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Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a key technique for mapping the distribution of histone posttranslational modifications (PTMs) and chromatin-associated factors across genomes. There is a perceived challenge to define a quantitative scale for ChIP-seq data, and as such, several approaches making use of exogenous additives, or 'spike-ins', have recently been developed. Herein, we report on the development of a quantitative, physical model defining ChIP-seq. The quantitative scale on which ChIP-seq results should be compared emerges from the model. To test the model and demonstrate the quantitative scale, we examine the impacts of an EZH2 inhibitor through the lens of ChIP-seq. We report a significant increase in immunoprecipitation of presumed off-target histone PTMs after inhibitor treatment, a trend predicted by the model but contrary to spike-in based indications. Our work also identifies a sensitivity issue in spike-in normalization that has not been considered in the literature, placing limitations on its utility and trustworthiness. We call our new approach the sans-spike-in method for quantitative ChIP-sequencing (siQ-ChIP).  A number of changes in community practice of ChIP-seq, data reporting, and analysis are motivated by this work.

Aging is an intricate process that is characterized by multiple hallmarks including stem cell exhaustion, genome instability, epigenome alteration, impaired proteostasis, and cellular senescence. While each of these is detrimental at the cellular level, it remains unclear how they are interconnected to cause systemic organ deterioration. Here we show that abrogating Brap, a BRCA1 associated protein, results in cellular senescence with persistent DNA double-strand breaks and elevation of histone H2A mono- and poly-ubiquitination (H2Aub). The high H2Aub initiates proteasome-dependent histone proteolysis, leading to global epigenetic alteration, ubiquitinated protein accumulation, and senescence reinforcement. When these defects occur in mice carrying Brap deletions in cerebral cortical neural progenitors or postnatal neurons, they accelerate brain aging, induce neurodegeneration, and shorten lifespan. As we show H2Aub is also increased in human brain tissues of Alzheimer disease, these data together suggest that chromatin aberrations mediated by H2Aub act as a nexus of multiple aging hallmarks.

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