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vonHoldt B, Heppenheimer E, Petrenko V, Croonquist P, Rutledge LY. Ancestry-Specific Methylation Patterns in Admixed Offspring from an Experimental Coyote and Gray Wolf Cross. J Hered 2017; 108:341-348. [PMID: 28182234 DOI: 10.1093/jhered/esx004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/19/2017] [Indexed: 12/18/2022] Open
Abstract
Reduced fitness of admixed individuals is typically attributed to genetic incompatibilities. Although mismatched genomes can lead to fitness changes, in some cases the reduction in hybrid fitness is subtle. The potential role of transcriptional regulation in admixed genomes could provide a mechanistic explanation for these discrepancies, but evidence is lacking for nonmodel organisms. Here, we explored the intersection of genetics and gene regulation in admixed genomes derived from an experimental cross between a western gray wolf and western coyote. We found a significant positive association between methylation and wolf ancestry, and identified outlier genes that have been previously implicated in inbreeding-related, or otherwise deleterious, phenotypes. We describe a pattern of site-specific, rather than genome-wide, methylation driven by inter-specific hybridization. Epigenetic variation is thus suggested to play a nontrivial role in both maintaining and combating mismatched genotypes through putative transcriptional mechanisms. We conclude that the regulation of gene expression is an underappreciated key component of hybrid genome functioning, but could also act as a potential source of novel and beneficial adaptive variation in hybrid offspring.
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Affiliation(s)
- Bridgett vonHoldt
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
| | - Elizabeth Heppenheimer
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
| | - Vladimir Petrenko
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
| | - Paula Croonquist
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
| | - Linda Y Rutledge
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
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Yadav S, Shekhawat M, Jahagirdar D, Kumar Sharma N. Natural and artificial small RNAs: a promising avenue of nucleic acid therapeutics for cancer. Cancer Biol Med 2017; 14:242-253. [PMID: 28884041 PMCID: PMC5570601 DOI: 10.20892/j.issn.2095-3941.2017.0038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/22/2017] [Indexed: 01/02/2023] Open
Abstract
Since the failure of traditional therapy, gene therapy using functional DNA sequence and small RNA/DNA molecules (oligonucleotide) has become a promising avenue for cancer treatment. The discovery of RNA molecules has impelled researchers to investigate small regulatory RNA from various natural and artificial sources and determine a cogent target for controlling tumor progression. Small regulatory RNAs are used for therapeutic silencing of oncogenes and aberrant DNA repair response genes. Despite their advantages, therapies based on small RNAs exhibit limitations in terms of stability of therapeutic drugs, precision-based delivery in tissues, precision-based intercellular and intracellular targeting, and tumor heterogeneity-based responses. In this study, we summarize the potential and drawbacks of small RNAs in nucleic acid therapeutics for cancer.
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Affiliation(s)
- Sunny Yadav
- Cancer and Translational Research Lab, Dr. D.Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India
| | - Mamta Shekhawat
- Cancer and Translational Research Lab, Dr. D.Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India
| | - Devashree Jahagirdar
- Cancer and Translational Research Lab, Dr. D.Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India
| | - Nilesh Kumar Sharma
- Cancer and Translational Research Lab, Dr. D.Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India
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Stratigi K, Chatzidoukaki O, Garinis GA. DNA damage-induced inflammation and nuclear architecture. Mech Ageing Dev 2016; 165:17-26. [PMID: 27702596 DOI: 10.1016/j.mad.2016.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/20/2016] [Accepted: 09/25/2016] [Indexed: 12/12/2022]
Abstract
Nuclear architecture and the chromatin state affect most-if not all- DNA-dependent transactions, including the ability of cells to sense DNA lesions and restore damaged DNA back to its native form. Recent evidence points to functional links between DNA damage sensors, DNA repair mechanisms and the innate immune responses. The latter raises the question of how such seemingly disparate processes operate within the intrinsically complex nuclear landscape and the chromatin environment. Here, we discuss how DNA damage-induced immune responses operate within chromatin and the distinct sub-nuclear compartments highlighting their relevance to chronic inflammation.
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Affiliation(s)
- Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Ourania Chatzidoukaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece; Department of Biology, University of Crete, Vassilika Vouton, GR71409, Heraklion, Crete, Greece.
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Krivega I, Dean A. Chromosome togetherness at the onset of ESC differentiation. Cell Stem Cell 2016; 16:213-4. [PMID: 25748925 DOI: 10.1016/j.stem.2015.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pairing of homologous alleles is a phenomenon generally associated with imprinted and mono-allelically expressed loci. In this issue, Hogan et al. (2015) examine the earliest steps between pluripotency and lineage commitment in ESCs and find a critical role for transient pairing of Oct4 alleles in exiting the pluripotent state.
