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Cantarella S, Vezzoli M, Carnevali D, Morselli M, Zemke NR, Montanini B, Daussy CF, Wodrich H, Teichmann M, Pellegrini M, Berk AJ, Dieci G, Ferrari R. Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler. Nucleic Acids Res 2024:gkae615. [PMID: 39011896 DOI: 10.1093/nar/gkae615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 04/29/2024] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
Alu retrotransposons, which form the largest family of mobile DNA elements in the human genome, have recently come to attention as a potential source of regulatory novelties, most notably by participating in enhancer function. Even though Alu transcription by RNA polymerase III is subjected to tight epigenetic silencing, their expression has long been known to increase in response to various types of stress, including viral infection. Here we show that, in primary human fibroblasts, adenovirus small e1a triggered derepression of hundreds of individual Alus by promoting TFIIIB recruitment by Alu-bound TFIIIC. Epigenome profiling revealed an e1a-induced decrease of H3K27 acetylation and increase of H3K4 monomethylation at derepressed Alus, making them resemble poised enhancers. The enhancer nature of e1a-targeted Alus was confirmed by the enrichment, in their upstream regions, of the EP300/CBP acetyltransferase, EP400 chromatin remodeler and YAP1 and FOS transcription factors. The physical interaction of e1a with EP400 was critical for Alu derepression, which was abrogated upon EP400 ablation. Our data suggest that e1a targets a subset of enhancer Alus whose transcriptional activation, which requires EP400 and is mediated by the e1a-EP400 interaction, may participate in the manipulation of enhancer activity by adenoviruses.
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Affiliation(s)
- Simona Cantarella
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marco Vezzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Davide Carnevali
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marco Morselli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Nathan R Zemke
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Barbara Montanini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Coralie F Daussy
- Bordeaux University, CNRS UMR 5234, Fundamental Microbiology and Pathogenicity, Bordeaux, France
| | - Harald Wodrich
- Bordeaux University, CNRS UMR 5234, Fundamental Microbiology and Pathogenicity, Bordeaux, France
| | - Martin Teichmann
- Bordeaux University, Inserm U 1312, Bordeaux Institute of Oncology, 33076 Bordeaux, France
| | - Matteo Pellegrini
- Department of Molecular Cellular and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Arnold J Berk
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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Nie Z, Zhao Y, Yu S, Mai J, Gao H, Fan Z, Bao Y, Li R, Xiao J. NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species. J Mol Biol 2024:168655. [PMID: 38878855 DOI: 10.1016/j.jmb.2024.168655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/24/2024] [Accepted: 06/07/2024] [Indexed: 06/24/2024]
Abstract
Nucleosome dynamics plays important roles in many biological processes, such as DNA replication and gene expression. NucMap (https://ngdc.cncb.ac.cn/nucmap) is the first database of genome-wide nucleosome positioning maps across species. Here, we present an updated version, NucMap 2.0, by incorporating more species and MNase-seq samples. In addition, we integrate other related omics data for each MNase-seq sample to provide a comprehensive view of nucleosome positioning, such as gene expression, transcription factor binding sites, histone modifications and DNA methylation. In particular, NucMap 2.0 integrates and pre-analyzes RNA-seq data and ChIP-seq data of human-related samples, which facilitates the interpretation of nucleosome positioning in humans. All processed data are integrated into an in-built genome browser, and users can make comprehensive side-by-side analyses. In addition, more online analytical functions are developed, which allows researchers to identify differential nucleosome regions and explore potential gene regulatory regions. All resources are open access with a user-friendly web interface.
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Affiliation(s)
- Zhi Nie
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yongbing Zhao
- University of Chinese Academy of Sciences, Beijing 100049, China; Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Shuhuan Yu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jialin Mai
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hao Gao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhuojing Fan
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
| | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Rujiao Li
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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Zhou J, Zhu L. Shared genetic links between hypothyroidism and psychiatric disorders: evidence from a comprehensive genetic analysis. Front Endocrinol (Lausanne) 2024; 15:1370019. [PMID: 38904036 PMCID: PMC11187243 DOI: 10.3389/fendo.2024.1370019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024] Open
Abstract
Background Epidemiologic studies have suggested co-morbidity between hypothyroidism and psychiatric disorders. However, the shared genetic etiology and causal relationship between them remain currently unclear. Methods We assessed the genetic correlations between hypothyroidism and psychiatric disorders [anxiety disorders (ANX), schizophrenia (SCZ), major depressive disorder (MDD), and bipolar disorder (BIP)] using summary association statistics from genome-wide association studies (GWAS). Two disease-associated pleiotropic risk loci and genes were identified, and pathway enrichment, tissue enrichment, and other analyses were performed to determine their specific functions. Furthermore, we explored the causal relationship between them through Mendelian randomization (MR) analysis. Results We found significant genetic correlations between hypothyroidism with ANX, SCZ, and MDD, both in the Linkage disequilibrium score regression (LDSC) approach and the high-definition likelihood (HDL) approach. Meanwhile, the strongest correlation was observed between hypothyroidism and MDD (LDSC: rg=0.264, P=7.35×10-12; HDL: rg=0.304, P=4.14×10-17). We also determined a significant genetic correlation between MDD with free thyroxine (FT4) and thyroid-stimulating hormone (TSH) levels. A total of 30 pleiotropic risk loci were identified between hypothyroidism and psychiatric disorders, of which the 15q14 locus was identified in both ANX and SCZ (P values are 6.59×10-11 and 2.10×10-12, respectively) and the 6p22.1 locus was identified in both MDD and SCZ (P values are 1.05×10-8 and 5.75×10-14, respectively). Sixteen pleiotropic risk loci were identified between MDD and indicators of thyroid function, of which, four loci associated with MDD (1p32.3, 6p22.1, 10q21.1, 11q13.4) were identified in both FT4 normal level and Hypothyroidism. Further, 79 pleiotropic genes were identified using Magma gene analysis (P<0.05/18776 = 2.66×10-6). Tissue-specific enrichment analysis revealed that these genes were highly enriched into six brain-related tissues. The pathway analysis mainly involved nucleosome assembly and lipoprotein particles. Finally, our two-sample MR analysis showed a significant causal effect of MDD on the increased risk of hypothyroidism, and BIP may reduce TSH normal levels. Conclusions Our findings not only provided evidence of a shared genetic etiology between hypothyroidism and psychiatric disorders, but also provided insights into the causal relationships and biological mechanisms that underlie their relationship. These findings contribute to a better understanding of the pleiotropy between hypothyroidism and psychiatric disorders, while having important implications for intervention and treatment goals for these disorders.
