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Hua H, Wang Y, Wang X, Wang S, Zhou Y, Liu Y, Liang Z, Ren H, Lu S, Wu S, Jiang Y, Pu Y, Zheng X, Tang C, Shen Z, Li C, Du Y, Deng H. Remodeling ceramide homeostasis promotes functional maturation of human pluripotent stem cell-derived β cells. Cell Stem Cell 2024; 31:850-865.e10. [PMID: 38697109 DOI: 10.1016/j.stem.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 03/21/2024] [Accepted: 04/12/2024] [Indexed: 05/04/2024]
Abstract
Human pluripotent stem cell-derived β cells (hPSC-β cells) show the potential to restore euglycemia. However, the immature functionality of hPSC-β cells has limited their efficacy in application. Here, by deciphering the continuous maturation process of hPSC-β cells post transplantation via single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq), we show that functional maturation of hPSC-β cells is an orderly multistep process during which cells sequentially undergo metabolic adaption, removal of negative regulators of cell function, and establishment of a more specialized transcriptome and epigenome. Importantly, remodeling lipid metabolism, especially downregulating the metabolic activity of ceramides, the central hub of sphingolipid metabolism, is critical for β cell maturation. Limiting intracellular accumulation of ceramides in hPSC-β cells remarkably enhanced their function, as indicated by improvements in insulin processing and glucose-stimulated insulin secretion. In summary, our findings provide insights into the maturation of human pancreatic β cells and highlight the importance of ceramide homeostasis in function acquisition.
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Affiliation(s)
- Huijuan Hua
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yaqi Wang
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China
| | | | - Shusen Wang
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Yunlu Zhou
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yinan Liu
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhen Liang
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Huixia Ren
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Sufang Lu
- Hangzhou Reprogenix Bioscience, Hangzhou, China
| | | | - Yong Jiang
- Hangzhou Reprogenix Bioscience, Hangzhou, China
| | - Yue Pu
- Hangzhou Reprogenix Bioscience, Hangzhou, China
| | - Xiang Zheng
- Hangzhou Repugene Technology, Hangzhou, China
| | - Chao Tang
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhongyang Shen
- Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, China
| | - Cheng Li
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing, China.
| | - Yuanyuan Du
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - Hongkui Deng
- MOE Engineering Research Center of Regenerative Medicine, School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Changping Laboratory, Beijing, China.
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2
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Perez AA, Goronzy IN, Blanco MR, Guo JK, Guttman M. ChIP-DIP: A multiplexed method for mapping hundreds of proteins to DNA uncovers diverse regulatory elements controlling gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571730. [PMID: 38187704 PMCID: PMC10769186 DOI: 10.1101/2023.12.14.571730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Gene expression is controlled by the dynamic localization of thousands of distinct regulatory proteins to precise regions of DNA. Understanding this cell-type specific process has been a goal of molecular biology for decades yet remains challenging because most current DNA-protein mapping methods study one protein at a time. To overcome this, we developed ChIP-DIP (ChIP Done In Parallel), a split-pool based method that enables simultaneous, genome-wide mapping of hundreds of diverse regulatory proteins in a single experiment. We demonstrate that ChIP-DIP generates highly accurate maps for all classes of DNA-associated proteins, including histone modifications, chromatin regulators, transcription factors, and RNA Polymerases. Using these data, we explore quantitative combinations of protein localization on genomic DNA to define distinct classes of regulatory elements and their functional activity. Our data demonstrate that ChIP-DIP enables the generation of 'consortium level', context-specific protein localization maps within any molecular biology lab.
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Zeng YL, Gao F, Zhang C, Ren PP, Ma L, Wang X, Wang R, Kang Y, Li K. USF1 modulates transcription and cellular functions by regulating multiple transcription factors in Huh7 cells. Oncol Lett 2023; 26:532. [PMID: 38020298 PMCID: PMC10655063 DOI: 10.3892/ol.2023.14119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/28/2023] [Indexed: 12/01/2023] Open
Abstract
Liver cancer, including hepatocellular carcinoma (HCC), is a malignant tumor that has high rates of metastasis and mortality worldwide. Upstream transcription factor 1 (USF1) is a canonical transcription factor (TF) and is associated with the pathogenesis of several cancers, but its biological functions and molecular targets in HCC remain unclear. Huh7 cells that overexpress USF1 were used with whole transcriptome profiling through RNA sequencing and chromatin immunoprecipitation (ChIP) sequencing methods to investigate the downstream targets of USF1. Reverse transcription-quantitative PCR was then used to validate the downstream targets. The results showed that USF1 significantly regulates 350 differentially expressed genes (DEGs). The upregulated DEGs were primarily protein-coding genes enriched in immune and inflammation response pathways, while the downregulated DEGs were mainly coding long non-coding (lnc)RNAs, indicating the regulatory function of USF1. It was also demonstrated that USF1 directly binds to the promoter region of 2,492 genes, which may be involved in the viral progression and cell proliferation pathways. By integrating these two datasets, 16 overlapped genes were detected, including downregulated lncRNA-NEAT1 and upregulated TF-ETV5. The downregulated lncRNA-NEAT1 showed reverse expression pattern and prognosis result compared with that of USF1 in patients with liver cancer, while upregulated TF-ETV5 showed consistent results with USF1. Promoter region motif analysis indicated that ETV5 has more binding motifs and genes than USF1 itself for USF1-regulated DEGs, indicating that USF1 may indirectly modulate gene expression by regulating ETV5 expression in Huh7 cells. The study also validated the direct interaction between USF1 and the promoter of ETV5 using ChIP-qPCR. In summary, the results demonstrated that USF1 binds to the promoter region of thousands of genes and affects a large part of DEGs indirectly. Downstream genes, including lncRNA-NEAT1 and TF-ETV5, may also have potential functions in the regulated network by USF1 and have potential functions in the progression of HCC. The present findings suggested that USF1 and its downstream targets could be potential targets for HCC therapy in the future.
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Affiliation(s)
- Yan-Li Zeng
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
- Department of Infectious Diseases, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, P.R. China
- Department of Infectious Diseases, Henan University People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Fei Gao
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Can Zhang
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Pei-Pei Ren
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Li Ma
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Xin Wang
- Department of Infectious Diseases, Henan University, Zhengzhou, Henan 450003, P.R. China
| | - Ruzhen Wang
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Yi Kang
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Ke Li
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
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Fu D, Si Q, Yu C, Han Z, Zang L. USF1-mediated ALKBH5 stabilizes FLII mRNA in an m6A-YTHDF2-dependent manner to repress glycolytic activity in prostate adenocarcinoma. Mol Carcinog 2023; 62:1700-1716. [PMID: 37493109 DOI: 10.1002/mc.23609] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
Upstream-stimulating factor 1 (USF1) is a ubiquitously expressed transcription factor implicated in multiple cellular processes, including metabolism and proliferation. This study focused on the function of USF1 in glycolysis and the malignant development of prostate adenocarcinoma (PRAD). Bioinformatics predictions suggested that USF1 is poorly expressed in PRAD. The clinical PRAD samples revealed a low level of USF1, which was correlated with an unfavorable prognosis. Artificial upregulation of USF1 significantly repressed glycolytic activity in PRAD cells and reduced cell growth and metastasis in vitro and in vivo. Potential downstream genes of USF1 were probed by integrated bioinformatics analyses. The chromatin immunoprecipitation and luciferase assays indicated that USF1 bound to the α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5) promoter for transcription activation. Flightless I (FLII) was identified as the gene showing the highest degree of correlation with ALKBH5. As an m6A demethylase, ALKBH5 enhanced FLII mRNA stability by inducing m6A demethylation in an m6A-YTH N6-methyladenosine RNA-binding protein F2 (YTHDF2)-dependent manner. Either silencing of ALKBH5 or FLII blocked the role of USF1 in PARD cells and restored glycolysis, cell proliferation, and invasion. This study demonstrates that USF1 activates ALKBH5 to stabilize FLII mRNA in an m6A-YTHDF2-dependent manner, thereby repressing glycolysis processes and the progression of PRAD.
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Affiliation(s)
- Dewang Fu
- Department of Urology Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, P.R. China
| | - Qingyue Si
- Department of Urology Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, P.R. China
| | - Chenxi Yu
- Department of Urology Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, P.R. China
| | - Zhifu Han
- Department of Urology Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, P.R. China
| | - Li'e Zang
- Department of Neurology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, P.R. China
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Cosenza G, Martin P, Garro G, Gallo D, Auzino B, Ciampolini R, Pauciullo A. A novel allelic donkey β-lactogobulin I protein isoform generated by a non-AUG translation initiation codon is associated with a nonsynonymous SNP. J Dairy Sci 2023; 106:4158-4170. [PMID: 37080792 DOI: 10.3168/jds.2022-22598] [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: 07/29/2022] [Accepted: 12/17/2022] [Indexed: 04/22/2023]
Abstract
β-Lactoglobulin I (β-LG I) is one of the most important whey proteins in donkey milk. However, to our knowledge, there has been no study focusing on the full nucleotide sequences of this gene (BLG I). Current investigation of donkey BLG I gene is very limited with only 2 variants (A and B) characterized so far at the protein level. Recently, a new β-LG I variant, with a significantly higher mass (+1,915 Da) than known variants has been detected. In this study, we report the whole nucleotide sequence of the BLG I gene from 2 donkeys, whose milk samples are characterized by the β-LG I SDS-PAGE band with a normal electrophoretic mobility (18,514.25 Da, β-LG I B1 form) the first, and by the presence of a unique β-LG I band with a higher electrophoretic mobility (20,428.5 Da, β-LG I D form) the latter. A high genetic variability was found all over the 2 sequenced BLG I alleles. In particular, 16 polymorphic sites were found in introns, one in the 5' flanking region, 3 SNPs in the 5' untranslated region and one SNP in the coding region (g.458G > A) located at the 40th nucleotide of exon 2 and responsible for the AA substitutions p.Asp28 > Asn in the mature protein. Two SNPs (g.920-922CAC > TGT and g.1871G/A) were genotyped in 93 donkeys of 2 Italian breeds (60 Ragusana and 33 Amiatina, respectively) and the overall frequencies of g.920-922CAC and g.1871A were 0.3065 and 0.043, respectively. Only the rare allele g.1871A was observed to be associated with the slower migrating β-LG I. Considering this genetic diversity and those found in the database, it was possible to deduce at least 5 different alleles (BLG I A, B, B1, C, D) responsible for 4 potential β-LG I translations. Among these alleles, B1 and D are those characterized in the present research, with the D allele of real novel identification. Haplotype data analysis suggests an evolutionary pathway of donkey BLG I gene and a possible phylogenetic map is proposed. Analyses of mRNA secondary structure showed relevant changes in the structures, as consequence of the g.1871G > A polymorphism, that might be responsible for the recognition of an alternative initiation site providing an additional signal peptide. The extension of 19 AA sequence to the mature protein, corresponding to the canonical signal peptide with an additional alanine residue, is sufficient to provide the observed molecular weight of the slower migrating β-LG I encoded by the BLG I D allele.