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Affiliation(s)
- Ivan Krivega
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Stratigi K, Kapsetaki M, Aivaliotis M, Town T, Flavell RA, Spilianakis CG. Spatial proximity of homologous alleles and long noncoding RNAs regulate a switch in allelic gene expression. Proc Natl Acad Sci U S A 2015; 112:E1577-86. [PMID: 25770217 PMCID: PMC4386343 DOI: 10.1073/pnas.1502182112] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Physiological processes rely on the regulation of total mRNA levels in a cell. In diploid organisms, the transcriptional activation of one or both alleles of a gene may involve trans-allelic interactions that provide a tight spatial and temporal level of gene expression regulation. The mechanisms underlying such interactions still remain poorly understood. Here, we demonstrate that lipopolysaccharide stimulation of murine macrophages rapidly resulted in the actin-mediated and transient homologous spatial proximity of Tnfα alleles, which was necessary for the mono- to biallelic switch in gene expression. We identified two new complementary long noncoding RNAs transcribed from the TNFα locus and showed that their knockdown had opposite effects in Tnfα spatial proximity and allelic expression. Moreover, the observed spatial proximity of Tnfα alleles depended on pyruvate kinase muscle isoform 2 (PKM2) and T-helper-inducing POZ-Krüppel-like factor (ThPOK). This study suggests a role for lncRNAs in the regulation of somatic homologous spatial proximity and allelic expression control necessary for fine-tuning mammalian immune responses.
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Affiliation(s)
- Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, GR70013 Heraklion, Greece; Department of Biology, University of Crete, GR70013 Heraklion, Greece
| | - Manouela Kapsetaki
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, GR70013 Heraklion, Greece
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, GR70013 Heraklion, Greece
| | - Terrence Town
- Department of Physiology and Biophysics, Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089; and
| | - Richard A Flavell
- Department of Immunobiology and Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520
| | - Charalampos G Spilianakis
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, GR70013 Heraklion, Greece; Department of Biology, University of Crete, GR70013 Heraklion, Greece;
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Krueger C, King MR, Krueger F, Branco MR, Osborne CS, Niakan KK, Higgins MJ, Reik W. Pairing of homologous regions in the mouse genome is associated with transcription but not imprinting status. PLoS One 2012; 7:e38983. [PMID: 22802932 PMCID: PMC3389011 DOI: 10.1371/journal.pone.0038983] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 05/17/2012] [Indexed: 01/09/2023] Open
Abstract
Although somatic homologous pairing is common in Drosophila it is not generally observed in mammalian cells. However, a number of regions have recently been shown to come into close proximity with their homologous allele, and it has been proposed that pairing might be involved in the establishment or maintenance of monoallelic expression. Here, we investigate the pairing properties of various imprinted and non-imprinted regions in mouse tissues and ES cells. We find by allele-specific 4C-Seq and DNA FISH that the Kcnq1 imprinted region displays frequent pairing but that this is not dependent on monoallelic expression. We demonstrate that pairing involves larger chromosomal regions and that the two chromosome territories come close together. Frequent pairing is not associated with imprinted status or DNA repair, but is influenced by chromosomal location and transcription. We propose that homologous pairing is not exclusive to specialised regions or specific functional events, and speculate that it provides the cell with the opportunity of trans-allelic effects on gene regulation.
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Affiliation(s)
- Christel Krueger
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- * E-mail: (CK); (WR)
| | - Michelle R. King
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Miguel R. Branco
- Genome Function Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, London, United Kingdom
| | - Cameron S. Osborne
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Kathy K. Niakan
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- Anne McLaren Laboratory for Regenerative Medicine, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Michael J. Higgins
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (CK); (WR)
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Abstract
The rDNA genes are transcribed by RNA polymerase I to make structural RNAs for ribosomes. Hundreds of rDNA genes are typically arranged in an array that spans megabase pairs of DNA. These arrays are the major sites of transcription in growing cells, accounting for as much as 50% of RNA synthesis. The repetitive rDNA arrays are thought to use heterochromatic gene silencing as a mechanism for metabolic regulation, since repeated sequences nucleate heterochromatin formation in eukaryotes. Drosophila melanogaster carries an rDNA array on the X chromosome and on the Y chromosome, and genetic analysis has suggested that both are transcribed. However, using a chromatin-marking assay, we find that the entire X chromosome rDNA array is normally silenced in D. melanogaster males, while the Y chromosome rDNA array is dominant and expressed. This resembles "nucleolar dominance," a phenomenon that occurs in interspecific hybrids where an rDNA array from one parental species is silenced, and that from the other parent is preferentially transcribed. Interspecies nucleolar dominance is thought to result from incompatibilities between species-specific transcription factors and the rDNA promoters in the hybrid, but our results show that nucleolar dominance is a normal feature of rDNA regulation. Nucleolar dominance within D. melanogaster is only partially dependent on known components of heterochromatic gene silencing, implying that a distinctive chromatin regulatory system may act at rDNA genes. Finally, we isolate variant Y chromosomes that allow X chromosome array expression and suggest that the large-scale organization of rDNA arrays contribute to nucleolar dominance. This is the first example of allelic inactivation in D. melanogaster.
