a uniform grid-invalid. In this work, we present a method to infer a curl-free model of a sensor's underlying pixel grid from flat-field images, incorporating the superposition of all electrostatic sensor effects-both known and unknown-present in flat-field data. We use these pixel grid models to estimate the overall impact of sensor systematics on photometry, astrometry, and PSF shape measurements in a representative sensor from the Dark Energy Camera (DECam) and a prototype LSST sensor. Applying the method to DECam data recovers known significant sensor effects for which corrections are currently being developed within DES. For an LSST prototype CCD with pixel-response non-uniformity (PRNU) of 0.4%, we find the impact of \"improper\" flat fielding on these observables is negligible in nominal .7″ seeing conditions. These errors scale linearly with the PRNU, so for future LSST production sensors, which may have larger PRNU, our method provides a way to assess whether pixel-level calibration beyond flat fielding will be required.

The Iowa Pore Index (IPI) test has been useful in prediction of freezing-and-thawing damage susceptibility of aggregate used in concrete pavements. However, the index is based on larger top size gradations that have been used in the past. This study was performed to identify size corrections that would allow aggregate gradations of smaller nominal maximum sizes, other than the standard 1/2 to 3/4 in. (12.5 to 19 mm) fraction, to be used in the index test method. In addition to the size corrections, several modifications to the method were developed to reduce variability in the test, and material re-testability was shown to be feasible. A new method of additional data collection from the IPI test was developed that allows for the measurement of water that is retained in and expelled from the aggregate after depressurization. These data have shown to have a better correlation with freezing-andthawing testing data than IPI.

The ambitious goals of precision cosmology with wide-field optical surveys such as the Dark Energy Survey (DES) and the Large Synoptic Survey Telescope (LSST) demand precision CCD astronomy as their foundation. This in turn requires an understanding of previously uncharacterized sources of systematic error in CCD sensors, many of which manifest themselves as static effective variations in pixel area. Such variation renders a critical assumption behind the traditional procedure of flat fielding—that a sensor’s pixels comprise a uniform grid—invalid. In this work, we present a method to infer a curl-free model of a sensor’s underlying pixel grid from flat-field images, incorporating the superposition of all electrostatic sensor effects—both known and unknown—present in flat-field data. We use these pixel grid models to estimate the overall impact of sensor systematics on photometry, astrometry, and PSF shape measurements in a representative sensor from the Dark Energy Camera (DECam) and a prototype LSST sensor. Applying the method to DECam data recovers known significant sensor effects for which corrections are currently being developed within DES. For an LSST prototype CCD with pixel-response non-uniformity (PRNU) of 0.4%, we find the impact of “improper” flat fielding on these observables is negligible in nominal .7″ seeing conditions. These errors scale linearly with the PRNU, so for future LSST production sensors, which may have larger PRNU, our method provides a way to assess whether pixel-level calibration beyond flat fielding will be required.

The Iowa Pore Index (IPI) test has been useful in prediction of freezing-and-thawing damage susceptibility of aggregate used in concrete pavements. However, the index is based on larger top size gradations that have been used in the past. This study was performed to identify size corrections that would allow aggregate gradations of smaller nominal maximum sizes, other than the standard 1/2 to 3/4 in. (12.5 to 19 mm) fraction, to be used in the index test method. In addition to the size corrections, several modifications to the method were developed to reduce variability in the test, and material re-testability was shown to be feasible. A new method of additional data collection from the IPI test was developed that allows for the measurement of water that is retained in and expelled from the aggregate after depressurization. These data have shown to have a better correlation with freezing-andthawing testing data than IPI. Keywords: aggregate; durability; freezing-and-thawing resistance.

Post-translational modifications of histone tails alter chromatin accessibility to regulate gene expression. Some viruses exploit the importance of histone modifications by expressing histone mimetic proteins that contain histone-like sequences to sequester complexes that recognize modified histones. Here we identify an evolutionarily conserved and ubiquitously expressed, endogenous mammalian protein Nucleolar protein 16 (NOP16) that functions as a H3K27 mimic. NOP16 binds to EED in the H3K27 trimethylation PRC2 complex and to the H3K27 demethylase JMJD3. NOP16 knockout selectively globally increases H3K27me3, a heterochromatin mark, without altering methylation of H3K4, H3K9, or H3K36 or acetylation of H3K27. NOP16 is overexpressed and linked to poor prognosis in breast cancer. Depletion of NOP16 in breast cancer cell lines causes cell cycle arrest, decreases cell proliferation and selectively decreases expression of E2F target genes and of genes involved in cell cycle, growth and apoptosis. Conversely, ectopic NOP16 expression in triple negative breast cancer cell lines increases cell proliferation, cell migration and invasivity and tumor growth , while NOP16 knockout or knockdown has the opposite effect. Thus, NOP16 is a histone mimic that competes with Histone H3 for H3K27 methylation and demethylation. When it is overexpressed in cancer, it derepresses genes that promote cell cycle progression to augment breast cancer growth.

Mammalian development requires effective mechanisms to repress genes whose expression would generate inappropriately specified cells. The Polycomb Repressive Complex 1 (PRC1) family complexes are central to maintaining this repression1. These include a set of canonical PRC1 complexes that each contain four core proteins, including one from the CBX family. These complexes have previously been shown to reside in membraneless organelles called Polycomb bodies, leading to speculation that canonical PRC1 might be found in a separate phase from the rest of the nucleus2,3. We show here that reconstituted PRC1 readily phase separates into droplets in vitro at low concentrations and physiological salt conditions. This behavior is driven by the CBX2 subunit. Point mutations in an internal domain of CBX2 eliminate phase separation. These same point mutations eliminate the formation of puncta in cells, and have previously been shown to eliminate nucleosome compaction in vitro4 and to generate axial patterning defects in mice5. Thus, a single domain in CBX2 is required for phase separation and nucleosome compaction, a finding that relates these functions to each other and to proper development.