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Affiliation(s)
- Jianlong Zhou
- People’s Hospital of Deyang City, Affiliated to Chengdu University of Traditional Chinese Medicine, Deyang, China
| | - Lv Zhu
- Department of Integrative Medicine, West China Hospital, Sichuan University, Chengdu, China
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Bai X, Bao Y, Bei S, Bu C, Cao R, Cao Y, Cen H, Chao J, Chen F, Chen H, Chen K, Chen M, Chen M, Chen M, Chen Q, Chen R, Chen S, Chen T, Chen X, Chen X, Cheng Y, Chu Y, Cui Q, Dong L, Du Z, Duan G, Fan S, Fan Z, Fang X, Fang Z, Feng Z, Fu S, Gao F, Gao G, Gao H, Gao W, Gao X, Gao X, Gao X, Gong J, Gong J, Gou Y, Gu S, Guo AY, Guo G, Guo X, Han C, Hao D, Hao L, He Q, He S, He S, Hu W, Huang K, Huang T, Huang X, Huang Y, Jia P, Jia Y, Jiang C, Jiang M, Jiang S, Jiang T, Jiang X, Jin E, Jin W, Kang H, Kang H, Kong D, Lan L, Lei W, Li CY, Li C, Li C, Li H, Li J, Li J, Li L, Li P, Li R, Li X, Li Y, Li Y, Li Z, Liao X, Lin S, Lin Y, Ling Y, Liu B, Liu CJ, Liu D, Liu GH, Liu L, Liu S, Liu W, Liu X, Liu X, Liu Y, Liu Y, Lu M, Lu T, Luo H, Luo H, Luo M, Luo S, Luo X, Ma L, Ma Y, Mai J, Meng J, Meng X, Meng Y, Meng Y, Miao W, Miao YR, Ni L, Nie Z, Niu G, Niu X, Niu Y, Pan R, Pan S, Peng D, Peng J, Qi J, Qi Y, Qian Q, Qin Y, Qu H, Ren J, Ren J, Sang Z, Shang K, Shen WK, Shen Y, Shi Y, Song S, Song T, Su T, Sun J, Sun Y, Sun Y, Sun Y, Tang B, Tang D, Tang Q, Tang Z, Tian D, Tian F, Tian W, Tian Z, Wang A, Wang G, Wang G, Wang J, Wang J, Wang P, Wang P, Wang W, Wang Y, Wang Y, Wang Y, Wang Y, Wang Z, Wei H, Wei Y, Wei Z, Wu D, Wu G, Wu S, Wu S, Wu W, Wu W, Wu Z, Xia Z, Xiao J, Xiao L, Xiao Y, Xie G, Xie GY, Xie J, Xie Y, Xiong J, Xiong Z, Xu D, Xu S, Xu T, Xu T, Xue Y, Xue Y, Yan C, Yang D, Yang F, Yang F, Yang H, Yang J, Yang K, Yang N, Yang QY, Yang S, Yang X, Yang X, Yang X, Yang YG, Ye W, Yu C, Yu F, Yu S, Yuan C, Yuan H, Zeng J, Zhai S, Zhang C, Zhang F, Zhang G, Zhang M, Zhang P, Zhang Q, Zhang R, Zhang S, Zhang W, Zhang W, Zhang W, Zhang X, Zhang X, Zhang Y, Zhang Y, Zhang Y, Zhang YE, Zhang Y, Zhang Z, Zhang Z, Zhao D, Zhao F, Zhao G, Zhao M, Zhao W, Zhao W, Zhao X, Zhao Y, Zhao Y, Zhao Z, Zheng X, Zheng Y, Zhou C, Zhou H, Zhou X, Zhou X, Zhou Y, Zhou Y, Zhu J, Zhu L, Zhu R, Zhu T, Zong W, Zou D, Zuo Z. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024. Nucleic Acids Res 2024; 52:D18-D32. [PMID: 38018256 PMCID: PMC10767964 DOI: 10.1093/nar/gkad1078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/12/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
The National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support the global academic and industrial communities. With the rapid accumulation of multi-omics data at an unprecedented pace, CNCB-NGDC continuously expands and updates core database resources through big data archiving, integrative analysis and value-added curation. Importantly, NGDC collaborates closely with major international databases and initiatives to ensure seamless data exchange and interoperability. Over the past year, significant efforts have been dedicated to integrating diverse omics data, synthesizing expanding knowledge, developing new resources, and upgrading major existing resources. Particularly, several database resources are newly developed for the biodiversity of protists (P10K), bacteria (NTM-DB, MPA) as well as plant (PPGR, SoyOmics, PlantPan) and disease/trait association (CROST, HervD Atlas, HALL, MACdb, BioKA, BioKA, RePoS, PGG.SV, NAFLDkb). All the resources and services are publicly accessible at https://ngdc.cncb.ac.cn.
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Lu D, Wu X, Wu W, Wu S, Li H, Zhang Y, Yan X, Zhai J, Dong X, Feng S, Zhang X, Sun F, Wang S, Cai K. Plasma cell-free DNA 5-hydroxymethylcytosine and whole-genome sequencing signatures for early detection of esophageal cancer. Cell Death Dis 2023; 14:843. [PMID: 38114477 PMCID: PMC10730877 DOI: 10.1038/s41419-023-06329-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/05/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023]
Abstract
Esophageal cancer is a highly incidence and deadly disease with a poor prognosis, especially in developing countries. Owing to the lack of specific symptoms and early diagnostic biomarkers, most patients are diagnosed with advanced disease, leading to a 5-year survival rate of less than 15%. Early (n = 50) and middle-advanced (n = 50) esophageal squamous cell carcinoma (ESCC) patients, as well as 71 healthy individuals, underwent 5-hydroxymethylcytosine (5hmC) sequencing on their plasma cell-free DNA (cfDNA). A Northern Chinese cohort of cfDNA 5hmC dataset of 150 ESCC patients and 183 healthy individuals were downloaded for validation. A diagnostic model was developed using cfDNA 5hmC signatures and then improved by low-pass whole genome sequencing (WGS) features of cfDNA. Conserved cfDNA 5hmC modification motifs were observed in the two independent ESCC cohorts. The diagnostic model with 5hmC features achieved an AUC of 0.810 and 0.862 in the Southern and Northern cohorts, respectively, with sensitivities of 69.3-74.3% and specificities of 82.4-90.7%. The performance was well maintained in Stage I to Stage IV, with accuracy of 70-100%, but low in Stage 0, 33.3%. Low-pass WGS of cfDNA improved the AUC to 0.934 with a sensitivity of 82.4%, a specificity of 88.2%, and an accuracy of 84.3%, particularly significantly in Stage 0, with an accuracy up to 80%. 5hmC and WGS could efficiently differentiate very early ESCC from healthy individuals. These findings imply a non-invasive and convenient method for ESCC detection when clinical treatments are available and may eventually prolong survival.