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Affiliation(s)
- G Cosenza
- Department of Agricultural Sciences, University of Naples "Federico II," 80055 Portici (Na), Italy.
| | - P Martin
- Université Paris-Saclay, INRAE, MICALIS Institute, PAPPSO, 78350 Jouy-en-Josas, France
| | - G Garro
- Department of Agricultural Sciences, University of Naples "Federico II," 80055 Portici (Na), Italy
| | - D Gallo
- Department of Agricultural Sciences, University of Naples "Federico II," 80055 Portici (Na), Italy
| | - B Auzino
- Department of Veterinary Science, University of Pisa, 56100, Italy
| | - R Ciampolini
- Department of Veterinary Science, University of Pisa, 56100, Italy.
| | - A Pauciullo
- Department of Agriculture, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy
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Beeram H, Siddamalla S, Tumu VR, KV V, Vidala A, Deenadayal M, Sisinthy S, Bhanoori M. Genetic Variants of VDR and PGC-1α Are Not Associated with the Risk of Endometriosis in Indian Women. DNA Cell Biol 2022; 41:987-995. [DOI: 10.1089/dna.2022.0350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Himabindu Beeram
- Department of Biochemistry, Osmania University, Hyderabad, India
| | | | | | - Veena KV
- Department of Biochemistry, Osmania University, Hyderabad, India
| | - Akanksha Vidala
- Department of Biochemistry, Osmania University, Hyderabad, India
| | - Mamata Deenadayal
- Infertility Institute and Research Centre (IIRC), Secunderabad, India
| | - Shivaji Sisinthy
- Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
- Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad, India
| | - Manjula Bhanoori
- Department of Biochemistry, Osmania University, Hyderabad, India
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7
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Veena KV, Siddamalla S, Deenadayal M, Sisinthy S, Bhanoori M. Histone deacetylase 1, Sirtuin 1, and Sirtuin 3 single-nucleotide polymorphisms and the risk of endometriosis in South Indian women. J OBSTET GYNAECOL 2022; 42:3230-3235. [PMID: 35980861 DOI: 10.1080/01443615.2022.2109955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The aim of the study was to investigate the association between Histone deacetylase 1 (HDAC1), Sirtuin1 (SIRT1), and Sirtuin3 (SIRT3) single-nucleotide polymorphisms (SNPs) and risk of endometriosis in South Indian women. A total of 300 subjects were recruited in this case-control study comprising 150 affected women and 150 women with no evidence of disease. All the subjects were of South Indian origin. The genotyping of HDAC1, SIRT1, and SIRT3 SNPs (rs1741981T/C, rs144124002A/G, and rs536715G/A) was carried out on DNA from subjects by PCR-RFLP and sequencing analysis. The genotype (p = .00782) and allele (p = .02561) frequencies of the HDAC1 rs1741981 polymorphism showed significant difference between cases and controls. In contrast, SIRT1 (rs144124002) and SIRT3 (rs536715) SNPs did not show significant association with the disease. The HDAC1 polymorphism may constitute a heritable risk factor for endometriosis in South Indian women. To date, there is no reported study on the association of polymorphisms in HDAC1, SIRT1, and SIRT3 with endometriosis risk. Impact StatementWhat is already known on this subject? Endometriosis is a benign gynaecological disease characterised by the implantation of functional endometrial tissue at ectopic positions, associated with an increased risk of malignant transformation. Epigenetic mechanisms are essential for normal development and maintenance of tissue-specific gene expression patterns. Histone modification, including deacetylation of lysine residues by HDACs, is a key epigenetic mechanism of gene expression regulation in endometriosis, therefore genetic variation in HDACs causing epigenetic control defects might lead to disease susceptibility.What do the results of this study add? Our study shows that the HDAC1 SNP is significantly associated with endometriosis in South Indian women, whereas the SNPs of SIRT1 and SIRT3 could not show any association with the disease.What are the implications of these findings for clinical practice and/or further research? The polymorphism of HDAC1 rs1741981 could be used as an important marker of genetic susceptibility to endometriosis development. Analysis of this SNP might help to identify patients at high risk for disease outcome.
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Affiliation(s)
- K V Veena
- Department of Biochemistry, Osmania University, Hyderabad, India
| | | | - Mamata Deenadayal
- Infertility Institute and Research Centre (IIRC), Secundrabad, India
| | - Shivaji Sisinthy
- Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Manjula Bhanoori
- Department of Biochemistry, Osmania University, Hyderabad, India
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8
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Functional Genomics Analysis to Disentangle the Role of Genetic Variants in Major Depression. Genes (Basel) 2022; 13:genes13071259. [PMID: 35886042 PMCID: PMC9320424 DOI: 10.3390/genes13071259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 02/06/2023] Open
Abstract
Understanding the molecular basis of major depression is critical for identifying new potential biomarkers and drug targets to alleviate its burden on society. Leveraging available GWAS data and functional genomic tools to assess regulatory variation could help explain the role of major depression-associated genetic variants in disease pathogenesis. We have conducted a fine-mapping analysis of genetic variants associated with major depression and applied a pipeline focused on gene expression regulation by using two complementary approaches: cis-eQTL colocalization analysis and alteration of transcription factor binding sites. The fine-mapping process uncovered putative causally associated variants whose proximal genes were linked with major depression pathophysiology. Four colocalizing genetic variants altered the expression of five genes, highlighting the role of SLC12A5 in neuronal chlorine homeostasis and MYRF in nervous system myelination and oligodendrocyte differentiation. The transcription factor binding analysis revealed the potential role of rs62259947 in modulating P4HTM expression by altering the YY1 binding site, altogether regulating hypoxia response. Overall, our pipeline could prioritize putative causal genetic variants in major depression. More importantly, it can be applied when only index genetic variants are available. Finally, the presented approach enabled the proposal of mechanistic hypotheses of these genetic variants and their role in disease pathogenesis.
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9
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Ishihara T, Hickford D, Fenelon JC, Griffith OW, Suzuki S, Renfree MB. Evolution of the short form of DNMT3A, DNMT3A2, occurred in the common ancestor of mammals. Genome Biol Evol 2022; 14:6615359. [PMID: 35749276 PMCID: PMC9254654 DOI: 10.1093/gbe/evac094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting is found in marsupial and eutherian mammals, but not in monotremes. While the primary regulator of genomic imprinting in eutherians is differential DNA methylation between parental alleles, conserved imprinted genes in marsupials tend to lack DNA methylation at their promoters. DNA methylation at eutherian imprinted genes is mainly catalysed by a DNA methyltransferase (DNMT) enzyme, DNMT3A. There are two isoforms of eutherian DNMT3A: DNMT3A and DNMT3A2. DNMT3A2 is the primary isoform for establishing DNA methylation at eutherian imprinted genes and is essential for eutherian genomic imprinting. In this study, we investigated whether DNMT3A2 is also present in the two other mammalian lineages, marsupials and monotremes. We identified DNMT3A2 in both marsupials and monotremes, although imprinting has not been identified in monotremes. By analysing genomic sequences and transcriptome data across vertebrates, we concluded that the evolution of DNMT3A2 occurred in the common ancestor of mammals. In addition, DNMT3A/3A2 gene and protein expression during gametogenesis showed distinct sexual dimorphisms in a marsupial, the tammar wallaby, and this pattern coincided with the sex-specific DNA methylation reprogramming in this species as it does in mice. Our results show that DNMT3A2 is present in all mammalian groups and suggests that the basic DNMT3A/3A2-based DNA methylation mechanism is conserved at least in therian mammals.
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Affiliation(s)
- Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Danielle Hickford
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jane C Fenelon
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Oliver W Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Shunsuke Suzuki
- Department of Agricultural and Life Sciences, Shinshu University, Nagano, Japan
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
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10
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Yang C, Croteau S, Hardy P. Histone deacetylase (HDAC) 9: versatile biological functions and emerging roles in human cancer. Cell Oncol (Dordr) 2021; 44:997-1017. [PMID: 34318404 PMCID: PMC8516780 DOI: 10.1007/s13402-021-00626-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/02/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND HDAC9 (histone deacetylase 9) belongs to the class IIa family of histone deacetylases. This enzyme can shuttle freely between the nucleus and cytoplasm and promotes tissue-specific transcriptional regulation by interacting with histone and non-histone substrates. HDAC9 plays an essential role in diverse physiological processes including cardiac muscle development, bone formation, adipocyte differentiation and innate immunity. HDAC9 inhibition or activation is therefore a promising avenue for therapeutic intervention in several diseases. HDAC9 overexpression is also common in cancer cells, where HDAC9 alters the expression and activity of numerous relevant proteins involved in carcinogenesis. CONCLUSIONS This review summarizes the most recent discoveries regarding HDAC9 as a crucial regulator of specific physiological systems and, more importantly, highlights the diverse spectrum of HDAC9-mediated posttranslational modifications and their contributions to cancer pathogenesis. HDAC9 is a potential novel therapeutic target, and the restoration of aberrant expression patterns observed among HDAC9 target genes and their related signaling pathways may provide opportunities to the design of novel anticancer therapeutic strategies.
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Affiliation(s)
- Chun Yang
- Research Center of CHU Sainte-Justine, University of Montréal, 3175 Côte-Sainte-Catherine, Room 2.17.004, Montréal, Québec H3T 1C5 Canada
| | - Stéphane Croteau
- Departments of Medicine, Pediatrics, Pharmacology and Physiology, University of Montréal, Montréal, QC Canada
| | - Pierre Hardy
- Research Center of CHU Sainte-Justine, University of Montréal, 3175 Côte-Sainte-Catherine, Room 2.17.004, Montréal, Québec H3T 1C5 Canada
- Departments of Medicine, Pediatrics, Pharmacology and Physiology, University of Montréal, Montréal, QC Canada
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11
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Lai WKM, Mariani L, Rothschild G, Smith ER, Venters BJ, Blanda TR, Kuntala PK, Bocklund K, Mairose J, Dweikat SN, Mistretta K, Rossi MJ, James D, Anderson JT, Phanor SK, Zhang W, Zhao Z, Shah AP, Novitzky K, McAnarney E, Keogh MC, Shilatifard A, Basu U, Bulyk ML, Pugh BF. A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells. Genome Res 2021; 31:1663-1679. [PMID: 34426512 PMCID: PMC8415381 DOI: 10.1101/gr.275472.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
Antibodies offer a powerful means to interrogate specific proteins in a complex milieu. However, antibody availability and reliability can be problematic, whereas epitope tagging can be impractical in many cases. To address these limitations, the Protein Capture Reagents Program (PCRP) generated over a thousand renewable monoclonal antibodies (mAbs) against human presumptive chromatin proteins. However, these reagents have not been widely field-tested. We therefore performed a screen to test their ability to enrich genomic regions via chromatin immunoprecipitation (ChIP) and a variety of orthogonal assays. Eight hundred eighty-seven unique antibodies against 681 unique human transcription factors (TFs) were assayed by ultra-high-resolution ChIP-exo/seq, generating approximately 1200 ChIP-exo data sets, primarily in a single pass in one cell type (K562). Subsets of PCRP mAbs were further tested in ChIP-seq, CUT&RUN, STORM super-resolution microscopy, immunoblots, and protein binding microarray (PBM) experiments. About 5% of the tested antibodies displayed high-confidence target (i.e., cognate antigen) enrichment across at least one assay and are strong candidates for additional validation. An additional 34% produced ChIP-exo data that were distinct from background and thus warrant further testing. The remaining 61% were not substantially different from background, and likely require consideration of a much broader survey of cell types and/or assay optimizations. We show and discuss the metrics and challenges to antibody validation in chromatin-based assays.
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Affiliation(s)
- William K M Lai
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Luca Mariani
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Edwin R Smith
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | - Thomas R Blanda
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Prashant K Kuntala
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Kylie Bocklund
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Joshua Mairose
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah N Dweikat
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Katelyn Mistretta
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Matthew J Rossi
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Daniela James
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - James T Anderson
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sabrina K Phanor
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wanwei Zhang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Zibo Zhao
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Avani P Shah
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | | | | | | | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics and the Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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12
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Abstract
Evolutionary processes, including mutation, migration and natural selection, have influenced the prevalence and distribution of various disorders in humans. However, despite a few well-known examples, such as the APOL1 variants - which have undergone positive genetic selection for their ability to confer resistance to Trypanosoma brucei infection but confer a higher risk of chronic kidney disease - little is known about the effects of evolutionary processes that have shaped genetic variation on kidney disease. An understanding of basic concepts in evolutionary genetics provides an opportunity to consider how findings from ancient and archaic genomes could inform our knowledge of evolution and provide insights into how population migration and genetic admixture have shaped the current distribution and landscape of human kidney-associated diseases. Differences in exposures to infectious agents, environmental toxins, dietary components and climate also have the potential to influence the evolutionary genetics of kidneys. Of note, selective pressure on loci associated with kidney disease is often from non-kidney diseases, and thus it is important to understand how the link between genome-wide selected loci and kidney disease occurs in relation to secondary nephropathies.
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13
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Irrelevance of USF2 rs916145 polymorphism with the risk of biliary atresia susceptibility in Southern Chinese children. Biosci Rep 2020; 40:222122. [PMID: 32109289 PMCID: PMC7048685 DOI: 10.1042/bsr20193623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/06/2020] [Accepted: 02/13/2020] [Indexed: 02/07/2023] Open
Abstract
Backgrounds: Biliary atresia (BA) is a very rare neonatal disease, however, it has been the most common cause of obstructive jaundice in infancy. The complex pathogenesis of BA is not entirely clear and a lot of possible pathogenic mechanisms have been proposed to explain the etiology of BA, including genetic, inflammatory, environmental and developmental abnormalities. As a transcription factor, USF2 gene rs916145 polymorphism has been shown to be related to the risk of BA. Methods: We examined the USF2 rs916145 genotype in a large case–control study consisting of 506 BA patients and 1473 healthy controls, using the MassARRAY iPLEX Gold system (Sequenom). Odds ratios (ORs) and 95% confidence intervals (CIs) were used to evaluate the association between the USF2 gene rs916145 polymorphism and BA susceptibility. Results: The frequency of different genotypes showed no statistical significance (GG/GC, OR: 1.09, P=0.470, 95% CI: 0.87–1.35; GG/CC, OR: 0.86, P=0.378, 95% CI: 0.62–1.20). No obvious association was revealed between the USF2 gene rs916145 polymorphism and BA susceptibility. Conclusion:USF2 rs916145 polymorphism may not be the best predictor of BA.
