No abstract

Diversified histone modifications (HMs) are essential epigenetic features. They play important roles in fundamental biological processes including transcription, DNA repair and DNA replication. Chromatin regulators (CRs), which are indispensable in epigenetics, can mediate HMs to adjust chromatin structures and functions. With the development of ChIP-Seq technology, there is an opportunity to study CR and HM profiles at the whole-genome scale. However, no specific resource for the integration of CR ChIP-Seq data or CR-HM ChIP-Seq linkage pairs is currently available. Therefore, we constructed the CR Cistrome database, available online at http://compbio.tongji.edu.cn/cr and http://cistrome.org/cr/, to further elucidate CR functions and CR-HM linkages. Within this database, we collected all publicly available ChIP-Seq data on CRs in human and mouse and categorized the data into four cohorts: the reader, writer, eraser and remodeler cohorts, together with curated introductions and ChIP-Seq data analysis results. For the HM readers, writers and erasers, we provided further ChIP-Seq analysis data for the targeted HMs and schematized the relationships between them. We believe CR Cistrome is a valuable resource for the epigenetics community.

Professional association football is a game of talent. The success of a professional club hinges largely on its ability of assembling the best team. Building on a dataset of player transfer records among more than 400 clubs in 24 world-wide top class leagues from 2011 to 2015, this study aims to relate a club’s success to its activities in the player transfer market from a network perspective. We confirm that modern professional football is indeed a money game, in which larger investment spent on the acquisition of talented players generally yields better team performance. However, further investigation shows that professional football clubs can actually play different strategies in surviving or even excelling this game, and the success of strategies is strongly associated to their network properties in the football player transfer network.

Muscle-invasive bladder cancers are characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival. Transcriptionally, FOXA1, GATA3, and PPARG are shown to be essential for luminal subtype-specific gene regulation and subtype switching, while TP63, STAT3, and TFAP2 family members are critical for regulation of basal subtype-specific genes. Despite these advances, the underlying epigenetic mechanisms and 3D chromatin architecture responsible for subtype-specific regulation in bladder cancer remain unknown. Result We determine the genome-wide transcriptome, enhancer landscape, and transcription factor binding profiles of FOXA1 and GATA3 in luminal and basal subtypes of bladder cancer. Furthermore, we report the first-ever mapping of genome-wide chromatin interactions by Hi-C in both bladder cancer cell lines and primary patient tumors. We show that subtype-specific transcription is accompanied by specific open chromatin and epigenomic marks, at least partially driven by distinct transcription factor binding at distal enhancers of luminal and basal bladder cancers. Finally, we identify a novel clinically relevant transcription factor, Neuronal PAS Domain Protein 2 (NPAS2), in luminal bladder cancers that regulates other subtype-specific genes and influences cancer cell proliferation and migration. Conclusion In summary, our work identifies unique epigenomic signatures and 3D genome structures in luminal and basal urinary bladder cancers and suggests a novel link between the circadian transcription factor NPAS2 and a clinical bladder cancer subtype.

Mechanoreceptor cells develop a specialized cytoskeleton that plays structural and sensory roles at the site of mechanotransduction. However, little is known about how the cytoskeleton is organized and formed. Using electron tomography and live-cell imaging, we resolve the 3D structure and dynamics of the microtubule-based cytoskeleton in fly campaniform mechanosensory cilia. Investigating the formation of the cytoskeleton, we find that katanin p60-like 1 (kat-60L1), a neuronal type of microtubule-severing enzyme, serves two functions. First, it amplifies the mass of microtubules to form the dense microtubule arrays inside the sensory cilia. Second, it generates short microtubules that are required to build the nanoscopic cytoskeleton at the mechanotransduction site. Additional analyses further reveal the functional roles of Patronin and other potential factors in the local regulatory network. In all, our results characterize the specialized cytoskeleton in fly external mechanosensory cilia at near-molecular resolution and provide mechanistic insights into how it is formed.

Background Significant sex differences exist in hearing physiology, while few human studies have investigated sex differences in noise-induced hearing loss (NIHL), and the sex bias in previous studies resulted in inadequate female data. The study aims to investigate sex differences in the characteristics of NIHL to provide insight into sex-specific risk factors, prevention strategies and treatment for NIHL. Methods This cross-sectional study included 2280 industrial noise-exposed shipyard workers (1140 males and 1140 females matched for age, job and employment length) in China. Individual noise exposure levels were measured to calculate the cumulative noise exposure (CNE), and an audiometric test was performed by an experienced technician in a soundproof booth. Sex differences in and influencing factors of low-frequency (LFHL) and high-frequency hearing loss (HFHL) were analyzed using logistic regression models stratified by age and CNE. Results At comparable noise exposure levels and ages, the prevalence of HFHL was significantly higher in males (34.4%) than in females (13.8%), and males had a higher prevalence of HFHL (OR = 4.19, 95% CI 3.18 to 5.52) after adjusting for age, CNE, and other covariates. Sex differences were constant and highly remarkable among subjects aged 30 to 40 years and those with a CNE of 80 to 95 dB(A). Alcohol consumption might be a risk factor for HFHL in females (OR = 3.12, 95% CI 1.10 to 8.89). Conclusions This study indicates significant sex differences in NIHL. Males are at higher risk of HFHL than females despite equivalent noise exposure and age. The risk factors for NIHL might be different in males and females.

Chromatin regulators play an important role in the development of human diseases. In this study, we focused on Plant Homeo Domain Finger protein 8 (PHF8), a chromatin regulator that has attracted special concern recently. PHF8 is a histone lysine demethylase ubiquitously expressed in nuclei. Mutations of PHF8 are associated with X-linked mental retardation. It usually functions as a transcriptional co-activator by associating with H3K4me3 and RNA polymerase II. We found that PHF8 may associate with another regulator, REST/NRSF, predominately at promoter regions via studying several published PHF8 chromatin immunoprecipitation-sequencing (ChIP-Seq) datasets. Our analysis suggested that PHF8 not only activates but may also repress gene expression.

Objective The aim of this study was to investigate the satisfaction of age-related hearing loss (ARHL) or presbycusis patients with individual, accurate, and precise fitting progress, which is a priority for bilateral hearing aids, and to explore the related influencing factors and their role in predicting the efficiency of hearing aids. Methods A total of 73 cases of presbycusis patients aged 60–95 years old underwent pure tone audiometry and speech recognition ability examination to obtain the pure tone audiometry of the better ear (BPTA) and maximum speech recognition rate of the better ear (BSRR) in quiet environment before hearing aid fitting. Audiologists evaluated the efficiency and satisfaction of participants according to the International Outcome Inventory for Hearing Aids (IOI-HA) questionnaire scores by face-to-face or telephone investigations after using the hearing aids for at least 3 months. The data were analyzed related to possible influencing factors. Results Total satisfaction percentage according to IOI-HA scores was 86.3%. There was no significant correlation between age, first fitting age, unilateral or bilateral hearing aids, BPTA, and IOI-HA total score. BSRR was strongly correlated to total IOI-HA scores ( r =0.768). According to the multiple linear regression analysis, BPTA and BSRR both had a statistically significant effect on the total IOI-HA scores after hearing aid intervention. Conclusion ARHL patients with accurate hearing aid fitting will have high satisfaction and bilateral hearing aids are better than unilateral ones. Age and first fitting age are not meaningful to satisfaction with hearing aids. A higher maximum speech recognition rate before hearing aids fitting could predict better efficiency and satisfaction with hearing aids. Therefore, completing speech recognition ability examination before fitting would make a great contribution to the efficiency of hearing aids, and help ARHL patients have realistic expectations.