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Affiliation(s)
- Di Lu
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xuanzhen Wu
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wendy Wu
- Berry Oncology Corporation, Beijing, 100102, China
| | - Shuangxiu Wu
- Berry Oncology Corporation, Beijing, 100102, China
| | - Hui Li
- Berry Oncology Corporation, Beijing, 100102, China
| | - Yuhong Zhang
- Berry Oncology Corporation, Beijing, 100102, China
| | - Xuebin Yan
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Jianxue Zhai
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoying Dong
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Siyang Feng
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | | | - Fuming Sun
- Berry Oncology Corporation, Beijing, 100102, China
| | - Shaobo Wang
- Berry Oncology Corporation, Beijing, 100102, China
| | - Kaican Cai
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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An Y, Zhao X, Zhang Z, Xia Z, Yang M, Ma L, Zhao Y, Xu G, Du S, Wu X, Zhang S, Hong X, Jin X, Sun K. DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation. Nat Commun 2023; 14:287. [PMID: 36653380 PMCID: PMC9849216 DOI: 10.1038/s41467-023-35959-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Plasma cell-free DNA (cfDNA) are small molecules generated through a non-random fragmentation procedure. Despite commendable translational values in cancer liquid biopsy, however, the biology of cfDNA, especially the principles of cfDNA fragmentation, remains largely elusive. Through orientation-aware analyses of cfDNA fragmentation patterns against the nucleosome structure and integration with multidimensional functional genomics data, here we report a DNA methylation - nuclease preference - cutting end - size distribution axis, demonstrating the role of DNA methylation as a functional molecular regulator of cfDNA fragmentation. Hence, low-level DNA methylation could increase nucleosome accessibility and alter the cutting activities of nucleases during DNA fragmentation, which further leads to variation in cutting sites and size distribution of cfDNA. We further develop a cfDNA ending preference-based metric for cancer diagnosis, whose performance has been validated by multiple pan-cancer datasets. Our work sheds light on the molecular basis of cfDNA fragmentation towards broader applications in cancer liquid biopsy.
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Affiliation(s)
- Yunyun An
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Xin Zhao
- Hepato-Biliary Surgery Division, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, 518100, Shenzhen, China
| | - Ziteng Zhang
- Hepato-Biliary Surgery Division, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, 518100, Shenzhen, China
| | - Zhaohua Xia
- Thoracic Surgical Department, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, 518100, Shenzhen, China
| | - Mengqi Yang
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Li Ma
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, 518107, Shenzhen, China
| | - Gang Xu
- Department of Liver Surgery and Liver Transplant Center, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College Hospital, PUMC and Chinese Academy of Medical Sciences, 100730, Beijing, Dongcheng, China
| | - Xiang'an Wu
- Department of Liver Surgery, Peking Union Medical College Hospital, PUMC and Chinese Academy of Medical Sciences, 100730, Beijing, Dongcheng, China
| | - Shuowen Zhang
- Department of Liver Surgery, Peking Union Medical College Hospital, PUMC and Chinese Academy of Medical Sciences, 100730, Beijing, Dongcheng, China
| | - Xin Hong
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xin Jin
- BGI-Shenzhen, 518083, Shenzhen, China. .,School of Medicine, South China University of Technology, 510006, Guangzhou, Guangdong, China.
| | - Kun Sun
- Institute of Cancer Research, Shenzhen Bay Laboratory, 518132, Shenzhen, China.
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Kasavi C. Gene co-expression network analysis revealed novel biomarkers for ovarian cancer. Front Genet 2022; 13:971845. [PMID: 36338962 PMCID: PMC9627302 DOI: 10.3389/fgene.2022.971845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/10/2022] [Indexed: 09/18/2023] Open
Abstract
Ovarian cancer is the second most common gynecologic cancer and remains the leading cause of death of all gynecologic oncologic disease. Therefore, understanding the molecular mechanisms underlying the disease, and the identification of effective and predictive biomarkers are invaluable for the development of diagnostic and treatment strategies. In the present study, a differential co-expression network analysis was performed via meta-analysis of three transcriptome datasets of serous ovarian adenocarcinoma to identify novel candidate biomarker signatures, i.e. genes and miRNAs. We identified 439 common differentially expressed genes (DEGs), and reconstructed differential co-expression networks using common DEGs and considering two conditions, i.e. healthy ovarian surface epithelia samples and serous ovarian adenocarcinoma epithelia samples. The modular analyses of the constructed networks indicated a co-expressed gene module consisting of 17 genes. A total of 11 biomarker candidates were determined through receiver operating characteristic (ROC) curves of gene expression of module genes, and miRNAs targeting these genes were identified. As a result, six genes (CDT1, CNIH4, CRLS1, LIMCH1, POC1A, and SNX13), and two miRNAs (mir-147a, and mir-103a-3p) were suggested as novel candidate prognostic biomarkers for ovarian cancer. Further experimental and clinical validation of the proposed biomarkers could help future development of potential diagnostic and therapeutic innovations in ovarian cancer.
