1
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Morgan D, DeMeo DL, Glass K. Using methylation data to improve transcription factor binding prediction. Epigenetics 2024; 19:2309826. [PMID: 38300850 PMCID: PMC10841018 DOI: 10.1080/15592294.2024.2309826] [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: 08/07/2023] [Accepted: 01/01/2024] [Indexed: 02/03/2024] Open
Abstract
Modelling the regulatory mechanisms that determine cell fate, response to external perturbation, and disease state depends on measuring many factors, a task made more difficult by the plasticity of the epigenome. Scanning the genome for the sequence patterns defined by Position Weight Matrices (PWM) can be used to estimate transcription factor (TF) binding locations. However, this approach does not incorporate information regarding the epigenetic context necessary for TF binding. CpG methylation is an epigenetic mark influenced by environmental factors that is commonly assayed in human cohort studies. We developed a framework to score inferred TF binding locations using methylation data. We intersected motif locations identified using PWMs with methylation information captured in both whole-genome bisulfite sequencing and Illumina EPIC array data for six cell lines, scored motif locations based on these data, and compared with experimental data characterizing TF binding (ChIP-seq). We found that for most TFs, binding prediction improves using methylation-based scoring compared to standard PWM-scores. We also illustrate that our approach can be generalized to infer TF binding when methylation information is only proximally available, i.e. measured for nearby CpGs that do not directly overlap with a motif location. Overall, our approach provides a framework for inferring context-specific TF binding using methylation data. Importantly, the availability of DNA methylation data in existing patient populations provides an opportunity to use our approach to understand the impact of methylation on gene regulatory processes in the context of human disease.
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Affiliation(s)
- Daniel Morgan
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, USA
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Flora P, Li MY, Zhou Y, Mercédes M, Zheng XY, Galbo PM, Zheng D, Ezhkova E. H2AK119ub dynamics controls hair follicle stem cell quiescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.10.617646. [PMID: 39416158 PMCID: PMC11482967 DOI: 10.1101/2024.10.10.617646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
The transition of stem cells from a quiescent state to an active state is a finely tuned process that requires the dismantling of the quiescence program and the establishment of a cell cycle-promoting transcriptional landscape. Whether epigenetic processes control stem cell states to promote the regeneration of adult tissues remains elusive. In this study, we show that a repressive histone modification, H2AK119ub, is dynamic between quiescent and active hair follicle stem cells (HFSCs) in the adult murine skin. Ablation of H2AK119ub in HFSCs leads to impaired quiescence leading to premature activation and an eventual exhaustion of HFSC pool. Transcriptional and chromatin studies revealed that H2AK119ub directly represses a proliferation promoting transcriptional program in the HFSCs to preserve quiescence. Lastly, we identify that the inhibitory FGF signaling produced by the hair follicle niche keratinocytes maintains H2AK119ub in quiescent HFSCs. Together, these findings reveal that a repressive histone mark, H2AK119ub, is under the dynamic regulation of inhibitory niche signaling to prevent the untimely establishment of an activated state to preserve SC function and longevity.
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3
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Yuan D, Zhang X, Yang Y, Wei L, Li H, Zhao T, Guo M, Li Z, Huang Z, Wang M, Dai Z, Li P, Xia Q, Qian W, Cheng D. Schlank orchestrates insect developmental transition by switching H3K27 acetylation to trimethylation in the prothoracic gland. Proc Natl Acad Sci U S A 2024; 121:e2401861121. [PMID: 39167603 PMCID: PMC11363265 DOI: 10.1073/pnas.2401861121] [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: 01/30/2024] [Accepted: 07/22/2024] [Indexed: 08/23/2024] Open
Abstract
Insect developmental transitions are precisely coordinated by ecdysone and juvenile hormone (JH). We previously revealed that accumulated H3K27 trimethylation (H3K27me3) at the locus encoding JH signal transducer Hairy is involved in the larval-pupal transition in insects, but the underlying mechanism remains to be fully defined. Here, we show in Drosophila and Bombyx that Rpd3-mediated H3K27 deacetylation in the prothoracic gland during the last larval instar promotes ecdysone biosynthesis and the larval-pupal transition by enabling H3K27me3 accumulation at the Hairy locus to induce its transcriptional repression. Importantly, we find that the homeodomain transcription factor Schlank acts to switch active H3K27 acetylation (H3K27ac) to repressive H3K27me3 at the Hairy locus by directly binding to the Hairy promoter and then recruiting the histone deacetylase Rpd3 and the histone methyltransferase PRC2 component Su(z)12 through physical interactions. Moreover, Schlank inhibits Hairy transcription to facilitate the larval-pupal transition, and the Schlank signaling cascade is suppressed by JH but regulated in a positive feedback manner by ecdysone. Together, our data uncover that Schlank mediates epigenetic reprogramming of H3K27 modifications in hormone actions during insect developmental transition.
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Affiliation(s)
- Dongqin Yuan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Xing Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Yan Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Ling Wei
- School of Life Sciences, Southwest University, Chongqing400715, China
| | - Hao Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Tujing Zhao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Mengge Guo
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Zheng Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Zhu Huang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Min Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Zongcai Dai
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Peixin Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Wenliang Qian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
| | - Daojun Cheng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing400715, China
- State Key Laboratory of Resource Insects, Biological Science Research Center,Southwest University, Chongqing400715, China
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4
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Yao YM, Miodownik I, O'Hagan MP, Jbara M, Afek A. Deciphering the dynamic code: DNA recognition by transcription factors in the ever-changing genome. Transcription 2024:1-25. [PMID: 39033307 DOI: 10.1080/21541264.2024.2379161] [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: 03/15/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Transcription factors (TFs) intricately navigate the vast genomic landscape to locate and bind specific DNA sequences for the regulation of gene expression programs. These interactions occur within a dynamic cellular environment, where both DNA and TF proteins experience continual chemical and structural perturbations, including epigenetic modifications, DNA damage, mechanical stress, and post-translational modifications (PTMs). While many of these factors impact TF-DNA binding interactions, understanding their effects remains challenging and incomplete. This review explores the existing literature on these dynamic changes and their potential impact on TF-DNA interactions.
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Affiliation(s)
- Yumi Minyi Yao
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Irina Miodownik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michael P O'Hagan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ariel Afek
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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Williams CJ, Dai D, Tran KA, Monroe JG, Williams BP. Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants. Genome Biol 2023; 24:227. [PMID: 37828516 PMCID: PMC10571256 DOI: 10.1186/s13059-023-03059-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND In several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA is well understood, gene body methylation is not associated with transcriptional repression, and its biological importance remains unclear. RESULTS We report a newly discovered type of GbM in plants, which is under constitutive addition and removal by dynamic methylation modifiers in all cells, including the germline. Methylation at Dynamic GbM genes is removed by the DRDD demethylation pathway and added by an unknown source of de novo methylation, most likely the maintenance methyltransferase MET1. We show that the Dynamic GbM state is present at homologous genes across divergent lineages spanning over 100 million years, indicating evolutionary conservation. We demonstrate that Dynamic GbM is tightly associated with the presence of a promoter or regulatory chromatin state within the gene body, in contrast to other gene body methylated genes. We find Dynamic GbM is associated with enhanced gene expression plasticity across development and diverse physiological conditions, whereas stably methylated GbM genes exhibit reduced plasticity. Dynamic GbM genes exhibit reduced dynamic range in drdd mutants, indicating a causal link between DNA demethylation and enhanced gene expression plasticity. CONCLUSIONS We propose a new model for GbM in regulating gene expression plasticity, including a novel type of GbM in which increased gene expression plasticity is associated with the activity of DNA methylation writers and erasers and the enrichment of a regulatory chromatin state.
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Affiliation(s)
- Clara J Williams
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | - Dawei Dai
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | - Kevin A Tran
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | - J Grey Monroe
- Department of Plant Sciences, University of California, Davis, USA
| | - Ben P Williams
- Department of Plant & Microbial Biology, University of California, Berkeley, USA.
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Regulation of human ZNF687, a gene associated with Paget's disease of bone. Int J Biochem Cell Biol 2023; 154:106332. [PMID: 36372390 DOI: 10.1016/j.biocel.2022.106332] [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: 06/01/2022] [Revised: 10/31/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Mutations in Zinc finger 687 (ZNF687) were associated with Paget's disease of bone (PDB), a disease characterized by increased bone resorption and excessive bone formation. It was suggested that ZNF687 plays a role in bone differentiation and development. However, the mechanisms involved in ZNF687 regulation remain unknown. This study aimed to obtain novel knowledge regarding ZNF687 transcriptional and epigenetic regulation. Through in silico analysis, we hypothesized three ZNF687 promoter regions located upstream exon 1 A, 1B, and 1 C and denominated promoter regions 1, 2, and 3, respectively. Their functionality was confirmed by luciferase activity assays and positive/negative regulatory regions were identified using promoter deletions constructs. In silico analysis revealed a high density of CpG islands in these promoter regions and in vitro methylation suppressed promoters' activity. Using bioinformatic approaches, bone-associated transcription factor binding sites containing CpG dinucleotides were identified, including those for NFκB, PU.1, DLX5, and SOX9. By co-transfection in HEK293 and hFOB cells, we found that DLX5 specifically activated ZNF687 promoter region 1, and its methylation impaired DLX5-driven promoter stimulation. NFκB repressed and activated promoter regions 1 and 2, respectively, and these activities were affected by methylation. PU.1 induced ZNF687 promoter region 1 which was affected by methylation. SOX9 differentially regulated ZNF687 promoters in HEK293 and hFOB cells that were impaired after methylation. In conclusion, this study provides novel insights into ZNF687 regulation by demonstrating that NFκB, PU.1, DLX5, and SOX9 are regulators of ZNF687 promoters, and DNA methylation influences their activity. The contribution of the dysregulation of these mechanisms in PDB should be further elucidated.
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7
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Integrated Analysis of Gene Expression and Methylation Data to Identify Potential Biomarkers Related to Atherosclerosis Onset. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5493051. [PMID: 35915606 PMCID: PMC9338736 DOI: 10.1155/2022/5493051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/29/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
Abstract
Atherosclerosis is a kind of chronic inflammatory cardiovascular disease. Epigenetic regulation plays a crucial role in atherosclerosis. Our study was aimed at finding potential biomarkers associated with the occurrence of atherosclerosis. Two datasets were downloaded from the Gene Expression Omnibus (GEO) database. The epigenome-wide association study (EWAS) analysis was performed on methylation data using CpGassoc package. The differential expression analysis was conducted on mRNA data using limma package. The GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) functional enrichment was done in clusterProfiler package. Finally, the logistic regression model was constructed using generalized linear model (glm) function. Between atherosclerotic vs. nonatherosclerotic samples, totally 4980 cytosine-phosphate-guanine (CpG) sites (annotated to 2860 genes) and 132 differentially expressed genes (DEGs) related to atherosclerosis were identified. The annotated 2860 genes and 132 DEGs were significantly enriched in 9 and 4 KEGG pathways and 289 and 132 GO terms, respectively. After cross-analysis, 6 crucial CpG sites were screened to build the model, including cg01187920, cg03422911, cg08018825, cg10967350, cg14473924, and cg25313204. The diagnostic model could reliably separate the atherosclerosis samples from nonatherosclerotic samples. In conclusion, the 6 CpG sites are probably potential diagnostic biomarkers for atherosclerosis, including cg01187920, cg03422911, cg08018825, cg10967350, cg14473924, and cg25313204.
