Highlights d SETD5 is an epigenetic driver of pancreatic cancer resistance to MEK1/2 inhibition d SETD5 has no intrinsic methylation activity on histones, including at H3 lysine 36 d A SETD5 co-repressor complex regulates a network of drug resistance pathways d Co-targeting of MEK1/2 and the SETD5 complex results in sustained tumor inhibition

HIV infection often involves the development of AIDS-related dementia complex, a variety of neurologic, neuropsychologic, and neuropathologic impairments. A possible contributor to AIDS-related dementia complex is the HIV envelope glycoprotein gp120, which damages neurons via a complex glutamate receptor-and calcium-dependent cascade. We demonstrate an endocrine modulation of the deleterious effects of gp120 in primary hippocampal and cortical cultures. Specifically, we observe that gp120-induced calcium mobilization and neurotoxicity are exacerbated by glucocorticoids, the adrenal steroids secreted during stress. Importantly, this deleterious synergy can occur between gp120 and synthetic glucocorticoids (such as prednisone or dexamethasone) that are used clinically in high concentrations to treat severe cases of the Pneumocystis carinii pneumonia typical of HIV infection. Conversely, we also observe that estradiol protects neurons from the deleterious actions of gp120, reducing toxicity and calcium mobilization.

Overexpression of bcl-2 protects neurons from numerous necrotic insults, both in vitro and in vivo. While the bulk of such protection is thought to arise from Bcl-2 blocking cytochrome c release from mitochondria, thereby blocking apoptosis, the protein can target other steps in apoptosis, and can protect against necrotic cell death as well. There is evidence that these additional actions may be antioxidant in nature, in that Bcl-2 has been reported to protect against generators of reactive oxygen species (ROS), to increase antioxidant defenses and to decrease levels of ROS and of oxidative damage. Despite this, there are also reports arguing against either the occurrence, or the importance of these antioxidant actions. We have examined these issues in neuron-enriched primary hippocampal cultures, with overexpression of bcl-2 driven by a herpes simplex virus amplicon: (i) Bcl-2 protected strongly against glutamate, whose toxicity is at least partially ROS-dependent. Such protection involved reduction in mitochondrially derived superoxide. Despite that, Bcl-2 had no effect on levels of lipid peroxidation, which is thought to be the primary locus of glutamate-induced oxidative damage; (ii) Bcl-2 was also mildly protective against the pro-oxidant adriamycin. However, it did so without reducing levels of superoxide, hydrogen peroxide or lipid peroxidation; (iii) Bcl-2 protected against permanent anoxia, an insult likely to involve little to no ROS generation. These findings suggest that Bcl-2 can have antioxidant actions that may nonetheless not be central to its protective effects, can protect against an ROS generator without targeting steps specific to oxidative biochemistry, and can protect in the absence of ROS generation. Thus, the antioxidant actions of Bcl-2 are neither necessary nor sufficient to explain its protective actions against these insults in hippocampal neurons.

Nuc-MS characterizes histone modifications and variants directly from intact endogenous nucleosomes. Preserving whole nucleosome particles enables precise interrogation of their protein content, as for H3.3-containing nucleosomes which had 6fold co-enrichment of variant H2A.Z over bulk chromatin. Nuc-MS, validated by ChIPseq, showed co-occurrence of oncogenic H3.3K27M with euchromatic marks (e.g., H4K16ac and >15-fold enrichment of H3K79me2). By capturing the entire epigenetic landscape, Nuc-MS provides a new, quantitative readout of nucleosome-level biology. MainThe post-translational modifications (PTMs) decorating the four core histones in an intact nucleosome encode information for nuclear effectors that trigger defined cellular events critical to health and disease. [1][2][3][4] For decades, affinity reagents, mass spectrometry and proteomics have played key roles in characterizing the many histone isoforms and PTMs involved in epigenetic regulation. [5][6][7] However, the standard practice of relying on digestion 8 and/or denaturation 5 removes the linkage between modifications and their nucleosomes of origin (Fig. 1a, at left). By digesting histone mixtures into small peptides, correlations among PTMs are forfeited, precluding strong assertions about the original composition of the intact histone. Similarly, when a nucleosome population is denatured, information about co-localization of histone isoforms and PTMs within the same nucleosome particle is lost. This inference problem diminishes our understanding of the organization and impact of co-occurring modifications, isoforms and mutations in epigenetics and disease pathogenesis. 9,10

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Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized "codes" that are read by specialized regions (reader domains) in chromatin associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP-histone PTM] specificity, and thus decipher the histone code / guide epigenetic therapies. However, this has largely been done using a reductive approach of isolated reader domains and histone peptides, with the assumption that PTM readout is unaffected by any higher order factors. Here we show that CAP-histone PTM interaction is in fact dependent on nucleosome context. Our results indicate this is due to histone tail accessibility and the associated impact on binding potential of reader domains. We further demonstrate that the in vitro specificity of a tandem reader for PTM-defined nucleosomes is recapitulated in a cellular context. This necessitates we refine the "histone code" concept and interrogate it at the nucleosome level.

Mutations in the PHIP/BRWD2 chromatin regulator cause the human neurodevelopmental disorder Chung-Jansen syndrome, while alterations in PHIP expression are linked to cancer. Precisely how PHIP functions in these contexts is not fully understood. Here we demonstrate that PHIP is a chromatin-associated CRL4 ubiquitin ligase substrate receptor and is required for CRL4 recruitment to chromatin. PHIP binds to chromatin through a trivalent reader domain consisting of a H3K4-methyl binding Tudor domain and two bromodomains (BD1 and BD2). Using semisynthetic nucleosomes with defined histone post-translational modifications, we characterize PHIPs BD1 and BD2 as respective readers of H3K14ac and H4K12ac, and identify human disease-associated mutations in each domain and the intervening linker region that likely disrupt chromatin binding. These findings provide new insight into the biological function of this enigmatic chromatin protein and set the stage for the identification of both upstream chromatin modifiers and downstream targets of PHIP in human disease.

Abbreviations: ammonium acetate (AmAc); background electrolyte (BGE); conductive liquid (CL); capillary zone electrophoresis (CZE); designer Nucleosome (dNuc); extracted ion electropherogram (EIE); endogenous nucleosomes (endoNucs); electrospray ionization (ESI); full-width at half maximum (FWHM); acetic acid (HAc), higher-energy collisional dissociation (HCD), hydrochloric acid (HCl); limit of detection (LOD); methylation equivalents (ME); micrococcal nuclease (MNase); molecular weight cut-off (MWCO); native capillary zone electrophoresis (nCZE); native mass spectrometry (nMS), mononucleosome (Nuc), orbitrap (OT); post-translational modification (PTM); Q Exactive HF MS with Extended Mass Range (QE-EMR); recombinant Nucleosome (rNuc); separation line (SL); signal-to-noise ratio (SNR); total ion electropherogram (TIE); top-down mass spectrometry (TDMS); Ultra High Mass Range (UHMR).