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Day K, Waite LL, Thalacker-Mercer A, West A, Bamman MM, Brooks JD, Myers RM, Absher D. Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape. Genome Biol 2015; 14:R102. [PMID: 24034465 PMCID: PMC4053985 DOI: 10.1186/gb-2013-14-9-r102] [Citation(s) in RCA: 242] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 08/22/2013] [Indexed: 12/30/2022] Open
Abstract
Background DNA methylation is an epigenetic modification that changes with age in human tissues, although the mechanisms and specificity of this process are still poorly understood. We compared CpG methylation changes with age across 283 human blood, brain, kidney, and skeletal muscle samples using methylation arrays to identify tissue-specific age effects. Results We found age-associated CpGs (ageCGs) that are both tissue-specific and common across tissues. Tissue-specific ageCGs are frequently located outside CpG islands with decreased methylation, and common ageCGs show the opposite trend. AgeCGs are significantly associated with poorly expressed genes, but those with decreasing methylation are linked with higher tissue-specific expression levels compared with increasing methylation. Therefore, tissue-specific gene expression may protect against common age-dependent methylation. Distinguished from other tissues, skeletal muscle ageCGs are more associated with expression, enriched near genes related to myofiber contraction, and closer to muscle-specific CTCF binding sites. Kidney-specific ageCGs are more increasingly methylated compared to other tissues as measured by affiliation with kidney-specific expressed genes. Underlying chromatin features also mark common and tissue-specific age effects reflective of poised and active chromatin states, respectively. In contrast with decreasingly methylated ageCGs, increasingly methylated ageCGs are also generally further from CTCF binding sites and enriched within lamina associated domains. Conclusions Our data identified common and tissue-specific DNA methylation changes with age that are reflective of CpG landscape and suggests both common and unique alterations within human tissues. Our findings also indicate that a simple epigenetic drift model is insufficient to explain all age-related changes in DNA methylation.
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352
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Jajodia A, Singh KD, Singhal A, Vig S, Datta M, Singh Y, Karthikeyan M, Kukreti R. Methylation of a HTR3A promoter variant alters the binding of transcription factor CTCF. RSC Adv 2015. [DOI: 10.1039/c5ra04455c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Genetic studies pertaining to effector molecules have been pivotal in schizophrenia research.
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Affiliation(s)
- Ajay Jajodia
- Genomics and Molecular Medicine
- CSIR-Institute of Genomics and Integrative Biology
- Delhi-110007
- India
| | | | - Anshika Singhal
- Genomics and Molecular Medicine
- CSIR-Institute of Genomics and Integrative Biology
- Delhi-110007
- India
| | - Saurabh Vig
- Genomics and Molecular Medicine
- CSIR-Institute of Genomics and Integrative Biology
- Delhi-110007
- India
| | - Malabika Datta
- Genomics and Molecular Medicine
- CSIR-Institute of Genomics and Integrative Biology
- Delhi-110007
- India
| | - Yogendra Singh
- Genomics and Molecular Medicine
- CSIR-Institute of Genomics and Integrative Biology
- Delhi-110007
- India
| | | | - Ritushree Kukreti
- Genomics and Molecular Medicine
- CSIR-Institute of Genomics and Integrative Biology
- Delhi-110007
- India
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353
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Magbanua JP, Runneburger E, Russell S, White R. A variably occupied CTCF binding site in the ultrabithorax gene in the Drosophila bithorax complex. Mol Cell Biol 2015; 35:318-30. [PMID: 25368383 PMCID: PMC4295388 DOI: 10.1128/mcb.01061-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 09/10/2014] [Accepted: 10/25/2014] [Indexed: 11/20/2022] Open
Abstract
Although the majority of genomic binding sites for the insulator protein CCCTC-binding factor (CTCF) are constitutively occupied, a subset show variable occupancy. Such variable sites provide an opportunity to assess context-specific CTCF functions in gene regulation. Here, we have identified a variably occupied CTCF site in the Drosophila Ultrabithorax (Ubx) gene. This site is occupied in tissues where Ubx is active (third thoracic leg imaginal disc) but is not bound in tissues where the Ubx gene is repressed (first thoracic leg imaginal disc). Using chromatin conformation capture, we show that this site preferentially interacts with the Ubx promoter region in the active state. The site lies close to Ubx enhancer elements and is also close to the locations of several gypsy transposon insertions that disrupt Ubx expression, leading to the bx mutant phenotype. gypsy insertions carry the Su(Hw)-dependent gypsy insulator and were found to affect both CTCF binding at the variable site and the chromatin topology. This suggests that insertion of the gypsy insulator in this region interferes with CTCF function and supports a model for the normal function of the variable CTCF site as a chromatin loop facilitator, promoting interaction between Ubx enhancers and the Ubx transcription start site.
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Affiliation(s)
- Jose Paolo Magbanua
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Estelle Runneburger
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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354
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Tan EJ, Kahata K, Idås O, Thuault S, Heldin CH, Moustakas A. The high mobility group A2 protein epigenetically silences the Cdh1 gene during epithelial-to-mesenchymal transition. Nucleic Acids Res 2014; 43:162-78. [PMID: 25492890 PMCID: PMC4288184 DOI: 10.1093/nar/gku1293] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The loss of the tumour suppressor E-cadherin (Cdh1) is a key event during tumourigenesis and epithelial-mesenchymal transition (EMT). Transforming growth factor-β (TGFβ) triggers EMT by inducing the expression of non-histone chromatin protein High Mobility Group A2 (HMGA2). We have previously shown that HMGA2, together with Smads, regulate a network of EMT-transcription factors (EMT-TFs) like Snail1, Snail2, ZEB1, ZEB2 and Twist1, most of which are well-known repressors of the Cdh1 gene. In this study, we show that the Cdh1 promoter is hypermethylated and epigenetically silenced in our constitutive EMT cell model, whereby HMGA2 is ectopically expressed in mammary epithelial NMuMG cells and these cells are highly motile and invasive. Furthermore, HMGA2 remodels the chromatin to favour binding of de novo DNA methyltransferase 3A (DNMT3A) to the Cdh1 promoter. E-cadherin expression could be restored after treatment with the DNA de-methylating agent 5-aza-2'-deoxycytidine. Here, we describe a new epigenetic role for HMGA2, which follows the actions that HMGA2 initiates via the EMT-TFs, thus achieving sustained silencing of E-cadherin expression and promoting tumour cell invasion.
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Affiliation(s)
- E-Jean Tan
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Kaoru Kahata
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Oskar Idås
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Sylvie Thuault
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Carl-Henrik Heldin
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Aristidis Moustakas
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala SE-75123, Sweden
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355
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Chatterjee R, He X, Huang D, FitzGerald P, Smith A, Vinson C. High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes. Epigenetics Chromatin 2014; 7:35. [PMID: 25699092 PMCID: PMC4333159 DOI: 10.1186/1756-8935-7-35] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/04/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genome-wide DNA methylation at a single nucleotide resolution in different primary cells of the mammalian genome helps to determine the characteristics and functions of tissue-specific hypomethylated regions (TS-HMRs). We determined genome-wide cytosine methylation maps at 91X and 36X coverage of newborn female mouse primary dermal fibroblasts and keratinocytes and compared with mRNA-seq gene expression data. RESULTS These high coverage methylation maps were used to identify HMRs in both cell types. A total of 2.91% of the genome are in keratinocyte HMRs, and 2.15% of the genome are in fibroblast HMRs with 1.75% being common. Half of the TS-HMRs are extensions of common HMRs, and the remaining are unique TS-HMRs. Four levels of CG methylation are observed: 1) total unmethylation for CG dinucleotides in HMRs in CGIs that are active in all tissues; 2) 10% to 40% methylation for TS-HMRs; 3) 60% methylation for TS-HMRs in cells types where they are not in HMRs; and 4) 70% methylation for the nonfunctioning part of the genome. SINE elements are depleted inside the TS-HMRs, while highly enriched in the surrounding regions. Hypomethylation at the last exon shows gene repression, while demethylation toward the gene body positively correlates with gene expression. The overlapping HMRs have a more complex relationship with gene expression. The common HMRs and TS-HMRs are each enriched for distinct Transcription Factor Binding Sites (TFBS). C/EBPβ binds to methylated regions outside of HMRs while CTCF prefers to bind in HMRs, highlighting these two parts of the genome and their potential interactions. CONCLUSIONS Keratinocytes and fibroblasts are of epithelial and mesenchymal origin. High-resolution methylation maps in these two cell types can be used as reference methylomes for analyzing epigenetic mechanisms in several diseases including cancer. Please see related article at the following link: http://www.epigeneticsandchromatin.com/content/7/1/34.
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Affiliation(s)
- Raghunath Chatterjee
- />Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892 USA
- />Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India
| | - Ximiao He
- />Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892 USA
| | - Di Huang
- />NCBI, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Peter FitzGerald
- />Genome Analysis Unit, Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892 USA
| | - Andrew Smith
- />Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089 USA
| | - Charles Vinson
- />Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892 USA
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356
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Zeng TB, He HJ, Han ZB, Zhang FW, Huang ZJ, Liu Q, Cui W, Wu Q. DNA methylation dynamics of a maternally methylated DMR in the mouseDlk1-Dio3domain. FEBS Lett 2014; 588:4665-71. [DOI: 10.1016/j.febslet.2014.10.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/26/2014] [Accepted: 10/30/2014] [Indexed: 10/24/2022]
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357
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Neri F, Dettori D, Incarnato D, Krepelova A, Rapelli S, Maldotti M, Parlato C, Paliogiannis P, Oliviero S. TET1 is a tumour suppressor that inhibits colon cancer growth by derepressing inhibitors of the WNT pathway. Oncogene 2014; 34:4168-76. [PMID: 25362856 DOI: 10.1038/onc.2014.356] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/22/2014] [Accepted: 09/16/2014] [Indexed: 12/17/2022]
Abstract
Ten eleven translocation (TET) enzymes catalyse the oxidative reactions of 5-methylcytosine (5mC) to promote the demethylation process. The reaction intermediate 5-hydroxymethylcytosine (5hmC) has been shown to be abundant in embryonic stem cells and tissues but strongly depleted in human cancers. Genetic mutations of TET2 gene were associated with leukaemia, whereas TET1 downregulation has been shown to promote malignancy in breast cancer. Here we report that TET1 is downregulated in colon tumours from the initial stage. TET1 silencing in primary epithelial colon cells increase their cellular proliferation while its re-expression in colon cancer cells inhibits their proliferation and the growth of tumour xenografts even at later stages. We found that TET1 binds to the promoter of the DKK gene inhibitors of the WNT signalling to maintain them hypomethylated. Downregulation of TET1 during colon cancer initiation leads to repression, by DNA methylation, the promoters of the inhibitors of the WNT pathway resulting in a constitutive activation of the WNT pathway. Thus the DNA hydroxymethylation mediated by TET1 controlling the WNT signalling is a key player of tumour growth. These results provide new insights for understanding how tumours escape cellular controls.