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14
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Taghizadeh E, Mirzaei F, Jalilian N, Ghayour Mobarhan M, Ferns GA, Pasdar A. A novel mutation in
USF1
gene is associated with familial combined hyperlipidemia. IUBMB Life 2019; 72:616-623. [DOI: 10.1002/iub.2186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/01/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Eskandar Taghizadeh
- Department of Medical Genetics, Faculty of MedicineMashhad University of Medical Sciences Mashhad Iran
- Cellular and Molecular Research CenterYasuj University of Medical Sciences Yasuj Iran
| | - Farzaneh Mirzaei
- Department of Medical Genetics, Faculty of MedicineMashhad University of Medical Sciences Mashhad Iran
| | - Nazanin Jalilian
- Department of Clinical biochemistry, School of MedicineKermanshah University of Medical Sciences Kermanshah Iran
| | - Majid Ghayour Mobarhan
- Metabolic Syndrome Research Centre, School of MedicineMashhad University of Medical Sciences Mashhad Iran
| | - Gordon A. Ferns
- Department of Medical EducationBrighton and Sussex Medical School Perso Falmer Brighton UK
| | - Alireza Pasdar
- Department of Medical Genetics, Faculty of MedicineMashhad University of Medical Sciences Mashhad Iran
- Medical Genetics Research Centre, Faculty of MedicineMashhad University of Medical Sciences Mashhad Iran
- Division of Applied Medicine, Medical School, University of Aberdeen Foresterhill Aberdeen UK
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15
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Chi TF, Horbach T, Götz C, Kietzmann T, Dimova EY. Cyclin-Dependent Kinase 5 (CDK5)-Mediated Phosphorylation of Upstream Stimulatory Factor 2 (USF2) Contributes to Carcinogenesis. Cancers (Basel) 2019; 11:cancers11040523. [PMID: 31013770 PMCID: PMC6521020 DOI: 10.3390/cancers11040523] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 03/30/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
The transcription factor USF2 is supposed to have an important role in tumor development. However, the regulatory mechanisms contributing to the function of USF2 are largely unknown. Cyclin-dependent kinase 5 (CDK5) seems to be of importance since high levels of CDK5 were found in different cancers associated with high USF2 expression. Here, we identified USF2 as a phosphorylation target of CDK5. USF2 is phosphorylated by CDK5 at two serine residues, serine 155 and serine 222. Further, phosphorylation of USF2 at these residues was shown to stabilize the protein and to regulate cellular growth and migration. Altogether, these results delineate the importance of the CDK5-USF2 interplay in cancer cells.
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Affiliation(s)
- Tabughang Franklin Chi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; (T.F.C.); (T.K.)
| | - Tina Horbach
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; (T.F.C.); (T.K.)
| | - Claudia Götz
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany;
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; (T.F.C.); (T.K.)
| | - Elitsa Y. Dimova
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland; (T.F.C.); (T.K.)
- Correspondence: ; Tel.: +358-0-294-485-785; Fax: +358-8-553-114
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16
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Guo J, Fang W, Chen X, Lin Y, Hu G, Wei J, Zhang X, Yang C, Li J. Upstream stimulating factor 1 suppresses autophagy and hepatic lipid droplet catabolism by activating mTOR. FEBS Lett 2018; 592:2725-2738. [PMID: 30054905 PMCID: PMC6175420 DOI: 10.1002/1873-3468.13203] [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] [Received: 03/15/2018] [Revised: 07/16/2018] [Accepted: 07/23/2018] [Indexed: 12/16/2022]
Abstract
Previous studies indicate that the transcription factor upstream stimulating factor 1 (USF1) is involved in the regulation of lipid and glucose metabolism. However, the role of USF1 in lipid-induced autophagy remains unknown. Interestingly, we found that USF1 overexpression suppresses autophagy-related gene expression in HepG2 cells. Further assays confirmed that USF1 could transcriptionally activate mTOR expression, thereby suppressing rapamycin-induced autophagy in HepG2 cells. Moreover, pharmacological activation of autophagy with rapamycin decreases the numbers and sizes of lipid droplets (LDs) in HepG2 cells exposed to an oleate/palmitate mixture. Of note, USF1 upregulation decreases colocalization of LDs and autophagosomes. In conclusion, our data provide evidence that USF1 contributes to abnormal lipid accumulation in the liver by suppressing autophagy via regulation of mTOR transcription.
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Affiliation(s)
- Jun Guo
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Weiwei Fang
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, China.,Department of Blood Transfusion, Cancer Institute/Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiehui Chen
- Department of Geriatrics Cardiovascular Medicine, Shenzhen Sun Yat-Sen Cardiovascular Hospital, Shenzhen, China
| | - Yajun Lin
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Gang Hu
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Jie Wei
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Xiaoyi Zhang
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Chunxiao Yang
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Jian Li
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, China
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17
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Song X, Zhu M, Li H, Liu B, Yan Z, Wang W, Li H, Sun J, Li S. USF1 promotes the development of knee osteoarthritis by activating the NF-κB signaling pathway. Exp Ther Med 2018; 16:3518-3524. [PMID: 30233704 PMCID: PMC6143875 DOI: 10.3892/etm.2018.6608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/19/2018] [Indexed: 01/16/2023] Open
Abstract
The current study mainly aims to evaluate the expression pattern and underlying mechanism of upstream stimulating factor 1 (USF1) in the muscle tissues of knee osteoarthritis (KOA) patients. In accordance with previous findings, our data showed that muscle strength was significantly decreased in KOA patients compared with controls. Furthermore, several inflammatory factors, including tumor necrosis factor α (TNFα), IL-8, IL-6 and MCP-1, were associated with reduced muscle strength in KOA patients. Not surprisingly, NF-κB signaling was significantly activated in the muscle tissues of KOA patients compared with control individuals. Furthermore, we showed that USF1 was increased in the muscles of KOA patients compared with controls. More importantly, overexpression of USF1 in primary human skeletal muscle cells significantly increased the activation of NF-κB signaling as well as the levels of pro-inflammatory factors. In summary, we showed novel data that the upregulation of USF1 promoted NF-κB activation-induced inflammatory responses in muscle tissues of KOA patients.
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Affiliation(s)
- Xiandong Song
- Department of Orthopedics, Hongqi Hospital Affiliated with Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Min Zhu
- Department of Radiology, Hongqi Hospital Affiliated with Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Hao Li
- Department of Radiology, Hongqi Hospital Affiliated with Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Bo Liu
- Department of Orthopedics, Hongqi Hospital Affiliated with Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Zhaowei Yan
- Department of Orthopedics, Hongqi Hospital Affiliated with Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Weican Wang
- Department of Orthopedics, Hongqi Hospital Affiliated with Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Hongyi Li
- Department of Radiology, Hongqi Hospital Affiliated with Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Jiping Sun
- Department of Radiology, Hongqi Hospital Affiliated with Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Shixing Li
- Department of Radiology, Hongqi Hospital Affiliated with Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
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18
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Guo WL, Huang DS. An efficient method to transcription factor binding sites imputation via simultaneous completion of multiple matrices with positional consistency. MOLECULAR BIOSYSTEMS 2018; 13:1827-1837. [PMID: 28718849 DOI: 10.1039/c7mb00155j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Transcription factors (TFs) are DNA-binding proteins that have a central role in regulating gene expression. Identification of DNA-binding sites of TFs is a key task in understanding transcriptional regulation, cellular processes and disease. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) enables genome-wide identification of in vivo TF binding sites. However, it is still difficult to map every TF in every cell line owing to cost and biological material availability, which poses an enormous obstacle for integrated analysis of gene regulation. To address this problem, we propose a novel computational approach, TFBSImpute, for predicting additional TF binding profiles by leveraging information from available ChIP-seq TF binding data. TFBSImpute fuses the dataset to a 3-mode tensor and imputes missing TF binding signals via simultaneous completion of multiple TF binding matrices with positional consistency. We show that signals predicted by our method achieve overall similarity with experimental data and that TFBSImpute significantly outperforms baseline approaches, by assessing the performance of imputation methods against observed ChIP-seq TF binding profiles. Besides, motif analysis shows that TFBSImpute preforms better in capturing binding motifs enriched in observed data compared with baselines, indicating that the higher performance of TFBSImpute is not simply due to averaging related samples. We anticipate that our approach will constitute a useful complement to experimental mapping of TF binding, which is beneficial for further study of regulation mechanisms and disease.
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Affiliation(s)
- Wei-Li Guo
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai, 201804, China.
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19
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Sa L, Li Y, Zhao L, Liu Y, Wang P, Liu L, Li Z, Ma J, Cai H, Xue Y. The Role of HOTAIR/miR-148b-3p/USF1 on Regulating the Permeability of BTB. Front Mol Neurosci 2017; 10:194. [PMID: 28701916 PMCID: PMC5487514 DOI: 10.3389/fnmol.2017.00194] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/01/2017] [Indexed: 12/19/2022] Open
Abstract
Homeobox transcript antisense intergenic RNA (HOTAIR), as a long non-coding RNA (lncRNA), has been considered to play critical roles in the biological properties of various tumors. The purposes of this study were to investigate the role and possible molecular mechanisms of HOTAIR in regulating the permeability of blood tumor barrier (BTB) in vitro. Our present study elucidated that the expressions of HOTAIR and upstream stimulatory factor 1 (USF1) was up-regulated, but miR-148b-3p was down-regulated in glioma microvascular endothelial cells (GECs). Knockdown of HOTAIR could increase the permeability of BTB as well as down-regulated the expressions of tight junction related proteins ZO-1, occludin, claudin-5, but up-regulated miR-148b-3p expressions in GECs. Meanwhile, dual-luciferase reporter assays demonstrated that HOTAIR was a target RNA of miR-148b-3p. Furthermore, overexpression of miR-148b-3p increased the permeability of BTB by down-regulating the expressions of tight junction related proteins and USF1 in GECs, and vice versa. And further result revealed USF1 was a target of miR-148b-3p. Silence of USF1 increased the permeability of BTB duo to their interaction with the promoters of ZO-1, occludin, and claudin-5 in GECs. Taken together, our finding indicated that knockdown of HOTAIR increased BTB permeability via binding to miR-148b-3p, which further reducing tight junction related proteins in GECs by targeting USF1. Thus, HOTAIR will attract more attention since it can serve as a potential target of drug delivery across BTB and may provide novel strategies for glioma treatment.