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Affiliation(s)
- Ceyda Kasavi
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Turkey
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8
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Abstract
A study of the plant Arabidopsis thaliana detected lower mutation rates in genomic regions where mutations are more likely to be deleterious, challenging the principle that mutagenesis is blind to its consequence. To examine the generality of this finding, we analyze large mutational data from baker's yeast and humans. The yeast data do not exhibit this trend, whereas the human data show an opposite trend that disappears upon the control of potential confounders. We find that the Arabidopsis study identified substantially more mutations than reported in the original data-generating studies and expected from Arabidopsis' mutation rate. These extra mutations are enriched in polynucleotide tracts and have relatively low sequencing qualities so are likely sequencing errors. Furthermore, the polynucleotide “mutations” can produce the purported mutational trend in Arabidopsis. Together, our results do not support lower mutagenesis of genomic regions of stronger selective constraints in the plant, fungal, and animal models examined.
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Affiliation(s)
- Haoxuan Liu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Evolutionary and Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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9
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Kong S, Lu Y, Tan S, Li R, Gao Y, Li K, Zhang Y. Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape. Genes (Basel) 2022; 13:genes13071114. [PMID: 35885897 PMCID: PMC9323251 DOI: 10.3390/genes13071114] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 12/04/2022] Open
Abstract
Genetic information is loaded on chromatin, which involves DNA sequence arrangement and the epigenetic landscape. The epigenetic information including DNA methylation, nucleosome positioning, histone modification, 3D chromatin conformation, and so on, has a crucial impact on gene transcriptional regulation. Out of them, nucleosomes, as basal chromatin structural units, play an important central role in epigenetic code. With the discovery of nucleosomes, various nucleosome-level technologies have been developed and applied, pushing epigenetics to a new climax. As the underlying methodology, next-generation sequencing technology has emerged and allowed scientists to understand the epigenetic landscape at a genome-wide level. Combining with NGS, nucleosome-omics (or nucleosomics) provides a fresh perspective on the epigenetic code and 3D genome landscape. Here, we summarized and discussed research progress in technology development and application of nucleosome-omics. We foresee the future directions of epigenetic development at the nucleosome level.
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10
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Li K, Oiwa NN, Mishra SK, Heermann DW. Inter-nucleosomal potentials from nucleosomal positioning data. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2022; 45:33. [PMID: 35403917 PMCID: PMC9001623 DOI: 10.1140/epje/s10189-022-00185-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
No systematic method exists to derive inter-nucleosomal potentials between nucleosomes along a chromosome consistently across a given genome. Such potentials can yield information on nucleosomal ordering, thermal as well as mechanical properties of chromosomes. Thus, indirectly, they shed light on a possible mechanical genomic code along a chromosome. To develop a method yielding effective inter-nucleosomal potentials between nucleosomes, a generalized Lennard-Jones potential for the parameterization is developed based on nucleosomal positioning data. This approach eliminates some of the problems that the underlying nucleosomal positioning data have, rendering the extraction difficult on the individual nucleosomal level. Furthermore, patterns on which to base a classification along a chromosome appear on larger domains, such as hetero- and euchromatin. An intuitive selection strategy for the noisy optimization problem is employed to derive effective exponents for the generalized potential. The method is tested on the Candida albicans genome. Applying k-means clustering based on potential parameters and thermodynamic compressibilities, a genome-wide clustering of nucleosome sequences is obtained for C. albicans. This clustering shows that a chromosome beyond the classical dichotomic categories of hetero- and euchromatin is more feature-rich.
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Affiliation(s)
- Kunhe Li
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, D-69120, Heidelberg, Germany
| | - Nestor Norio Oiwa
- Department of Basic Science, Universidade Federal Fluminense, Rua Doutor Sílvio Henrique Braune 22, Centro, Nova Friburgo, 28625-650, Brazil
| | - Sujeet Kumar Mishra
- Center for Computational Biology and Bioinformatics, School of Computational and Integrative Sciences (SCIS) Jawaharlal Nehru University, New Delhi, India
| | - Dieter W Heermann
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, D-69120, Heidelberg, Germany.
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11
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Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome. Life (Basel) 2022; 12:life12040541. [PMID: 35455033 PMCID: PMC9026121 DOI: 10.3390/life12040541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/16/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
Nucleosome positioning plays an important role in crucial biological processes such as replication, transcription, and gene regulation. It has been widely used to predict the genome’s function and chromatin organisation. So far, the studies of patterns in nucleosome positioning have been limited to transcription start sites, CTCFs binding sites, and some promoter and loci regions. The genome-wide organisational pattern remains unknown. We have developed a theoretical model to coarse-grain nucleosome positioning data in order to obtain patterns in their distribution. Using hierarchical clustering on the auto-correlation function of this coarse-grained nucleosome positioning data, a genome-wide clustering is obtained for Candida albicans. The clustering shows the existence beyond hetero- and eu-chromatin inside the chromosomes. These non-trivial clusterings correspond to different nucleosome distributions and gene densities governing differential gene expression patterns. Moreover, these distribution patterns inside the chromosome appeared to be conserved throughout the genome and within species. The pipeline of the coarse grain nucleosome positioning sequence to identify underlying genomic organisation used in our study is novel, and the classifications obtained are unique and consistent.
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12
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Oiwa NN, Li K, Cordeiro CE, Heermann DW. Prediction and comparative analysis of CTCF binding sites based on a first principle approach. Phys Biol 2022; 19. [PMID: 35290214 DOI: 10.1088/1478-3975/ac5dca] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/09/2022] [Indexed: 11/12/2022]
Abstract
We calculated the patterns for the CCCTC transcription factor (CTCF) binding sites across many genomes on a first principle approach. The validation of the first principle method was done on the human as well as on the mouse genome. The predicted human CTCF binding sites are consistent with the consensus sequence, ChIP-seq data for the K562 cell, nucleosome positions for IMR90 cell as well as the CTCF binding sites in the mouse HOXA gene. The analysis of Homo sapiens, Mus musculus, Sus scrofa, Capra hircus and Drosophila melanogaster whole genomes shows: binding sites are organized in cluster-like groups, where two consecutive sites obey a power-law with coefficient ranging from to 0.3292 0.0068 to 0.5409 0.0064; the distance between these groups varies from 18.08 0.52kbp to 42.1 2.0kbp. The genome of Aedes aegypti does not show a power law, but 19.9% of binding sites are 144 4 and 287 5bp distant of each other. We run negative tests, confirming the under-representation of CTCF binding sites in Caenorhabditis elegans, Plasmodium falciparum and Arabidopsis thaliana complete genomes.