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Affiliation(s)
- F Neri
- Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy
| | - D Dettori
- Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy
| | - D Incarnato
- 1] Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy [2] Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Siena, Italy
| | - A Krepelova
- 1] Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy [2] Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Siena, Italy
| | - S Rapelli
- 1] Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy [2] Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Siena, Italy
| | - M Maldotti
- Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy
| | - C Parlato
- Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy
| | - P Paliogiannis
- Dipartimento di Scienze Chirurgiche, Microchirurgiche e Mediche, Università di Sassari, Sassari, Italy
| | - S Oliviero
- 1] Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy [2] Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino Torino, Italy
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358
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Sipahi L, Wildman DE, Aiello AE, Koenen KC, Galea S, Abbas A, Uddin M. Longitudinal epigenetic variation of DNA methyltransferase genes is associated with vulnerability to post-traumatic stress disorder. Psychol Med 2014; 44:3165-79. [PMID: 25065861 PMCID: PMC4530981 DOI: 10.1017/s0033291714000968] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
BACKGROUND Epigenetic differences exist between trauma-exposed individuals with and without post-traumatic stress disorder (PTSD). It is unclear whether these epigenetic differences pre-exist, or arise following, trauma and PTSD onset. METHOD In pre- and post-trauma samples from a subset of Detroit Neighborhood Health Study participants, DNA methylation (DNAm) was measured at DNA methyltransferase 1 (DNMT1), DNMT3A, DNMT3B and DNMT3L. Pre-trauma DNAm differences and changes in DNAm from pre- to post-trauma were assessed between and within PTSD cases (n = 30) and age-, gender- and trauma exposure-matched controls (n = 30). Pre-trauma DNAm was tested for association with post-trauma symptom severity (PTSS) change. Potential functional consequences of DNAm differences were explored via bioinformatic search for putative transcription factor binding sites (TFBS). RESULTS DNMT1 DNAm increased following trauma in PTSD cases (p = 0.001), but not controls (p = 0.067). DNMT3A and DNMT3B DNAm increased following trauma in both cases (DNMT3A: p = 0.009; DNMT3B: p < 0.001) and controls (DNMT3A: p = 0.002; DNMT3B: p < 0.001). In cases only, pre-trauma DNAm was lower at a DNMT3B CpG site that overlaps with a TFBS involved in epigenetic regulation (p = 0.001); lower pre-trauma DNMT3B DNAm at this site was predictive of worsening of PTSS post-trauma (p = 0.034). Some effects were attenuated following correction for multiple hypothesis testing. CONCLUSIONS DNAm among trauma-exposed individuals shows both longitudinal changes and pre-existing epigenetic states that differentiate individuals who are resilient versus susceptible to PTSD. These distinctive DNAm differences within DNMT loci may contribute to genome-wide epigenetic profiles of PTSD.
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Affiliation(s)
- Levent Sipahi
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI
| | - Derek E. Wildman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Allison E. Aiello
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC
| | - Karestan C. Koenen
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY
| | - Sandro Galea
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY
| | - Asad Abbas
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI
| | - Monica Uddin
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI
- Department of Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, Detroit, MI
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359
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Schoborg T, Labrador M. Expanding the roles of chromatin insulators in nuclear architecture, chromatin organization and genome function. Cell Mol Life Sci 2014; 71:4089-113. [PMID: 25012699 PMCID: PMC11113341 DOI: 10.1007/s00018-014-1672-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/31/2014] [Accepted: 06/23/2014] [Indexed: 01/08/2023]
Abstract
Of the numerous classes of elements involved in modulating eukaryotic chromosome structure and function, chromatin insulators arguably remain the most poorly understood in their contribution to these processes in vivo. Indeed, our view of chromatin insulators has evolved dramatically since their chromatin boundary and enhancer blocking properties were elucidated roughly a quarter of a century ago as a result of recent genome-wide, high-throughput methods better suited to probing the role of these elements in their native genomic contexts. The overall theme that has emerged from these studies is that chromatin insulators function as general facilitators of higher-order chromatin loop structures that exert both physical and functional constraints on the genome. In this review, we summarize the result of recent work that supports this idea as well as a number of other studies linking these elements to a diverse array of nuclear processes, suggesting that chromatin insulators exert master control over genome organization and behavior.
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Affiliation(s)
- Todd Schoborg
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996 USA
- Present Address: Laboratory of Molecular Machines and Tissue Architecture, Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, 50 South Dr Rm 2122, Bethesda, MD 20892 USA
| | - Mariano Labrador
- Department of Biochemistry, Cellular and Molecular Biology, The University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996 USA
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360
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Abstract
Gene expression frequently requires chromatin-remodeling complexes, and it is assumed that these complexes have common gene targets across cell types. Contrary to this belief, we show by genome-wide expression profiling that Bptf, an essential and unique subunit of the nucleosome-remodeling factor (NURF), predominantly regulates the expression of a unique set of genes between diverse cell types. Coincident with its functions in gene expression, we observed that Bptf is also important for regulating nucleosome occupancy at nucleosome-free regions (NFRs), many of which are located at sites occupied by the multivalent factors Ctcf and cohesin. NURF function at Ctcf binding sites could be direct, because Bptf occupies Ctcf binding sites in vivo and has physical interactions with CTCF and the cohesin subunit SA2. Assays of several Ctcf binding sites using reporter assays showed that their regulatory activity requires Bptf in two different cell types. Focused studies at H2-K1 showed that Bptf regulates the ability of Klf4 to bind near an upstream Ctcf site, possibly influencing gene expression. In combination, these studies demonstrate that gene expression as regulated by NURF occurs partly through physical and functional interactions with the ubiquitous and multivalent factors Ctcf and cohesin.
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361
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Franco MM, Prickett AR, Oakey RJ. The role of CCCTC-binding factor (CTCF) in genomic imprinting, development, and reproduction. Biol Reprod 2014; 91:125. [PMID: 25297545 DOI: 10.1095/biolreprod.114.122945] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CCCTC-binding factor (CTCF) is the major protein involved in insulator activity in vertebrates, with widespread DNA binding sites in the genome. CTCF participates in many processes related to global chromatin organization and remodeling, contributing to the repression or activation of gene transcription. It is also involved in epigenetic reprogramming and is essential during gametogenesis and embryo development. Abnormal DNA methylation patterns at CTCF motifs may impair CTCF binding to DNA, and are related to fertility disorders in mammals. Therefore, CTCF and its binding sites are important candidate regions to be investigated as molecular markers for gamete and embryo quality. This article reviews the role of CTCF in genomic imprinting, gametogenesis, and early embryo development and, moreover, highlights potential opportunities for environmental influences associated with assisted reproductive techniques (ARTs) to affect CTCF-mediated processes. We discuss the potential use of CTCF as a molecular marker for assessing gamete and embryo quality in the context of improving the efficiency and safety of ARTs.
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Affiliation(s)
- Maurício M Franco
- Embrapa Genetic Resources & Biotechnology, Laboratory of Animal Reproduction, Parque Estação Biológica, Brasília, Brazil
| | - Adam R Prickett
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Rebecca J Oakey
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
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362
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Mateo JL, van den Berg DLC, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Lu QR, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B. Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Res 2014; 25:41-56. [PMID: 25294244 PMCID: PMC4317172 DOI: 10.1101/gr.173435.114] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The gene regulatory network (GRN) that supports neural stem cell (NS cell) self-renewal has so far been poorly characterized. Knowledge of the central transcription factors (TFs), the noncoding gene regulatory regions that they bind to, and the genes whose expression they modulate will be crucial in unlocking the full therapeutic potential of these cells. Here, we use DNase-seq in combination with analysis of histone modifications to identify multiple classes of epigenetically and functionally distinct cis-regulatory elements (CREs). Through motif analysis and ChIP-seq, we identify several of the crucial TF regulators of NS cells. At the core of the network are TFs of the basic helix-loop-helix (bHLH), nuclear factor I (NFI), SOX, and FOX families, with CREs often densely bound by several of these different TFs. We use machine learning to highlight several crucial regulatory features of the network that underpin NS cell self-renewal and multipotency. We validate our predictions by functional analysis of the bHLH TF OLIG2. This TF makes an important contribution to NS cell self-renewal by concurrently activating pro-proliferation genes and preventing the untimely activation of genes promoting neuronal differentiation and stem cell quiescence.
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Affiliation(s)
- Juan L Mateo
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany;
| | - Debbie L C van den Berg
- Division of Molecular Neurobiology, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Maximilian Haeussler
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Daniela Drechsel
- Division of Molecular Neurobiology, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Zachary B Gaber
- Division of Molecular Neurobiology, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Diogo S Castro
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Paul Robson
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Gregory E Crawford
- Institute of Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Laurence Ettwiller
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany; New England Biolabs, Inc., Ipswich, Massachusetts 01938-2723, USA
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - François Guillemot
- Division of Molecular Neurobiology, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Ben Martynoga
- Division of Molecular Neurobiology, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom;
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363
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Lianos GD, Bali CD, Glantzounis GK, Katsios C, Roukos DH. BMI and lymph node ratio may predict clinical outcomes of gastric cancer. Future Oncol 2014; 10:249-55. [PMID: 24490611 DOI: 10.2217/fon.13.188] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
AIM BMI and the lymph node (LN) ratio can affect short- and long-term outcomes of patients with gastric cancer. PATIENTS & METHODS This study includes 104 consecutive patients with gastric adenocarcinoma who underwent curative gastrectomy divided in two groups: overweight group (group A) and normal weight group (group B). RESULTS We found that 53.4% of our patients were overweight (group A). The overall rate of postoperative complications was 16.3%, while mortality was 1%. Statistical analyses revealed that postoperative morbidity was significantly higher in group A (p < 0.05). Long-term survival was significantly higher in group B. Cox regression showed a statistically significant correlation between higher BMI and poor long-term survival after curative gastrectomy. Multivariate analysis has identified age and the LN ratios as independent prognostic factors of survival. CONCLUSION In this retrospective analysis, BMI and LN ratio were independently associated with survival in patients with gastric cancer. Further studies are needed to confirm our findings.
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Affiliation(s)
- Georgios D Lianos
- Department of Surgery, University Hospital of Ioannina, St. Niarchou Av, Ioannina 451 10, Greece
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364
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Gómez-Díaz E, Corces VG. Architectural proteins: regulators of 3D genome organization in cell fate. Trends Cell Biol 2014; 24:703-11. [PMID: 25218583 DOI: 10.1016/j.tcb.2014.08.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/10/2014] [Accepted: 08/12/2014] [Indexed: 12/20/2022]
Abstract
The relation between alterations in chromatin structure and changes in gene expression during cell differentiation has served as a paradigm to understand the link between genome organization and function. Yet, the factors involved and the mechanisms by which the 3D organization of the nucleus is established remain poorly understood. The use of Chromosome Conformation-Capture (3C)-based approaches has resulted in a new appreciation of the role of architectural proteins in the establishment of 3D genome organization. Architectural proteins orchestrate higher-order chromatin organization through the establishment of interactions between regulatory elements across multiple spatial scales. The regulation of these proteins, their interaction with DNA, and their co-occurrence in the genome, may be responsible for the plasticity of 3D chromatin architecture that dictates cell and time-specific blueprints of gene expression.
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Affiliation(s)
| | - Victor G Corces
- Department of Biology, Emory University, Atlanta, GA 30322, USA.