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Affiliation(s)
- Libo Sa
- Department of Neurobiology, College of Basic Medicine, China Medical UniversityShenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical UniversityShenyang, China
| | - Yan Li
- No. 1 English Department, School of Fundamental Sciences, China Medical UniversityShenyang, China
| | - Lini Zhao
- Department of Neurobiology, College of Basic Medicine, China Medical UniversityShenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical UniversityShenyang, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical UniversityShenyang, China.,Liaoning Research Center for Translational Medicine in Nervous System DiseaseShenyang, China
| | - Ping Wang
- Department of Neurobiology, College of Basic Medicine, China Medical UniversityShenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical UniversityShenyang, China
| | - Libo Liu
- Department of Neurobiology, College of Basic Medicine, China Medical UniversityShenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical UniversityShenyang, China
| | - Zhen Li
- Department of Neurosurgery, Shengjing Hospital of China Medical UniversityShenyang, China.,Liaoning Research Center for Translational Medicine in Nervous System DiseaseShenyang, China
| | - Jun Ma
- Department of Neurobiology, College of Basic Medicine, China Medical UniversityShenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical UniversityShenyang, China
| | - Heng Cai
- Department of Neurosurgery, Shengjing Hospital of China Medical UniversityShenyang, China.,Liaoning Research Center for Translational Medicine in Nervous System DiseaseShenyang, China
| | - Yixue Xue
- Department of Neurobiology, College of Basic Medicine, China Medical UniversityShenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical UniversityShenyang, China
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20
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Laurila PP, Soronen J, Kooijman S, Forsström S, Boon MR, Surakka I, Kaiharju E, Coomans CP, Van Den Berg SAA, Autio A, Sarin AP, Kettunen J, Tikkanen E, Manninen T, Metso J, Silvennoinen R, Merikanto K, Ruuth M, Perttilä J, Mäkelä A, Isomi A, Tuomainen AM, Tikka A, Ramadan UA, Seppälä I, Lehtimäki T, Eriksson J, Havulinna A, Jula A, Karhunen PJ, Salomaa V, Perola M, Ehnholm C, Lee-Rueckert M, Van Eck M, Roivainen A, Taskinen MR, Peltonen L, Mervaala E, Jalanko A, Hohtola E, Olkkonen VM, Ripatti S, Kovanen PT, Rensen PCN, Suomalainen A, Jauhiainen M. USF1 deficiency activates brown adipose tissue and improves cardiometabolic health. Sci Transl Med 2016; 8:323ra13. [PMID: 26819196 DOI: 10.1126/scitranslmed.aad0015] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
USF1 (upstream stimulatory factor 1) is a transcription factor associated with familial combined hyperlipidemia and coronary artery disease in humans. However, whether USF1 is beneficial or detrimental to cardiometabolic health has not been addressed. By inactivating USF1 in mice, we demonstrate protection against diet-induced dyslipidemia, obesity, insulin resistance, hepatic steatosis, and atherosclerosis. The favorable plasma lipid profile, including increased high-density lipoprotein cholesterol and decreased triglycerides, was coupled with increased energy expenditure due to activation of brown adipose tissue (BAT). Usf1 inactivation directs triglycerides from the circulation to BAT for combustion via a lipoprotein lipase-dependent mechanism, thus enhancing plasma triglyceride clearance. Mice lacking Usf1 displayed increased BAT-facilitated, diet-induced thermogenesis with up-regulation of mitochondrial respiratory chain complexes, as well as increased BAT activity even at thermoneutrality and after BAT sympathectomy. A direct effect of USF1 on BAT activation was demonstrated by an amplified adrenergic response in brown adipocytes after Usf1 silencing, and by augmented norepinephrine-induced thermogenesis in mice lacking Usf1. In humans, individuals carrying SNP (single-nucleotide polymorphism) alleles that reduced USF1 mRNA expression also displayed a beneficial cardiometabolic profile, featuring improved insulin sensitivity, a favorable lipid profile, and reduced atherosclerosis. Our findings identify a new molecular link between lipid metabolism and energy expenditure, and point to the potential of USF1 as a therapeutic target for cardiometabolic disease.
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Affiliation(s)
- Pirkka-Pekka Laurila
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland. Department of Medical Genetics, University of Helsinki, Helsinki FI-00014, Finland. Institute for Molecular Medicine Finland, FIMM, Helsinki FI-00251, Finland.
| | - Jarkko Soronen
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland. Institute for Molecular Medicine Finland, FIMM, Helsinki FI-00251, Finland. Minerva Foundation Institute for Medical Research, Helsinki FI-00290, Finland
| | - Sander Kooijman
- Department of Endocrinology and Metabolic Diseases, Leiden University Medical Center, Leiden 2333 ZA, Netherlands. Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden 2333 ZA, Netherlands
| | - Saara Forsström
- Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki FI-00014, Finland
| | - Mariëtte R Boon
- Department of Endocrinology and Metabolic Diseases, Leiden University Medical Center, Leiden 2333 ZA, Netherlands. Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden 2333 ZA, Netherlands
| | - Ida Surakka
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland. Institute for Molecular Medicine Finland, FIMM, Helsinki FI-00251, Finland
| | - Essi Kaiharju
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland
| | - Claudia P Coomans
- Department of Endocrinology and Metabolic Diseases, Leiden University Medical Center, Leiden 2333 ZA, Netherlands. Department of Molecular Cell Biology, Leiden University Medical Center, Leiden 2333 ZA, Netherlands
| | | | - Anu Autio
- Turku PET Centre, University of Turku and Turku University Hospital, Turku FI-20520, Finland
| | - Antti-Pekka Sarin
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland. Institute for Molecular Medicine Finland, FIMM, Helsinki FI-00251, Finland
| | - Johannes Kettunen
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland. Institute for Molecular Medicine Finland, FIMM, Helsinki FI-00251, Finland. Computational Medicine, Institute of Health Sciences, University of Oulu and Oulu University Hospital, Oulu FI-90014, Finland
| | - Emmi Tikkanen
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland. Institute for Molecular Medicine Finland, FIMM, Helsinki FI-00251, Finland. Hjelt Institute, University of Helsinki, Helsinki FI-00014, Finland
| | - Tuula Manninen
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland. Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki FI-00014, Finland
| | - Jari Metso
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland
| | | | - Krista Merikanto
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland
| | - Maija Ruuth
- Wihuri Research Institute, Helsinki FI-00290, Finland
| | - Julia Perttilä
- Minerva Foundation Institute for Medical Research, Helsinki FI-00290, Finland
| | - Anne Mäkelä
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland
| | - Ayaka Isomi
- Hiroshima University, Hiroshima 730-0053, Japan
| | - Anita M Tuomainen
- Institute of Dentistry, University of Helsinki, Helsinki FI-00014, Finland
| | - Anna Tikka
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland
| | - Usama Abo Ramadan
- Experimental MRI Laboratory, Department of Neurology, Helsinki University Central Hospital, Helsinki FI-00290, Finland
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories, and Tampere University School of Medicine, Tampere FI-33014, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Tampere University School of Medicine, Tampere FI-33014, Finland
| | - Johan Eriksson
- Department of Health, National Institute for Health and Welfare, Helsinki FI-00271, Finland. Folkhälsan Research Centre, Helsinki FI-00251, Finland. Unit of General Practice, Helsinki University Central Hospital, Helsinki FI-00290, Finland. Department of General Practice and Primary Health Care, University of Helsinki, Helsinki FI-00014, Finland
| | - Aki Havulinna
- Department of Health, National Institute for Health and Welfare, Helsinki FI-00271, Finland
| | - Antti Jula
- Department of Health, National Institute for Health and Welfare, Helsinki FI-00271, Finland
| | - Pekka J Karhunen
- Department of Clinical Chemistry, Fimlab Laboratories, and Tampere University School of Medicine, Tampere FI-33014, Finland
| | - Veikko Salomaa
- Department of Health, National Institute for Health and Welfare, Helsinki FI-00271, Finland
| | - Markus Perola
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland
| | - Christian Ehnholm
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland
| | | | - Miranda Van Eck
- Department of Endocrinology and Metabolic Diseases, Leiden University Medical Center, Leiden 2333 ZA, Netherlands
| | - Anne Roivainen
- Turku PET Centre, University of Turku and Turku University Hospital, Turku FI-20520, Finland. Turku Center for Disease Modeling, University of Turku, Turku FI-20520, Finland
| | - Marja-Riitta Taskinen
- Diabetes and Obesity Research Program, University of Helsinki, Helsinki FI-00014, Finland
| | | | - Eero Mervaala
- Institute of Biomedicine, University of Helsinki, Helsinki FI-00014, Finland
| | - Anu Jalanko
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland
| | - Esa Hohtola
- Department of Genetics and Physiology, University of Oulu, Oulu FI-90014, Finland
| | - Vesa M Olkkonen
- Minerva Foundation Institute for Medical Research, Helsinki FI-00290, Finland
| | - Samuli Ripatti
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland. Institute for Molecular Medicine Finland, FIMM, Helsinki FI-00251, Finland. Hjelt Institute, University of Helsinki, Helsinki FI-00014, Finland. Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Patrick C N Rensen
- Department of Endocrinology and Metabolic Diseases, Leiden University Medical Center, Leiden 2333 ZA, Netherlands. Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden 2333 ZA, Netherlands
| | - Anu Suomalainen
- Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki FI-00014, Finland. Department of Neurology, Helsinki University Central Hospital, Helsinki FI-00290, Finland. Neuroscience Center, University of Helsinki, Helsinki FI-00014, Finland
| | - Matti Jauhiainen
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki FI-00251, Finland.
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Diamanti K, Umer HM, Kruczyk M, Dąbrowski MJ, Cavalli M, Wadelius C, Komorowski J. Maps of context-dependent putative regulatory regions and genomic signal interactions. Nucleic Acids Res 2016; 44:9110-9120. [PMID: 27625394 PMCID: PMC5100580 DOI: 10.1093/nar/gkw800] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 08/31/2016] [Indexed: 12/24/2022] Open
Abstract
Gene transcription is regulated mainly by transcription factors (TFs). ENCODE and Roadmap Epigenomics provide global binding profiles of TFs, which can be used to identify regulatory regions. To this end we implemented a method to systematically construct cell-type and species-specific maps of regulatory regions and TF-TF interactions. We illustrated the approach by developing maps for five human cell-lines and two other species. We detected ∼144k putative regulatory regions among the human cell-lines, with the majority of them being ∼300 bp. We found ∼20k putative regulatory elements in the ENCODE heterochromatic domains suggesting a large regulatory potential in the regions presumed transcriptionally silent. Among the most significant TF interactions identified in the heterochromatic regions were CTCF and the cohesin complex, which is in agreement with previous reports. Finally, we investigated the enrichment of the obtained putative regulatory regions in the 3D chromatin domains. More than 90% of the regions were discovered in the 3D contacting domains. We found a significant enrichment of GWAS SNPs in the putative regulatory regions. These significant enrichments provide evidence that the regulatory regions play a crucial role in the genomic structural stability. Additionally, we generated maps of putative regulatory regions for prostate and colorectal cancer human cell-lines.
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Affiliation(s)
- Klev Diamanti
- Department of Cell and Molecular Biology, Uppsala University, Uppsala SE-751-24, Sweden
| | - Husen M Umer
- Department of Cell and Molecular Biology, Uppsala University, Uppsala SE-751-24, Sweden
| | - Marcin Kruczyk
- Department of Cell and Molecular Biology, Uppsala University, Uppsala SE-751-24, Sweden
| | - Michał J Dąbrowski
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala SE-751-08, Sweden
| | - Marco Cavalli
- Institute of Computer Science, Polish Academy of Sciences, Warsaw 012-48, Poland
| | - Claes Wadelius
- Institute of Computer Science, Polish Academy of Sciences, Warsaw 012-48, Poland
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Uppsala University, Uppsala SE-751-24, Sweden .,Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala SE-751-08, Sweden
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22
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Yamanaka T, Tosaki A, Kurosawa M, Shimogori T, Hattori N, Nukina N. Genome-wide analyses in neuronal cells reveal that upstream transcription factors regulate lysosomal gene expression. FEBS J 2016; 283:1077-87. [DOI: 10.1111/febs.13650] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/17/2015] [Accepted: 01/08/2016] [Indexed: 12/01/2022]
Affiliation(s)
- Tomoyuki Yamanaka
- Laboratory of Structural Neuropathology; Doshisha University Graduate School of Brain Science; Kyoto Japan
- Laboratory for Structural Neuropathology; RIKEN Brain Science Institute; Saitama Japan
- Department of Neuroscience for Neurodegenerative Disorders; Juntendo University Graduate School of Medicine; Tokyo Japan
- Laboratory for Molecular Mechanisms of Thalamus Development; RIKEN Brain Science Institute; Saitama Japan
| | - Asako Tosaki
- Laboratory for Structural Neuropathology; RIKEN Brain Science Institute; Saitama Japan
| | - Masaru Kurosawa
- Laboratory for Structural Neuropathology; RIKEN Brain Science Institute; Saitama Japan
- Department of Neuroscience for Neurodegenerative Disorders; Juntendo University Graduate School of Medicine; Tokyo Japan
| | - Tomomi Shimogori
- Laboratory for Molecular Mechanisms of Thalamus Development; RIKEN Brain Science Institute; Saitama Japan
| | - Nobutaka Hattori
- Department of Neurology; Juntendo University Graduate School of Medicine; Tokyo Japan
| | - Nobuyuki Nukina
- Laboratory of Structural Neuropathology; Doshisha University Graduate School of Brain Science; Kyoto Japan
- Laboratory for Structural Neuropathology; RIKEN Brain Science Institute; Saitama Japan
- Department of Neuroscience for Neurodegenerative Disorders; Juntendo University Graduate School of Medicine; Tokyo Japan
- Laboratory for Molecular Mechanisms of Thalamus Development; RIKEN Brain Science Institute; Saitama Japan
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23
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Busche S, Shao X, Caron M, Kwan T, Allum F, Cheung WA, Ge B, Westfall S, Simon MM, Barrett A, Bell JT, McCarthy MI, Deloukas P, Blanchette M, Bourque G, Spector TD, Lathrop M, Pastinen T, Grundberg E. Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation. Genome Biol 2015; 16:290. [PMID: 26699896 PMCID: PMC4699357 DOI: 10.1186/s13059-015-0856-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/09/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND CpG methylation variation is involved in human trait formation and disease susceptibility. Analyses within populations have been biased towards CpG-dense regions through the application of targeted arrays. We generate whole-genome bisulfite sequencing data for approximately 30 adipose and blood samples from monozygotic and dizygotic twins for the characterization of non-genetic and genetic effects at single-site resolution. RESULTS Purely invariable CpGs display a bimodal distribution with enrichment of unmethylated CpGs and depletion of fully methylated CpGs in promoter and enhancer regions. Population-variable CpGs account for approximately 15-20 % of total CpGs per tissue, are enriched in enhancer-associated regions and depleted in promoters, and single nucleotide polymorphisms at CpGs are a frequent confounder of extreme methylation variation. Differential methylation is primarily non-genetic in origin, with non-shared environment accounting for most of the variance. These non-genetic effects are mainly tissue-specific. Tobacco smoking is associated with differential methylation in blood with no evidence of this exposure impacting cell counts. Opposite to non-genetic effects, genetic effects of CpG methylation are shared across tissues and thus limit inter-tissue epigenetic drift. CpH methylation is rare, and shows similar characteristics of variation patterns as CpGs. CONCLUSIONS Our study highlights the utility of low pass whole-genome bisulfite sequencing in identifying methylome variation beyond promoter regions, and suggests that targeting the population dynamic methylome of tissues requires assessment of understudied intergenic CpGs distal to gene promoters to reveal the full extent of inter-individual variation.