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8
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Yashar WM, Kong G, VanCampen J, Curtiss BM, Coleman DJ, Carbone L, Yardimci GG, Maxson JE, Braun TP. GoPeaks: histone modification peak calling for CUT&Tag. Genome Biol 2022; 23:144. [PMID: 35788238 PMCID: PMC9252088 DOI: 10.1186/s13059-022-02707-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 06/15/2022] [Indexed: 12/27/2022] Open
Abstract
Genome-wide mapping of histone modifications is critical to understanding transcriptional regulation. CUT&Tag is a new method for profiling histone modifications, offering improved sensitivity and decreased cost compared with ChIP-seq. Here, we present GoPeaks, a peak calling method specifically designed for histone modification CUT&Tag data. We compare the performance of GoPeaks against commonly used peak calling algorithms to detect histone modifications that display a range of peak profiles and are frequently used in epigenetic studies. We find that GoPeaks robustly detects genome-wide histone modifications and, notably, identifies a substantial number of H3K27ac peaks with improved sensitivity compared to other standard algorithms.
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Affiliation(s)
- William M. Yashar
- Knight Cancer Institute, Oregon Health & Science University, Portland, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, USA
| | - Garth Kong
- Knight Cancer Institute, Oregon Health & Science University, Portland, USA
| | - Jake VanCampen
- Knight Cancer Institute, Oregon Health & Science University, Portland, USA
| | | | - Daniel J. Coleman
- Knight Cancer Institute, Oregon Health & Science University, Portland, USA
| | - Lucia Carbone
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, USA
| | - Galip Gürkan Yardimci
- Knight Cancer Institute, Oregon Health & Science University, Portland, USA
- Center for Early Cancer Detection, Oregon Health & Science University, Portland, USA
| | - Julia E. Maxson
- Knight Cancer Institute, Oregon Health & Science University, Portland, USA
- Division of Oncologic Sciences, Oregon Health & Science University, Portland, USA
| | - Theodore P. Braun
- Knight Cancer Institute, Oregon Health & Science University, Portland, USA
- Division of Oncologic Sciences, Oregon Health & Science University, Portland, USA
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, USA
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9
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Li H, Guan Y. Asymmetric predictive relationships across histone modifications. NAT MACH INTELL 2022; 4:288-299. [DOI: 10.1038/s42256-022-00455-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Rodríguez-Sanabria JS, Escutia-Gutiérrez R, Rosas-Campos R, Armendáriz-Borunda JS, Sandoval-Rodríguez A. An Update in Epigenetics in Metabolic-Associated Fatty Liver Disease. Front Med (Lausanne) 2022; 8:770504. [PMID: 35087844 PMCID: PMC8787199 DOI: 10.3389/fmed.2021.770504] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2022] Open
Abstract
Metabolic-associated fatty liver disease (MAFLD) is characterized by hepatic steatosis accompanied by one of three features: overweight or obesity, T2DM, or lean or normal weight with evidence of metabolic dysregulation. It is distinguished by excessive fat accumulation in hepatocytes, and a decrease in the liver's ability to oxidize fats, the accumulation of ectopic fat, and the activation of proinflammatory pathways. Chronic damage will keep this pathophysiologic cycle active causing progression from hepatic steatosis to cirrhosis and eventually, hepatocarcinoma. Epigenetics affecting gene expression without altering DNA sequence allows us to study MAFLD pathophysiology from a different perspective, in which DNA methylation processes, histone modifications, and miRNAs expression have been closely associated with MAFLD progression. However, these considerations also faced us with the circumstance that modifying those epigenetics patterns might lead to MAFLD regression. Currently, epigenetics is an area of great interest because it could provide new insights in therapeutic targets and non-invasive biomarkers. This review comprises an update on the role of epigenetic patterns, as well as innovative therapeutic targets and biomarkers in MAFLD.
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Affiliation(s)
- J Samael Rodríguez-Sanabria
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico
| | - Rebeca Escutia-Gutiérrez
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico
| | - Rebeca Rosas-Campos
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico
| | - Juan S Armendáriz-Borunda
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico.,School of Medicine and Health Sciences, Tecnologico de Monterrey, Campus Guadalajara, Zapopan, Mexico
| | - Ana Sandoval-Rodríguez
- Department of Molecular Biology and Genomics, Institute for Molecular Biology in Medicine and Gene Therapy, CUCS, University of Guadalajara, Guadalajara, Mexico
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Jiang L, Liang J, Huang W, Ma J, Park KH, Wu Z, Chen P, Zhu H, Ma JJ, Cai W, Paul C, Niu L, Fan GC, Wang HS, Kanisicak O, Xu M, Wang Y. CRISPR activation of endogenous genes reprograms fibroblasts into cardiovascular progenitor cells for myocardial infarction therapy. Mol Ther 2022; 30:54-74. [PMID: 34678511 PMCID: PMC8753567 DOI: 10.1016/j.ymthe.2021.10.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/27/2021] [Accepted: 10/18/2021] [Indexed: 01/07/2023] Open
Abstract
Fibroblasts can be reprogrammed into cardiovascular progenitor cells (CPCs) using transgenic approaches, although the underlying mechanism remains unclear. We determined whether activation of endogenous genes such as Gata4, Nkx2.5, and Tbx5 can rapidly establish autoregulatory loops and initiate CPC generation in adult extracardiac fibroblasts using a CRISPR activation system. The induced fibroblasts (>80%) showed phenotypic changes as indicated by an Nkx2.5 cardiac enhancer reporter. The progenitor characteristics were confirmed by colony formation and expression of cardiovascular genes. Cardiac sphere induction segregated the early and late reprogrammed cells that can generate functional cardiomyocytes and vascular cells in vitro. Therefore, they were termed CRISPR-induced CPCs (ciCPCs). Transcriptomic analysis showed that cell cycle and heart development pathways were important to accelerate CPC formation during the early reprogramming stage. The CRISPR system opened the silenced chromatin locus, thereby allowing transcriptional factors to access their own promoters and eventually forming a positive feedback loop. The regenerative potential of ciCPCs was assessed after implantation in mouse myocardial infarction models. The engrafted ciCPCs differentiated into cardiovascular cells in vivo but also significantly improved contractile function and scar formation. In conclusion, multiplex gene activation was sufficient to drive CPC reprogramming, providing a new cell source for regenerative therapeutics.
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Affiliation(s)
- Lin Jiang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Jialiang Liang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA.
| | - Wei Huang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Jianyong Ma
- Department of Pharmacology and Systems Physiology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Ki Ho Park
- Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Zhichao Wu
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Peng Chen
- Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Hua Zhu
- Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jian-Jie Ma
- Department of Surgery, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Wenfeng Cai
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Christian Paul
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Liang Niu
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Guo-Chang Fan
- Department of Pharmacology and Systems Physiology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Hong-Sheng Wang
- Department of Pharmacology and Systems Physiology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Onur Kanisicak
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Meifeng Xu
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Yigang Wang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA.
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12
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Zurek M, Aavik E, Mallick R, Ylä-Herttuala S. Epigenetic Regulation of Vascular Smooth Muscle Cell Phenotype Switching in Atherosclerotic Artery Remodeling: A Mini-Review. Front Genet 2021; 12:719456. [PMID: 34422021 PMCID: PMC8375552 DOI: 10.3389/fgene.2021.719456] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/19/2021] [Indexed: 12/11/2022] Open
Abstract
Atherosclerosis is a chronic inflammatory disease characterized by extensive remodeling of medium and large-sized arteries. Inward remodeling (=lumen shrinkage) of the vascular walls is the underlying cause for ischemia in target organs. Therefore, inward remodeling can be considered the predominant feature of atherosclerotic pathology. Outward remodeling (=lumen enlargement) is a physiological response compensating for lumen shrinkage caused by neointimal hyperplasia, but as a pathological response to changes in blood flow, outward remodeling leads to substantial arterial wall thinning. Thinned vascular walls are prone to rupture, and subsequent thrombus formation accounts for the majority of acute cardiovascular events. Pathological remodeling is driven by inflammatory cells which induce vascular smooth muscle cells to switch from quiescent to a proliferative and migratory phenotype. After decades of intensive research, the molecular mechanisms of arterial remodeling are starting to unfold. In this mini-review, we summarize the current knowledge of the epigenetic and transcriptional regulation of vascular smooth muscle cell phenotype switching from the contractile to the synthetic phenotype involved in arterial remodeling and discuss potential therapeutic options.
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Affiliation(s)
- Michelle Zurek
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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13
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Yu YL, Chen M, Zhu H, Zhuo MX, Chen P, Mao YJ, Li LY, Zhao Q, Wu M, Ye M. STAT1 epigenetically regulates LCP2 and TNFAIP2 by recruiting EP300 to contribute to the pathogenesis of inflammatory bowel disease. Clin Epigenetics 2021; 13:127. [PMID: 34112215 PMCID: PMC8194145 DOI: 10.1186/s13148-021-01101-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/10/2021] [Indexed: 12/23/2022] Open
Abstract
Background The aetiology of inflammatory bowel disease (IBD) is related to genetics and epigenetics. Epigenetic regulation of the pathogenesis of IBD has not been well defined. Here, we investigated the role of H3K27ac events in the pathogenesis of IBD. Based on previous ChIP-seq and RNA-seq assays, we studied signal transducer and activator of transcription 1 (STAT1) as a transcription factor (TF) and investigated whether the STAT1–EP300–H3K27ac axis contributes to the development of IBD. We performed ChIP-PCR to investigate the interaction between STAT1 and H3K27ac, and co-IP assays were performed to investigate the crosstalk between STAT1 and EP300. Results Lymphocyte cytosolic protein 2 (LCP2) and TNF-α‐inducible protein 2 (TNFAIP2) are target genes of STAT1. p-STAT1 binds to the enhancer loci of the two genes where H3K27ac is enriched, and EP300 subsequently binds to regulate their expression. In mice with dextran sulfate sodium (DSS)-induced acute colitis, an EP300 inhibitor significantly inhibited colitis. Conclusions p-STAT1 and EP300 promote TNFAIP2 and LCP2 expression through an increase in H3K27ac enrichment on their enhancers and contribute to the pathogenesis of chronic inflammation. Graphic abstract ![]()
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Affiliation(s)
- Ya-Li Yu
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China.,Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Meng Chen
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China.,Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Hua Zhu
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China.,Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Ming-Xing Zhuo
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China.,Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Ping Chen
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China.,Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Yu-Juan Mao
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China.,Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Lian-Yun Li
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Intestinal and Colorectal Diseases, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China.,Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Min Wu
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Intestinal and Colorectal Diseases, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Mei Ye
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China. .,Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China.
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14
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Shyamala N, Gundapaneni KK, Galimudi RK, Tupurani MA, Padala C, Puranam K, Kupsal K, Kummari R, Gantala SR, Nallamala KR, Sahu SK, Hanumanth SR. PCSK9 genetic (rs11591147) and epigenetic (DNA methylation) modifications associated with PCSK9 expression and serum proteins in CAD patients. J Gene Med 2021; 23:e3346. [PMID: 33885177 DOI: 10.1002/jgm.3346] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/07/2021] [Accepted: 04/17/2021] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Proprotein convertase subtilisin/kexin type 9 (PCSK9) genetic polymorphisms play a significant role in cholesterol homeostasis. Therefore, we aimed to investigate the association of PCSK9 genetic variations NM_174936.3:c.137G>T (R46L, rs11591147) and NM_174936.3:c.1120G>T (D374Y, rs137852912), as well as promoter DNA methylation status, with mRNA expression and circulating serum protein levels in coronary artery disease (CAD) patients. METHODS The present study includes 300 CAD cases and 300 controls from South India. Biochemical assays were performed using commercially available kits. PCSK9 rs11591147 and rs137852912 polymorphisms were analyzed by the polymerase chain reaction (PCR)-restriction fragment length polymorphism method, whereas promoter DNA methylation status and gene expression were determined using methylation specific PCR and quantitative PCR respectively. RESULTS The genotypic distribution of PCSK9 rs11591147 revealed that individuals with the TT-genotype and T-allele have a reduced risk for CAD. Furthermore, patients with the PCSK9 rs11591147 TT genotype have a significantly lower total cholesterol and low-density lipoprotein-cholesterol levels and also higher high-density lipoprotein-cholesterol levels than individuals with the GG genotype. Logistic regression analysis has shown that the GG and GT (p = 1.51 × 10-8 , p = 1.47 × 10-9 ) genotypes predicted the risk for CAD with an odds ratio of 5.8 and 7.3 respectively. In addition, individuals with the TT genotype were hypermethylated at promoter DNA of PCSK9, resulting in lower mRNA expression and circulating serum proteins than in individuals with the GG genotype. In silico analyses revealed that rs11591147 T-allele has protein destabilizing capacity. CONCLUSIONS In conclusion, the present study indicates that the PCSK9 gene expression and circulating serum protein levels are not only associated with rs11591147 genotype, but also with promoter DNA methylation. Furthermore, the findings with respect to both single nucleotide polymorphism and promoter DNA methylation may open avenues for novel treatment possibilities targeting PCSK9 for CAD management.