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Affiliation(s)
- Nestor Norio Oiwa
- Theoretical Physics, Heidelberg University, Philosophenweg 19, Heidelberg, Baden-Württemberg, 69120, GERMANY
| | - Kunhe Li
- Theoretical Physics, Heidelberg University, Philosophenweg 19, Heidelberg, 69117, GERMANY
| | - Claudette E Cordeiro
- Department of Physics, Universidade Federal Fluminense, Avenida Atlantica s/n, Gragoatal, Niteroi, Rio de Janeiro, 24220-900, BRAZIL
| | - Dieter W Heermann
- Theoretical Physics, Heidelberg University, Philosophenweg 19, Heidelberg, 69120, GERMANY
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13
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Zhang Y, Zou D, Zhu T, Xu T, Chen M, Niu G, Zong W, Pan R, Jing W, Sang J, Liu C, Xiong Y, Sun Y, Zhai S, Chen H, Zhao W, Xiao J, Bao Y, Hao L, Zhang Z. Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. Nucleic Acids Res 2022; 50:D1016-D1024. [PMID: 34591957 PMCID: PMC8728231 DOI: 10.1093/nar/gkab878] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 01/07/2023] Open
Abstract
Transcriptomic profiling is critical to uncovering functional elements from transcriptional and post-transcriptional aspects. Here, we present Gene Expression Nebulas (GEN, https://ngdc.cncb.ac.cn/gen/), an open-access data portal integrating transcriptomic profiles under various biological contexts. GEN features a curated collection of high-quality bulk and single-cell RNA sequencing datasets by using standardized data processing pipelines and a structured curation model. Currently, GEN houses a large number of gene expression profiles from 323 datasets (157 bulk and 166 single-cell), covering 50 500 samples and 15 540 169 cells across 30 species, which are further categorized into six biological contexts. Moreover, GEN integrates a full range of transcriptomic profiles on expression, RNA editing and alternative splicing for 10 bulk datasets, providing opportunities for users to conduct integrative analysis at both transcriptional and post-transcriptional levels. In addition, GEN provides abundant gene annotations based on value-added curation of transcriptomic profiles and delivers online services for data analysis and visualization. Collectively, GEN presents a comprehensive collection of transcriptomic profiles across multiple species, thus serving as a fundamental resource for better understanding genetic regulatory architecture and functional mechanisms from tissues to cells.
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Affiliation(s)
- Yuansheng Zhang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Tongtong Zhu
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianyi Xu
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Ming Chen
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangyi Niu
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenting Zong
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Pan
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Jing
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Sang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chang Liu
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujia Xiong
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100069, China
| | - Yubin Sun
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Shuang Zhai
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Huanxin Chen
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Wenming Zhao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Xiao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lili Hao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Zhang Zhang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Epigenomic signatures on paralogous genes reveal underappreciated universality of active histone codes adopted across animals. Comput Struct Biotechnol J 2022; 20:353-367. [PMID: 35035788 PMCID: PMC8741409 DOI: 10.1016/j.csbj.2021.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 11/21/2022] Open
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15
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Zaurin R, Ferrari R, Nacht AS, Carbonell J, Le Dily F, Font-Mateu J, de Llobet Cucalon LI, Vidal E, Lioutas A, Beato M, Vicent GP. A set of accessible enhancers enables the initial response of breast cancer cells to physiological progestin concentrations. Nucleic Acids Res 2021; 49:12716-12731. [PMID: 34850111 PMCID: PMC8682742 DOI: 10.1093/nar/gkab1125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 11/14/2022] Open
Abstract
Here, we report that in T47D breast cancer cells 50 pM progestin is sufficient to activate cell cycle entry and the progesterone gene expression program. At this concentration, equivalent to the progesterone blood levels found around the menopause, progesterone receptor (PR) binds only to 2800 genomic sites, which are accessible to ATAC cleavage prior to hormone exposure. These highly accessible sites (HAs) are surrounded by well-organized nucleosomes and exhibit breast enhancer features, including estrogen receptor alpha (ERα), higher FOXA1 and BRD4 (bromodomain containing 4) occupancy. Although HAs are enriched in RAD21 and CTCF, PR binding is the driving force for the most robust interactions with hormone-regulated genes. HAs show higher frequency of 3D contacts among themselves than with other PR binding sites, indicating colocalization in similar compartments. Gene regulation via HAs is independent of classical coregulators and ATP-activated remodelers, relying mainly on MAP kinase activation that enables PR nuclear engagement. HAs are also preferentially occupied by PR and ERα in breast cancer xenografts derived from MCF-7 cells as well as from patients, indicating their potential usefulness as targets for therapeutic intervention.
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Affiliation(s)
- Roser Zaurin
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Ana Silvina Nacht
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Jose Carbonell
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Francois Le Dily
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Jofre Font-Mateu
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Lara Isabel de Llobet Cucalon
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Enrique Vidal
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Antonios Lioutas
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, 08003, Spain
| | - Guillermo P Vicent
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Barcelona, 08003, Spain
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16
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Oveisi M, Shukla M, Seymen N, Ohno M, Taniguchi Y, Nahata S, Loos R, Mufti GJ, Allshire RC, Dimitrov S, Karimi MM. iNucs: Inter-Nucleosome Interactions. Bioinformatics 2021; 37:4562-4563. [PMID: 34623394 PMCID: PMC8652021 DOI: 10.1093/bioinformatics/btab698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022] Open
Abstract
MOTIVATION Deciphering nucleosome-nucleosome interactions is an important step towards mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available. RESULTS We developed iNucs, a user-friendly and efficient Python-based bioinformatics tool to compute and visualize nucleosome resolved interactions using standard pairs format input generated from pairtools. AVAILABILITY https://github.com/Karimi-Lab/inucs/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mehrdad Oveisi
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King’s College London, London SE5 8AF, UK
| | - Manu Shukla
- Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nogayhan Seymen
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King’s College London, London SE5 8AF, UK
| | - Masae Ohno
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan,Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Yuichi Taniguchi
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan,Laboratory for Cell Systems Control, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Sunil Nahata
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Remco Loos
- BMS Center for Innovation and Translational Research Europe (CITRE, a Bristol Myers Squibb Company), Pabellón de Italia, 41092 Sevilla, Spain
| | - Ghulam J Mufti
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King’s College London, London SE5 8AF, UK
| | - Robin C Allshire
- Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Stefan Dimitrov
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France,Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balçova, Izmir 35330, Turkey
| | - Mohammad M Karimi
- Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King’s College London, London SE5 8AF, UK,To whom correspondence should be addressed.