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365
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Dubois-Chevalier J, Oger F, Dehondt H, Firmin FF, Gheeraert C, Staels B, Lefebvre P, Eeckhoute J. A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation. Nucleic Acids Res 2014; 42:10943-59. [PMID: 25183525 PMCID: PMC4176165 DOI: 10.1093/nar/gku780] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
CCCTC-binding factor (CTCF) is a ubiquitously expressed multifunctional transcription factor characterized by chromatin binding patterns often described as largely invariant. In this context, how CTCF chromatin recruitment and functionalities are used to promote cell type-specific gene expression remains poorly defined. Here, we show that, in addition to constitutively bound CTCF binding sites (CTS), the CTCF cistrome comprises a large proportion of sites showing highly dynamic binding patterns during the course of adipogenesis. Interestingly, dynamic CTCF chromatin binding is positively linked with changes in expression of genes involved in biological functions defining the different stages of adipogenesis. Importantly, a subset of these dynamic CTS are gained at cell type-specific regulatory regions, in line with a requirement for CTCF in transcriptional induction of adipocyte differentiation. This relates to, at least in part, CTCF requirement for transcriptional activation of both the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARG) and its target genes. Functionally, we show that CTCF interacts with TET methylcytosine dioxygenase (TET) enzymes and promotes adipogenic transcriptional enhancer DNA hydroxymethylation. Our study reveals a dynamic CTCF chromatin binding landscape required for epigenomic remodeling of enhancers and transcriptional activation driving cell differentiation.
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Affiliation(s)
- Julie Dubois-Chevalier
- Inserm UMR U1011, F-59000 Lille, France Université Lille 2, F-59000 Lille, France Institut Pasteur de Lille, F-59019 Lille, France European Genomic Institute for Diabetes (EGID), FR 3508, F-59000 Lille, France
| | - Frédérik Oger
- Inserm UMR U1011, F-59000 Lille, France Université Lille 2, F-59000 Lille, France Institut Pasteur de Lille, F-59019 Lille, France European Genomic Institute for Diabetes (EGID), FR 3508, F-59000 Lille, France
| | - Hélène Dehondt
- Inserm UMR U1011, F-59000 Lille, France Université Lille 2, F-59000 Lille, France Institut Pasteur de Lille, F-59019 Lille, France European Genomic Institute for Diabetes (EGID), FR 3508, F-59000 Lille, France
| | - François F Firmin
- Inserm UMR U1011, F-59000 Lille, France Université Lille 2, F-59000 Lille, France Institut Pasteur de Lille, F-59019 Lille, France European Genomic Institute for Diabetes (EGID), FR 3508, F-59000 Lille, France
| | - Céline Gheeraert
- Inserm UMR U1011, F-59000 Lille, France Université Lille 2, F-59000 Lille, France Institut Pasteur de Lille, F-59019 Lille, France European Genomic Institute for Diabetes (EGID), FR 3508, F-59000 Lille, France
| | - Bart Staels
- Inserm UMR U1011, F-59000 Lille, France Université Lille 2, F-59000 Lille, France Institut Pasteur de Lille, F-59019 Lille, France European Genomic Institute for Diabetes (EGID), FR 3508, F-59000 Lille, France
| | - Philippe Lefebvre
- Inserm UMR U1011, F-59000 Lille, France Université Lille 2, F-59000 Lille, France Institut Pasteur de Lille, F-59019 Lille, France European Genomic Institute for Diabetes (EGID), FR 3508, F-59000 Lille, France
| | - Jérôme Eeckhoute
- Inserm UMR U1011, F-59000 Lille, France Université Lille 2, F-59000 Lille, France Institut Pasteur de Lille, F-59019 Lille, France European Genomic Institute for Diabetes (EGID), FR 3508, F-59000 Lille, France
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366
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Siggens L, Ekwall K. Epigenetics, chromatin and genome organization: recent advances from the ENCODE project. J Intern Med 2014; 276:201-14. [PMID: 24605849 DOI: 10.1111/joim.12231] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The organization of the genome into functional units, such as enhancers and active or repressed promoters, is associated with distinct patterns of DNA and histone modifications. The Encyclopedia of DNA Elements (ENCODE) project has advanced our understanding of the principles of genome, epigenome and chromatin organization, identifying hundreds of thousands of potential regulatory regions and transcription factor binding sites. Part of the ENCODE consortium, GENCODE, has annotated the human genome with novel transcripts including new noncoding RNAs and pseudogenes, highlighting transcriptional complexity. Many disease variants identified in genome-wide association studies are located within putative enhancer regions defined by the ENCODE project. Understanding the principles of chromatin and epigenome organization will help to identify new disease mechanisms, biomarkers and drug targets, particularly as ongoing epigenome mapping projects generate data for primary human cell types that play important roles in disease.
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Affiliation(s)
- L Siggens
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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367
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Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility. Nat Immunol 2014; 15:777-88. [PMID: 24997565 DOI: 10.1038/ni.2937] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 06/03/2014] [Indexed: 12/16/2022]
Abstract
A characteristic feature of asthma is the aberrant accumulation, differentiation or function of memory CD4(+) T cells that produce type 2 cytokines (TH2 cells). By mapping genome-wide histone modification profiles for subsets of T cells isolated from peripheral blood of healthy and asthmatic individuals, we identified enhancers with known and potential roles in the normal differentiation of human TH1 cells and TH2 cells. We discovered disease-specific enhancers in T cells that differ between healthy and asthmatic individuals. Enhancers that gained the histone H3 Lys4 dimethyl (H3K4me2) mark during TH2 cell development showed the highest enrichment for asthma-associated single nucleotide polymorphisms (SNPs), which supported a pathogenic role for TH2 cells in asthma. In silico analysis of cell-specific enhancers revealed transcription factors, microRNAs and genes potentially linked to human TH2 cell differentiation. Our results establish the feasibility and utility of enhancer profiling in well-defined populations of specialized cell types involved in disease pathogenesis.
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368
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Demars J, Shmela ME, Khan AW, Lee KS, Azzi S, Dehais P, Netchine I, Rossignol S, Le Bouc Y, El-Osta A, Gicquel C. Genetic variants within the second intron of the KCNQ1 gene affect CTCF binding and confer a risk of Beckwith-Wiedemann syndrome upon maternal transmission. J Med Genet 2014; 51:502-11. [PMID: 24996904 DOI: 10.1136/jmedgenet-2014-102368] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Disruption of 11p15 imprinting results in two fetal growth disorders with opposite phenotypes: the Beckwith-Wiedemann (BWS; MIM 130650) and the Silver-Russell (SRS; MIM 180860) syndromes. DNA methylation defects account for 60% of BWS and SRS cases and, in most cases, occur without any identified mutation in a cis-acting regulatory sequence or a trans-acting factor. METHODS We investigated whether 11p15 cis-acting sequence variants account for primary DNA methylation defects in patients with SRS and BWS with loss of DNA methylation at ICR1 and ICR2, respectively. RESULTS We identified a 4.5 kb haplotype that, upon maternal transmission, is associated with a risk of ICR2 loss of DNA methylation in patients with BWS. This novel region is located within the second intron of the KCNQ1 gene, 170 kb upstream of the ICR2 imprinting centre and encompasses two CTCF binding sites. We showed that, within the 4.5 kb region, two SNPs (rs11823023 and rs179436) affect CTCF occupancy at DNA motifs flanking the CTCF 20 bp core motif. CONCLUSIONS This study shows that genetic variants confer a risk of DNA methylation defect with a parent-of-origin effect and highlights the crucial role of CTCF for the regulation of genomic imprinting of the CDKN1C/KCNQ1 domain.
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Affiliation(s)
- Julie Demars
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia INRA, GenPhySE (Génétique, Physiologie et Systèmes d'Elevage), Castanet-Tolosan, France
| | - Mansur Ennuri Shmela
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Abdul Waheed Khan
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia University of Melbourne, Parkville, Australia
| | - Kai Syin Lee
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Salah Azzi
- APHP, Armand Trousseau Hôpital, Pediatric Endocrinology, INSERM, UMR_S 938, CDR Saint-Antoine, F-75012, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, F-75012, Paris, France
| | - Patrice Dehais
- INRA, GenPhySE (Génétique, Physiologie et Systèmes d'Elevage), Castanet-Tolosan, France
| | - Irène Netchine
- APHP, Armand Trousseau Hôpital, Pediatric Endocrinology, INSERM, UMR_S 938, CDR Saint-Antoine, F-75012, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, F-75012, Paris, France
| | - Sylvie Rossignol
- APHP, Armand Trousseau Hôpital, Pediatric Endocrinology, INSERM, UMR_S 938, CDR Saint-Antoine, F-75012, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, F-75012, Paris, France
| | - Yves Le Bouc
- APHP, Armand Trousseau Hôpital, Pediatric Endocrinology, INSERM, UMR_S 938, CDR Saint-Antoine, F-75012, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 938, CDR Saint-Antoine, F-75012, Paris, France
| | - Assam El-Osta
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia University of Melbourne, Parkville, Australia
| | - Christine Gicquel
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
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369
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Glastad KM, Hunt BG, Goodisman MA. Evolutionary insights into DNA methylation in insects. CURRENT OPINION IN INSECT SCIENCE 2014; 1:25-30. [PMID: 32846726 DOI: 10.1016/j.cois.2014.04.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/18/2014] [Accepted: 04/24/2014] [Indexed: 06/11/2023]
Abstract
Epigenetic information affects gene function and plays a critical role in development. DNA methylation is one of the most widespread epigenetic marks and has been linked to developmental plasticity in insects. Here, we review the patterns and functions of DNA methylation in insects. We specifically focus on how the application of an evolutionary framework has led to important insights into the role of DNA methylation. We discuss the importance of evolutionary variation in DNA methylation among insect taxa and show how comparative analyses have revealed conservation in targets of DNA methylation. We then show how the distribution of DNA methylation in insect genomes has been linked to evolutionary conserved patterns of histone modifications and variants. We conclude by discussing how the evolutionary conservation and variability of DNA methylation in insects can provide insight into the function of DNA methylation across eukaryotic systems.
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Affiliation(s)
- Karl M Glastad
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Griffin, GA 30223, USA
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370
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Daniel B, Nagy G, Nagy L. The intriguing complexities of mammalian gene regulation: how to link enhancers to regulated genes. Are we there yet? FEBS Lett 2014; 588:2379-91. [PMID: 24945732 DOI: 10.1016/j.febslet.2014.05.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 01/08/2023]
Abstract
The information encoded in genomes supports the differentiation and function of the more than 200 unique cell types, which exist in various mammalian species. The major mechanism driving cellular differentiation and specification is differential gene expression regulation. Cis-acting enhancers and silencers appear to have key roles in regulating the expression of mammalian genes. However, these cis-acting elements are often located very far away from the regulated gene. Therefore, it is hard to find all of them and link them to the regulated gene. An intriguing and unresolved issue of the field is to identify all of the enhancers of a particular gene and link these short regulatory sequences to the genes they regulate and thus, reliably identify gene regulatory enhancer networks. Recent advances in molecular biological methods coupled with Next-Generation Sequencing (NGS) technologies have opened up new possibilities in this area of genomics. In this review we summarize the technological advances, bioinformatics challenges and the potential molecular mechanisms allowing the construction of enhancer networks operating in specific cell types and/or activated by various signals.
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Affiliation(s)
- Bence Daniel
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., Debrecen H-4010, Hungary
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., Debrecen H-4010, Hungary
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., Debrecen H-4010, Hungary; MTA-DE "Lendület" Immunogenomics Research Group, University of Debrecen, Egyetem tér 1., Debrecen, Hungary; Sanford-Burnham Medical Research Institute, 6400 Sanger Road, Orlando, FL 32827, USA.