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Affiliation(s)
- Nivas Shyamala
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana State, India
| | | | - Rajesh Kumar Galimudi
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana State, India.,Vascular and Renal Translational Research Group, Institut de Recerca Biomèdica de Lleida (IRBLleida), Lleida, Spain
| | | | - Chiranjeevi Padala
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana State, India.,Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana State, India
| | - Kaushik Puranam
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana State, India
| | - Keerthi Kupsal
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana State, India
| | - Ramanjaneyulu Kummari
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana State, India
| | - Srilatha Reddy Gantala
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana State, India
| | - Krishna Reddy Nallamala
- CARE cardiac center, Durgabai Deshmukh Hospital and Research Centre, Hyderabad, Telangana State, India
| | - Sanjib K Sahu
- CARE cardiac center, Durgabai Deshmukh Hospital and Research Centre, Hyderabad, Telangana State, India
| | - Surekha Rani Hanumanth
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, Telangana State, India
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15
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Fischer J, Ardakani FB, Kattler K, Walter J, Schulz MH. CpG content-dependent associations between transcription factors and histone modifications. PLoS One 2021; 16:e0249985. [PMID: 33857234 PMCID: PMC8049299 DOI: 10.1371/journal.pone.0249985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/30/2021] [Indexed: 11/18/2022] Open
Abstract
Understanding the factors that underlie the epigenetic regulation of genes is crucial to understand the gene regulatory machinery as a whole. Several experimental and computational studies examined the relationship between different factors involved. Here we investigate the relationship between transcription factors (TFs) and histone modifications (HMs), based on ChIP-seq data in cell lines. As it was shown that gene regulation by TFs differs depending on the CpG class of a promoter, we study the impact of the CpG content in promoters on the associations between TFs and HMs. We suggest an approach based on sparse linear regression models to infer associations between TFs and HMs with respect to CpG content. A study of the partial correlation of HMs for the two classes of high and low CpG content reveals possible CpG dependence and potential candidates for confounding factors in our models. We show that the models are accurate, inferred associations reflect known biological relationships, and we give new insight into associations with respect to CpG content. Moreover, analysis of a ChIP-seq dataset in HepG2 cells of the HM H3K122ac, an HM about little is known, reveals novel TF associations and supports a previously established link to active transcription.
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Affiliation(s)
- Jonas Fischer
- Max Planck Institute for Informatics, Databases and Information Systems, Saarbrücken, Germany
- Cluster of Excellence for Multimodal Computing and Interaction, High Throughput Genomics and Systems Biology, Saarbrücken, Germany
- * E-mail:
| | - Fatemeh Behjati Ardakani
- Max Planck Institute for Informatics, Computational Biology and Applied Algorithmics, Saarbrücken, Germany
- Cluster of Excellence for Multimodal Computing and Interaction, High Throughput Genomics and Systems Biology, Saarbrücken, Germany
- Institute of Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
| | - Kathrin Kattler
- Department of Genetics, University of Saarland, Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics, University of Saarland, Saarbrücken, Germany
| | - Marcel H. Schulz
- Max Planck Institute for Informatics, Computational Biology and Applied Algorithmics, Saarbrücken, Germany
- Cluster of Excellence for Multimodal Computing and Interaction, High Throughput Genomics and Systems Biology, Saarbrücken, Germany
- Institute of Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
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16
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Cao Y, Kitanovski S, Hoffmann D. intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data. BMC Genomics 2020; 21:802. [PMID: 33372591 PMCID: PMC7771091 DOI: 10.1186/s12864-020-07205-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND RNA-Seq, the high-throughput sequencing (HT-Seq) of mRNAs, has become an essential tool for characterizing gene expression differences between different cell types and conditions. Gene expression is regulated by several mechanisms, including epigenetically by post-translational histone modifications which can be assessed by ChIP-Seq (Chromatin Immuno-Precipitation Sequencing). As more and more biological samples are analyzed by the combination of ChIP-Seq and RNA-Seq, the integrated analysis of the corresponding data sets becomes, theoretically, a unique option to study gene regulation. However, technically such analyses are still in their infancy. RESULTS Here we introduce intePareto, a computational tool for the integrative analysis of RNA-Seq and ChIP-Seq data. With intePareto we match RNA-Seq and ChIP-Seq data at the level of genes, perform differential expression analysis between biological conditions, and prioritize genes with consistent changes in RNA-Seq and ChIP-Seq data using Pareto optimization. CONCLUSION intePareto facilitates comprehensive understanding of high dimensional transcriptomic and epigenomic data. Its superiority to a naive differential gene expression analysis with RNA-Seq and available integrative approach is demonstrated by analyzing a public dataset.
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Affiliation(s)
- Yingying Cao
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr.2, Essen, 45141, Germany.
| | - Simo Kitanovski
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr.2, Essen, 45141, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr.2, Essen, 45141, Germany
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17
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Haddad-Mashadrizeh A, Hemmat J, Aslamkhan M. Intronic regions of the human coagulation factor VIII gene harboring transcription factor binding sites with a strong bias towards the short-interspersed elements. Heliyon 2020; 6:e04727. [PMID: 32944665 PMCID: PMC7481535 DOI: 10.1016/j.heliyon.2020.e04727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/03/2019] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Increasing data show that intronic derived regulatory elements, such as transcription factor binding sites (TFBs), play key roles in gene regulation, and malfunction. Accordingly, characterizing the sequence context of the intronic regions of the human coagulation factor VIII (hFVIII) gene can be important. In this study, the intronic regions of the hFVIII gene were scrutinized based on in-silico methods. The results disclosed that these regions harbor a rich array of functional elements such as repetitive elements (REs), splicing sites, and transcription factor binding sites (TFBs). Among these elements, TFBs and REs showed a significant distribution and correlation to each other. This survey indicated that 31% of TFBs are localized in the intronic regions of the gene. Moreover, TFBs indicate a strong bias in the regions far from splice sites of introns with mapping to different REs. Accordingly, TFBs showed highly bias toward Short Interspersed Elements (SINEs), which in turn they covering about 12% of the total of REs. However, the distribution pattern of TFBs-REs showed different bias in the intronic regions, spatially into the Introns 13 and 25. The rich array of SINE-TFBs and CR1-TFBs were situated within 5′UTR of the gene that may be an important driving force for regulatory innovation of the hFVIII gene. Taken together, these data may lead to revealing intronic regions with the capacity to renewing gene regulatory networks of the hFVIII gene. On the other hand, these correlations might provide the novel idea for a new hypothesis of molecular evolution of the FVIII gene, and treatment of Hemophilia A which should be considered in future studies.
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Affiliation(s)
- Aliakbar Haddad-Mashadrizeh
- Recombinant Proteins Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Jafar Hemmat
- Biotechnology Department, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Muhammad Aslamkhan
- Human Genetics & Molecular Biology Dept., University of Health Sciences, Lahore, Pakistan.,Honorary Senior Lecturer in the School of the Medicine University of Liverpool, Liverpool, UK
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18
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Grzybkowska D, Nowak K, Gaj MD. Hypermethylation of Auxin-Responsive Motifs in the Promoters of the Transcription Factor Genes Accompanies the Somatic Embryogenesis Induction in Arabidopsis. Int J Mol Sci 2020; 21:E6849. [PMID: 32961931 PMCID: PMC7555384 DOI: 10.3390/ijms21186849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022] Open
Abstract
The auxin-induced embryogenic reprogramming of plant somatic cells is associated with extensive modulation of the gene expression in which epigenetic modifications, including DNA methylation, seem to play a crucial role. However, the function of DNA methylation, including the role of auxin in epigenetic regulation of the SE-controlling genes, remains poorly understood. Hence, in the present study, we analysed the expression and methylation of the TF genes that play a critical regulatory role during SE induction (LEC1, LEC2, BBM, WUS and AGL15) in auxin-treated explants of Arabidopsis. The results showed that auxin treatment substantially affected both the expression and methylation patterns of the SE-involved TF genes in a concentration-dependent manner. The auxin treatment differentially modulated the methylation of the promoter (P) and gene body (GB) sequences of the SE-involved genes. Relevantly, the SE-effective auxin treatment (5.0 µM of 2,4-D) was associated with the stable hypermethylation of the P regions of the SE-involved genes and a significantly higher methylation of the P than the GB fragments was a characteristic feature of the embryogenic culture. The presence of auxin-responsive (AuxRE) motifs in the hypermethylated P regions suggests that auxin might substantially contribute to the DNA methylation-mediated control of the SE-involved genes.
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Affiliation(s)
| | | | - Małgorzata D. Gaj
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland; (D.G.); (K.N.)
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19
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Huang Y, Zhou D, Wang Y, Zhang X, Su M, Wang C, Sun Z, Jiang Q, Sun B, Zhang Y. Prediction of transcription factors binding events based on epigenetic modifications in different human cells. Epigenomics 2020; 12:1443-1456. [PMID: 32921165 DOI: 10.2217/epi-2019-0321] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Aim: We aim to predict transcription factor (TF) binding events from knowledge of gene expression and epigenetic modifications. Materials & methods: TF-binding events based on the Encode project and The Cancer Genome Atlas data were analyzed by the random forest method. Results: We showed the high performance of TF-binding predictive models in GM12878, HeLa, HepG2 and K562 cell lines and applied them to other cell lines and tissues. The genes bound by the top TFs (MAX and MAZ) were significantly associated with cancer-related processes such as cell proliferation and DNA repair. Conclusion: We successfully constructed TF-binding predictive models in cell lines and applied them in tissues.
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Affiliation(s)
- Yan Huang
- School of Life Science & Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Dianshuang Zhou
- School of Life Science & Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Yihan Wang
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin 150081, China
| | - Xingda Zhang
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin 150081, China
| | - Mu Su
- School of Life Science & Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Cong Wang
- School of Life Science & Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Zhongyi Sun
- School of Life Science & Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Qinghua Jiang
- School of Life Science & Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Baoqing Sun
- Department of Allergy & Clinical Immunology, Guangzhou Institute of Respiratory health, State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yan Zhang
- School of Life Science & Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China.,Department of Allergy & Clinical Immunology, Guangzhou Institute of Respiratory health, State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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20
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Hemerich D, Pei J, Harakalova M, van Setten J, Boymans S, Boukens BJ, Efimov IR, Michels M, van der Velden J, Vink A, Cheng C, van der Harst P, Moore JH, Mokry M, Tragante V, Asselbergs FW. Integrative Functional Annotation of 52 Genetic Loci Influencing Myocardial Mass Identifies Candidate Regulatory Variants and Target Genes. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 12:e002328. [PMID: 30681347 DOI: 10.1161/circgen.118.002328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Regulatory elements may be involved in the mechanisms by which 52 loci influence myocardial mass, reflected by abnormal amplitude and duration of the QRS complex on the ECG. Functional annotation thus far did not take into account how these elements are affected in disease context. METHODS We generated maps of regulatory elements on hypertrophic cardiomyopathy patients (ChIP-seq N=14 and RNA-seq N=11) and nondiseased hearts (ChIP-seq N=4 and RNA-seq N=11). We tested enrichment of QRS-associated loci on elements differentially acetylated and directly regulating differentially expressed genes between hypertrophic cardiomyopathy patients and controls. We further performed functional annotation on QRS-associated loci using these maps of differentially active regulatory elements. RESULTS Regions differentially affected in disease showed a stronger enrichment ( P=8.6×10-5) for QRS-associated variants than those not showing differential activity ( P=0.01). Promoters of genes differentially regulated between hypertrophic cardiomyopathy patients and controls showed more enrichment ( P=0.001) than differentially acetylated enhancers ( P=0.8) and super-enhancers ( P=0.025). We also identified 74 potential causal variants overlapping these differential regulatory elements. Eighteen of the genes mapped confirmed previous findings, now also pinpointing the potentially affected regulatory elements and candidate causal variants. Fourteen new genes were also mapped. CONCLUSIONS Our results suggest differentially active regulatory elements between hypertrophic cardiomyopathy patients and controls can offer more insights into the mechanisms of QRS-associated loci than elements not affected by disease.
