High Enhancer Activity is an Epigenetic Feature of HPV Negative Atypical Head and Neck Squamous Cell Carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease with significant morbidity and mortality and frequent recurrence. Pre-NGS efforts to transcriptionally classify HNSCC into groups of varying prognosis have identified four accepted molecular subtypes of disease: Atypical (AT), Basal (BA), Classical (CL), and Mesenchymal (MS). Here, we investigated the active enhancer landscapes of these subtypes using representative HNSCC cell lines and identified samples belonging to the AT subtype as having increased enhancer activity compared to the other 3 HNSCC subtypes. Cell lines belonging to atypical subtype were more resistant to bromodomain inhibitors (BETi). PRO-Seq experiments that both TCGA tumors and AT cell lines showed higher eRNA transcripts for enhancers controlling BETi resistance pathways, such as lipid metabolism and MAPK signaling. Additionally, HiChIP experiments suggested higher enhancer-promoter (E-P) contacts in the AT subtype, including on genes identified in the eRNA analysis. Consistently, known BETi resistance pathways were upregulated upon exposure to these inhibitors. Together, our results identify that the AT subtype of HNSCC is associated with high enhancer activity, resistance to BET inhibition, and signaling pathways that could serve as future targets for sensitizing HNSCC to BET inhibition.

Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay

In eukaryotes, histone variant distribution within the genome is the key epigenetic feature. To understand how each histone variant is targeted to the genome, we developed a new method, the RhIP (Reconstituted histone complex Incorporation into chromatin of Permeabilized cell) assay, in which epitope-tagged histone complexes are introduced into permeabilized cells and incorporated into their chromatin. Using this method, we found that H3.1 and H3.3 were incorporated into chromatin in replication-dependent and -independent manners, respectively. We further found that the incorporation of histones H2A and H2A.Z mainly occurred at less condensed chromatin (open), suggesting that condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. Our study revealed that the combination of chromatin structure and DNA replication dictates the differential histone deposition to maintain the epigenetic chromatin states.

An Information Gain-based Method for Evaluating the Classification Power of Features Towards Identifying Enhancers

Background: Enhancers are cis-regulatory elements that enhance gene expression on DNA sequences. Since most of enhancers are located far from transcription start sites, it is difficult to identify them. As other regulatory elements, the regions around enhancers contain a variety of features, which can help in enhancer recognition. Objective: The classification power of features differs significantly, the performances of existing methods that use one or a few features for identifying enhancer vary greatly. Therefore, evaluating the classification power of each feature can improve the predictive performance of enhancers. Methods: We present an evaluation method based on Information Gain (IG) that captures the entropy change of enhancer recognition according to features. To validate the performance of our method, experiments using the Single Feature Prediction Accuracy (SFPA) were conducted on each feature. Results: The average IG values of the sequence feature, transcriptional feature and epigenetic feature are 0.068, 0.213, and 0.299, respectively. Through SFPA, the average AUC values of the sequence feature, transcriptional feature and epigenetic feature are 0.534, 0.605, and 0.647, respectively. The verification results are consistent with our evaluation results. Conclusion: This IG-based method can effectively evaluate the classification power of features for identifying enhancers. Compared with sequence features, epigenetic features are more effective for recognizing enhancers.

Global Research on DNA methylation from 2000 to 2019: Bibliometric Analysis and Visualization

Introduction:DNA methylation is the most common epigenetic feature in human somatic cells, it has played a crucial role in regulating related genes and diagnosing cancer. However, few studies used bibliometric method to systematically analyze the development of DNA methylation. The purpose of this study was to systematically analyze the trends of DNA methylation research from 2000 to 2019. Methods:The published studies were searched between January, 2000 and December 31st, 2019 in the Web of Science. We only included peer-reviewed reviews and articles. The language was limited to English, and no species limitations were specified. A total of 11,127 publications met the inclusion criteria. CiteSpace V was used to analyze the trends of DNA methylation research. Results:The results showed the publications had a statistical increase over time in the DNA methylation research(P<0.005) by linear regression analyses. USA had the largest number of published papers (4263). Plos One contributed to the most publications (4.52%). The most prolific institution is Chinese Acad Sci (237). In accordance with subject categories of Web of Science, Genetics Heredity subject category had the largest number of publications (2,516) and citations (119,113). Biochemistry Molecular Biology subject category had the highest number of H-index (154). On the basis of the co-citation map of references, the “specific dna methylation” was labeled as the largest cluster. Most recent burst keywords were as follows: “pregnancy” (2017~2019), “obesity” (2017~2019), “growth” (2017~2019). Conclusions: This study provides useful information for DNA methylation researchers to find fresh viewpoints related to collaborators, cooperative institutions, popular topics. It also reminds us to pay attention to some new research trends.

Identification and characterization of the hypoxia response regulatory elements in the accessible genome

Hypoxia is commonly observed in the solid tumor and contributes to the drug resistance in cancer therapy. Deciphering the epigenetic feature under the hypoxia condition in the solid tumor is critical for us to understand the tumorigenesis and design the precision therapy. Using the time series of ATAC-seq data under the hypoxia treatment from the epithelia cells, we identified the hypoxia response regulatory elements (HRREs) in the accessible genome. We found that these different HRREs have unique genomic features and are enriched with different transcriptional factors (TFs). Our study provides insights into the chromatin structure response to the hypoxia treatment and identifies useful genomic features for a better understanding of the hypoxia biology in the solid tumor.

Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay

In eukaryotes, histone variant distribution within the genome is the key epigenetic feature. To understand how each histone variant is targeted to the genome, we developed a new method, in which epitope-tagged histone complexes are introduced into permeabilized cells and incorporated into their chromatin. We found that the incorporation of histones H2A and H2A.Z mainly occurred at less condensed chromatin (open), suggesting that the condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. This led to the recapitulation of the pre-existing chromatin structure: the genome-wide even distribution of H2A and the exclusion of H2A.Z from the closed chromatin. Intriguingly, an H2A.Z mutant with mutations in the developmentally essential region was incorporated into closed chromatin. Our study revealed that the combination of chromatin structure and DNA replication dictates the differential histone deposition for maintaining the epigenetic chromatin states.