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371
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Taberlay PC, Statham AL, Kelly TK, Clark SJ, Jones PA. Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res 2014; 24:1421-32. [PMID: 24916973 PMCID: PMC4158760 DOI: 10.1101/gr.163485.113] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
It is well established that cancer-associated epigenetic repression occurs concomitant with CpG island hypermethylation and loss of nucleosomes at promoters, but the role of nucleosome occupancy and epigenetic reprogramming at distal regulatory elements in cancer is still poorly understood. Here, we evaluate the scope of global epigenetic alterations at enhancers and insulator elements in prostate and breast cancer cells using simultaneous genome-wide mapping of DNA methylation and nucleosome occupancy (NOMe-seq). We find that the genomic location of nucleosome-depleted regions (NDRs) is mostly cell type specific and preferentially found at enhancers in normal cells. In cancer cells, however, we observe a global reconfiguration of NDRs at distal regulatory elements coupled with a substantial reorganization of the cancer methylome. Aberrant acquisition of nucleosomes at enhancer-associated NDRs is associated with hypermethylation and epigenetic silencing marks, and conversely, loss of nucleosomes with demethylation and epigenetic activation. Remarkably, we show that nucleosomes remain strongly organized and phased at many facultative distal regulatory elements, even in the absence of a NDR as an anchor. Finally, we find that key transcription factor (TF) binding sites also show extensive peripheral nucleosome phasing, suggesting the potential for TFs to organize NDRs genome-wide and contribute to deregulation of cancer epigenomes. Together, our findings suggest that “decommissioning” of NDRs and TFs at distal regulatory elements in cancer cells is accompanied by DNA hypermethylation susceptibility of enhancers and insulator elements, which in turn may contribute to an altered genome-wide architecture and epigenetic deregulation in malignancy.
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Affiliation(s)
- Phillippa C Taberlay
- Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia
| | - Aaron L Statham
- Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Theresa K Kelly
- Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; Active Motif, Inc., Carlsbad, California 92008, USA
| | - Susan J Clark
- Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia;
| | - Peter A Jones
- Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
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372
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Sandi C, Sandi M, Anjomani Virmouni S, Al-Mahdawi S, Pook MA. Epigenetic-based therapies for Friedreich ataxia. Front Genet 2014; 5:165. [PMID: 24917884 PMCID: PMC4042889 DOI: 10.3389/fgene.2014.00165] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/19/2014] [Indexed: 11/29/2022] Open
Abstract
Friedreich ataxia (FRDA) is a lethal autosomal recessive neurodegenerative disorder caused primarily by a homozygous GAA repeat expansion mutation within the first intron of the FXN gene, leading to inhibition of FXN transcription and thus reduced frataxin protein expression. Recent studies have shown that epigenetic marks, comprising chemical modifications of DNA and histones, are associated with FXN gene silencing. Such epigenetic marks can be reversed, making them suitable targets for epigenetic-based therapy. Furthermore, since FRDA is caused by insufficient, but functional, frataxin protein, epigenetic-based transcriptional re-activation of the FXN gene is an attractive therapeutic option. In this review we summarize our current understanding of the epigenetic basis of FXN gene silencing and we discuss current epigenetic-based FRDA therapeutic strategies.
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Affiliation(s)
| | | | | | | | - Mark A. Pook
- Division of Biosciences, School of Health Sciences and Social Care, Brunel University LondonUxbridge, UK
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373
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Stong N, Deng Z, Gupta R, Hu S, Paul S, Weiner AK, Eichler EE, Graves T, Fronick CC, Courtney L, Wilson RK, Lieberman PM, Davuluri RV, Riethman H. Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline. Genome Res 2014; 24:1039-50. [PMID: 24676094 PMCID: PMC4032850 DOI: 10.1101/gr.166983.113] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 03/26/2014] [Indexed: 12/25/2022]
Abstract
Mapping genome-wide data to human subtelomeres has been problematic due to the incomplete assembly and challenges of low-copy repetitive DNA elements. Here, we provide updated human subtelomere sequence assemblies that were extended by filling telomere-adjacent gaps using clone-based resources. A bioinformatic pipeline incorporating multiread mapping for annotation of the updated assemblies using short-read data sets was developed and implemented. Annotation of subtelomeric sequence features as well as mapping of CTCF and cohesin binding sites using ChIP-seq data sets from multiple human cell types confirmed that CTCF and cohesin bind within 3 kb of the start of terminal repeat tracts at many, but not all, subtelomeres. CTCF and cohesin co-occupancy were also enriched near internal telomere-like sequence (ITS) islands and the nonterminal boundaries of subtelomere repeat elements (SREs) in transformed lymphoblastoid cell lines (LCLs) and human embryonic stem cell (ES) lines, but were not significantly enriched in the primary fibroblast IMR90 cell line. Subtelomeric CTCF and cohesin sites predicted by ChIP-seq using our bioinformatics pipeline (but not predicted when only uniquely mapping reads were considered) were consistently validated by ChIP-qPCR. The colocalized CTCF and cohesin sites in SRE regions are candidates for mediating long-range chromatin interactions in the transcript-rich SRE region. A public browser for the integrated display of short-read sequence-based annotations relative to key subtelomere features such as the start of each terminal repeat tract, SRE identity and organization, and subtelomeric gene models was established.
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Affiliation(s)
- Nicholas Stong
- Graduate Group in Genomics and Computational Biology, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Zhong Deng
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Ravi Gupta
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Sufen Hu
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Shiela Paul
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | | | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Tina Graves
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Catrina C. Fronick
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Laura Courtney
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Richard K. Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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374
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Kemp CJ, Moore JM, Moser R, Bernard B, Teater M, Smith LE, Rabaia NA, Gurley KE, Guinney J, Busch SE, Shaknovich R, Lobanenkov VV, Liggitt D, Shmulevich I, Melnick A, Filippova GN. CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer. Cell Rep 2014; 7:1020-9. [PMID: 24794443 PMCID: PMC4040130 DOI: 10.1016/j.celrep.2014.04.004] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 03/05/2014] [Accepted: 04/03/2014] [Indexed: 01/02/2023] Open
Abstract
Epigenetic alterations, particularly in DNA methylation, are ubiquitous in cancer, yet the molecular origins and the consequences of these alterations are poorly understood. CTCF, a DNA-binding protein that regulates higher-order chromatin organization, is frequently altered by hemizygous deletion or mutation in human cancer. To date, a causal role for CTCF in cancer has not been established. Here, we show that Ctcf hemizygous knockout mice are markedly susceptible to spontaneous, radiation-, and chemically induced cancer in a broad range of tissues. Ctcf(+/-) tumors are characterized by increased aggressiveness, including invasion, metastatic dissemination, and mixed epithelial/mesenchymal differentiation. Molecular analysis of Ctcf(+/-) tumors indicates that Ctcf is haploinsufficient for tumor suppression. Tissues with hemizygous loss of CTCF exhibit increased variability in CpG methylation genome wide. These findings establish CTCF as a prominent tumor-suppressor gene and point to CTCF-mediated epigenetic stability as a major barrier to neoplastic progression.
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Affiliation(s)
- Christopher J Kemp
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - James M Moore
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Russell Moser
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Brady Bernard
- Institute for Systems Biology, Seattle, WA 98106, USA
| | - Matt Teater
- Division of Hematology/Oncology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Leslie E Smith
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Natalia A Rabaia
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kay E Gurley
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Justin Guinney
- Sage Bionetworks, 1100 Fairview Avenue, Seattle, WA 98109, USA
| | - Stephanie E Busch
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rita Shaknovich
- Division of Hematology/Oncology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Victor V Lobanenkov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD 20852, USA
| | - Denny Liggitt
- Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | | | - Ari Melnick
- Division of Hematology/Oncology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Galina N Filippova
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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375
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Teif VB, Beshnova DA, Vainshtein Y, Marth C, Mallm JP, Höfer T, Rippe K. Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development. Genome Res 2014; 24:1285-95. [PMID: 24812327 PMCID: PMC4120082 DOI: 10.1101/gr.164418.113] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
During differentiation of embryonic stem cells, chromatin reorganizes to establish cell type-specific expression programs. Here, we have dissected the linkages between DNA methylation (5mC), hydroxymethylation (5hmC), nucleosome repositioning, and binding of the transcription factor CTCF during this process. By integrating MNase-seq and ChIP-seq experiments in mouse embryonic stem cells (ESC) and their differentiated counterparts with biophysical modeling, we found that the interplay between these factors depends on their genomic context. The mostly unmethylated CpG islands have reduced nucleosome occupancy and are enriched in cell type-independent binding sites for CTCF. The few remaining methylated CpG dinucleotides are preferentially associated with nucleosomes. In contrast, outside of CpG islands most CpGs are methylated, and the average methylation density oscillates so that it is highest in the linker region between nucleosomes. Outside CpG islands, binding of TET1, an enzyme that converts 5mC to 5hmC, is associated with labile, MNase-sensitive nucleosomes. Such nucleosomes are poised for eviction in ESCs and become stably bound in differentiated cells where the TET1 and 5hmC levels go down. This process regulates a class of CTCF binding sites outside CpG islands that are occupied by CTCF in ESCs but lose the protein during differentiation. We rationalize this cell type-dependent targeting of CTCF with a quantitative biophysical model of competitive binding with the histone octamer, depending on the TET1, 5hmC, and 5mC state.
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Affiliation(s)
- Vladimir B Teif
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Daria A Beshnova
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Yevhen Vainshtein
- Division Theoretical Systems Biology, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Caroline Marth
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Jan-Philipp Mallm
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Thomas Höfer
- Division Theoretical Systems Biology, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Karsten Rippe
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
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376
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Nordin M, Bergman D, Halje M, Engström W, Ward A. Epigenetic regulation of the Igf2/H19 gene cluster. Cell Prolif 2014; 47:189-99. [PMID: 24738971 DOI: 10.1111/cpr.12106] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 01/14/2014] [Indexed: 12/13/2022] Open
Abstract
Igf2 (insulin-like growth factor 2) and H19 genes are imprinted in mammals; they are expressed unevenly from the two parental alleles. Igf2 is a growth factor expressed in most normal tissues, solely from the paternal allele. H19 gene is transcribed (but not translated to a protein) from the maternal allele. Igf2 protein is a growth factor particularly important during pregnancy, where it promotes both foetal and placental growth and also nutrient transfer from mother to offspring via the placenta. This article reviews epigenetic regulation of the Igf2/H19 gene-cluster that leads to parent-specific expression, with current models including parental allele-specific DNA methylation and chromatin modifications, DNA-binding of insulator proteins (CTCFs) and three-dimensional partitioning of DNA in the nucleus. It is emphasized that key genomic features are conserved among mammals and have been functionally tested in mouse. 'The enhancer competition model', 'the boundary model' and 'the chromatin-loop model' are three models based on differential methylation as the epigenetic mark responsible for the imprinted expression pattern. Pathways are discussed that can account for allelic methylation differences; there is a recent study that contradicts the previously accepted fact that biallelic expression is accompanied with loss of differential methylation pattern.
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Affiliation(s)
- M Nordin
- Faculty of Veterinary Medicine, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
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377
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Duncan EJ, Gluckman PD, Dearden PK. Epigenetics, plasticity, and evolution: How do we link epigenetic change to phenotype? JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 322:208-20. [PMID: 24719220 DOI: 10.1002/jez.b.22571] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 03/13/2014] [Accepted: 03/15/2014] [Indexed: 12/12/2022]
Abstract
Epigenetic mechanisms are proposed as an important way in which the genome responds to the environment. Epigenetic marks, including DNA methylation and Histone modifications, can be triggered by environmental effects, and lead to permanent changes in gene expression, affecting the phenotype of an organism. Epigenetic mechanisms have been proposed as key in plasticity, allowing environmental exposure to shape future gene expression. While we are beginning to understand how these mechanisms have roles in human biology and disease, we have little understanding of their roles and impacts on ecology and evolution. In this review, we discuss different types of epigenetic marks, their roles in gene expression and plasticity, methods for assaying epigenetic changes, and point out the future advances we require to understand fully the impact of this field.