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Affiliation(s)
- Stephan Busche
- />Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec Canada
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
| | - Xiaojian Shao
- />Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec Canada
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
| | - Maxime Caron
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
| | - Tony Kwan
- />Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec Canada
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
| | - Fiona Allum
- />Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec Canada
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
| | - Warren A. Cheung
- />Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec Canada
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
| | - Bing Ge
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
| | - Susan Westfall
- />Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec Canada
| | - Marie-Michelle Simon
- />Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec Canada
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
| | - The Multiple Tissue Human Expression Resource
- />Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec Canada
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
- />Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford, UK
- />Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
- />Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- />Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Headington, Oxford, UK
- />William Harvey Research Institute, Queen Mary University of London, London, UK
- />Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- />School of Computer Science, McGill University, Montreal, Quebec Canada
| | - Amy Barrett
- />Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford, UK
| | - Jordana T. Bell
- />Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Mark I. McCarthy
- />Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford, UK
- />Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- />Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Headington, Oxford, UK
| | - Panos Deloukas
- />William Harvey Research Institute, Queen Mary University of London, London, UK
- />Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Mathieu Blanchette
- />School of Computer Science, McGill University, Montreal, Quebec Canada
| | - Guillaume Bourque
- />Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec Canada
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
| | - Timothy D. Spector
- />Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Mark Lathrop
- />Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec Canada
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
| | - Tomi Pastinen
- />Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec Canada
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
| | - Elin Grundberg
- />Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec Canada
- />McGill University and Genome Quebec Innovation Centre, Montreal, Quebec Canada
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Analysis of tandem E-box motifs within human Complement receptor 2 (CR2/CD21) promoter reveals cell specific roles for RP58, E2A, USF and localized chromatin accessibility. Int J Biochem Cell Biol 2015; 64:107-19. [DOI: 10.1016/j.biocel.2015.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/03/2015] [Accepted: 03/18/2015] [Indexed: 02/06/2023]
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Bornelöv S, Komorowski J, Wadelius C. Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription. BMC Genomics 2015; 16:300. [PMID: 25881024 PMCID: PMC4446127 DOI: 10.1186/s12864-015-1485-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 03/25/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several post-translational histone modifications are mainly found in gene promoters and are associated with the promoter activity. It has been hypothesized that histone modifications regulate the transcription, as opposed to the traditional view with transcription factors as the key regulators. Promoters of most active genes do not only initiate transcription of the coding sequence, but also a substantial amount of transcription of the antisense strand upstream of the transcription start site (TSS). This promoter feature has generally not been considered in previous studies of histone modifications and transcription factor binding. RESULTS We annotated protein-coding genes as bi- or unidirectional depending on their mode of transcription and compared histone modifications and transcription factor occurrences between them. We found that H3K4me3, H3K9ac, and H3K27ac were significantly more enriched upstream of the TSS in bidirectional genes compared with the unidirectional ones. In contrast, the downstream histone modification signals were similar, suggesting that the upstream histone modifications might be a consequence of transcription rather than a cause. Notably, we found well-positioned CTCF and RAD21 peaks approximately 60-80 bp upstream of the TSS in the unidirectional genes. The peak heights were related to the amount of antisense transcription and we hypothesized that CTCF and cohesin act as a barrier against antisense transcription. CONCLUSIONS Our results provide insights into the distribution of histone modifications at promoters and suggest a novel role of CTCF and cohesin as regulators of transcriptional direction.
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Affiliation(s)
- Susanne Bornelöv
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, SE-751 24, Sweden.
- Current affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-751 23, Sweden.
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, SE-751 24, Sweden.
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, 01-248, Poland.
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, SE-751 08, Sweden.
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Horbach T, Götz C, Kietzmann T, Dimova EY. Protein kinases as switches for the function of upstream stimulatory factors: implications for tissue injury and cancer. Front Pharmacol 2015; 6:3. [PMID: 25741280 PMCID: PMC4332324 DOI: 10.3389/fphar.2015.00003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/07/2015] [Indexed: 01/30/2023] Open
Abstract
The upstream stimulatory factors (USFs) are regulators of important cellular processes. Both USF1 and USF2 are supposed to have major roles in metabolism, tissue protection and tumor development. However, the knowledge about the mechanisms that control the function of USFs, in particular in tissue protection and cancer, is limited. Phosphorylation is a versatile tool to regulate protein functions. Thereby, phosphorylation can positively or negatively affect different aspects of transcription factor function including protein stability, protein-protein interaction, cellular localization, or DNA binding. The present review aims to summarize the current knowledge about the regulation of USFs by direct phosphorylation and the consequences for USF functions in tissue protection and cancer.
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Affiliation(s)
- Tina Horbach
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu , Oulu, Finland ; Department of Chemistry, University of Kaiserslautern , Kaiserslautern, Germany
| | - Claudia Götz
- Medical Biochemistry and Molecular Biology, Saarland University , Homburg, Germany
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu , Oulu, Finland
| | - Elitsa Y Dimova
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu , Oulu, Finland
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27
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Significant association between upstream transcription factor 1 rs2516839 polymorphism and hepatocellular carcinoma risk: a case–control study. Tumour Biol 2014; 36:2551-8. [DOI: 10.1007/s13277-014-2871-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 11/18/2014] [Indexed: 12/13/2022] Open
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Glass K, Quackenbush J, Silverman EK, Celli B, Rennard SI, Yuan GC, DeMeo DL. Sexually-dimorphic targeting of functionally-related genes in COPD. BMC SYSTEMS BIOLOGY 2014; 8:118. [PMID: 25431000 PMCID: PMC4269917 DOI: 10.1186/s12918-014-0118-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/09/2014] [Indexed: 12/23/2022]
Abstract
BACKGROUND There is growing evidence that many diseases develop, progress, and respond to therapy differently in men and women. This variability may manifest as a result of sex-specific structures in gene regulatory networks that influence how those networks operate. However, there are few methods to identify and characterize differences in network structure, slowing progress in understanding mechanisms driving sexual dimorphism. RESULTS Here we apply an integrative network inference method, PANDA (Passing Attributes between Networks for Data Assimilation), to model sex-specific networks in blood and sputum samples from subjects with Chronic Obstructive Pulmonary Disease (COPD). We used a jack-knifing approach to build an ensemble of likely networks for each sex. By adapting statistical methods to compare these network ensembles, we were able to identify strong differential-targeting patterns associated with functionally-related sets of genes, including those involved in mitochondrial function and energy metabolism. Network analysis also identified several potential sex- and disease-specific transcriptional regulators of these pathways. CONCLUSIONS Network analysis yielded insight into potential mechanisms driving sexual dimorphism in COPD that were not evident from gene expression analysis alone. We believe our ensemble approach to network analysis provides a principled way to capture sex-specific regulatory relationships and could be applied to identify differences in gene regulatory patterns in a wide variety of diseases and contexts.
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Affiliation(s)
- Kimberly Glass
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Bartolome Celli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Stephen I Rennard
- Division of Pulmonary, Critical Care, Sleep and Allergy, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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Roson-Burgo B, Sanchez-Guijo F, Del Cañizo C, De Las Rivas J. Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placenta. BMC Genomics 2014; 15:910. [PMID: 25326687 PMCID: PMC4287589 DOI: 10.1186/1471-2164-15-910] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 09/24/2014] [Indexed: 02/08/2023] Open
Abstract
Background Human Mesenchymal Stromal/Stem Cells (MSCs) are adult multipotent cells that behave in a highly plastic manner, inhabiting the stroma of several tissues. The potential utility of MSCs is nowadays strongly investigated in the field of regenerative medicine and cell therapy, although many questions about their molecular identity remain uncertain. Results MSC primary cultures from human bone marrow (BM) and placenta (PL) were derived and verified by their immunophenotype standard pattern and trilineage differentiation potential. Then, a broad characterization of the transcriptome of these MSCs was performed using RNA deep sequencing (RNA-Seq). Quantitative analysis of these data rendered an extensive expression footprint that includes 5,271 protein-coding genes. Flow cytometry assays of canonical MSC CD-markers were congruent with their expression levels detected by the RNA-Seq. Expression of other recently proposed MSC markers (CD146, Nestin and CD271) was tested in the placenta samples, finding only CD146 and Nestin. Functional analysis revealed enrichment in stem cell related genes and mesenchymal regulatory transcription factors (TFs). Analysis of TF binding sites (TFBSs) identified 11 meta-regulators, including factors KLF4 and MYC among them. Epigenetically, hypomethylated promoter patterns supported the active expression of the MSC TFs found. An interaction network of these TFs was built to show up their links and relations. Assessment of dissimilarities between cell origins (BM versus PL) disclosed two hundred differentially expressed genes enrolled in microenvironment processes related to the cellular niche, as regulation of bone formation and blood vessel morphogenesis for the case of BM-MSCs. By contrast genes overexpressed in PL-MSCs showed functional enrichment on mitosis, negative regulation of cell-death and embryonic morphogenesis that supported the higher growth rates observed in the cultures of these fetal cells and their closer links with development processes. Conclusions The results present a transcriptomic portrait of the human MSCs isolated from bone marrow and placenta. The data are released as a cell-specific resource, providing a comprehensive expression footprint of the MSCs useful to better understand their cellular and molecular biology and for further investigations on the isolation and biomedical use of these multipotent cells. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-910) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Javier De Las Rivas
- Bioinformatics and Functional Genomics Group, Cancer Research Center (IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Cientificas (CSIC), Salamanca, Spain.
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Pdx1 and USF transcription factors co-ordinately regulate Alx3 gene expression in pancreatic β-cells. Biochem J 2014; 463:287-96. [DOI: 10.1042/bj20140643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We investigated the transcriptional mechanisms regulating the expression of Alx3 in pancreatic islets. We found that the transcriptional transactivation of Alx3 in β-cells requires the co-operation of the islet-specific homeoprotein Pdx1 with the transcription factors USF1 and USF2.
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Integration of genome-wide of Stat3 binding and epigenetic modification mapping with transcriptome reveals novel Stat3 target genes in glioma cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1341-50. [PMID: 25111868 DOI: 10.1016/j.bbagrm.2014.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/18/2014] [Accepted: 07/14/2014] [Indexed: 01/04/2023]
Abstract
BACKGROUND Signal transducer and activator of transcription 3 (STAT3) is constitutively activated in many human tumors, including gliomas, and regulates the expression of genes implicated in proliferation, survival, apoptosis, angiogenesis and immune regulation. Only a small fraction of those genes has been proven to be direct STAT3 targets. In gliomas, STAT3 can play tumor suppressive or oncogenic roles depending on the tumor genetic background with target genes being largely unknown. RESULTS We used chromatin immunoprecipitation, promoter microarrays and deep sequencing to assess the genome-wide occupancy of phospho (p)-Stat3 and epigenetic modifications of H3K4me3 and H3ac in C6 glioma cells. This combined assessment identified a list of 1200 genes whose promoters have both Stat3 binding sites and epigenetic marks characteristic for actively transcribed genes. The Stat3 and histone markings data were also intersected with a set of microarray data from C6 glioma cells after inhibition of Jak2/Stat3 signaling. Subsequently, we found 284 genes characterized by p-Stat3 occupancy, activating histone marks and transcriptional changes. Novel genes were screened for their potential involvement in oncogenesis, and the most interesting hits were verified by ChIP-PCR and STAT3 knockdown in human glioma cells. CONCLUSIONS Non-random association between silent genes, histone marks and p-Stat3 binding near transcription start sites was observed, consistent with its repressive role in transcriptional regulation of target genes in glioma cells with specific genetic background.