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Affiliation(s)
- Daiane Hemerich
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands.,CAPES Foundation, Ministry of Education of Brazil, Brasília (D.H.)
| | - Jiayi Pei
- CAPES Foundation, Ministry of Education of Brazil, Brasília (D.H.).,Department of Nephrology and Hypertension (J.P., C.C.), UMC Utrecht
| | - Magdalena Harakalova
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands
| | - Jessica van Setten
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands
| | - Sander Boymans
- Department of Genetics, Center for Molecular Medicine, Cancer Genomics Netherlands (S.B.), UMC Utrecht
| | - Bas J Boukens
- Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands (B.J.B.)
| | - Igor R Efimov
- Department of Biomedical Engineering, The George Washington University, Washington, DC (I.R.E.)
| | - Michelle Michels
- Department of Cardiology, Erasmus MC, Rotterdam, The Netherlands (M. Michels)
| | - Jolanda van der Velden
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center (J.v.d.V.)
| | - Aryan Vink
- Department of Pathology (A.V.), UMC Utrecht, Utrecht University, The Netherlands
| | - Caroline Cheng
- Department of Nephrology and Hypertension (J.P., C.C.), UMC Utrecht
| | | | - Jason H Moore
- Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, University of Pennsylvania, PA (J.H.M.)
| | - Michal Mokry
- Department of Pediatrics, Wilhelmina Children's Hospital, Utrecht (M. Mokry.)
| | - Vinicius Tragante
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology (D.H., M.H., J.v.S., V.T., F.W.A.), UMC Utrecht, Utrecht University, The Netherlands.,Durrer Center for Cardiogenetic Research, ICINNetherlands Heart Institute, Utrecht (F.W.A.).,Institute of Cardiovascular Science, Faculty of Population Health Sciences (F.W.A.), University College London, United Kingdom.,Health Data Research UK London, Institute of Health Informatics F.W.A.), University College London, United Kingdom
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21
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Comprehensive functional annotation of susceptibility variants associated with asthma. Hum Genet 2020; 139:1037-1053. [PMID: 32240371 DOI: 10.1007/s00439-020-02151-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/18/2020] [Indexed: 01/02/2023]
Abstract
Genome-wide association studies (GWAS) have identified hundreds of primarily non-coding disease-susceptibility variants that further need functional interpretation to prioritize and discriminate the disease-relevant variants. We present a comprehensive genome-wide non-coding variant prioritization scheme followed by validation using Pyrosequencing and TaqMan assays in asthma. We implemented a composite Functional Annotation Score (cFAS) to investigate over 32,000 variants consisting of 1525 GWAS-lead asthma-susceptibility variants and their LD proxies (r2 ≥ 0.80). Functional annotation pipeline in cFAS revealed 274 variants with significant score at 1% false discovery rate. This study implicates a novel locus 4p16 (SLC26A1) with eQTL variant (rs11936407) and known loci in 17q12-21 and 5q22 which encode ORM1-like protein 3 (ORMDL3, rs406527, and rs12936231) and thymic stromal lymphopoietin (TSLP, rs3806932 and rs10073816) epithelial gene, respectively. Follow-up validation analysis through pyrosequencing of CpG sites in and nearby rs4065275 and rs11936407 showed genotype-dependent hypomethylation on asthma cases compared with healthy controls. Prioritized variants are enriched for asthma-specific histone modification associated with active chromatin (H3K4me1 and H3K27ac) in T cells, B cells, lung, and immune-related interferon gamma signaling pathways. Our findings, together with those from prior studies, suggest that SNPs can affect asthma by regulating enhancer activity, and our comprehensive bioinformatics and functional analysis could lead to biological insights into asthma pathogenesis.Graphic abstract.
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22
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Wu J, Zhang L, Song Q, Yu L, Wang S, Zhang B, Wang W, Xia P, Chen X, Xiao Y, Xu C. Systematical identification of cell-specificity of CTCF-gene binding based on epigenetic modifications. Brief Bioinform 2020; 22:589-600. [PMID: 32022856 DOI: 10.1093/bib/bbaa004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 12/22/2022] Open
Abstract
The CCCTC-binding factor (CTCF) mediates transcriptional regulation and implicates epigenetic modifications in cancers. However, the systematically unveiling inverse regulatory relationship between CTCF and epigenetic modifications still remains unclear, especially the mechanism by which histone modification mediates CTCF binding. Here, we developed a systematic approach to investigate how epigenetic changes affect CTCF binding. Through integration analysis of CTCF binding in 30 cell lines, we concluded that CTCF generally binds with higher intensity in normal cell lines than that in cancers, and higher intensity in genome regions closed to transcription start sites. To facilitate the better understanding of their associations, we constructed linear mixed-effect models to analyze the effects of the epigenetic modifications on CTCF binding in four cancer cell lines and six normal cell lines, and identified seven epigenetic modifications as potential epigenetic patterns that influence CTCF binding intensity in promoter regions and six epigenetic modifications in enhancer regions. Further analysis of the effects in different locations revealed that the epigenetic regulation of CTCF binding was location-specific and cancer cell line-specific. Moreover, H3K4me2 and H3K9ac showed the potential association with immune regulation of disease. Taken together, our method can contribute to improve the understanding of the epigenetic regulation of CTCF binding and provide potential therapeutic targets for treating tumors associated with CTCF.
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Affiliation(s)
- Jie Wu
- Bioinformatics at Harbin Medical University, China
| | - Li Zhang
- Bioinformatics at Harbin Medical University, China
| | - Qian Song
- Bioinformatics at Harbin Medical University, China
| | - Lei Yu
- Bioinformatics at Harbin Medical University, China
| | - Shuyuan Wang
- Bioinformatics at Harbin Medical University, China
| | - Bo Zhang
- Bioinformatics at Harbin Medical University, China
| | - Weida Wang
- Bioinformatics at Harbin Medical University, China
| | - Peng Xia
- Bioinformatics at Harbin Medical University, China
| | - Xiaowen Chen
- Bioinformatics at Harbin Medical University, China
| | - Yun Xiao
- Bioinformatics at Harbin Medical University, China
| | - Chaohan Xu
- Bioinformatics at Harbin Medical University, China
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23
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Gan W, Luo J, Li YZ, Guo JL, Zhu M, Li ML. A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information. BMC Genomics 2019; 20:980. [PMID: 31881832 PMCID: PMC6933632 DOI: 10.1186/s12864-019-6303-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background The three-dimensional (3D) structure of chromatins plays significant roles during cell differentiation and development. Hi-C and other 3C-based technologies allow us to look deep into the chromatin architectures. Many studies have suggested that topologically associating domains (TAD), as the structure and functional unit, are conserved across different organs. However, our understanding about the underlying mechanism of the TAD boundary formation is still limited. Results We developed a computational method, TAD–Lactuca, to infer this structure by taking the contextual information of the epigenetic modification signals and the primary DNA sequence information on the genome. TAD–Lactuca is found stable in the case of multi-resolutions and different datasets. It could achieve high accuracy and even outperforms the state-of-art methods when the sequence patterns were incorporated. Moreover, several transcript factor binding motifs, besides the well-known CCCTC-binding factor (CTCF) motif, were found significantly enriched on the boundaries. Conclusions We provided a low cost, effective method to predict TAD boundaries. Above results suggested the incorporation of sequence features could significantly improve the performance. The sequence motif enrichment analysis indicates several gene regulation motifs around the boundaries, which is consistent with TADs may serve as the functional units of gene regulation and implies the sequence patterns would be important in chromatin folding.
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Affiliation(s)
- Wei Gan
- College of Computer Science, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Juan Luo
- College of Chemistry, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Yi Zhou Li
- College of Cybersecurity, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jia Li Guo
- College of Chemistry, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Min Zhu
- College of Computer Science, Sichuan University, Chengdu, 610064, People's Republic of China.
| | - Meng Long Li
- College of Chemistry, Sichuan University, Chengdu, 610064, People's Republic of China.
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24
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Guarasci F, D'Aquila P, Montesanto A, Corsonello A, Bellizzi D, Passarino G. Individual DNA Methylation Profile is Correlated with Age and can be Targeted to Modulate Healthy Aging and Longevity. Curr Pharm Des 2019; 25:4139-4149. [DOI: 10.2174/1381612825666191112095655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023]
Abstract
:Patterns of DNA methylation, the best characterized epigenetic modification, are modulated by aging. In humans, different studies at both site-specific and genome-wide levels have reported that modifications of DNA methylation are associated with the chronological aging process but also with the quality of aging (or biological aging), providing new perspectives for establishing powerful biomarkers of aging.:In this article, the role of DNA methylation in aging and longevity has been reviewed by analysing literature data about DNA methylation variations occurring during the lifetime in response to environmental factors and genetic background, and their association with the aging process and, in particular, with the quality of aging. Special attention has been devoted to the relationship between nuclear DNA methylation patterns, mitochondrial DNA epigenetic modifications, and longevity. Mitochondrial DNA has recently been reported to modulate global DNA methylation levels of the nuclear genome during the lifetime, and, in spite of the previous belief, it has been found to be the target of methylation modifications.:Analysis of DNA methylation profiles across lifetime shows that a remodeling of the methylome occurs with age and/or with age-related decline. Thus, it can be an excellent biomarker of aging and of the individual decline and frailty status. The knowledge about the mechanisms underlying these modifications is crucial since it might allow the opportunity for targeted treatment to modulate the rate of aging and longevity.