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Affiliation(s)
- Elizabeth J Duncan
- Genetics Otago and Gravida, The National Centre for Growth and Development, Biochemistry Department, University of Otago, Dunedin, New Zealand
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378
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Thorwarth A, Schnittert-Hübener S, Schrumpf P, Müller I, Jyrch S, Dame C, Biebermann H, Kleinau G, Katchanov J, Schuelke M, Ebert G, Steininger A, Bönnemann C, Brockmann K, Christen HJ, Crock P, deZegher F, Griese M, Hewitt J, Ivarsson S, Hübner C, Kapelari K, Plecko B, Rating D, Stoeva I, Ropers HH, Grüters A, Ullmann R, Krude H. Comprehensive genotyping and clinical characterisation reveal 27 novel NKX2-1 mutations and expand the phenotypic spectrum. J Med Genet 2014; 51:375-87. [PMID: 24714694 DOI: 10.1136/jmedgenet-2013-102248] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND NKX2-1 encodes a transcription factor with large impact on the development of brain, lung and thyroid. Germline mutations of NKX2-1 can lead to dysfunction and malformations of these organs. Starting from the largest coherent collection of patients with a suspected phenotype to date, we systematically evaluated frequency, quality and spectrum of phenotypic consequences of NKX2-1 mutations. METHODS After identifying mutations by Sanger sequencing and array CGH, we comprehensively reanalysed the phenotype of affected patients and their relatives. We employed electrophoretic mobility shift assay (EMSA) to detect alterations of NKX2-1 DNA binding. Gene expression was monitored by means of in situ hybridisation and compared with the expression level of MBIP, a candidate gene presumably involved in the disorders and closely located in close genomic proximity to NKX2-1. RESULTS Within 101 index patients, we detected 17 point mutations and 10 deletions. Neurological symptoms were the most consistent finding (100%), followed by lung affection (78%) and thyroidal dysfunction (75%). Novel symptoms associated with NKX2-1 mutations comprise abnormal height, bouts of fever and cardiac septum defects. In contrast to previous reports, our data suggest that missense mutations in the homeodomain of NKX2-1 not necessarily modify its DNA binding capacity and that this specific type of mutations may be associated with mild pulmonary phenotypes such as asthma. Two deletions did not include NKX2-1, but MBIP, whose expression spatially and temporarily coincides with NKX2-1 in early murine development. CONCLUSIONS The high incidence of NKX2-1 mutations strongly recommends the routine screen for mutations in patients with corresponding symptoms. However, this analysis should not be confined to the exonic sequence alone, but should take advantage of affordable NGS technology to expand the target to adjacent regulatory sequences and the NKX2-1 interactome in order to maximise the yield of this diagnostic effort.
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Affiliation(s)
- Anne Thorwarth
- Institute for Experimental Pediatric Endocrinology, Charité University Medicine, Berlin, Germany Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sarah Schnittert-Hübener
- Institute for Experimental Pediatric Endocrinology, Charité University Medicine, Berlin, Germany
| | - Pamela Schrumpf
- Institute for Experimental Pediatric Endocrinology, Charité University Medicine, Berlin, Germany
| | - Ines Müller
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sabine Jyrch
- Institute for Experimental Pediatric Endocrinology, Charité University Medicine, Berlin, Germany
| | - Christof Dame
- Department of Neonatology, Charité University Medicine, Berlin, Germany
| | - Heike Biebermann
- Institute for Experimental Pediatric Endocrinology, Charité University Medicine, Berlin, Germany
| | - Gunnar Kleinau
- Institute for Experimental Pediatric Endocrinology, Charité University Medicine, Berlin, Germany
| | - Juri Katchanov
- Department of Neurology, Charité University Medicine, Berlin, Germany
| | - Markus Schuelke
- Department of Neuropediatrics, Charité University Medicine, Berlin, Germany
| | - Grit Ebert
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anne Steininger
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Carsten Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Knut Brockmann
- Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, University Medical Center, Georg August University, Göttingen, Germany
| | - Hans-Jürgen Christen
- Department for Neuropediatrics, Children's and Youth Hospital "Auf der Bult", Hannover, Germany
| | - Patricia Crock
- Division of Pediatric Endocrinology & Diabetes, John Hunter Children's Hospital, Newcastle, Australia
| | - Francis deZegher
- Department of Woman and Child, University of Leuven, Leuven, Belgium
| | - Matthias Griese
- Dr. von Haunersches Kinderspital, Member of the German Center for Lung Research, University of Munich, Munich, Germany
| | - Jacqueline Hewitt
- Division of Endocrinology & Diabetes, Royal Children's Hospital Melbourne, Melbourne, Australia
| | - Sten Ivarsson
- Department of Clinical Sciences- Pediatric Endocrinology, University Hospital MAS, Malmö, Sweden
| | - Christoph Hübner
- Department of Neuropediatrics, Charité University Medicine, Berlin, Germany
| | - Klaus Kapelari
- Department of Pediatric and Adolescent Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Barbara Plecko
- Division of Child Neurology, University Childrens Hospital Zurich, Zurich, Switzerland
| | - Dietz Rating
- Department for Neuropediatrics, Heidelberg University Hospital, Heidelberg, Germany
| | - Iva Stoeva
- Department of Paediatric Endocrinology Screening and Functional Endocrine Diagnostics, University Paediatric Hospital, Medical University Sofia, Sofia, Bulgaria
| | | | - Annette Grüters
- Institute for Experimental Pediatric Endocrinology, Charité University Medicine, Berlin, Germany
| | | | - Heiko Krude
- Institute for Experimental Pediatric Endocrinology, Charité University Medicine, Berlin, Germany
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379
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Gupta A, Christensen RG, Bell HA, Goodwin M, Patel RY, Pandey M, Enuameh MS, Rayla AL, Zhu C, Thibodeau-Beganny S, Brodsky MH, Joung JK, Wolfe SA, Stormo GD. An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins. Nucleic Acids Res 2014; 42:4800-12. [PMID: 24523353 PMCID: PMC4005693 DOI: 10.1093/nar/gku132] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/21/2014] [Accepted: 01/22/2014] [Indexed: 11/17/2022] Open
Abstract
Cys(2)-His(2) zinc finger proteins (ZFPs) are the largest family of transcription factors in higher metazoans. They also represent the most diverse family with regards to the composition of their recognition sequences. Although there are a number of ZFPs with characterized DNA-binding preferences, the specificity of the vast majority of ZFPs is unknown and cannot be directly inferred by homology due to the diversity of recognition residues present within individual fingers. Given the large number of unique zinc fingers and assemblies present across eukaryotes, a comprehensive predictive recognition model that could accurately estimate the DNA-binding specificity of any ZFP based on its amino acid sequence would have great utility. Toward this goal, we have used the DNA-binding specificities of 678 two-finger modules from both natural and artificial sources to construct a random forest-based predictive model for ZFP recognition. We find that our recognition model outperforms previously described determinant-based recognition models for ZFPs, and can successfully estimate the specificity of naturally occurring ZFPs with previously defined specificities.
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Affiliation(s)
- Ankit Gupta
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan G. Christensen
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Heather A. Bell
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Mathew Goodwin
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Ronak Y. Patel
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Manishi Pandey
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Metewo Selase Enuameh
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy L. Rayla
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Cong Zhu
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Stacey Thibodeau-Beganny
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael H. Brodsky
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - J. Keith Joung
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Scot A. Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Gary D. Stormo
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
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380
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Villar D, Flicek P, Odom DT. Evolution of transcription factor binding in metazoans - mechanisms and functional implications. Nat Rev Genet 2014; 15:221-33. [PMID: 24590227 PMCID: PMC4175440 DOI: 10.1038/nrg3481] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Differences in transcription factor binding can contribute to organismal evolution by altering downstream gene expression programmes. Genome-wide studies in Drosophila melanogaster and mammals have revealed common quantitative and combinatorial properties of in vivo DNA binding, as well as marked differences in the rate and mechanisms of evolution of transcription factor binding in metazoans. Here, we review the recently discovered rapid 're-wiring' of in vivo transcription factor binding between related metazoan species and summarize general principles underlying the observed patterns of evolution. We then consider what might explain the differences in genome evolution between metazoan phyla and outline the conceptual and technological challenges facing this research field.
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Affiliation(s)
- Diego Villar
- University of Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB1 01SD, UK
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
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381
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Medvedeva YA, Khamis AM, Kulakovskiy IV, Ba-Alawi W, Bhuyan MSI, Kawaji H, Lassmann T, Harbers M, Forrest ARR, Bajic VB. Effects of cytosine methylation on transcription factor binding sites. BMC Genomics 2014; 15:119. [PMID: 24669864 PMCID: PMC3986887 DOI: 10.1186/1471-2164-15-119] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 08/16/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND DNA methylation in promoters is closely linked to downstream gene repression. However, whether DNA methylation is a cause or a consequence of gene repression remains an open question. If it is a cause, then DNA methylation may affect the affinity of transcription factors (TFs) for their binding sites (TFBSs). If it is a consequence, then gene repression caused by chromatin modification may be stabilized by DNA methylation. Until now, these two possibilities have been supported only by non-systematic evidence and they have not been tested on a wide range of TFs. An average promoter methylation is usually used in studies, whereas recent results suggested that methylation of individual cytosines can also be important. RESULTS We found that the methylation profiles of 16.6% of cytosines and the expression profiles of neighboring transcriptional start sites (TSSs) were significantly negatively correlated. We called the CpGs corresponding to such cytosines "traffic lights". We observed a strong selection against CpG "traffic lights" within TFBSs. The negative selection was stronger for transcriptional repressors as compared with transcriptional activators or multifunctional TFs as well as for core TFBS positions as compared with flanking TFBS positions. CONCLUSIONS Our results indicate that direct and selective methylation of certain TFBS that prevents TF binding is restricted to special cases and cannot be considered as a general regulatory mechanism of transcription.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Vladimir B Bajic
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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382
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Erhard F, Haas J, Lieber D, Malterer G, Jaskiewicz L, Zavolan M, Dölken L, Zimmer R. Widespread context dependency of microRNA-mediated regulation. Genome Res 2014; 24:906-19. [PMID: 24668909 PMCID: PMC4032855 DOI: 10.1101/gr.166702.113] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Gene expression is regulated in a context-dependent, cell-type-specific manner. Condition-specific transcription is dependent on the presence of transcription factors (TFs) that can activate or inhibit its target genes (global context). Additional factors, such as chromatin structure, histone, or DNA modifications, also influence the activity of individual target genes (individual context). The role of the global and individual context for post-transcriptional regulation has not systematically been investigated on a large scale and is poorly understood. Here we show that global and individual context dependency is a pervasive feature of microRNA-mediated regulation. Our comprehensive and highly consistent data set from several high-throughput technologies (PAR-CLIP, RIP-chip, 4sU-tagging, and SILAC) provides strong evidence that context-dependent microRNA target sites (CDTS) are as frequent and functionally relevant as constitutive target sites (CTS). Furthermore, we found the global context to be insufficient to explain the CDTS, and that flanking sequence motifs provide individual context that is an equally important factor. Our results demonstrate that, similar to TF-mediated regulation, global and individual context dependency are prevalent in microRNA-mediated gene regulation, implying a much more complex post-transcriptional regulatory network than is currently known. The necessary tools to unravel post-transcriptional regulations and mechanisms need to be much more involved, and much more data will be needed for particular cell types and cellular conditions in order to understand microRNA-mediated regulation and the context-dependent post-transcriptional regulatory network.