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17
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Chen X, Yang H, Liu G, Zhang Y. NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes. BMC Bioinformatics 2021; 22:321. [PMID: 34120586 PMCID: PMC8201709 DOI: 10.1186/s12859-021-04239-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 06/06/2021] [Indexed: 12/02/2022] Open
Abstract
Background Nucleosome organization is involved in many regulatory activities in various organisms. However, studies integrating nucleosome organization in mammalian genomes are very limited mainly due to the lack of comprehensive data quality control (QC) assessment and uneven data quality of public data sets. Results The NUCOME is a database focused on filtering qualified nucleosome organization referenced landscapes covering various cell types in human and mouse based on QC metrics. The filtering strategy guarantees the quality of nucleosome organization referenced landscapes and exempts users from redundant data set selection and processing. The NUCOME database provides standardized, qualified data source and informative nucleosome organization features at a whole-genome scale and on the level of individual loci. Conclusions The NUCOME provides valuable data resources for integrative analyses focus on nucleosome organization. The NUCOME is freely available at http://compbio-zhanglab.org/NUCOME. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04239-9.
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Affiliation(s)
- Xiaolan Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Hui Yang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Guifen Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
| | - Yong Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
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18
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Nasrollahzadeh D, Roshandel G, Delhomme TM, Avogbe PH, Foll M, Saidi F, Poustchi H, Sotoudeh M, Malekzadeh R, Brennan P, Mckay J, Hainaut P, Abedi-Ardekani B. TP53 Targeted Deep Sequencing of Cell-Free DNA in Esophageal Squamous Cell Carcinoma Using Low-Quality Serum: Concordance with Tumor Mutation. Int J Mol Sci 2021; 22:5627. [PMID: 34073316 PMCID: PMC8197963 DOI: 10.3390/ijms22115627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/28/2021] [Accepted: 05/17/2021] [Indexed: 12/30/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) is emerging as a potential tumor biomarker. CfDNA-based biomarkers may be applicable in tumors without an available non-invasive screening method among at-risk populations. Esophageal squamous cell carcinoma (ESCC) and residents of the Asian cancer belt are examples of those malignancies and populations. Previous epidemiological studies using cfDNA have pointed to the need for high volumes of good quality plasma (i.e., >1 mL plasma with 0 or 1 cycles of freeze-thaw) rather than archival serum, which is often the main available source of cfDNA in retrospective studies. Here, we have investigated the concordance of TP53 mutations in tumor tissue and cfDNA extracted from archival serum left-over from 42 cases and 39 matched controls (age, gender, residence) in a high-risk area of Northern Iran (Golestan). Deep sequencing of TP53 coding regions was complemented with a specialized variant caller (Needlestack). Overall, 23% to 31% of mutations were concordantly detected in tumor and serum cfDNA (based on two false discovery rate thresholds). Concordance was positively correlated with high cfDNA concentration, smoking history (p-value = 0.02) and mutations with a high potential of neoantigen formation (OR; 95%CI = 1.9 (1.11-3.29)), suggesting that tumor DNA release in the bloodstream might reflect the effects of immune and inflammatory context on tumor cell turnover. We identified TP53 mutations in five controls, one of whom was subsequently diagnosed with ESCC. Overall, the results showed that cfDNA mutations can be reliably identified by deep sequencing of archival serum, with a rate of success comparable to plasma. Nonetheless, 70% non-identifiable mutations among cancer patients and 12% mutation detection in controls are the main challenges in applying cfDNA to detect tumor-related variants when blindly targeting whole coding regions of the TP53 gene in ESCC.
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Affiliation(s)
- Dariush Nasrollahzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Gholamreza Roshandel
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan 49177-44563, Iran;
| | - Tiffany Myriam Delhomme
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
| | - Patrice Hodonou Avogbe
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Matthieu Foll
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Farrokh Saidi
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Hossein Poustchi
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Masoud Sotoudeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - James Mckay
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Inserm 1209 CNRS 5309 UGA, 38700 Grenoble, France;
| | - Behnoush Abedi-Ardekani
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
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19
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Chen L, Abou-Alfa GK, Zheng B, Liu JF, Bai J, Du LT, Qian YS, Fan R, Liu XL, Wu L, Hou JL, Wang HY. Genome-scale profiling of circulating cell-free DNA signatures for early detection of hepatocellular carcinoma in cirrhotic patients. Cell Res 2021; 31:589-592. [PMID: 33589745 PMCID: PMC8089097 DOI: 10.1038/s41422-020-00457-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Affiliation(s)
- Lei Chen
- National Center for Liver Cancer, Shanghai, 210822 China ,International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, 200438 China
| | - Ghassan K. Abou-Alfa
- Memorial Sloan Kettering Cancer Center, New York, NY USA ,Weill Medical College at Cornell University, New York, NY USA
| | - Bo Zheng
- National Center for Liver Cancer, Shanghai, 210822 China ,International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, 200438 China
| | - Jing-Feng Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian 350025 China
| | - Jian Bai
- Berry Oncology Corporation, Beijing, 100102 China
| | - Lu-Tao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, Shandong 250033 China ,The Clinical Research Center of Shandong Province for Clinical Laboratory, 247 Beiyuan Street, Jinan, Shandong 250033 China
| | - Yun-Song Qian
- Hepatology Department, Ningbo Hwamei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang 315010 China
| | - Rong Fan
- Department of Infectious Diseases, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515 China
| | - Xiao-Long Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian 350025 China
| | - Lin Wu
- Berry Oncology Corporation, Beijing, 100102 China
| | - Jin-Lin Hou
- Department of Infectious Diseases, State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515 China
| | - Hong-Yang Wang
- National Center for Liver Cancer, Shanghai, 210822 China ,International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, 200438 China ,Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, 200438 China ,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai, 200438 China
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20
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Yu X, Singh PK, Tabrejee S, Sinha S, Buck MJ. ΔNp63 is a pioneer factor that binds inaccessible chromatin and elicits chromatin remodeling. Epigenetics Chromatin 2021; 14:20. [PMID: 33865440 PMCID: PMC8053304 DOI: 10.1186/s13072-021-00394-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/02/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND ΔNp63 is a master transcriptional regulator playing critical roles in epidermal development and other cellular processes. Recent studies suggest that ΔNp63 functions as a pioneer factor that can target its binding sites within inaccessible chromatin and induce chromatin remodeling. METHODS In order to examine if ΔNp63 can bind to inaccessible chromatin and to determine if specific histone modifications are required for binding, we induced ΔNp63 expression in two p63-naïve cell lines. ΔNp63 binding was then examined by ChIP-seq and the chromatin at ΔNp63 targets sites was examined before and after binding. Further analysis with competitive nucleosome binding assays was used to determine how ΔNp63 directly interacts with nucleosomes. RESULTS Our results show that before ΔNp63 binding, targeted sites lack histone modifications, indicating ΔNp63's capability to bind at unmodified chromatin. Moreover, the majority of the sites that are bound by ectopic ΔNp63 expression exist in an inaccessible state. Once bound, ΔNp63 induces acetylation of the histone and the repositioning of nucleosomes at its binding sites. Further analysis with competitive nucleosome binding assays reveal that ΔNp63 can bind directly to nucleosome edges with significant binding inhibition occurring within 50 bp of the nucleosome dyad. CONCLUSION Overall, our results demonstrate that ΔNp63 is a pioneer factor that binds nucleosome edges at inaccessible and unmodified chromatin sites and induces histone acetylation and nucleosome repositioning.