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Faisal M, Waseem D, Ismatullah H, Taqi MM. A molecular prospective provides new insights into implication of PDYN and OPRK1 genes in alcohol dependence. Comput Biol Med 2014; 53:250-7. [PMID: 25177835 DOI: 10.1016/j.compbiomed.2014.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 07/24/2014] [Accepted: 07/26/2014] [Indexed: 12/15/2022]
Abstract
Single nucleotide polymorphisms (SNPs) both in coding and non-coding regions govern gene functions prompting differential vulnerability to diseases, heterogeneous response to pharmaceutical regimes and environmental anomalies. These genetic variations, SNPs, may alter an individual׳s susceptibility for alcohol dependence by remodeling DNA-protein interaction patterns in prodynorphin (PDYN) and the κ-opioid receptor (OPRK1) genes. In order to elaborate the underlying molecular mechanism behind these susceptibility differences we used bioinformatics tools to retrieve differential DNA-protein interactions at PDYN and OPRK1 SNPs significantly associated with alcohol dependence. Our results show allele-specific DNA-protein interactions depicting allele-specific mechanisms implicated in differential regulation of gene expression. Several transcription factors, for instance, VDR, RXR-alpha, NFYA, CTF family, USF-1, USF2, ER, AR and predominantly SP family show an allele-specific binding affinity with PDYN gene; likewise, GATA, TBP, AP-1, USF-2, C/EBPbeta, Cart-1 and ER interact with OPRK1 SNPs on intron 2 in an allele-specific manner. In a nutshell, transition of a single nucleotide may modify differential DNA-protein interactions at OPRK1 and PDYN׳s SNPs, significantly associated with pathology that may lead to altered individual vulnerability for alcohol dependence.
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Affiliation(s)
- Muhammad Faisal
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Durdana Waseem
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Humaira Ismatullah
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad, Pakistan
| | - Malik Mumtaz Taqi
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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Zubeldia-Brenner L, Gutierrez-Uzquiza A, Barrio-Real L, Wang H, Kazanietz MG, Leskow FC. β3-chimaerin, a novel member of the chimaerin Rac-GAP family. Mol Biol Rep 2014; 41:2067-76. [PMID: 24430297 DOI: 10.1007/s11033-014-3055-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 01/04/2014] [Indexed: 12/11/2022]
Abstract
Chimaerins are a family of diacylglycerol- and phorbol ester-regulated GTPase activating proteins (GAPs) for the small G-protein Rac. Extensive evidence indicates that these proteins play important roles in development, axon guidance, metabolism, cell motility, and T cell activation. Four isoforms have been reported to-date, which are products of CHN1 (α1- and α2-chimaerins) and CHN2 (β1- and β2-chimaerins) genes. Although these gene products are assumed to be generated by alternative splicing, bioinformatics analysis of the CHN2 gene revealed that β1- and β2-chimaerins are the products of alternative transcription start sites (TSSs) in different promoter regions. Furthermore, we found an additional TSS in CHN2 gene that leads to a novel product, which we named β3-chimaerin. Expression profile analysis revealed predominantly low levels for the β3-chimaerin transcript, with higher expression levels in epididymis, plasma blood leucocytes, spleen, thymus, as well as various areas of the brain. In addition to the prototypical SH2, C1, and Rac-GAP domains, β3-chimaerin has a unique N-terminal domain. Studies in cells established that β3-chimaerin has Rac-GAP activity and is responsive to phorbol esters. The enhanced responsiveness of β3-chimaerin for phorbol ester-induced translocation relative to β2-chimaerin suggests differential ligand accessibility to the C1 domain.
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Affiliation(s)
- Lautaro Zubeldia-Brenner
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, IQUIBICEN-CONICET, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
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34
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Bysani M, Wallerman O, Bornelöv S, Zatloukal K, Komorowski J, Wadelius C. ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer. BMC Med Genomics 2013; 6:50. [PMID: 24206787 PMCID: PMC3831757 DOI: 10.1186/1755-8794-6-50] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 10/31/2013] [Indexed: 02/06/2023] Open
Abstract
Background Steatohepatitis occurs in alcoholic liver disease and may progress to liver cirrhosis and hepatocellular carcinoma. Its molecular pathogenesis is to a large degree unknown. Histone modifications play a key role in transcriptional regulations as marks for silencing and activation of gene expression and as marks for functional elements. Many transcription factors (TFs) are crucial for the control of the genes involved in metabolism, and abnormality in their function may lead to disease. Methods We performed ChIP-seq of the histone modifications H3K4me1, H3K4me3 and H3K27ac and a candidate transcription factor (USF1) in liver tissue from patients with steatohepatitis and normal livers and correlated results to mRNA-expression and genotypes. Results We found several regions that are differentially enriched for histone modifications between disease and normal tissue, and qRT-PCR results indicated that the expression of the tested genes strongly correlated with differential enrichment of histone modifications but is independent of USF1 enrichment. By gene ontology analysis of differentially modified genes we found many disease associated genes, some of which had previously been implicated in the etiology of steatohepatitis. Importantly, the genes associated to the strongest histone peaks in the patient were over-represented in cancer specific pathways suggesting that the tissue was on a path to develop to cancer, a common complication to the disease. We also found several novel SNPs and GWAS catalogue SNPs that are candidates to be functional and therefore needs further study. Conclusion In summary we find that analysis of chromatin features in tissue samples provides insight into disease mechanisms.
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Affiliation(s)
| | | | | | | | | | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Uppsala University, PO BOX 815, Uppsala, SE 751 08, Sweden.
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35
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Grundberg E, Meduri E, Sandling J, Hedman Å, Keildson S, Buil A, Busche S, Yuan W, Nisbet J, Sekowska M, Wilk A, Barrett A, Small K, Ge B, Caron M, Shin SY, Lathrop M, Dermitzakis ET, McCarthy MI, Spector TD, Bell JT, Deloukas P. Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Am J Hum Genet 2013; 93:876-90. [PMID: 24183450 PMCID: PMC3824131 DOI: 10.1016/j.ajhg.2013.10.004] [Citation(s) in RCA: 288] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/13/2013] [Accepted: 10/04/2013] [Indexed: 12/28/2022] Open
Abstract
Epigenetic modifications such as DNA methylation play a key role in gene regulation and disease susceptibility. However, little is known about the genome-wide frequency, localization, and function of methylation variation and how it is regulated by genetic and environmental factors. We utilized the Multiple Tissue Human Expression Resource (MuTHER) and generated Illumina 450K adipose methylome data from 648 twins. We found that individual CpGs had low variance and that variability was suppressed in promoters. We noted that DNA methylation variation was highly heritable (h(2)median = 0.34) and that shared environmental effects correlated with metabolic phenotype-associated CpGs. Analysis of methylation quantitative-trait loci (metQTL) revealed that 28% of CpGs were associated with nearby SNPs, and when overlapping them with adipose expression quantitative-trait loci (eQTL) from the same individuals, we found that 6% of the loci played a role in regulating both gene expression and DNA methylation. These associations were bidirectional, but there were pronounced negative associations for promoter CpGs. Integration of metQTL with adipose reference epigenomes and disease associations revealed significant enrichment of metQTL overlapping metabolic-trait or disease loci in enhancers (the strongest effects were for high-density lipoprotein cholesterol and body mass index [BMI]). We followed up with the BMI SNP rs713586, a cg01884057 metQTL that overlaps an enhancer upstream of ADCY3, and used bisulphite sequencing to refine this region. Our results showed widespread population invariability yet sequence dependence on adipose DNA methylation but that incorporating maps of regulatory elements aid in linking CpG variation to gene regulation and disease risk in a tissue-dependent manner.
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Affiliation(s)
- Elin Grundberg
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Eshwar Meduri
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Johanna K. Sandling
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- Molecular Medicine, Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, 751 23 Uppsala, Sweden
| | - Åsa K. Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX37BN Oxford, UK
| | - Sarah Keildson
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX37BN Oxford, UK
| | - Alfonso Buil
- Department of Genetic Medicine and Development and Institute for Genetics and Genomics in Geneva, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Stephan Busche
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - Wei Yuan
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - James Nisbet
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
| | | | - Alicja Wilk
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
| | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology, & Metabolism, University of Oxford, Churchill Hospital, OX37LJ Oxford, UK
| | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Bing Ge
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
| | - Mark Lathrop
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development and Institute for Genetics and Genomics in Geneva, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX37BN Oxford, UK
- Oxford Centre for Diabetes, Endocrinology, & Metabolism, University of Oxford, Churchill Hospital, OX37LJ Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, OX3 7LE Oxford, UK
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
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36
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Vacca GM, Dettori ML, Balia F, Luridiana S, Mura MC, Carcangiu V, Pazzola M. Sequence polymorphisms at the growth hormone GH1/GH2-N and GH2-Z gene copies and their relationship with dairy traits in domestic sheep (Ovis aries). Mol Biol Rep 2013; 40:5285-94. [PMID: 23653010 DOI: 10.1007/s11033-013-2629-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 04/30/2013] [Indexed: 11/29/2022]
Abstract
The purpose was to analyze the growth hormone GH1/GH2-N and GH2-Z gene copies and to assess their possible association with milk traits in Sarda sheep. Two hundred multiparous lactating ewes were monitored. The two gene copies were amplified separately and each was used as template for a nested PCR, to investigate single strand conformation polymorphism (SSCP) of the 5'UTR, exon-1, exon-5 and 3'UTR DNA regions. SSCP analysis revealed marked differences in the number of polymorphic patterns between the two genes. Sequencing revealed five nucleotide changes at the GH1/GH2-N gene. Five nucleotide changes occurred at the GH2-Z gene: one was located in exon-5 (c.556G > A) and resulted in a putative amino acid substitution G186S. All the nucleotide changes were copy-specific, except c.*30delT, which was common to both GH1/GH2-N and GH2-Z. Variability in the promoter regions of each gene might have consequences on the expression level, due to the involvement in potential transcription factor binding sites. Both gene copies influenced milk yield. A correlation with milk protein and casein content was also evidenced. These results may have implications that make them useful for future breeding strategies in dairy sheep breeding.
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Affiliation(s)
- G M Vacca
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, via Vienna 2, 07100, Sassari, Italy
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37
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Ernst J, Kellis M. Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types. Genome Res 2013; 23:1142-54. [PMID: 23595227 PMCID: PMC3698507 DOI: 10.1101/gr.144840.112] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The regions bound by sequence-specific transcription factors can be highly variable across different cell types despite the static nature of the underlying genome sequence. This has been partly attributed to changes in chromatin accessibility, but a systematic picture has been hindered by the lack of large-scale data sets. Here, we use 456 binding experiments for 119 regulators and 84 chromatin maps generated by the ENCODE in six human cell types, and relate those to a global map of regulatory motif instances for these factors. We find specific and robust chromatin state preferences for each regulator beyond the previously reported open-chromatin association, suggesting a much richer chromatin landscape beyond simple accessibility. The preferentially bound chromatin states of regulators were enriched for sequence motifs of regulators relative to all states, suggesting that these preferences are at least partly encoded by the genomic sequence. Relative to all regions bound by a regulator, however, regulatory motifs were surprisingly depleted in the regulator's preferentially bound states, suggesting additional non-sequence-specific binding beyond the level predicted by the regulatory motifs. Such permissive binding was largely restricted to open-chromatin regions showing histone modification marks characteristic of active enhancer and promoter regions, whereas open-chromatin regions lacking such marks did not show permissive binding. Lastly, the vast majority of cobinding of regulator pairs is predicted by the chromatin state preferences of individual regulators. Overall, our results suggest a joint role of sequence motifs and specific chromatin states beyond mere accessibility in mediating regulator binding dynamics across different cell types.