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Affiliation(s)
- Florian Erhard
- Institut für Informatik, Ludwig-Maximilians-Universität München, 80333 München, Germany
| | - Jürgen Haas
- Max-von-Pettenkofer Institut, Virologie, Ludwig-Maximilians-Universität München, 80336 München, Germany; Division of Pathway Medicine, University of Edinburgh, Edinburgh EH17 8TR, United Kingdom
| | - Diana Lieber
- Max-von-Pettenkofer Institut, Virologie, Ludwig-Maximilians-Universität München, 80336 München, Germany; Institut für Virologie, Universitätsklinikum Ulm, 89081 Ulm, Germany
| | - Georg Malterer
- Max-von-Pettenkofer Institut, Virologie, Ludwig-Maximilians-Universität München, 80336 München, Germany
| | - Lukasz Jaskiewicz
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland
| | - Lars Dölken
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, CB20QQ Cambridge, United Kingdom
| | - Ralf Zimmer
- Institut für Informatik, Ludwig-Maximilians-Universität München, 80333 München, Germany
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383
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Majumder P, Scharer CD, Choi NM, Boss JM. B cell differentiation is associated with reprogramming the CCCTC binding factor-dependent chromatin architecture of the murine MHC class II locus. THE JOURNAL OF IMMUNOLOGY 2014; 192:3925-35. [PMID: 24634495 DOI: 10.4049/jimmunol.1303205] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The transcriptional insulator CCCTC binding factor (CTCF) was shown previously to be critical for human MHC class II (MHC-II) gene expression. Whether the mechanisms used by CTCF in humans were similar to that of the mouse and whether the three-dimensional chromatin architecture created was specific to B cells were not defined. Genome-wide CTCF occupancy was defined for murine B cells and LPS-derived plasmablasts by chromatin immunoprecipitation sequencing. Fifteen CTCF sites within the murine MHC-II locus were associated with high CTCF binding in B cells. Only one-third of these sites displayed significant CTCF occupancy in plasmablasts. CTCF was required for maximal MHC-II gene expression in mouse B cells. In B cells, a subset of the CTCF regions interacted with each other, creating a three-dimensional architecture for the locus. Additional interactions occurred between MHC-II promoters and the CTCF sites. In contrast, a novel configuration occurred in plasma cells, which do not express MHC-II genes. Ectopic CIITA expression in plasma cells to induce MHC-II expression resulted in high levels of MHC-II proteins, but did not alter the plasma cell architecture completely. These data suggest that reorganizing the three-dimensional chromatin architecture is an epigenetic mechanism that accompanies the silencing of MHC-II genes as part of the cell fate commitment of plasma cells.
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Affiliation(s)
- Parimal Majumder
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
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384
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Ong CT, Corces VG. CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet 2014; 15:234-46. [PMID: 24614316 DOI: 10.1038/nrg3663] [Citation(s) in RCA: 703] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The eukaryotic genome is organized in the three-dimensional nuclear space in a specific manner that is both a cause and a consequence of its function. This organization is partly established by a special class of architectural proteins, of which CCCTC-binding factor (CTCF) is the best characterized. Although CTCF has been assigned various roles that are often contradictory, new results now help to draw a unifying model to explain the many functions of this protein. CTCF creates boundaries between topologically associating domains in chromosomes and, within these domains, facilitates interactions between transcription regulatory sequences. Thus, CTCF links the architecture of the genome to its function.
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Affiliation(s)
- Chin-Tong Ong
- Department of Biology, Emory University, 1510 Clifton Rd NE, Atlanta, Georgia 30322, USA
| | - Victor G Corces
- Department of Biology, Emory University, 1510 Clifton Rd NE, Atlanta, Georgia 30322, USA
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385
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Lake RJ, Tsai PF, Choi I, Won KJ, Fan HY. RBPJ, the major transcriptional effector of Notch signaling, remains associated with chromatin throughout mitosis, suggesting a role in mitotic bookmarking. PLoS Genet 2014; 10:e1004204. [PMID: 24603501 PMCID: PMC3945225 DOI: 10.1371/journal.pgen.1004204] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 01/13/2014] [Indexed: 01/07/2023] Open
Abstract
Mechanisms that maintain transcriptional memory through cell division are important to maintain cell identity, and sequence-specific transcription factors that remain associated with mitotic chromatin are emerging as key players in transcriptional memory propagation. Here, we show that the major transcriptional effector of Notch signaling, RBPJ, is retained on mitotic chromatin, and that this mitotic chromatin association is mediated through the direct association of RBPJ with DNA. We further demonstrate that RBPJ binds directly to nucleosomal DNA in vitro, with a preference for sites close to the entry/exit position of the nucleosomal DNA. Genome-wide analysis in the murine embryonal-carcinoma cell line F9 revealed that roughly 60% of the sites occupied by RBPJ in asynchronous cells were also occupied in mitotic cells. Among them, we found that a fraction of RBPJ occupancy sites shifted between interphase and mitosis, suggesting that RBPJ can be retained on mitotic chromatin by sliding on DNA rather than disengaging from chromatin during mitotic chromatin condensation. We propose that RBPJ can function as a mitotic bookmark, marking genes for efficient transcriptional activation or repression upon mitotic exit. Strikingly, we found that sites of RBPJ occupancy were enriched for CTCF-binding motifs in addition to RBPJ-binding motifs, and that RBPJ and CTCF interact. Given that CTCF regulates transcription and bridges long-range chromatin interactions, our results raise the intriguing hypothesis that by collaborating with CTCF, RBPJ may participate in establishing chromatin domains and/or long-range chromatin interactions that could be propagated through cell division to maintain gene expression programs. How does a cell remember what it should be after cell division? One mechanism that is beginning to emerge is the retention of a few key regulatory proteins on the highly condensed mitotic chromatin during cell division. These proteins are called mitotic bookmarks, as they are believed to offer critical information as to how genetic information should be read immediately after mitosis. We have found that a protein called RBPJ, which plays pivotal roles in regulating cell-fate choices, is retained on mitotic chromatin. RBPJ transmits to DNA signals elicited by the Notch pathway: a pathway that conveys information resulting from the communication between two adjacent cells. Unlike many other factors, we found that RBPJ can bind to nucleosomes, which are the basic unit of packaged DNA consisting of DNA wrapped around eight histone proteins. We also found that RBPJ interacts with and binds to DNA sites regulated by the CTCF protein, which plays important roles in regulating long-range DNA interactions. Together, our results suggest that RBPJ can function as a mitotic bookmarking factor, to help maintain genetic programs, higher-order structural information and consequently the memory of cell identity through cell division.
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Affiliation(s)
- Robert J. Lake
- Epigenetics Program, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Pei-Fang Tsai
- Epigenetics Program, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Inchan Choi
- Institute for Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kyoung-Jae Won
- Institute for Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (KJW); (HYF)
| | - Hua-Ying Fan
- Epigenetics Program, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (KJW); (HYF)
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386
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Wilson GA, Butcher LM, Foster HR, Feber A, Roos C, Walter L, Woszczek G, Beck S, Bell CG. Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases. Genome Med 2014; 6:19. [PMID: 24598577 PMCID: PMC4062055 DOI: 10.1186/gm536] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 02/24/2014] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Common human diseases are caused by the complex interplay of genetic susceptibility as well as environmental factors. Due to the environment's influence on the epigenome, and therefore genome function, as well as conversely the genome's facilitative effect on the epigenome, analysis of this level of regulation may increase our knowledge of disease pathogenesis. METHODS In order to identify human-specific epigenetic influences, we have performed a novel genome-wide DNA methylation analysis comparing human, chimpanzee and rhesus macaque. RESULTS We have identified that the immunological Leukotriene B4 receptor (LTB4R, BLT1 receptor) is the most epigenetically divergent human gene in peripheral blood in comparison with other primates. This difference is due to the co-ordinated active state of human-specific hypomethylation in the promoter and human-specific increased gene body methylation. This gene is significant in innate immunity and the LTB4/LTB4R pathway is involved in the pathogenesis of the spectrum of human inflammatory diseases. This finding was confirmed by additional neutrophil-only DNA methylome and lymphoblastoid H3K4me3 chromatin comparative data. Additionally we show through functional analysis that this receptor has increased expression and a higher response to the LTB4 ligand in human versus rhesus macaque peripheral blood mononuclear cells. Genome-wide we also find human species-specific differentially methylated regions (human s-DMRs) are more prevalent in CpG island shores than within the islands themselves, and within the latter are associated with the CTCF motif. CONCLUSIONS This result further emphasises the exclusive nature of the human immunological system, its divergent adaptation even from very closely related primates, and the power of comparative epigenomics to identify and understand human uniqueness.
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Affiliation(s)
- Gareth A Wilson
- Medical Genomics, UCL Cancer Institute, University College London, London, UK ; Current address: Translational Cancer Therapeutics, CR-UK London Research Institute, Lincoln's Inn Fields, London, UK
| | - Lee M Butcher
- Medical Genomics, UCL Cancer Institute, University College London, London, UK
| | - Holly R Foster
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, Division of Asthma, Allergy and Lung Biology, King's College London, London, UK
| | - Andrew Feber
- Medical Genomics, UCL Cancer Institute, University College London, London, UK
| | - Christian Roos
- Genebank of Primates and Primate Genetics Laboratory, German Primate Centre, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Lutz Walter
- Genebank of Primates and Primate Genetics Laboratory, German Primate Centre, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Grzegorz Woszczek
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, Division of Asthma, Allergy and Lung Biology, King's College London, London, UK
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London, UK
| | - Christopher G Bell
- Medical Genomics, UCL Cancer Institute, University College London, London, UK ; Current address: Department of Twin Research & Genetic Epidemiology, St Thomas' Hospital, King's College London, London, UK
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387
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Shi J, Marconett CN, Duan J, Hyland PL, Li P, Wang Z, Wheeler W, Zhou B, Campan M, Lee DS, Huang J, Zhou W, Triche T, Amundadottir L, Warner A, Hutchinson A, Chen PH, Chung BSI, Pesatori AC, Consonni D, Bertazzi PA, Bergen AW, Freedman M, Siegmund KD, Berman BP, Borok Z, Chatterjee N, Tucker MA, Caporaso NE, Chanock SJ, Laird-Offringa IA, Landi MT. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nat Commun 2014; 5:3365. [PMID: 24572595 PMCID: PMC3982882 DOI: 10.1038/ncomms4365] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 01/31/2014] [Indexed: 12/17/2022] Open
Abstract
The genetic regulation of the human epigenome is not fully appreciated. Here we describe the effects of genetic variants on the DNA methylome in human lung based on methylation-quantitative trait loci (meQTL) analyses. We report 34,304 cis- and 585 trans-meQTLs, a genetic-epigenetic interaction of surprising magnitude, including a regulatory hotspot. These findings are replicated in both breast and kidney tissues and show distinct patterns: cis-meQTLs mostly localize to CpG sites outside of genes, promoters and CpG islands (CGIs), while trans-meQTLs are over-represented in promoter CGIs. meQTL SNPs are enriched in CTCF-binding sites, DNaseI hypersensitivity regions and histone marks. Importantly, four of the five established lung cancer risk loci in European ancestry are cis-meQTLs and, in aggregate, cis-meQTLs are enriched for lung cancer risk in a genome-wide analysis of 11,587 subjects. Thus, inherited genetic variation may affect lung carcinogenesis by regulating the human methylome.