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Affiliation(s)
- Francesco Guarasci
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Patrizia D'Aquila
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Andrea Corsonello
- Unit of Geriatric Pharmacoepidemiology, Scientific Research Institute - Italian National Research Center on Aging (IRCCS INRCA), Cosenza, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
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25
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Berest I, Arnold C, Reyes-Palomares A, Palla G, Rasmussen KD, Giles H, Bruch PM, Huber W, Dietrich S, Helin K, Zaugg JB. Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF. Cell Rep 2019; 29:3147-3159.e12. [DOI: 10.1016/j.celrep.2019.10.106] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 09/20/2019] [Accepted: 10/28/2019] [Indexed: 12/26/2022] Open
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26
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Horvath A, Daniel B, Szeles L, Cuaranta-Monroy I, Czimmerer Z, Ozgyin L, Steiner L, Kiss M, Simandi Z, Poliska S, Giannakis N, Raineri E, Gut IG, Nagy B, Nagy L. Labelled regulatory elements are pervasive features of the macrophage genome and are dynamically utilized by classical and alternative polarization signals. Nucleic Acids Res 2019; 47:2778-2792. [PMID: 30799488 PMCID: PMC6451134 DOI: 10.1093/nar/gkz118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/14/2019] [Indexed: 01/09/2023] Open
Abstract
The concept of tissue-specific gene expression posits that lineage-determining transcription factors (LDTFs) determine the open chromatin profile of a cell via collaborative binding, providing molecular beacons to signal-dependent transcription factors (SDTFs). However, the guiding principles of LDTF binding, chromatin accessibility and enhancer activity have not yet been systematically evaluated. We sought to study these features of the macrophage genome by the combination of experimental (ChIP-seq, ATAC-seq and GRO-seq) and computational approaches. We show that Random Forest and Support Vector Regression machine learning methods can accurately predict chromatin accessibility using the binding patterns of the LDTF PU.1 and four other key TFs of macrophages (IRF8, JUNB, CEBPA and RUNX1). Any of these TFs alone were not sufficient to predict open chromatin, indicating that TF binding is widespread at closed or weakly opened chromatin regions. Analysis of the PU.1 cistrome revealed that two-thirds of PU.1 binding occurs at low accessible chromatin. We termed these sites labelled regulatory elements (LREs), which may represent a dormant state of a future enhancer and contribute to macrophage cellular plasticity. Collectively, our work demonstrates the existence of LREs occupied by various key TFs, regulating specific gene expression programs triggered by divergent macrophage polarizing stimuli.
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Affiliation(s)
- Attila Horvath
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Bence Daniel
- Johns Hopkins University School of Medicine, Department of Medicine and Biological Chemistry, Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, Saint Petersburg, FL 33701, USA
| | - Lajos Szeles
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Ixchelt Cuaranta-Monroy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Zsolt Czimmerer
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Lilla Ozgyin
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Laszlo Steiner
- UD-GenoMed Medical Genomic Technologies Ltd., Nagyerdei krt. 98., H-4032 Debrecen, Hungary
| | - Mate Kiss
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Zoltan Simandi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Szilard Poliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.,UD-GenoMed Medical Genomic Technologies Ltd., Nagyerdei krt. 98., H-4032 Debrecen, Hungary
| | - Nikolas Giannakis
- UD-GenoMed Medical Genomic Technologies Ltd., Nagyerdei krt. 98., H-4032 Debrecen, Hungary
| | - Emanuele Raineri
- Centro Nacional de Analisis Genomico (CNAG-CRG), Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), C/Baldiri Reixac 4, 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002, Barcelona, Spain
| | - Ivo G Gut
- Centro Nacional de Analisis Genomico (CNAG-CRG), Center for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), C/Baldiri Reixac 4, 08028 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, 08002, Barcelona, Spain
| | - Benedek Nagy
- Department of Mathematics, Eastern Mediterranean University, Famagusta, North Cyprus, Mersin 10, Turkey
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.,Johns Hopkins University School of Medicine, Department of Medicine and Biological Chemistry, Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, Saint Petersburg, FL 33701, USA
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27
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Huilgol D, Venkataramani P, Nandi S, Bhattacharjee S. Transcription Factors That Govern Development and Disease: An Achilles Heel in Cancer. Genes (Basel) 2019; 10:E794. [PMID: 31614829 PMCID: PMC6826716 DOI: 10.3390/genes10100794] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/22/2022] Open
Abstract
Development requires the careful orchestration of several biological events in order to create any structure and, eventually, to build an entire organism. On the other hand, the fate transformation of terminally differentiated cells is a consequence of erroneous development, and ultimately leads to cancer. In this review, we elaborate how development and cancer share several biological processes, including molecular controls. Transcription factors (TF) are at the helm of both these processes, among many others, and are evolutionarily conserved, ranging from yeast to humans. Here, we discuss four families of TFs that play a pivotal role and have been studied extensively in both embryonic development and cancer-high mobility group box (HMG), GATA, paired box (PAX) and basic helix-loop-helix (bHLH) in the context of their role in development, cancer, and their conservation across several species. Finally, we review TFs as possible therapeutic targets for cancer and reflect on the importance of natural resistance against cancer in certain organisms, yielding knowledge regarding TF function and cancer biology.
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Affiliation(s)
- Dhananjay Huilgol
- Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA.
| | | | - Saikat Nandi
- Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA.
| | - Sonali Bhattacharjee
- Bungtown Road, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA.
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28
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Lin Y, Li Y, Zhu X, Huang Y, Li Y, Li M. Genetic Contexts Characterize Dynamic Histone Modification Patterns Among Cell Types. Interdiscip Sci 2019; 11:698-710. [PMID: 31165438 DOI: 10.1007/s12539-019-00338-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/18/2019] [Accepted: 05/27/2019] [Indexed: 11/29/2022]
Abstract
Histone modifications play critical roles in mammalian development, regulating chromatin structure and gene expression. Dynamic histone modifications among cell types have been shown to associate with changes in mammalian development. However, how to quantitatively measure the histone modification alterations and how histone modifications vary across cell types under different genetic contexts remain largely unexplored and whether these changes are related to the primary DNA sequence remains limited. Here, we employed an entropy-based method to measure histone modification alterations in six definite genomic regions across five cell types and identified lineage-specific histone modification genes. We observed that histone modification alterations prefer to enrich in 5'-UTR exons, and also in 3'-UTR exons and its downstream. Then we built a model to predict the histone modification patterns from the primary DNA sequence. We found that the frequencies of k-mer sequence compositions are predictive of histone modification patterns, suggesting that the primary DNA sequence correlated with the histone modification alterations among cell types. Additionally, the lineage-specific histone modification genes display a higher conservation and lower GC-content. Together, we performed a systematic analysis for histone modification alterations and demonstrated how to identify genomic region-specific elements of epigenetic and genetic regulation and histone modification patterns across different cell types.
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Affiliation(s)
- Yanmei Lin
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yan Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Xingyong Zhu
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yuyao Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yizhou Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China. .,College of Cybersecurity, Sichuan University, Chengdu, 610064, Sichuan, China.
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
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29
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Epigenetic Reprogramming of TGF-β Signaling in Breast Cancer. Cancers (Basel) 2019; 11:cancers11050726. [PMID: 31137748 PMCID: PMC6563130 DOI: 10.3390/cancers11050726] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 12/16/2022] Open
Abstract
The Transforming Growth Factor-β (TGF-β) signaling pathway has a well-documented, context-dependent role in breast cancer development. In normal and premalignant cells, it acts as a tumor suppressor. By contrast, during the malignant phases of breast cancer progression, the TGF-β signaling pathway elicits tumor promoting effects particularly by driving the epithelial to mesenchymal transition (EMT), which enhances tumor cell migration, invasion and ultimately metastasis to distant organs. The molecular and cellular mechanisms that govern this dual capacity are being uncovered at multiple molecular levels. This review will focus on recent advances relating to how epigenetic changes such as acetylation and methylation control the outcome of TGF-β signaling and alter the fate of breast cancer cells. In addition, we will highlight how this knowledge can be further exploited to curb tumorigenesis by selective targeting of the TGF-β signaling pathway.
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30
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Zhao X, Yin H, Li N, Zhu Y, Shen W, Qian S, He G, Li J, Wang X. An Integrated Regulatory Network Based on Comprehensive Analysis of mRNA Expression, Gene Methylation and Expression of Long Non-coding RNAs (lncRNAs) in Myelodysplastic Syndromes. Front Oncol 2019; 9:200. [PMID: 30984623 PMCID: PMC6450213 DOI: 10.3389/fonc.2019.00200] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/08/2019] [Indexed: 12/12/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of disorders characterized by ineffective hematopoiesis, defective differentiation of hematopoietic precursors, and expansion of the abnormal clones. The prevalence of MDS has raised great concerns worldwide, but its pathogenetic mechanisms remain elusive. To provide insights on novel biomarkers for the diagnosis and therapy of MDS, we performed high-throughput genome-wide mRNA expression profiling, DNA methylation analysis, and long non-coding RNAs (lncRNA) analysis on bone marrows from four MDS patients and four age-matched healthy controls. We identified 1,937 differentially expressed genes (DEGs), 515 methylated genes, and 214 lncRNA that showed statistically significant differences. As the most significant module-related DEGs, TCL1A, PTGS2, and MME were revealed to be enriched in regulation of cell differentiation and cell death pathways. In addition, the GeneGo pathway maps identified by top DEGs were shown to converge on cancer, immunoregulation, apoptosis and regulation of actin cytoskeleton, most of which are known contributors in MDS etiology and pathogenesis. Notably, as potential biomarkers for diagnosis of MDS, four specific genes (ABAT, FADD, DAPP1, and SMPD3) were further subjected to detailed pathway analysis. Our integrative analysis on mRNA expression, gene methylation and lncRNAs profiling facilitates further understanding of the pathogenesis of MDS, and may promote the diagnosis and novel therapeutics for this disease.
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Affiliation(s)
- Xiaoli Zhao
- Key Laboratory of Hematology, Department of Hematology, Collaborative Innovation Center for Cancer Personalized Medicine, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China.,Department of Haematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Hua Yin
- Key Laboratory of Hematology, Department of Hematology, Collaborative Innovation Center for Cancer Personalized Medicine, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Nianyi Li
- Department of Haematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yu Zhu
- Key Laboratory of Hematology, Department of Hematology, Collaborative Innovation Center for Cancer Personalized Medicine, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Wenyi Shen
- Key Laboratory of Hematology, Department of Hematology, Collaborative Innovation Center for Cancer Personalized Medicine, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Sixuan Qian
- Key Laboratory of Hematology, Department of Hematology, Collaborative Innovation Center for Cancer Personalized Medicine, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Guangsheng He
- Key Laboratory of Hematology, Department of Hematology, Collaborative Innovation Center for Cancer Personalized Medicine, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Jianyong Li
- Key Laboratory of Hematology, Department of Hematology, Collaborative Innovation Center for Cancer Personalized Medicine, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, China
| | - Xiaoqin Wang
- Department of Haematology, Huashan Hospital, Fudan University, Shanghai, China
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31
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van der Kroef M, Castellucci M, Mokry M, Cossu M, Garonzi M, Bossini-Castillo LM, Chouri E, Wichers CGK, Beretta L, Trombetta E, Silva-Cardoso S, Vazirpanah N, Carvalheiro T, Angiolilli C, Bekker CPJ, Affandi AJ, Reedquist KA, Bonte-Mineur F, Zirkzee EJM, Bazzoni F, Radstake TRDJ, Rossato M. Histone modifications underlie monocyte dysregulation in patients with systemic sclerosis, underlining the treatment potential of epigenetic targeting. Ann Rheum Dis 2019; 78:529-538. [PMID: 30793699 DOI: 10.1136/annrheumdis-2018-214295] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/24/2018] [Accepted: 01/02/2019] [Indexed: 01/23/2023]
Abstract
BACKGROUND AND OBJECTIVE Systemic sclerosis (SSc) is a severe autoimmune disease, in which the pathogenesis is dependent on both genetic and epigenetic factors. Altered gene expression in SSc monocytes, particularly of interferon (IFN)-responsive genes, suggests their involvement in SSc development. We investigated the correlation between epigenetic histone marks and gene expression in SSc monocytes. METHODS Chromatin immunoprecipitation followed by sequencing (ChIPseq) for histone marks H3K4me3 and H3K27ac was performed on monocytes of nine healthy controls and 14 patients with SSc. RNA sequencing was performed in parallel to identify aberrantly expressed genes and their correlation with the levels of H3K4me3 and H3K27ac located nearby their transcription start sites. ChIP-qPCR assays were used to verify the role of bromodomain proteins, H3K27ac and STATs on IFN-responsive gene expression. RESULTS 1046 and 534 genomic loci showed aberrant H3K4me3 and H3K27ac marks, respectively, in SSc monocytes. The expression of 381 genes was directly and significantly proportional to the levels of such chromatin marks present near their transcription start site. Genes correlated to altered histone marks were enriched for immune, IFN and antiviral pathways and presented with recurrent binding sites for IRF and STAT transcription factors at their promoters. IFNα induced the binding of STAT1 and STAT2 at the promoter of two of these genes, while blocking acetylation readers using the bromodomain BET family inhibitor JQ1 suppressed their expression. CONCLUSION SSc monocytes have altered chromatin marks correlating with their IFN signature. Enzymes modulating these reversible marks may provide interesting therapeutic targets to restore monocyte homeostasis to treat or even prevent SSc.