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Affiliation(s)
- Xinyang Yu
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, 14203, USA.,Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, Guangdong, China
| | - Prashant K Singh
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, 14203, USA
| | - Shamira Tabrejee
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, 14203, USA
| | - Satrajit Sinha
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, 14203, USA.
| | - Michael J Buck
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, 14203, USA. .,Department of Biomedical Informatics, Jacobs School of Medicine & Biomedical Sciences, Buffalo, USA.
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21
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Gómez-García PA, Portillo-Ledesma S, Neguembor MV, Pesaresi M, Oweis W, Rohrlich T, Wieser S, Meshorer E, Schlick T, Cosma MP, Lakadamyali M. Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation. Cell Rep 2021; 34:108614. [PMID: 33440158 PMCID: PMC7842188 DOI: 10.1016/j.celrep.2020.108614] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 10/29/2020] [Accepted: 12/16/2020] [Indexed: 01/01/2023] Open
Abstract
Nucleosomes form heterogeneous groups in vivo, named clutches. Clutches are smaller and less dense in mouse embryonic stem cells (ESCs) compared to neural progenitor cells (NPCs). Using coarse-grained modeling of the pluripotency Pou5f1 gene, we show that the genome-wide clutch differences between ESCs and NPCs can be reproduced at a single gene locus. Larger clutch formation in NPCs is associated with changes in the compaction and internucleosome contact probability of the Pou5f1 fiber. Using single-molecule tracking (SMT), we further show that the core histone protein H2B is dynamic, and its local mobility relates to the structural features of the chromatin fiber. H2B is less stable and explores larger areas in ESCs compared to NPCs. The amount of linker histone H1 critically affects local H2B dynamics. Our results have important implications for how nucleosome organization and H2B dynamics contribute to regulate gene activity and cell identity.
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Affiliation(s)
- Pablo Aurelio Gómez-García
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; Institute of Photonic Sciences (ICFO), The Barcelona Institute of Science and Technology (BIST), Castelldefels, 08860 Barcelona, Spain
| | - Stephanie Portillo-Ledesma
- Department of Chemistry, 1021 Silver Center, 100 Washington Square East, New York University, New York, NY 10003, USA
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Martina Pesaresi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Walaa Oweis
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Talia Rohrlich
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Stefan Wieser
- Institute of Photonic Sciences (ICFO), The Barcelona Institute of Science and Technology (BIST), Castelldefels, 08860 Barcelona, Spain
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel; The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Tamar Schlick
- Department of Chemistry, 1021 Silver Center, 100 Washington Square East, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, 251 Mercer Street, New York University, New York, NY 10012, USA; NYU-ECNU Center for Computational Chemistry at New York University Shanghai, 340 Geography Building, 3663 North Zhongshan Road, Shanghai 3663, China
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain; Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Melike Lakadamyali
- Perelman School of Medicine, Department of Physiology, University of Pennsylvania, Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104, USA; Perelman School of Medicine, Department of Cell and Developmental Biology, University of Pennsylvania, Biomedical Research Building, 421 Curie Boulevard, Philadelphia, PA 19104, USA.
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22
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Sandholtz SH, Kannan D, Beltran BG, Spakowitz AJ. Chromosome Structural Mechanics Dictates the Local Spreading of Epigenetic Marks. Biophys J 2020; 119:1630-1639. [PMID: 33010237 DOI: 10.1016/j.bpj.2020.08.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/07/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022] Open
Abstract
We present a theoretical model that demonstrates the integral role chromosome organization and structural mechanics play in the spreading of histone modifications involved in epigenetic regulation. Our model shows that heterogeneous nucleosome positioning, and the resulting position-dependent mechanical properties, must be included to reproduce several qualitative features of experimental data of histone methylation spreading around an artificially induced "nucleation site." We show that our model recreates both the extent of spreading and the presence of a subdominant peak upstream of the transcription start site. Our model indicates that the spreading of epigenetic modifications is sensitive to heterogeneity in chromatin organization and the resulting variability in the chromatin's mechanical properties, suggesting that nucleosome spacing can directly control the conferral of epigenetic marks by modifying the structural mechanics of the chromosome. It further illustrates how the physical organization of the DNA polymer may play a significant role in re-establishing the epigenetic code upon cell division.
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Affiliation(s)
| | - Deepti Kannan
- Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Bruno G Beltran
- Biophysics Program, Stanford University, Stanford, California
| | - Andrew J Spakowitz
- Biophysics Program, Stanford University, Stanford, California; Chemical Engineering Department, Stanford University, Stanford, California; Department of Materials Science and Engineering, Stanford University, Stanford, California; Department of Applied Physics, Stanford University, Stanford, California.