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Affiliation(s)
- Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Crystal N Marconett
- 1] Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA
| | - Jubao Duan
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, North Shore University Health System Research Institute, University of Chicago Pritzker School of Medicine, Evanston, Illinois 60201, USA
| | - Paula L Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Peng Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - William Wheeler
- Information Management Services Inc., Rockville, Maryland 20852, USA
| | - Beiyun Zhou
- Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, USC Keck School of Medicine, Los Angeles, California 90089, USA
| | - Mihaela Campan
- 1] Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA
| | - Diane S Lee
- 1] Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA
| | - Jing Huang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Tim Triche
- Bioinformatics Division, Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Laufey Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Andrew Warner
- Pathology/Histotechnology Laboratory, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Po-Han Chen
- 1] Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA
| | - Brian S I Chung
- 1] Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA
| | - Angela C Pesatori
- Unit of Epidemiology, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Dario Consonni
- Unit of Epidemiology, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Pier Alberto Bertazzi
- Unit of Epidemiology, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Andrew W Bergen
- Molecular Genetics Program, Center for Health Sciences, SRI, Menlo Park, California 94025, USA
| | - Mathew Freedman
- 1] Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts 02142, USA [2] Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Kimberly D Siegmund
- Bioinformatics Division, Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Benjamin P Berman
- 1] Bioinformatics Division, Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089, USA [2] USC Epigenome Center and USC/Norris Comprehensive Cancer Center, Los Angeles, California 90089, USA
| | - Zea Borok
- 1] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, USC Keck School of Medicine, Los Angeles, California 90089, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
| | - Ite A Laird-Offringa
- 1] Department of Surgery, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA [2] Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, California 90089, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland 20892, USA
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Luo X, Chae M, Krishnakumar R, Danko CG, Kraus WL. Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses. BMC Genomics 2014; 15:155. [PMID: 24564208 PMCID: PMC3945043 DOI: 10.1186/1471-2164-15-155] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/05/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Defining cell type-specific transcriptomes in mammals can be challenging, especially for unannotated regions of the genome. We have developed an analytical pipeline called groHMM for annotating primary transcripts using global nuclear run-on sequencing (GRO-seq) data. Herein, we use this pipeline to characterize the transcriptome of an immortalized adult human ventricular cardiomyocyte cell line (AC16) in response to signaling by tumor necrosis factor alpha (TNFα), which is controlled in part by NF-κB, a key transcriptional regulator of inflammation. A unique aspect of this work is the use of the RNA polymerase II (Pol II) inhibitor α-amanitin, which we used to define a set of RNA polymerase I and III (Pol I and Pol III) transcripts. RESULTS Using groHMM, we identified ~30,000 coding and non-coding transcribed regions in AC16 cells, which includes a set of unique Pol I and Pol III primary transcripts. Many of these transcripts have not been annotated previously, including enhancer RNAs originating from NF-κB binding sites. In addition, we observed that AC16 cells rapidly and dynamically reorganize their transcriptomes in response to TNFα stimulation in an NF-κB-dependent manner, switching from a basal state to a proinflammatory state affecting a spectrum of cardiac-associated protein-coding and non-coding genes. Moreover, we observed distinct Pol II dynamics for up- and downregulated genes, with a rapid release of Pol II into productive elongation for TNFα-stimulated genes. As expected, the TNFα-induced changes in the AC16 transcriptome resulted in corresponding changes in cognate mRNA and protein levels in a similar manner, but with delayed kinetics. CONCLUSIONS Our studies illustrate how computational genomics can be used to characterize the signal-regulated transcriptome in biologically relevant cell types, providing new information about how the human genome is organized, transcribed and regulated. In addition, they show how α-amanitin can be used to reveal the Pol I and Pol III transcriptome. Furthermore, they shed new light on the regulation of the cardiomyocyte transcriptome in response to a proinflammatory signal and help to clarify the link between inflammation and cardiomyocyte function at the transcriptional level.
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Affiliation(s)
- Xin Luo
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Graduate School of Biomedical Sciences, Program in Genetics and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Minho Chae
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Raga Krishnakumar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
- Current address: Institute for Regenerative Medicine, University of California, San Francisco 94143, USA
| | - Charles G Danko
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Graduate School of Biomedical Sciences, Program in Genetics and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
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389
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Maksimenko O, Georgiev P. Mechanisms and proteins involved in long-distance interactions. Front Genet 2014; 5:28. [PMID: 24600469 PMCID: PMC3927085 DOI: 10.3389/fgene.2014.00028] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/25/2014] [Indexed: 12/28/2022] Open
Abstract
Due to advances in genome-wide technologies, consistent distant interactions within chromosomes of higher eukaryotes have been revealed. In particular, it has been shown that enhancers can specifically and directly interact with promoters by looping out intervening sequences, which can be up to several hundred kilobases long. This review is focused on transcription factors that are supposed to be involved in long-range interactions. Available data are in agreement with the model that several known transcription factors and insulator proteins belong to an abundant but poorly studied class of proteins that are responsible for chromosomal architecture.
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Affiliation(s)
- Oksana Maksimenko
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences Moscow, Russia
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390
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Liao BY, Chang A. Accumulation of CTCF-binding sites drives expression divergence between tandemly duplicated genes in humans. BMC Genomics 2014; 15 Suppl 1:S8. [PMID: 24564680 PMCID: PMC4046690 DOI: 10.1186/1471-2164-15-s1-s8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background During eukaryotic genome evolution, tandem gene duplication is the most frequent event giving rise to clustered gene families. However, how expression divergence between tandemly duplicated genes has emerged and maintained remain unclear. In particular, it is unknown if epigenetic regulators have been involved in the process. Results We demonstrate that CCCTC-binding factor (CTCF), the master epigenetic regulator and the only known insulator protein in humans, has played a predominant role in generating divergence in both expression profiles and expression levels between adjacent paralogs in the human genome. This phenomenon was not observed for non-paralogous adjacent genes. After tandem duplication events, CTCF-binding sites gradually accumulate between paralogs. This trend was more prominent for genes involved in particular functions. Conclusions The accumulation of CTCF-binding sites drives expression divergence of tandemly duplicated genes. This process is likely targeted by natural selection. Our study reveals the importance of CTCF to the evolution of animal diversity and complexity. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-S1-S8) contains supplementary material, which is available to authorized users.
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391
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Eggeling R, Gohr A, Keilwagen J, Mohr M, Posch S, Smith AD, Grosse I. On the value of intra-motif dependencies of human insulator protein CTCF. PLoS One 2014; 9:e85629. [PMID: 24465627 PMCID: PMC3899044 DOI: 10.1371/journal.pone.0085629] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/05/2013] [Indexed: 01/08/2023] Open
Abstract
The binding affinity of DNA-binding proteins such as transcription factors is mainly determined by the base composition of the corresponding binding site on the DNA strand. Most proteins do not bind only a single sequence, but rather a set of sequences, which may be modeled by a sequence motif. Algorithms for de novo motif discovery differ in their promoter models, learning approaches, and other aspects, but typically use the statistically simple position weight matrix model for the motif, which assumes statistical independence among all nucleotides. However, there is no clear justification for that assumption, leading to an ongoing debate about the importance of modeling dependencies between nucleotides within binding sites. In the past, modeling statistical dependencies within binding sites has been hampered by the problem of limited data. With the rise of high-throughput technologies such as ChIP-seq, this situation has now changed, making it possible to make use of statistical dependencies effectively. In this work, we investigate the presence of statistical dependencies in binding sites of the human enhancer-blocking insulator protein CTCF by using the recently developed model class of inhomogeneous parsimonious Markov models, which is capable of modeling complex dependencies while avoiding overfitting. These findings lead to a more detailed characterization of the CTCF binding motif, which is only poorly represented by independent nucleotide frequencies at several positions, predominantly at the 3' end.
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Affiliation(s)
- Ralf Eggeling
- Institute of Computer Science, Martin Luther University Halle–Wittenberg, Halle/Saale, Germany
| | - André Gohr
- Institute of Computer Science, Martin Luther University Halle–Wittenberg, Halle/Saale, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Germany
| | - Michaela Mohr
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Germany
| | - Stefan Posch
- Institute of Computer Science, Martin Luther University Halle–Wittenberg, Halle/Saale, Germany
| | - Andrew D. Smith
- Molecular and Computational Biology, University of Southern California, Los Angeles, United States of America
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle–Wittenberg, Halle/Saale, Germany
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Germany
- German Center of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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392
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Li Y, Umbach DM, Li L. T-KDE: a method for genome-wide identification of constitutive protein binding sites from multiple ChIP-seq data sets. BMC Genomics 2014; 15:27. [PMID: 24428924 PMCID: PMC3903014 DOI: 10.1186/1471-2164-15-27] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 01/13/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A protein may bind to its target DNA sites constitutively, i.e., regardless of cell type. Intuitively, constitutive binding sites should be biologically functional. A prerequisite for understanding their functional relevance is knowing all their locations for a protein of interest. Genome-wide discovery of constitutive binding sites requires robust and efficient computational methods to integrate results from numerous binding experiments. Such methods are lacking, however. RESULTS To locate constitutive binding sites for a protein using ChIP-seq data for that protein from multiple cell lines, we developed a method, T-KDE, which combines a binary range tree with a kernel density estimator. Using 132 CTCF (CCCTC-binding factor) ChIP-seq datasets, we showed that the number of constitutive sites identified by T-KDE is robust to the choice of tuning parameter and that T-KDE identifies binding site locations more accurately than a binning approach. Furthermore, T-KDE can identify constitutive sites that are missed by a motif-based approach either because a bound site failed to reach the motif significance cutoff or because the peak sequence scanned was too short. By studying sites declared constitutive by T-KDE but not by the motif-based approach, we discovered two new CTCF motif variants. Using ENCODE data on 22 transcription factors (TF) in 132 cell lines, we identified constitutive binding sites for each TF and provide evidence that, for some TFs, they may be biologically meaningful. CONCLUSIONS T-KDE is an efficient and effective method to predict constitutive protein binding sites using ChIP-seq peaks from multiple cell lines. Besides constitutive binding sites for a given protein, T-KDE can identify genomic "hot spots" where several different proteins bind and, conversely, cell-type-specific sites bound by a given protein.
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Affiliation(s)
| | | | - Leping Li
- Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Morrisville, NC 27709, USA.
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393
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Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, Flicek P. Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes. Genome Biol 2013; 14:R148. [PMID: 24380390 PMCID: PMC4056453 DOI: 10.1186/gb-2013-14-12-r148] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 12/31/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genomic binding of CTCF is highly conserved across mammals, but the mechanisms that underlie its stability are poorly understood. One transcription factor known to functionally interact with CTCF in the context of X-chromosome inactivation is the ubiquitously expressed YY1. Because combinatorial transcription factor binding can contribute to the evolutionary stabilization of regulatory regions, we tested whether YY1 and CTCF co-binding could in part account for conservation of CTCF binding. RESULTS Combined analysis of CTCF and YY1 binding in lymphoblastoid cell lines from seven primates, as well as in mouse and human livers, reveals extensive genome-wide co-localization specifically at evolutionarily stable CTCF-bound regions. CTCF-YY1 co-bound regions resemble regions bound by YY1 alone, as they enrich for active histone marks, RNA polymerase II and transcription factor binding. Although these highly conserved, transcriptionally active CTCF-YY1 co-bound regions are often promoter-proximal, gene-distal regions show similar molecular features. CONCLUSIONS Our results reveal that these two ubiquitously expressed, multi-functional zinc-finger proteins collaborate in functionally active regions to stabilize one another's genome-wide binding across primate evolution.