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Affiliation(s)
- Maarten van der Kroef
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Monica Castellucci
- Division of General Pathology, Department of Medicine, University of Verona, Verona, Italy
| | - Michal Mokry
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marta Cossu
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marianna Garonzi
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Lara M Bossini-Castillo
- Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Instituto de Parasitología y Biomedicina López-Neyra, PTS Granada, Granada, Spain.,Department of cellular genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Eleni Chouri
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Catharina G K Wichers
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Elena Trombetta
- Flow Cytometry Service, Analysis Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Sandra Silva-Cardoso
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nadia Vazirpanah
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Tiago Carvalheiro
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Chiara Angiolilli
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Cornelis P J Bekker
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Alsya J Affandi
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Kris A Reedquist
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Femke Bonte-Mineur
- Department of Rheumatology and Clinical Immunology, Maasstad Hospital, Rotterdam, The Netherlands
| | - Els J M Zirkzee
- Department of Rheumatology and Clinical Immunology, Maasstad Hospital, Rotterdam, The Netherlands
| | - Flavia Bazzoni
- Division of General Pathology, Department of Medicine, University of Verona, Verona, Italy
| | - Timothy R D J Radstake
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands .,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marzia Rossato
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Biotechnology, University of Verona, Verona, Italy
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32
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Banerjee S, Zhu H, Tang M, Feng WC, Wu X, Xie H. Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells. Front Genet 2019; 9:731. [PMID: 30697231 PMCID: PMC6341026 DOI: 10.3389/fgene.2018.00731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/22/2018] [Indexed: 12/19/2022] Open
Abstract
Gene expression regulation is a complex process involving the interplay between transcription factors and chromatin states. Significant progress has been made toward understanding the impact of chromatin states on gene expression. Nevertheless, the mechanism of transcription factors binding combinatorially in different chromatin states to enable selective regulation of gene expression remains an interesting research area. We introduce a nonparametric Bayesian clustering method for inhomogeneous Poisson processes to detect heterogeneous binding patterns of multiple proteins including transcription factors to form regulatory modules in different chromatin states. We applied this approach on ChIP-seq data for mouse neural stem cells containing 21 proteins and observed different groups or modules of proteins clustered within different chromatin states. These chromatin-state-specific regulatory modules were found to have significant influence on gene expression. We also observed different motif preferences for certain TFs between different chromatin states. Our results reveal a degree of interdependency between chromatin states and combinatorial binding of proteins in the complex transcriptional regulatory process. The software package is available on Github at - https://github.com/BSharmi/DPM-LGCP.
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Affiliation(s)
- Sharmi Banerjee
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, United States.,Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States
| | - Hongxiao Zhu
- Department of Statistics, Virginia Tech, Blacksburg, VA, United States
| | - Man Tang
- Department of Statistics, Virginia Tech, Blacksburg, VA, United States
| | - Wu-Chun Feng
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
| | - Xiaowei Wu
- Department of Statistics, Virginia Tech, Blacksburg, VA, United States
| | - Hehuang Xie
- Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States.,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, United States.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States.,School of Neuroscience, Virginia Tech, Blacksburg, VA, United States
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Zhang L, Xue G, Liu J, Li Q, Wang Y. Revealing transcription factor and histone modification co-localization and dynamics across cell lines by integrating ChIP-seq and RNA-seq data. BMC Genomics 2018; 19:914. [PMID: 30598100 PMCID: PMC6311957 DOI: 10.1186/s12864-018-5278-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Interactions among transcription factors (TFs) and histone modifications (HMs) play an important role in the precise regulation of gene expression. The context specificity of those interactions and further its dynamics in normal and disease remains largely unknown. Recent development in genomics technology enables transcription profiling by RNA-seq and protein’s binding profiling by ChIP-seq. Integrative analysis of the two types of data allows us to investigate TFs and HMs interactions both from the genome co-localization and downstream target gene expression. Results We propose a integrative pipeline to explore the co-localization of 55 TFs and 11 HMs and its dynamics in human GM12878 and K562 by matched ChIP-seq and RNA-seq data from ENCODE. We classify TFs and HMs into three types based on their binding enrichment around transcription start site (TSS). Then a set of statistical indexes are proposed to characterize the TF-TF and TF-HM co-localizations. We found that Rad21, SMC3, and CTCF co-localized across five cell lines. High resolution Hi-C data in GM12878 shows that they associate most of the Hi-C peak loci with a specific CTCF-motif “anchor” and supports that CTCF, SMC3, and RAD2 co-localization serves important role in 3D chromatin structure. Meanwhile, 17 TF-TF pairs are highly dynamic between GM12878 and K562. We then build SVM models to correlate high and low expression level of target genes with TF binding and HM strength. We found that H3k9ac, H3k27ac, and three TFs (ELF1, TAF1, and POL2) are predictive with the accuracy about 85~92%. Conclusion We propose a pipeline to analyze the co-localization of TF and HM and their dynamics across cell lines from ChIP-seq, and investigate their regulatory potency by RNA-seq. The integrative analysis of two level data reveals new insight for the cooperation of TFs and HMs and is helpful in understanding cell line specificity of TF/HM interactions. Electronic supplementary material The online version of this article (10.1186/s12864-018-5278-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lirong Zhang
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, China.
| | - Gaogao Xue
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, China
| | - Junjie Liu
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, China
| | - Qianzhong Li
- School of Physical Science and Technology, Inner Mongolia University, Hohhot, Inner Mongolia, 010021, China.
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China. .,School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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Liu Z, Gao Y, Li X. Cancer epigenetics and the potential of epigenetic drugs for treating solid tumors. Expert Rev Anticancer Ther 2018; 19:139-149. [PMID: 30470148 DOI: 10.1080/14737140.2019.1552139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction: Epigenetic modification without DNA sequence mutation plays an important role in cancer development. Some small molecular inhibitors targeting key epigenetic molecules have been approved by the Food and Drug Administration to treat hematological malignancies. However, the anticancer effects of these drugs on solid tumors are not satisfactory, and the mechanisms of action remain largely unknown. Areas covered: The review summarizes the latest research on cancer epigenetics and discusses the potentials and limitations of using epigenetic drugs to treat solid tumors. An analysis of possible reasons for epigenetic drug treatment failure in solid tumors in some clinical trials is discussed along with prospects for future development. Expert commentary: Next-generation small molecule inhibitors will target novel epigenetic regulators with high cancer specificity. Combined modalities exploiting epigenetic drugs with chemo-/radiotherapy, molecular-targeting drugs, and immunotherapy will be able to effectively treat solid tumors in the near future.
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Affiliation(s)
- Zhenghui Liu
- a Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - Yingxue Gao
- a Xiangya Hospital, Central South University , Changsha , Hunan , China
| | - Xiong Li
- a Xiangya Hospital, Central South University , Changsha , Hunan , China
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35
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Xu Y, Zhao W, Olson SD, Prabhakara KS, Zhou X. Alternative splicing links histone modifications to stem cell fate decision. Genome Biol 2018; 19:133. [PMID: 30217220 PMCID: PMC6138936 DOI: 10.1186/s13059-018-1512-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Understanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-messenger RNA splicing, and cell-cycle progression. However, their intricate interrelations and joint contributions to ESC fate decision remain unclear. RESULTS We analyze the transcriptomes and epigenomes of human ESC and five types of differentiated cells. We identify thousands of alternatively spliced exons and reveal their development and lineage-dependent characterizations. Several histone modifications show dynamic changes in alternatively spliced exons and three are strongly associated with 52.8% of alternative splicing events upon hESC differentiation. The histone modification-associated alternatively spliced genes predominantly function in G2/M phases and ATM/ATR-mediated DNA damage response pathway for cell differentiation, whereas other alternatively spliced genes are enriched in the G1 phase and pathways for self-renewal. These results imply a potential epigenetic mechanism by which some histone modifications contribute to ESC fate decision through the regulation of alternative splicing in specific pathways and cell-cycle genes. Supported by experimental validations and extended datasets from Roadmap/ENCODE projects, we exemplify this mechanism by a cell-cycle-related transcription factor, PBX1, which regulates the pluripotency regulatory network by binding to NANOG. We suggest that the isoform switch from PBX1a to PBX1b links H3K36me3 to hESC fate determination through the PSIP1/SRSF1 adaptor, which results in the exon skipping of PBX1. CONCLUSION We reveal the mechanism by which alternative splicing links histone modifications to stem cell fate decision.
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Affiliation(s)
- Yungang Xu
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
- Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
- Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
| | - Scott D. Olson
- Department of Pediatric Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Karthik S. Prabhakara
- Department of Pediatric Surgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
- Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157 USA
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36
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Genome-wide analysis of H3K36me3 and its regulations to cancer-related genes expression in human cell lines. Biosystems 2018; 171:59-65. [DOI: 10.1016/j.biosystems.2018.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/01/2018] [Accepted: 07/09/2018] [Indexed: 01/11/2023]
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37
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Lambert M, Jambon S, Depauw S, David-Cordonnier MH. Targeting Transcription Factors for Cancer Treatment. Molecules 2018; 23:molecules23061479. [PMID: 29921764 PMCID: PMC6100431 DOI: 10.3390/molecules23061479] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022] Open
Abstract
Transcription factors are involved in a large number of human diseases such as cancers for which they account for about 20% of all oncogenes identified so far. For long time, with the exception of ligand-inducible nuclear receptors, transcription factors were considered as “undruggable” targets. Advances knowledge of these transcription factors, in terms of structure, function (expression, degradation, interaction with co-factors and other proteins) and the dynamics of their mode of binding to DNA has changed this postulate and paved the way for new therapies targeted against transcription factors. Here, we discuss various ways to target transcription factors in cancer models: by modulating their expression or degradation, by blocking protein/protein interactions, by targeting the transcription factor itself to prevent its DNA binding either through a binding pocket or at the DNA-interacting site, some of these inhibitors being currently used or evaluated for cancer treatment. Such different targeting of transcription factors by small molecules is facilitated by modern chemistry developing a wide variety of original molecules designed to specifically abort transcription factor and by an increased knowledge of their pathological implication through the use of new technologies in order to make it possible to improve therapeutic control of transcription factor oncogenic functions.
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Affiliation(s)
- Mélanie Lambert
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Samy Jambon
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Sabine Depauw
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Marie-Hélène David-Cordonnier
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
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38
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Lyu G, Zhang C, Ling T, Liu R, Zong L, Guan Y, Huang X, Sun L, Zhang L, Li C, Nie Y, Tao W. Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease. BMC Genomics 2018; 19:428. [PMID: 29866040 PMCID: PMC5987557 DOI: 10.1186/s12864-018-4814-7] [Citation(s) in RCA: 26] [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: 06/23/2017] [Accepted: 05/22/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is the leading non-infectious cause of death in infants. Monozygotic (MZ) twins share nearly all of their genetic variants before and after birth. Nevertheless, MZ twins are sometimes discordant for common complex diseases. The goal of this study is to identify genomic and epigenomic differences between a pair of twins discordant for a form of congenital heart disease, double outlet right ventricle (DORV). RESULTS A monoamniotic monozygotic (MZ) twin pair discordant for DORV were subjected to genome-wide sequencing and methylation analysis. We identified few genomic differences but 1566 differentially methylated regions (DMRs) between the MZ twins. Twenty percent (312/1566) of the DMRs are located within 2 kb upstream of transcription start sites (TSS), containing 121 binding sites of transcription factors. Particularly, ZIC3 and NR2F2 are found to have hypermethylated promoters in both the diseased twin and additional patients suffering from DORV. CONCLUSIONS The results showed a high correlation between hypermethylated promoters at ZIC3 and NR2F2 and down-regulated gene expression levels of these two genes in patients with DORV compared to normal controls, providing new insight into the potential mechanism of this rare form of CHD.