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23
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Amato D, Bosco GL, Rizzo R. CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification. BMC Bioinformatics 2020; 21:326. [PMID: 32938377 PMCID: PMC7493859 DOI: 10.1186/s12859-020-03627-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that nucleosomes are determined by the combined effects of several factors, including DNA sequence organization. Interestingly, the identification of nucleosomes on a genomic scale has been successfully performed by computational methods using DNA sequence as input data. RESULTS In this work, we propose CORENup, a deep learning model for nucleosome identification. CORENup processes a DNA sequence as input using one-hot representation and combines in a parallel fashion a fully convolutional neural network and a recurrent layer. These two parallel levels are devoted to catching both non periodic and periodic DNA string features. A dense layer is devoted to their combination to give a final classification. CONCLUSIONS Results computed on public data sets of different organisms show that CORENup is a state of the art methodology for nucleosome positioning identification based on a Deep Neural Network architecture. The comparisons have been carried out using two groups of datasets, currently adopted by the best performing methods, and CORENup has shown top performance both in terms of classification metrics and elapsed computation time.
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Affiliation(s)
- Domenico Amato
- Dipartimento di Matematica e Informatica, Università degli studi di Palermo, Via Archirafi, 34, Palermo, 90123, Italy
| | - Giosue' Lo Bosco
- Dipartimento di Matematica e Informatica, Università degli studi di Palermo, Via Archirafi, 34, Palermo, 90123, Italy. .,Dipartimento di Scienze per l'Innovazione tecnologica, Istituto Euro-Mediterraneo di Scienza e Tecnologia, Via Michele Miraglia, 20, Palermo, 9039, Italy.
| | - Riccardo Rizzo
- CNR-ICAR, National Research Council of Italy, Via Ugo La Malfa, 153, Palermo, 90146, Italy
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24
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Li Z, Sun R, Bishop TC. Genome Dashboards: Framework and Examples. Biophys J 2020; 118:2077-2085. [PMID: 32171420 PMCID: PMC7203004 DOI: 10.1016/j.bpj.2020.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 01/28/2020] [Accepted: 02/18/2020] [Indexed: 12/11/2022] Open
Abstract
Genomics is a sequence-based informatics science and a three-dimensional-structure-based material science. However, in practice, most genomics researchers utilize sequence-based informatics approaches or three-dimensional-structure-based material science techniques, not both. This division is, at least in part, the result of historical developments rather than a fundamental necessity. The underlying computational tools, experimental techniques, and theoretical models were developed independently. The primary result presented here is a framework for the unification of informatics- and physics-based data associated with DNA, nucleosomes, and chromatin. The framework is based on the mathematical representation of geometrically exact rods and the generalization of DNA basepair step parameters. Data unification enables researchers to integrate computational, experimental, and theoretical approaches for the study of chromatin biology. The framework can be implemented using model-view-controller design principles, existing genome browsers, and existing molecular visualization tools. We developed a minimal, web-based genome dashboard, G-Dash-min, and applied it to two simple examples to demonstrate the usefulness of data unification and proof of concept. Genome dashboards developed using the framework and design principles presented here are extensible and customizable and are therefore more broadly applicable than the examples presented. We expect a number of purpose-specific genome dashboards to emerge as a novel means of investigating structure-function relationships for genomes that range from basepairs to entire chromosomes and for generating, validating, and testing mechanistic hypotheses.
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Affiliation(s)
- Zilong Li
- Chemistry and Physics, Louisiana Tech University, Ruston, Louisiana
| | - Ran Sun
- Chemistry and Physics, Louisiana Tech University, Ruston, Louisiana
| | - Thomas C Bishop
- Chemistry and Physics, Louisiana Tech University, Ruston, Louisiana.
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25
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Ferrari R, de Llobet Cucalon LI, Di Vona C, Le Dilly F, Vidal E, Lioutas A, Oliete JQ, Jochem L, Cutts E, Dieci G, Vannini A, Teichmann M, de la Luna S, Beato M. TFIIIC Binding to Alu Elements Controls Gene Expression via Chromatin Looping and Histone Acetylation. Mol Cell 2020; 77:475-487.e11. [PMID: 31759822 PMCID: PMC7014570 DOI: 10.1016/j.molcel.2019.10.020] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/20/2019] [Accepted: 10/13/2019] [Indexed: 12/15/2022]
Abstract
How repetitive elements, epigenetic modifications, and architectural proteins interact ensuring proper genome expression remains poorly understood. Here, we report regulatory mechanisms unveiling a central role of Alu elements (AEs) and RNA polymerase III transcription factor C (TFIIIC) in structurally and functionally modulating the genome via chromatin looping and histone acetylation. Upon serum deprivation, a subset of AEs pre-marked by the activity-dependent neuroprotector homeobox Protein (ADNP) and located near cell-cycle genes recruits TFIIIC, which alters their chromatin accessibility by direct acetylation of histone H3 lysine-18 (H3K18). This facilitates the contacts of AEs with distant CTCF sites near promoter of other cell-cycle genes, which also become hyperacetylated at H3K18. These changes ensure basal transcription of cell-cycle genes and are critical for their re-activation upon serum re-exposure. Our study reveals how direct manipulation of the epigenetic state of AEs by a general transcription factor regulates 3D genome folding and expression.
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Affiliation(s)
- Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Lara Isabel de Llobet Cucalon
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Chiara Di Vona
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - François Le Dilly
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Vidal
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Antonios Lioutas
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Javier Quilez Oliete
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Laura Jochem
- The Institute of Cancer Research (ICR), London, UK
| | - Erin Cutts
- The Institute of Cancer Research (ICR), London, UK
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alessandro Vannini
- The Institute of Cancer Research (ICR), London, UK; Human Technopole. Via Cristina Belgioioso, 171, 20157 Milano MI, Italy
| | - Martin Teichmann
- Université de Bordeaux, INSERM U1212 CNRS UMR 5320 146, Bordeaux, France
| | - Susana de la Luna
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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26
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Song S, Zhang Z. Database Resources in BIG Data Center: Submission, Archiving, and Integration of Big Data in Plant Science. MOLECULAR PLANT 2019; 12:279-281. [PMID: 30716410 DOI: 10.1016/j.molp.2019.01.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/26/2019] [Accepted: 01/27/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Shuhui Song
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhang Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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27
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Mörl MC, Zülske T, Schöpflin R, Wedemann G. Data formats for modelling the spatial structure of chromatin based on experimental positions of nucleosomes. AIMS BIOPHYSICS 2019. [DOI: 10.3934/biophy.2019.3.83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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