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Affiliation(s)
- Petra C Schwalie
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Current address: Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Michelle C Ward
- University of Cambridge, Cancer Research UK-Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK
- Current address: Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Carolyn E Cain
- Current address: Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Andre J Faure
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Yoav Gilad
- Current address: Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK-Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
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394
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Batlle-López A, Cortiguera MG, Rosa-Garrido M, Blanco R, del Cerro E, Torrano V, Wagner SD, Delgado MD. Novel CTCF binding at a site in exon1A of BCL6 is associated with active histone marks and a transcriptionally active locus. Oncogene 2013; 34:246-56. [PMID: 24362533 DOI: 10.1038/onc.2013.535] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 10/01/2013] [Accepted: 11/01/2013] [Indexed: 12/14/2022]
Abstract
BCL6 is a zinc-finger transcriptional repressor, which is highly expressed in germinal centre B-cells and is essential for germinal centre formation and T-dependent antibody responses. Constitutive BCL6 expression is sufficient to produce lymphomas in mice. Deregulated expression of BCL6 due to chromosomal rearrangements, mutations of a negative autoregulatory site in the BCL6 promoter region and aberrant post-translational modifications have been detected in a number of human lymphomas. Tight lineage and temporal regulation of BCL6 is, therefore, required for normal immunity, and abnormal regulation occurs in lymphomas. CCCTC-binding factor (CTCF) is a multi-functional chromatin regulator, which has recently been shown to bind in a methylation-sensitive manner to sites within the BCL6 first intron. We demonstrate a novel CTCF-binding site in BCL6 exon1A within a potential CpG island, which is unmethylated both in cell lines and in primary lymphoma samples. CTCF binding, which was found in BCL6-expressing cell lines, correlated with the presence of histone variant H2A.Z and active histone marks, suggesting that CTCF induces chromatin modification at a transcriptionally active BCL6 locus. CTCF binding to exon1A was required to maintain BCL6 expression in germinal centre cells by avoiding BCL6-negative autoregulation. Silencing of CTCF in BCL6-expressing cells reduced BCL6 mRNA and protein expression, which is sufficient to induce B-cell terminal differentiation toward plasma cells. Moreover, lack of CTCF binding to exon1A shifts the BCL6 local chromatin from an active to a repressive state. This work demonstrates that, in contexts in which BCL6 is expressed, CTCF binding to BCL6 exon1A associates with epigenetic modifications indicative of transcriptionally open chromatin.
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Affiliation(s)
- A Batlle-López
- 1] Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) and Departamento de Biología Molecular, Universidad de Cantabria, CSIC, SODERCAN, Santander, Spain [2] Servicio de Hematología, Hospital U. Marqués de Valdecilla, and IFIMAV-FMV, Santander, Spain
| | - M G Cortiguera
- 1] Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) and Departamento de Biología Molecular, Universidad de Cantabria, CSIC, SODERCAN, Santander, Spain [2] Servicio de Hematología, Hospital U. Marqués de Valdecilla, and IFIMAV-FMV, Santander, Spain
| | - M Rosa-Garrido
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) and Departamento de Biología Molecular, Universidad de Cantabria, CSIC, SODERCAN, Santander, Spain
| | - R Blanco
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) and Departamento de Biología Molecular, Universidad de Cantabria, CSIC, SODERCAN, Santander, Spain
| | - E del Cerro
- Servicio de Hematología, Hospital U. Marqués de Valdecilla, and IFIMAV-FMV, Santander, Spain
| | - V Torrano
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) and Departamento de Biología Molecular, Universidad de Cantabria, CSIC, SODERCAN, Santander, Spain
| | - S D Wagner
- Department of Cancer Studies and Molecular Medicine and MRC Toxicology Unit, University of Leicester, Leicester, UK
| | - M D Delgado
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) and Departamento de Biología Molecular, Universidad de Cantabria, CSIC, SODERCAN, Santander, Spain
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395
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Marshall AD, Bailey CG, Rasko JEJ. CTCF and BORIS in genome regulation and cancer. Curr Opin Genet Dev 2013; 24:8-15. [PMID: 24657531 DOI: 10.1016/j.gde.2013.10.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/18/2013] [Accepted: 10/19/2013] [Indexed: 10/25/2022]
Abstract
CTCF plays a vital role in chromatin structure and function. CTCF is ubiquitously expressed and plays diverse roles in gene regulation, imprinting, insulation, intra/interchromosomal interactions, nuclear compartmentalisation, and alternative splicing. CTCF has a single paralogue, the testes-specific CTCF-like gene (CTCFL)/BORIS. CTCF and BORIS can be deregulated in cancer. The tumour suppressor gene CTCF can be mutated or deleted in cancer, or CTCF DNA binding can be altered by epigenetic changes. BORIS is aberrantly expressed frequently in cancer, leading some to propose a pro-tumourigenic role for BORIS. However, BORIS can inhibit cell proliferation, and is mutated in cancer similarly to CTCF suggesting BORIS activation in cancer may be due to global genetic or epigenetic changes typical of malignant transformation.
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Affiliation(s)
- Amy D Marshall
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia; Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, NSW, Australia.
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396
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Epigenetics and the regulation of stress vulnerability and resilience. Neuroscience 2013; 264:157-70. [PMID: 24333971 DOI: 10.1016/j.neuroscience.2013.12.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/29/2013] [Accepted: 12/03/2013] [Indexed: 12/13/2022]
Abstract
The human brain has a remarkable capacity to adapt to and learn from a wide range of variations in the environment. However, environmental challenges can also precipitate psychiatric disorders in susceptible individuals. Why any given experience should induce one brain to adapt while another is edged toward psychopathology remains poorly understood. Like all aspects of psychological function, both nature (genetics) and nurture (life experience) sculpt the brain's response to stressful stimuli. Here we review how these two influences intersect at the epigenetic regulation of neuronal gene transcription, and we discuss how the regulation of genomic DNA methylation near key stress-response genes may influence psychological susceptibility or resilience to environmental stressors. Our goal is to offer a perspective on the epigenetics of stress responses that works to bridge the gap between the study of this molecular process in animal models and its potential usefulness for understanding stress vulnerabilities in humans.
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397
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Chetverina D, Aoki T, Erokhin M, Georgiev P, Schedl P. Making connections: insulators organize eukaryotic chromosomes into independent cis-regulatory networks. Bioessays 2013; 36:163-72. [PMID: 24277632 DOI: 10.1002/bies.201300125] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Insulators play a central role in subdividing the chromosome into a series of discrete topologically independent domains and in ensuring that enhancers and silencers contact their appropriate target genes. In this review we first discuss the general characteristics of insulator elements and their associated protein factors. A growing collection of insulator proteins have been identified including a family of proteins whose expression is developmentally regulated. We next consider several unexpected discoveries that require us to completely rethink how insulators function (and how they can best be assayed). These discoveries also require a reevaluation of how insulators might restrict or orchestrate (by preventing or promoting) interactions between regulatory elements and their target genes. We conclude by connecting these new insights into the mechanisms of insulator action to dynamic changes in the three-dimensional topology of the chromatin fiber and the generation of specific patterns of gene activity during development and differentiation.
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Affiliation(s)
- Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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398
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Del Campo EP, Márquez JJT, Reyes-Vargas F, Intriago-Ortega MDP, Quintanar-Escorza MA, Burciaga-Nava JA, Sifuentes-Alvarez A, Reyes-Romero M. CTCF and CTCFL mRNA expression in 17β-estradiol-treated MCF7 cells. Biomed Rep 2013; 2:101-104. [PMID: 24649078 DOI: 10.3892/br.2013.200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 11/06/2013] [Indexed: 01/13/2023] Open
Abstract
Estrogens play a key role in breast cancer, with 60-70% of the cases expressing estrogen receptors (ERs), which are encoded by the ESR1 gene. CTCFL, a paralogue of the chromatin organizer CTCF, is a potential biomarker of breast cancer, but its expression in this disease is currently controversial. A positive correlation has been reported between CTCFL and ERs in breast tumors and there also exists a coordinated interaction between CTCF and ERs in breast cancer cells. Therefore, there appears to be an association between CTCF, CTCFL and estrogens in breast cancer; however, there has been no report on the effects of estrogens on CTCF and CTCFL expression. The aim of this study was to determine the effect of 17β-estradiol (E2) on the CTCF and CTCFL mRNA expression in the MCF7 breast cancer cell line. The promoter methylation status of CTCFL and data mining for estrogen response elements in promoters of the CTCF and CTCFL genes were also determined. The transcription of CTCF and CTCFL was performed by quantitative polymerase chain reaction (qPCR) and the promoter methylation status of CTCFL was determined by methylation-specific PCR. The MCF7 cells exhibited basal transcription of CTCF, which was significantly downregulated to 0.68 by 1 μM E2; basal or E2-regulated transcription of CTCFL was not detected. Under basal conditions, the CTCFL promoter was methylated. Through data mining, an estrogen response element was identified in the CTCF promoter, but no such element was found in CTCFL. These results suggested that estrogens may modulate CTCF expression, although there was no apparent association between ERs and CTCFL.
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Affiliation(s)
- Eduardo Portillo Del Campo
- Department of Molecular Medicine, Faculty of Medicine and Nutrition, Juárez University of the State of Durango, Durango 34000, Mexico
| | - José Jorge Talamás Márquez
- Department of Molecular Medicine, Faculty of Medicine and Nutrition, Juárez University of the State of Durango, Durango 34000, Mexico ; Department of Biochemistry, Faculty of Medicine and Nutrition, Juárez University of the State of Durango, Durango 34000, Mexico
| | | | - María Del Pilar Intriago-Ortega
- Department of Biochemistry, Faculty of Medicine and Nutrition, Juárez University of the State of Durango, Durango 34000, Mexico
| | | | - Jorge Alberto Burciaga-Nava
- Department of Biochemistry, Faculty of Medicine and Nutrition, Juárez University of the State of Durango, Durango 34000, Mexico
| | - Antonio Sifuentes-Alvarez
- Department of Biochemistry, Faculty of Medicine and Nutrition, Juárez University of the State of Durango, Durango 34000, Mexico
| | - Miguel Reyes-Romero
- Department of Molecular Medicine, Faculty of Medicine and Nutrition, Juárez University of the State of Durango, Durango 34000, Mexico
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399
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Buck MJ, Raaijmakers LM, Ramakrishnan S, Wang D, Valiyaparambil S, Liu S, Nowak NJ, Pili R. Alterations in chromatin accessibility and DNA methylation in clear cell renal cell carcinoma. Oncogene 2013; 33:4961-5. [DOI: 10.1038/onc.2013.455] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 08/28/2013] [Accepted: 09/14/2013] [Indexed: 12/13/2022]
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400
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Roukos DH, Baltogiannis GG, Baltogiannis G. Mapping inherited and somatic variation in regulatory DNA: new roadmap for common disease clinical discoveries. Expert Rev Mol Diagn 2013; 13:519-22. [PMID: 23895121 DOI: 10.1586/14737159.2013.811908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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