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Affiliation(s)
- Guoliang Lyu
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Chao Zhang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Te Ling
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Rui Liu
- Department of Cardiovascular Surgery, Center for Cardiovascular Regenerative Medicine, Fuwai Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100871 China
| | - Le Zong
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yiting Guan
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Xiaoke Huang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Lei Sun
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Lijun Zhang
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yu Nie
- Department of Cardiovascular Surgery, Center for Cardiovascular Regenerative Medicine, Fuwai Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100871 China
| | - Wei Tao
- Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
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Liu K, Beck D, Thoms JAI, Liu L, Zhao W, Pimanda JE, Zhou X. Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method. Bioinformatics 2018; 33:2622-2630. [PMID: 28472271 DOI: 10.1093/bioinformatics/btx280] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 04/22/2017] [Indexed: 02/01/2023] Open
Abstract
Motivation Long non-coding RNAs (lncRNAs) have been implicated in the regulation of diverse biological functions. The number of newly identified lncRNAs has increased dramatically in recent years but their expression and function have not yet been described from most diseases. To elucidate lncRNA function in human disease, we have developed a novel network based method (NLCFA) integrating correlations between lncRNA, protein coding genes and noncoding miRNAs. We have also integrated target gene associations and protein-protein interactions and designed our model to provide information on the combined influence of mRNAs, lncRNAs and miRNAs on cellular signal transduction networks. Results We have generated lncRNA expression profiles from the CD34+ haematopoietic stem and progenitor cells (HSPCs) from patients with Myelodysplastic syndromes (MDS) and healthy donors. We report, for the first time, aberrantly expressed lncRNAs in MDS and further prioritize biologically relevant lncRNAs using the NLCFA. Taken together, our data suggests that aberrant levels of specific lncRNAs are intimately involved in network modules that control multiple cancer-associated signalling pathways and cellular processes. Importantly, our method can be applied to prioritize aberrantly expressed lncRNAs for functional validation in other diseases and biological contexts. Availability and implementation The method is implemented in R language and Matlab. Contact xizhou@wakehealth.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Keqin Liu
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Dominik Beck
- Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, 2052, Australia.,Centre for Health Technologies and School of Software, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Julie A I Thoms
- Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, 2052, Australia
| | - Liang Liu
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Weiling Zhao
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - John E Pimanda
- Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, 2052, Australia.,Centre for Health Technologies and School of Software, University of Technology Sydney, Sydney, NSW, 2007, Australia.,Department of Haematology, Prince of Wales Hospital, Randwick, NSW, 2031, Australia
| | - Xiaobo Zhou
- Department of Radiology, Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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Homocysteine induces vascular inflammatory response via SMAD7 hypermethylation in human umbilical vein smooth muscle cells. Microvasc Res 2018; 120:8-12. [PMID: 29777793 DOI: 10.1016/j.mvr.2018.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 04/14/2018] [Accepted: 05/13/2018] [Indexed: 12/21/2022]
Abstract
Homocysteine (Hcy) can induce atherosclerosis through the inflammatory response and DNA methylation disorder. Our recent study has reported a novel epigenetic modified gene related to atherosclerosis -SMAD7. To further understand the pathogenesis of atherosclerosis, the current study was designed to investigate an inflammatory role of Hcy in human umbilical vein smooth muscle cells (HUVSMCs) through interfering with SMAD7 methylation. Using MALDI-TOF MS, we found that Hcy increased DNA methylation levels of SMAD7 promoter in a dose and time-dependent manner in HUVSMCs. Meanwhile, both SMAD7 mRNA and protein levels were decreased along with the increase of Hcy concentrations and treating time. Decreased SMAD7 levels led to up regulation of pro-inflammatory cytokines (TNF-α and IL-1β) expression in HUVSMCs. Furthermore, we found that activation of NF-κB pathway was the mechanism by which reduced Smad7 levels enhanced vascular inflammation. Thus, Hcy is able to activate NF-κB-mediated vascular inflammatory response via inducing hypermethylation of SMAD7 promoter in HUVSMCs. The in vitro findings supplement our recent clinical study that SMAD7 methylation as a novel marker in atherosclerosis and further elucidate the role of Hcy in atherogenesis.
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41
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Feng ZX, Li QZ, Meng JJ. Recognition of the long range enhancer-promoter interactions by further adding DNA structure properties and transcription factor binding motifs in human cell lines. J Theor Biol 2018; 445:136-150. [PMID: 29476833 DOI: 10.1016/j.jtbi.2018.02.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/07/2018] [Accepted: 02/20/2018] [Indexed: 11/17/2022]
Abstract
The enhancer-promoter interactions (EPIs) with strong tissue-specificity play an important role in cis-regulatory mechanism of human cell lines. However, it still remains a challenging work to predict these interactions so far. Due to that these interactions are regulated by the cooperativeness of diverse functional genomic signatures, DNA spatial structure and DNA sequence elements. In this paper, by adding DNA structure properties and transcription factor binding motifs, we presented an improved computational method to predict EPIs in human cell lines. In comparison with the results of other group on the same datasets, our best accuracies by cross-validation test were about 15%-24% higher in the same cell lines, and the accuracies by independent test were about 11%-15% higher in new cell lines. Meanwhile, we found that transcription factor binding motifs and DNA structure properties have important information that would largely determine long range EPIs prediction. From the distribution comparisons, we also found their distinct differences between interacting and non-interacting sets in each cell line. Then, the correlation analysis and network models for relationships among top-ranked functional genomic signatures indicated that diverse genomic signatures would cooperatively establish a complex regulatory network to facilitate long range EPIs. The experimental results provided additional insights about the roles of DNA intrinsic properties and functional genomic signatures in EPIs prediction.
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Affiliation(s)
- Zhen-Xing Feng
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China; The State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China.
| | - Jian-Jun Meng
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
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42
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Pursani V, Bhartiya D, Tanavde V, Bashir M, Sampath P. Transcriptional activator DOT1L putatively regulates human embryonic stem cell differentiation into the cardiac lineage. Stem Cell Res Ther 2018; 9:97. [PMID: 29631608 PMCID: PMC5891944 DOI: 10.1186/s13287-018-0810-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 02/12/2018] [Accepted: 02/20/2018] [Indexed: 01/09/2023] Open
Abstract
Background Commitment of pluripotent stem cells into differentiated cells and associated gene expression necessitate specific epigenetic mechanisms that modify the DNA and corresponding histone proteins to render the chromatin in an open or closed state. This in turn dictates the associated genetic machinery, including transcription factors, acknowledging the cellular signals provided. Activating histone methyltransferases represent crucial enzymes in the epigenetic machinery that cause transcription initiation by delivering the methyl mark on histone proteins. A number of studies have evidenced the vital role of one such histone modifier, DOT1L, in transcriptional regulation. Involvement of DOT1L in differentiating pluripotent human embryonic stem (hES) cells into the cardiac lineage has not yet been investigated. Methods The study was conducted on in-house derived (KIND1) and commercially available (HES3) human embryonic stem cell lines. Chromatin immunoprecipitation (ChIP) was performed followed by sequencing to uncover the cardiac genes harboring the DOT1L specific mark H3K79me2. Following this, dual immunofluorescence was employed to show the DOT1L co-occupancy along with the cardiac progenitor specific marker. DOT1L was knocked down by siRNA to further confirm its role during cardiac differentiation. Results ChIP sequencing revealed a significant number of peaks characterizing H3K79me2 occupancy in the proximity of the transcription start site. This included genes like MYOF, NR2F2, NKX2.5, and HAND1 in cardiac progenitors and cardiomyocytes, and POU5F1 and NANOG in pluripotent hES cells. Consistent with this observation, we also show that DOT1L co-localizes with the master cardiac transcription factor NKX2.5, suggesting its direct involvement during gene activation. Knockdown of DOT1L did not alter the pluripotency of hES cells, but it led to the disruption of cardiac differentiation observed morphologically as well as at transcript and protein levels. Conclusions Collectively, our data suggests the crucial role of H3K79me2 methyltransferase DOT1L for activation of NKX2.5 during the cardiac differentiation of hES cells. Electronic supplementary material The online version of this article (10.1186/s13287-018-0810-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Varsha Pursani
- Stem Cell Biology Department, ICMR-National Institute for Research in Reproductive Health, J.M. Street, Parel, Mumbai, Maharashtra, 400 012, India
| | - Deepa Bhartiya
- Stem Cell Biology Department, ICMR-National Institute for Research in Reproductive Health, J.M. Street, Parel, Mumbai, Maharashtra, 400 012, India.
| | - Vivek Tanavde
- Division of Biological & Life Sciences, School of Arts & Sciences, Ahmedabad University, Ahmedabad, 380009, India.,Genome and Gene Expression Data Analysis Division, A* Star-Bioinformatics Institute, Singapore, 138671, Singapore
| | - Mohsin Bashir
- Division of Translational Control of Disease, A* Star-Institute of Medical Biology, Singapore, 138648, Singapore
| | - Prabha Sampath
- Division of Translational Control of Disease, A* Star-Institute of Medical Biology, Singapore, 138648, Singapore
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Xin B, Rohs R. Relationship between histone modifications and transcription factor binding is protein family specific. Genome Res 2018; 28:321-333. [PMID: 29326300 PMCID: PMC5848611 DOI: 10.1101/gr.220079.116] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 01/10/2018] [Indexed: 12/20/2022]
Abstract
The very small fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies focusing on BSs within DNA regulatory regions found correlations between HM patterns and TF binding specificities. However, a mechanistic understanding of TF-DNA binding specificity determinants is still not available. The ability to predict in vivo TF binding on a genome-wide scale requires the identification of features that determine TF binding based on evolutionary relationships of DNA binding proteins. To reveal protein family-dependent mechanisms of TF binding, we conducted comprehensive comparisons of HM patterns surrounding BSs and non-BSs with exactly matched core motifs for TFs in three cell lines: 33 TFs in GM12878, 37 TFs in K562, and 18 TFs in H1-hESC. These TFs displayed protein family-specific preferences for HM patterns surrounding BSs, with high agreement among cell lines. Moreover, compared to models based on DNA sequence and shape at flanking regions of BSs, HM-augmented quantitative machine-learning methods resulted in increased performance in a TF family-specific manner. Analysis of the relative importance of features in these models indicated that TFs, displaying larger HM pattern differences between BSs and non-BSs, bound DNA in an HM-specific manner on a protein family-specific basis. We propose that TF family-specific HM preferences reveal distinct mechanisms that assist in guiding TFs to their cognate BSs by altering chromatin structure and accessibility.