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Affiliation(s)
- Jason Ernst
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, USA
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38
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Giannopoulou EG, Elemento O. Inferring chromatin-bound protein complexes from genome-wide binding assays. Genome Res 2013; 23:1295-306. [PMID: 23554462 PMCID: PMC3730103 DOI: 10.1101/gr.149419.112] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Genome-wide binding assays can determine where individual transcription factors bind in the genome. However, these factors rarely bind chromatin alone, but instead frequently bind to cis-regulatory elements (CREs) together with other factors thus forming protein complexes. Currently there are no integrative analytical approaches that can predict which complexes are formed on chromatin. Here, we describe a computational methodology to systematically capture protein complexes and infer their impact on gene expression. We applied our method to three human cell types, identified thousands of CREs, inferred known and undescribed complexes recruited to these CREs, and determined the role of the complexes as activators or repressors. Importantly, we found that the predicted complexes have a higher number of physical interactions between their members than expected by chance. Our work provides a mechanism for developing hypotheses about gene regulation via binding partners, and deciphering the interplay between combinatorial binding and gene expression.
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Affiliation(s)
- Eugenia G Giannopoulou
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, New York 10021, USA
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39
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Estécio MRH, Gallegos J, Dekmezian M, Lu Y, Liang S, Issa JPJ. SINE retrotransposons cause epigenetic reprogramming of adjacent gene promoters. Mol Cancer Res 2012; 10:1332-42. [PMID: 22952045 DOI: 10.1158/1541-7786.mcr-12-0351] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Almost half of the human genome and as much as 40% of the mouse genome is composed of repetitive DNA sequences. The majority of these repeats are retrotransposons of the SINE and LINE families, and such repeats are generally repressed by epigenetic mechanisms. It has been proposed that these elements can act as methylation centers from which DNA methylation spreads into gene promoters in cancer. Contradictory to a methylation center function, we have found that retrotransposons are enriched near promoter CpG islands that stay methylation-free in cancer. Clearly, it is important to determine which influence, if any, these repetitive elements have on nearby gene promoters. Using an in vitro system, we confirm here that SINE B1 elements can influence the activity of downstream gene promoters, with acquisition of DNA methylation and loss of activating histone marks, thus resulting in a repressed state. SINE sequences themselves did not immediately acquire DNA methylation but were marked by H3K9me2 and H3K27me3. Moreover, our bisulfite sequencing data did not support that gain of DNA methylation in gene promoters occurred by methylation spreading from SINE B1 repeats. Genome-wide analysis of SINE repeats distribution showed that their enrichment is directly correlated with the presence of USF1, USF2, and CTCF binding, proteins with insulator function. In summary, our work supports the concept that SINE repeats interfere negatively with gene expression and that their presence near gene promoters is counter-selected, except when the promoter is protected by an insulator element.
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Affiliation(s)
- Marcos R H Estécio
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA.
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40
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Auer S, Hahne P, Soyal SM, Felder T, Miller K, Paulmichl M, Krempler F, Oberkofler H, Patsch W. Potential Role of Upstream Stimulatory Factor 1 Gene Variant in Familial Combined Hyperlipidemia and Related Disorders. Arterioscler Thromb Vasc Biol 2012; 32:1535-44. [DOI: 10.1161/atvbaha.112.245639] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Objective—
Genetic studies implicated upstream stimulatory factor 1 (USF1) in familial combined hyperlipidemia because the rs2073658 minor allele was associated with reduced risk of familial combined hyperlipidemia and related disorders. The molecular mechanisms whereby rs2073658 influences trait expression have remained elusive.
Methods and Results—
Plasma lipids, rs2073658 genotypes (N=372), and hepatic transcript levels (N=96) of
USF1
and genes involved in hepatic lipoprotein production were determined in obese subjects. The rs2073658 minor allele was associated with reduced plasma triglycerides (TGs) (
P
<0.001), hepatic
USF1
(
P
<0.01), and microsomal TG transfer protein transcript levels (
P
<0.05). Functional studies in human hepatocellular carcinoma cells showed that rs2073658 is located in a forkhead box A2 (FOXA2) binding site and that major allele constructs displayed higher transcriptional activity than minor allele constructs. Knockdown of FOXA2 reduced the activity of major, but not minor allele constructs. Furthermore, an interaction between hepatic FOXA2 transcript levels and rs2073658 minor allele carrier status on hepatic
USF1
transcript levels was observed in vivo (
P
<0.05).
USF1
activated the transcription of FOXA2 and FOXA2 strongly activated the transcription of microsomal TG transfer protein.
Conclusion—
A feed-forward loop comprising activation of
USF1
transcription by FOXA2 and activation of FOXA2 transcription by
USF1
, driving microsomal TG transfer protein expression, is modulated by rs2073658. Hence, rs2073658 likely influences hepatic TG secretion.
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Affiliation(s)
- Simon Auer
- From the Department of Laboratory Medicine (S.A., P.H., S.M.S., T.F., H.O., W.P.) and Institute of Pharmacology (M.P., W.P.), Paracelsus Medical University, Salzburg, Austria; Departments of Surgery (K.M.) and Internal Medicine (F.K.), Krankenhaus Hallein, Salzburg, Austria
| | - Penelope Hahne
- From the Department of Laboratory Medicine (S.A., P.H., S.M.S., T.F., H.O., W.P.) and Institute of Pharmacology (M.P., W.P.), Paracelsus Medical University, Salzburg, Austria; Departments of Surgery (K.M.) and Internal Medicine (F.K.), Krankenhaus Hallein, Salzburg, Austria
| | - Selma M. Soyal
- From the Department of Laboratory Medicine (S.A., P.H., S.M.S., T.F., H.O., W.P.) and Institute of Pharmacology (M.P., W.P.), Paracelsus Medical University, Salzburg, Austria; Departments of Surgery (K.M.) and Internal Medicine (F.K.), Krankenhaus Hallein, Salzburg, Austria
| | - Thomas Felder
- From the Department of Laboratory Medicine (S.A., P.H., S.M.S., T.F., H.O., W.P.) and Institute of Pharmacology (M.P., W.P.), Paracelsus Medical University, Salzburg, Austria; Departments of Surgery (K.M.) and Internal Medicine (F.K.), Krankenhaus Hallein, Salzburg, Austria
| | - Karl Miller
- From the Department of Laboratory Medicine (S.A., P.H., S.M.S., T.F., H.O., W.P.) and Institute of Pharmacology (M.P., W.P.), Paracelsus Medical University, Salzburg, Austria; Departments of Surgery (K.M.) and Internal Medicine (F.K.), Krankenhaus Hallein, Salzburg, Austria
| | - Markus Paulmichl
- From the Department of Laboratory Medicine (S.A., P.H., S.M.S., T.F., H.O., W.P.) and Institute of Pharmacology (M.P., W.P.), Paracelsus Medical University, Salzburg, Austria; Departments of Surgery (K.M.) and Internal Medicine (F.K.), Krankenhaus Hallein, Salzburg, Austria
| | - Franz Krempler
- From the Department of Laboratory Medicine (S.A., P.H., S.M.S., T.F., H.O., W.P.) and Institute of Pharmacology (M.P., W.P.), Paracelsus Medical University, Salzburg, Austria; Departments of Surgery (K.M.) and Internal Medicine (F.K.), Krankenhaus Hallein, Salzburg, Austria
| | - Hannes Oberkofler
- From the Department of Laboratory Medicine (S.A., P.H., S.M.S., T.F., H.O., W.P.) and Institute of Pharmacology (M.P., W.P.), Paracelsus Medical University, Salzburg, Austria; Departments of Surgery (K.M.) and Internal Medicine (F.K.), Krankenhaus Hallein, Salzburg, Austria
| | - Wolfgang Patsch
- From the Department of Laboratory Medicine (S.A., P.H., S.M.S., T.F., H.O., W.P.) and Institute of Pharmacology (M.P., W.P.), Paracelsus Medical University, Salzburg, Austria; Departments of Surgery (K.M.) and Internal Medicine (F.K.), Krankenhaus Hallein, Salzburg, Austria
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Park S, Liu X, Davis DR, Sigmund CD. Gene trapping uncovers sex-specific mechanisms for upstream stimulatory factors 1 and 2 in angiotensinogen expression. Hypertension 2012; 59:1212-9. [PMID: 22547438 DOI: 10.1161/hypertensionaha.112.192971] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A single-nucleotide polymorphism (C/A) located within an E-box at the -20 position of the human angiotensinogen (AGT) promoter may regulate transcriptional activation through differential recruitment of the transcription factors upstream stimulatory factor (USF) 1 and 2. To study the contribution of USF1 on AGT gene expression, mice carrying a (-20C) human AGT (hAGT) transgene were bred with mice harboring a USF1 gene trap allele designed to knock down USF1 expression. USF1 mRNA was reduced relative to controls in liver (9 ± 1%), perigenital adipose (16 ± 3%), kidney (17 ± 1%), and brain (34 ± 2%) in double-transgenic mice. This decrease was confirmed by electrophoretic mobility shift assay. Chromatin immunoprecipitation analyses revealed a decrease in USF1, with retention of USF2 binding at the hAGT promoter in the liver of male mice. hAGT expression was reduced in the liver and other tissues of female but not male mice. The decrease in endogenous AGT expression was insufficient to alter systolic blood pressure at baseline but caused reduced systolic blood pressure in female USF1 gene trap mice fed a high-fat diet. Treatment of USF1 knockdown males with intravenous adenoviral short hairpin RNA targeting USF2 resulted in reduced expression of USF1, USF2, and hAGT protein. Our data from chromatin immunoprecipitation assays suggests that this decrease in hAGT is attributed to decreased USF2 binding to the hAGT promoter. In conclusion, both USF1 and USF2 are essential for AGT transcriptional regulation, and distinct sex-specific and tissue-specific mechanisms are involved in the activities of these transcription factors in vivo.
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Affiliation(s)
- Sungmi Park
- Department of Pharmacology, 3181 MERF, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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42
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Iglesias MJ, Reilly SJ, Emanuelsson O, Sennblad B, Pirmoradian Najafabadi M, Folkersen L, Mälarstig A, Lagergren J, Eriksson P, Hamsten A, Odeberg J. Combined chromatin and expression analysis reveals specific regulatory mechanisms within cytokine genes in the macrophage early immune response. PLoS One 2012; 7:e32306. [PMID: 22384210 PMCID: PMC3288078 DOI: 10.1371/journal.pone.0032306] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 01/26/2012] [Indexed: 11/19/2022] Open
Abstract
Macrophages play a critical role in innate immunity, and the expression of early response genes orchestrate much of the initial response of the immune system. Macrophages undergo extensive transcriptional reprogramming in response to inflammatory stimuli such as Lipopolysaccharide (LPS).To identify gene transcription regulation patterns involved in early innate immune responses, we used two genome-wide approaches--gene expression profiling and chromatin immunoprecipitation-sequencing (ChIP-seq) analysis. We examined the effect of 2 hrs LPS stimulation on early gene expression and its relation to chromatin remodeling (H3 acetylation; H3Ac) and promoter binding of Sp1 and RNA polymerase II phosphorylated at serine 5 (S5P RNAPII), which is a marker for transcriptional initiation. Our results indicate novel and alternative gene regulatory mechanisms for certain proinflammatory genes. We identified two groups of up-regulated inflammatory genes with respect to chromatin modification and promoter features. One group, including highly up-regulated genes such as tumor necrosis factor (TNF), was characterized by H3Ac, high CpG content and lack of TATA boxes. The second group, containing inflammatory mediators (interleukins and CCL chemokines), was up-regulated upon LPS stimulation despite lacking H3Ac in their annotated promoters, which were low in CpG content but did contain TATA boxes. Genome-wide analysis showed that few H3Ac peaks were unique to either +/-LPS condition. However, within these, an unpacking/expansion of already existing H3Ac peaks was observed upon LPS stimulation. In contrast, a significant proportion of S5P RNAPII peaks (approx 40%) was unique to either condition. Furthermore, data indicated a large portion of previously unannotated TSSs, particularly in LPS-stimulated macrophages, where only 28% of unique S5P RNAPII peaks overlap annotated promoters. The regulation of the inflammatory response appears to occur in a very specific manner at the chromatin level for specific genes and this study highlights the level of fine-tuning that occurs in the immune response.
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Affiliation(s)
- Maria Jesus Iglesias
- Atherosclerosis Research Unit, Department of Medicine, Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden.