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Affiliation(s)
- Beibei Xin
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Remo Rohs
- Computational Biology and Bioinformatics Program, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
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44
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Wei L, Zhao S, Wang G, Zhang S, Luo W, Qin Z, Bi X, Tan Y, Meng M, Qin J, Qin H, Tian D, Zhang A. SMAD7 methylation as a novel marker in atherosclerosis. Biochem Biophys Res Commun 2018; 496:700-705. [DOI: 10.1016/j.bbrc.2018.01.121] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 01/18/2018] [Indexed: 12/22/2022]
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45
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Mitchell AC, Javidfar B, Pothula V, Ibi D, Shen EY, Peter CJ, Bicks L, Fehr T, Jiang Y, Brennand KJ, Neve RL, Gonzalez-Maeso J, Akbarian S. MEF2C transcription factor is associated with the genetic and epigenetic risk architecture of schizophrenia and improves cognition in mice. Mol Psychiatry 2018; 23:123-132. [PMID: 28115742 PMCID: PMC5966823 DOI: 10.1038/mp.2016.254] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 10/30/2016] [Accepted: 12/06/2016] [Indexed: 12/20/2022]
Abstract
Large-scale consortia mapping the genomic risk architectures of schizophrenia provide vast amounts of molecular information, with largely unexplored therapeutic potential. We harnessed publically available information from the Psychiatric Genomics Consortium, and report myocyte enhancer factor 2C (MEF2C) motif enrichment in sequences surrounding the top scoring single-nucleotide polymorphisms within risk loci contributing by individual small effect to disease heritability. Chromatin profiling at base-pair resolution in neuronal nucleosomes extracted from prefrontal cortex of 34 subjects, including 17 cases diagnosed with schizophrenia, revealed MEF2C motif enrichment within cis-regulatory sequences, including neuron-specific promoters and superenhancers, affected by histone H3K4 hypermethylation in disease cases. Vector-induced short- and long-term Mef2c upregulation in mouse prefrontal projection neurons consistently resulted in enhanced cognitive performance in working memory and object recognition paradigms at baseline and after psychotogenic drug challenge, in conjunction with remodeling of local connectivity. Neuronal genome tagging in vivo by Mef2c-Dam adenine methyltransferase fusion protein confirmed the link between cognitive enhancement and MEF2C occupancy at promoters harboring canonical and variant MEF2C motifs. The multilayered integrative approaches presented here provide a roadmap to uncover the therapeutic potential of transcriptional regulators for schizophrenia and related disorders.
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Affiliation(s)
- Amanda C. Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Behnam Javidfar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Venu Pothula
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Daisuke Ibi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Erica Y. Shen
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Cyril J. Peter
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Lucy Bicks
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Tristan Fehr
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Yan Jiang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kristen J. Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Rachael L. Neve
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge MA02139, USA
| | - Javier Gonzalez-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University Medical School, Richmond, Virginia 23298, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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Adnan M, Zheng W, Islam W, Arif M, Abubakar YS, Wang Z, Lu G. Carbon Catabolite Repression in Filamentous Fungi. Int J Mol Sci 2017; 19:ijms19010048. [PMID: 29295552 PMCID: PMC5795998 DOI: 10.3390/ijms19010048] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 12/18/2022] Open
Abstract
Carbon Catabolite Repression (CCR) has fascinated scientists and researchers around the globe for the past few decades. This important mechanism allows preferential utilization of an energy-efficient and readily available carbon source over relatively less easily accessible carbon sources. This mechanism helps microorganisms to obtain maximum amount of glucose in order to keep pace with their metabolism. Microorganisms assimilate glucose and highly favorable sugars before switching to less-favored sources of carbon such as organic acids and alcohols. In CCR of filamentous fungi, CreA acts as a transcription factor, which is regulated to some extent by ubiquitination. CreD-HulA ubiquitination ligase complex helps in CreA ubiquitination, while CreB-CreC deubiquitination (DUB) complex removes ubiquitin from CreA, which causes its activation. CCR of fungi also involves some very crucial elements such as Hexokinases, cAMP, Protein Kinase (PKA), Ras proteins, G protein-coupled receptor (GPCR), Adenylate cyclase, RcoA and SnfA. Thorough study of molecular mechanism of CCR is important for understanding growth, conidiation, virulence and survival of filamentous fungi. This review is a comprehensive revision of the regulation of CCR in filamentous fungi as well as an updated summary of key regulators, regulation of different CCR-dependent mechanisms and its impact on various physical characteristics of filamentous fungi.
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Affiliation(s)
- Muhammad Adnan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Waqar Islam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Muhammad Arif
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yakubu Saddeeq Abubakar
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Key Laboratory of Bio-Pesticides and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Xu Y, Wang Y, Luo J, Zhao W, Zhou X. Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision. Nucleic Acids Res 2017; 45:12100-12112. [PMID: 29036709 PMCID: PMC5716079 DOI: 10.1093/nar/gkx870] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 09/08/2017] [Accepted: 09/15/2017] [Indexed: 01/31/2023] Open
Abstract
Alternative splicing (AS) is a genetically and epigenetically regulated pre-mRNA processing to increase transcriptome and proteome diversity. Comprehensively decoding these regulatory mechanisms holds promise in getting deeper insights into a variety of biological contexts involving in AS, such as development and diseases. We assembled splicing (epi)genetic code, DeepCode, for human embryonic stem cell (hESC) differentiation by integrating heterogeneous features of genomic sequences, 16 histone modifications with a multi-label deep neural network. With the advantages of epigenetic features, DeepCode significantly improves the performance in predicting the splicing patterns and their changes during hESC differentiation. Meanwhile, DeepCode reveals the superiority of epigenomic features and their dominant roles in decoding AS patterns, highlighting the necessity of including the epigenetic properties when assembling a more comprehensive splicing code. Moreover, DeepCode allows the robust predictions across cell lineages and datasets. Especially, we identified a putative H3K36me3-regulated AS event leading to a nonsense-mediated mRNA decay of BARD1. Reduced BARD1 expression results in the attenuation of ATM/ATR signalling activities and further the hESC differentiation. These results suggest a novel candidate mechanism linking histone modifications to hESC fate decision. In addition, when trained in different contexts, DeepCode can be expanded to a variety of biological and biomedical fields.
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Affiliation(s)
- Yungang Xu
- Center for Systems Medicine, School of Biomedical Bioinformatics, University of Texas Health Science Center at Houston, TX 77030, USA
- Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Yongcui Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
| | - Jiesi Luo
- Center for Systems Medicine, School of Biomedical Bioinformatics, University of Texas Health Science Center at Houston, TX 77030, USA
| | - Weiling Zhao
- Center for Systems Medicine, School of Biomedical Bioinformatics, University of Texas Health Science Center at Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Systems Medicine, School of Biomedical Bioinformatics, University of Texas Health Science Center at Houston, TX 77030, USA
- Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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Oxidative Stress Alters the Profile of Transcription Factors Related to Early Development on In Vitro Produced Embryos. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:1502489. [PMID: 29209446 PMCID: PMC5676474 DOI: 10.1155/2017/1502489] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 08/04/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023]
Abstract
High oxygen levels during in vitro culture (IVC) can induce oxidative stress through accumulation of reactive oxygen species (ROS), negatively affecting embryo development. This study evaluated the effect of different O2 tensions during IVC on bovine blastocyst development and transcriptional status, considering transcription factors that play an essential role during early embryo development. For this purpose, embryos were produced in vitro by conventional protocols and cultured in two different oxygen tensions, physiological (5%) and atmospheric (20%). Expanded blastocysts were subjected to transcript quantitation analysis by RT-qPCR with Biomark™ HD System (Fluidigm, US), using 67 TaqMan assays specific for Bos taurus. Differences were observed in genes related to oxidation-reduction processes, DNA-dependent transcription factors, and factors related to important functional pathways for embryo development. Blastocyst rate was higher in the 5% O2 group and the number of cells was assessed, with the 5% O2 group having a higher number of cells. ROS concentration was evaluated, with a higher ROS presence in the 20% O2 group. Taken together, these results allow us to conclude that IVC of embryos at atmospheric O2 tension affects the expression of important transcription factors involved in multiple cell biology pathways that can affect embryo development, quality, and viability.
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Richardson TG, Zheng J, Davey Smith G, Timpson NJ, Gaunt TR, Relton CL, Hemani G. Mendelian Randomization Analysis Identifies CpG Sites as Putative Mediators for Genetic Influences on Cardiovascular Disease Risk. Am J Hum Genet 2017; 101:590-602. [PMID: 28985495 PMCID: PMC5630190 DOI: 10.1016/j.ajhg.2017.09.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 09/06/2017] [Indexed: 01/10/2023] Open
Abstract
The extent to which genetic influences on cardiovascular disease risk are mediated by changes in DNA methylation levels has not been systematically explored. We developed an analytical framework that integrates genetic fine mapping and Mendelian randomization with epigenome-wide association studies to evaluate the causal relationships between methylation levels and 14 cardiovascular disease traits. We identified ten genetic loci known to influence proximal DNA methylation which were also associated with cardiovascular traits after multiple-testing correction. Bivariate fine mapping provided evidence that the individual variants responsible for the observed effects on cardiovascular traits at the ADCY3 and ADIPOQ loci were potentially mediated through changes in DNA methylation, although we highlight that we are unable to reliably separate causality from horizontal pleiotropy. Estimates of causal effects were replicated with results from large-scale consortia. Genetic variants and CpG sites identified in this study were enriched for histone mark peaks in relevant tissue types and gene promoter regions. Integrating our results with expression quantitative trait loci data, we provide evidence that variation at these regulatory regions is likely to also influence gene expression levels at these loci.
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Affiliation(s)
- Tom G Richardson
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
| | - Jie Zheng
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, Bristol Medical School (Population Health Sciences), University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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50
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Li H, Torres-Garcia J, Latrasse D, Benhamed M, Schilderink S, Zhou W, Kulikova O, Hirt H, Bisseling T. Plant-Specific Histone Deacetylases HDT1/2 Regulate GIBBERELLIN 2-OXIDASE2 Expression to Control Arabidopsis Root Meristem Cell Number. THE PLANT CELL 2017; 29:2183-2196. [PMID: 28855334 PMCID: PMC5635991 DOI: 10.1105/tpc.17.00366] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/20/2017] [Accepted: 08/29/2017] [Indexed: 05/02/2023]
Abstract
Root growth is modulated by environmental factors and depends on cell production in the root meristem (RM). New cells in the meristem are generated by stem cells and transit-amplifying cells, which together determine RM cell number. Transcription factors and chromatin-remodeling factors have been implicated in regulating the switch from stem cells to transit-amplifying cells. Here, we show that two Arabidopsis thaliana paralogs encoding plant-specific histone deacetylases, HDT1 and HDT2, regulate a second switch from transit-amplifying cells to expanding cells. Knockdown of HDT1/2 (hdt1,2i) results in an earlier switch and causes a reduced RM cell number. Our data show that HDT1/2 negatively regulate the acetylation level of the C19-GIBBERELLIN 2-OXIDASE2 (GA2ox2) locus and repress the expression of GA2ox2 in the RM and elongation zone. Overexpression of GA2ox2 in the RM phenocopies the hdt1,2i phenotype. Conversely, knockout of GA2ox2 partially rescues the root growth defect of hdt1,2i These results suggest that by repressing the expression of GA2ox2, HDT1/2 likely fine-tune gibberellin metabolism and they are crucial for regulating the switch from cell division to expansion to determine RM cell number. We propose that HDT1/2 function as part of a mechanism that modulates root growth in response to environmental factors.
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Affiliation(s)
- Huchen Li
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Jesus Torres-Garcia
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - David Latrasse
- Unité de Recherche en Génomique Végétale, UMR INRA 1165, Université d'Evry Val d'Essonne, ERL CNRS 8196, Saclay Plant Sciences, 91057 Evry, France
- Institut de Biologie des Plantes, CNRS-Université Paris-Sud 11, UMR 8618, 91405 Orsay cedex, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, CNRS-Université Paris-Sud 11, UMR 8618, 91405 Orsay cedex, France
- King Abdullah University of Sciences and Technology, Thuwal 23955, Saudi Arabia
| | - Stefan Schilderink
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Wenkun Zhou
- Department of Plant Sciences, Plant Developmental Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Olga Kulikova
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Heribert Hirt
- Unité de Recherche en Génomique Végétale, UMR INRA 1165, Université d'Evry Val d'Essonne, ERL CNRS 8196, Saclay Plant Sciences, 91057 Evry, France
- King Abdullah University of Sciences and Technology, Thuwal 23955, Saudi Arabia
| | - Ton Bisseling
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
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