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43
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Stone JL, McMillan RE, Skaar DA, Bradshaw JM, Jirtle RL, Sikes ML. DNA double-strand breaks relieve USF-mediated repression of Dβ2 germline transcription in developing thymocytes. THE JOURNAL OF IMMUNOLOGY 2012; 188:2266-75. [PMID: 22287717 DOI: 10.4049/jimmunol.1002931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Activation of germline promoters is central to V(D)J recombinational accessibility, driving chromatin remodeling, nucleosome repositioning, and transcriptional read-through of associated DNA. We have previously shown that of the two TCRβ locus (Tcrb) D segments, Dβ1 is flanked by an upstream promoter that directs its transcription and recombinational accessibility. In contrast, transcription within the DJβ2 segment cluster is initially restricted to the J segments and only redirected upstream of Dβ2 after D-to-J joining. The repression of upstream promoter activity prior to Tcrb assembly correlates with evidence that suggests DJβ2 recombination is less efficient than that of DJβ1. Because inefficient DJβ2 assembly offers the potential for V-to-DJβ2 recombination to rescue frameshifted V-to-DJβ1 joints, we wished to determine how Dβ2 promoter activity is modulated upon Tcrb recombination. In this study, we show that repression of the otherwise transcriptionally primed 5'Dβ2 promoter requires binding of upstream stimulatory factor (USF)-1 to a noncanonical E-box within the Dβ2 12-recombination signal sequence spacer prior to Tcrb recombination. USF binding is lost from both rearranged and germline Dβ2 sites in DNA-dependent protein kinase, catalytic subunit-competent thymocytes. Finally, genotoxic dsDNA breaks lead to rapid loss of USF binding and gain of transcriptionally primed 5'Dβ2 promoter activity in a DNA-dependent protein kinase, catalytic subunit-dependent manner. Together, these data suggest a mechanism by which V(D)J recombination may feed back to regulate local Dβ2 recombinational accessibility during thymocyte development.
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Affiliation(s)
- Jennifer L Stone
- Department of Microbiology, North Carolina State University, Raleigh, NC 27695, USA
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Saxena A, Carninci P. Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. Bioessays 2011; 33:830-9. [PMID: 21915889 PMCID: PMC3258546 DOI: 10.1002/bies.201100084] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/09/2011] [Accepted: 08/10/2011] [Indexed: 12/16/2022]
Abstract
Common themes are emerging in the molecular mechanisms of long non-coding RNA-mediated gene repression. Long non-coding RNAs (lncRNAs) participate in targeted gene silencing through chromatin remodelling, nuclear reorganisation, formation of a silencing domain and precise control over the entry of genes into silent compartments. The similarities suggest that these are fundamental processes of transcription regulation governed by lncRNAs. These findings have paved the way for analogous investigations on other lncRNAs and chromatin remodelling enzymes. Here we discuss these common mechanisms and provide our view on other molecules that warrant similar investigations. We also present our concepts on the possible mechanisms that may facilitate the exit of genes from the silencing domains and their potential therapeutic applications. Finally, we point to future areas of research and put forward our recommendations for improvements in resources and applications of existing technologies towards targeted outcomes in this active area of research.
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Affiliation(s)
- Alka Saxena
- Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro Cho, Tsurumi Ku, Yokohama, Kanagawa 230-0045, Japan
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Lyons MR, West AE. Mechanisms of specificity in neuronal activity-regulated gene transcription. Prog Neurobiol 2011; 94:259-95. [PMID: 21620929 PMCID: PMC3134613 DOI: 10.1016/j.pneurobio.2011.05.003] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 05/05/2011] [Accepted: 05/05/2011] [Indexed: 02/06/2023]
Abstract
The brain is a highly adaptable organ that is capable of converting sensory information into changes in neuronal function. This plasticity allows behavior to be accommodated to the environment, providing an important evolutionary advantage. Neurons convert environmental stimuli into long-lasting changes in their physiology in part through the synaptic activity-regulated transcription of new gene products. Since the neurotransmitter-dependent regulation of Fos transcription was first discovered nearly 25 years ago, a wealth of studies have enriched our understanding of the molecular pathways that mediate activity-regulated changes in gene transcription. These findings show that a broad range of signaling pathways and transcriptional regulators can be engaged by neuronal activity to sculpt complex programs of stimulus-regulated gene transcription. However, the shear scope of the transcriptional pathways engaged by neuronal activity raises the question of how specificity in the nature of the transcriptional response is achieved in order to encode physiologically relevant responses to divergent stimuli. Here we summarize the general paradigms by which neuronal activity regulates transcription while focusing on the molecular mechanisms that confer differential stimulus-, cell-type-, and developmental-specificity upon activity-regulated programs of neuronal gene transcription. In addition, we preview some of the new technologies that will advance our future understanding of the mechanisms and consequences of activity-regulated gene transcription in the brain.
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Affiliation(s)
- Michelle R Lyons
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
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Chatterjee TK, Idelman G, Blanco V, Blomkalns AL, Piegore MG, Weintraub DS, Kumar S, Rajsheker S, Manka D, Rudich SM, Tang Y, Hui DY, Bassel-Duby R, Olson EN, Lingrel JB, Ho SM, Weintraub NL. Histone deacetylase 9 is a negative regulator of adipogenic differentiation. J Biol Chem 2011; 286:27836-47. [PMID: 21680747 DOI: 10.1074/jbc.m111.262964] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Differentiation of preadipocytes into mature adipocytes capable of efficiently storing lipids is an important regulatory mechanism in obesity. Here, we examined the involvement of histone deacetylases (HDACs) and histone acetyltransferases (HATs) in the regulation of adipogenesis. We find that among the various members of the HDAC and HAT families, only HDAC9 exhibited dramatic down-regulation preceding adipogenic differentiation. Preadipocytes from HDAC9 gene knock-out mice exhibited accelerated adipogenic differentiation, whereas HDAC9 overexpression in 3T3-L1 preadipocytes suppressed adipogenic differentiation, demonstrating its direct role as a negative regulator of adipogenesis. HDAC9 expression was higher in visceral as compared with subcutaneous preadipocytes, negatively correlating with their potential to undergo adipogenic differentiation in vitro. HDAC9 localized in the nucleus, and its negative regulation of adipogenesis segregates with the N-terminal nuclear targeting domain, whereas the C-terminal deacetylase domain is dispensable for this function. HDAC9 co-precipitates with USF1 and is recruited with USF1 at the E-box region of the C/EBPα gene promoter in preadipocytes. Upon induction of adipogenic differentiation, HDAC9 is down-regulated, leading to its dissociation from the USF1 complex, whereas p300 HAT is up-regulated to allow its association with USF1 and accumulation at the E-box site of the C/EBPα promoter in differentiated adipocytes. This reciprocal regulation of HDAC9 and p300 HAT in the USF1 complex is associated with increased C/EBPα expression, a master regulator of adipogenic differentiation. These findings provide new insights into mechanisms of adipogenic differentiation and document a critical regulatory role for HDAC9 in adipogenic differentiation through a deacetylase-independent mechanism.
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Affiliation(s)
- Tapan K Chatterjee
- Department of Internal Medicine, Division of Cardiovascular Diseases, University of Cincinnati, Cincinnati, Ohio 45267, USA.
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Chromatin boundaries require functional collaboration between the hSET1 and NURF complexes. Blood 2011; 118:1386-94. [PMID: 21653943 DOI: 10.1182/blood-2010-11-319111] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Chromatin insulators protect erythroid genes from being silenced during erythropoiesis, and the disruption of barrier insulator function in erythroid membrane gene loci results in mild or severe anemia. We showed previously that the USF1/2-bound 5'HS4 insulator mediates chromatin barrier activity in the erythroid-specific chicken β-globin locus. It is currently not known how insulators establish such a barrier. To understand the function of USF1, we purified USF1-associated protein complexes and found that USF1 forms a multiprotein complex with hSET1 and NURF, thus exhibiting histone H3K4 methyltransferase- and ATP-dependent nucleosome remodeling activities, respectively. Both SET1 and NURF are recruited to the 5'HS4 insulator by USF1 to retain the active chromatin structure in erythrocytes. Knock-down of NURF resulted in a rapid loss of barrier activity accompanied by an alteration of nucleosome positioning, increased occupancy of the nucleosome-free linker region at the insulator site, and increased repressive H3K27me3 levels in the vicinity of the HS4 insulator. Furthermore, suppression of SET1 reduced barrier activity, decreased H3K4me2 and acH3K9/K14, and diminished the recruitment of BPTF at several erythroid-specific barrier insulator sites. Therefore, our data reveal a synergistic role of hSET1 and NURF in regulating the USF-bound barrier insulator to prevent erythroid genes from encroachment of heterochromatin.
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Role of helix-loop-helix proteins during differentiation of erythroid cells. Mol Cell Biol 2011; 31:1332-43. [PMID: 21282467 DOI: 10.1128/mcb.01186-10] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Helix-loop-helix (HLH) proteins play a profound role in the process of development and cellular differentiation. Among the HLH proteins expressed in differentiating erythroid cells are the ubiquitous proteins Myc, USF1, USF2, and TFII-I, as well as the hematopoiesis-specific transcription factor Tal1/SCL. All of these HLH proteins exhibit distinct functions during the differentiation of erythroid cells. For example, Myc stimulates the proliferation of erythroid progenitor cells, while the USF proteins and Tal1 regulate genes that specify the differentiated phenotype. This minireview summarizes the known activities of Myc, USF, TFII-I, and Tal11/SCL and discusses how they may function sequentially, cooperatively, or antagonistically in regulating expression programs during the differentiation of erythroid cells.
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Gomes NP, Espinosa JM. Disparate chromatin landscapes and kinetics of inactivation impact differential regulation of p53 target genes. Cell Cycle 2010; 9:3428-37. [PMID: 20818159 PMCID: PMC3047614 DOI: 10.4161/cc.9.17.12998] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 07/13/2010] [Indexed: 11/19/2022] Open
Abstract
The p53 transcription factor regulates the expression of genes involved in cellular responses to stress, including cell cycle arrest and apoptosis. The p53 transcriptional program is extremely malleable, with target gene expression varying in a stress- and cell type-specific fashion. The molecular mechanisms underlying differential p53 target gene expression remain elusive. Here we provide evidence for gene-specific mechanisms affecting expression of three important p53 target genes. First we show that transcription of the apoptotic gene PUMA is regulated through intragenic chromatin boundaries, as revealed by distinct histone modification territories that correlate with binding of the insulator factors CTCF, Cohesins and USF1/2. Interestingly, this mode of regulation produces an evolutionary conserved long non-coding RNA of unknown function. Second, we demonstrate that the kinetics of transcriptional competence of the cell cycle arrest gene p21 and the apoptotic gene FAS are markedly different in vivo, as predicted by recent biochemical dissection of their core promoter elements in vitro. After a pulse of p53 activity in cells, assembly of the transcriptional apparatus on p21 is rapidly reversed, while FAS transcriptional activation is more sustained. Collectively these data add to a growing list of p53-autonomous mechanisms that impact differential regulation of p53 target genes.
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Affiliation(s)
- Nathan P Gomes
- Howard Hughes Medical Institute, Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
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Enroth S, Andersson R, Wadelius C, Komorowski J. SICTIN: Rapid footprinting of massively parallel sequencing data. BioData Min 2010; 3:4. [PMID: 20707885 PMCID: PMC2928217 DOI: 10.1186/1756-0381-3-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 08/13/2010] [Indexed: 01/29/2023] Open
Abstract
Background Massively parallel sequencing allows for genome-wide hypothesis-free investigation of for instance transcription factor binding sites or histone modifications. Although nucleotide resolution detailed information can easily be generated, biological insight often requires a more general view of patterns (footprints) over distinct genomic features such as transcription start sites, exons or repetitive regions. The construction of these footprints is however a time consuming task. Methods The presented software generates a binary representation of the signals enabling fast and scalable lookup. This representation allows for footprint generation in mere minutes on a desktop computer. Several different input formats are accepted, e.g. the SAM format, bed-files and the UCSC wiggle track. Conclusions Hypothesis-free investigation of genome wide interactions allows for biological data mining at a scale never before seen. Until recently, the main focus of analysis of sequencing data has been targeted on signal patterns around transcriptional start sites which are in manageable numbers. Today, focus is shifting to a wider perspective and numerous genomic features are being studied. To this end, we provide a system allowing for fast querying in the order of hundreds of thousands of features.
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Affiliation(s)
- Stefan Enroth
- Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-75124 Uppsala, Sweden.
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