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Yang C, Wu J, Zheng YG. Function of the active site lysine autoacetylation in Tip60 catalysis. PLoS One 2012; 7:e32886. [PMID: 22470428 PMCID: PMC3314657 DOI: 10.1371/journal.pone.0032886] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 02/01/2012] [Indexed: 01/01/2023] Open
Abstract
The 60-kDa HIV-Tat interactive protein (Tip60) is a key member of the MYST family of histone acetyltransferases (HATs) that plays critical roles in multiple cellular processes. We report here that Tip60 undergoes autoacetylation at several lysine residues, including a key lysine residue (i.e. Lys-327) in the active site of the MYST domain. The mutation of K327 to arginine led to loss of both the autoacetylation activity and the cognate HAT activity. Interestingly, deacetylated Tip60 still kept a substantial degree of HAT activity. We also investigated the effect of cysteine 369 and glutamate 403 in Tip60 autoacetylation in order to understand the molecular pathway of the autoacetylation at K327. Together, we conclude that the acetylation of K327 which is located in the active site of Tip60 regulates but is not obligatory for the catalytic activity of Tip60. Since acetylation at this key residue appears to be evolutionarily conserved amongst all MYST proteins, our findings provide an interesting insight into the regulatory mechanism of MYST activities.
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Affiliation(s)
| | | | - Y. George Zheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia, United States of America
- * E-mail:
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Lee JT. Gracefully ageing at 50, X-chromosome inactivation becomes a paradigm for RNA and chromatin control. Nat Rev Mol Cell Biol 2011; 12:815-26. [DOI: 10.1038/nrm3231] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Shoemaker R, Wang W, Zhang K. Mediators and dynamics of DNA methylation. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 3:281-98. [PMID: 20878927 DOI: 10.1002/wsbm.124] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As an inherited epigenetic marker occurring mainly on cytosines at CpG dinucleotides, DNA methylation occurs across many higher eukaryotic organisms. Looking at methylation patterns genome-wide classifies cell types uniquely and in several cases discriminates between healthy and cancerous cell types. DNA methylation can occur allele-specifically, which allows the cellular regulatory machinery to recognize each allele separately. Although only a small number of allele specifically methylated (ASM) regions are known, genome-wide experiments show that ASM is prevalent throughout the human genome. These DNA methylation patterns can be modified via DNA demethylation, which is important for induced pluripotent stem reprogramming and primordial germ cells. Recent evidence shows that the protein activation-induced cytidine deaminase plays a critical role in these demethylation events. Many transcription factors mediate DNA methylation patterns. Some transcription factors bind specifically to methylated or unmethylated sequences and other transcription factors protect genomic regions (e.g., promoter regions) from nearby DNA methylation encroachment. Possibly acting as another epigenetic regulatory layer, methylated cytosines are also converted to 5-hydroxyethylcyotines, which is a new modification type whose biological significance has yet been defined.
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Affiliation(s)
- Robert Shoemaker
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, USA
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12
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Abstract
The X-linked region now known as the "X-inactivation center" (Xic) was once dominated by protein-coding genes but, with the rise of Eutherian mammals some 150-200 million years ago, became infiltrated by genes that produce long noncoding RNA (ncRNA). Some of the noncoding genes have been shown to play crucial roles during X-chromosome inactivation (XCI), including the targeting of chromatin modifiers to the X. The rapid establishment of ncRNA hints at a possible preference for long transcripts in some aspects of epigenetic regulation. This article discusses the role of RNA in XCI and considers the advantages RNA offers in delivering allelic, cis-limited, and locus-specific control. Unlike proteins and small RNAs, long ncRNAs are tethered to the site of transcription and effectively tag the allele of origin. Furthermore, long ncRNAs are drawn from larger sequence space than proteins and can mark a unique region in a complex genome. Thus, like their small RNA cousins, long ncRNAs may emerge as versatile and powerful regulators of the epigenome.
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Abstract
Transcriptome studies are revealing that the eukaryotic genome actively transcribes a diverse repertoire of large noncoding RNAs (ncRNAs), many of which are unannotated and distinct from the small RNAs that have garnered much attention in recent years. Why are they so pervasive, and do they have a function? X-chromosome inactivation (XCI) is a classic epigenetic phenomenon associated with many large ncRNAs. Here, I provide a perspective on how XCI is achieved in mice and suggest how this knowledge can be applied to the rest of the genome. Emerging data indicate that long ncRNAs can function as guides and tethers, and may be the molecules of choice for epigenetic regulation: First, unlike proteins and small RNAs, large ncRNAs remain tethered to the site of transcription, and can therefore uniquely direct allelic regulation. Second, ncRNAs command a much larger sequence space than proteins, and can therefore achieve very precise spatiotemporal control of development. These properties imply that long noncoding transcripts may ultimately rival small RNAs and proteins in their versatility as epigenetic regulators, particularly for locus- and allele-specific control.
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Affiliation(s)
- Jeannie T Lee
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA.
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Abstract
The development of genetic sex determination and cytologically distinct sex chromosomes leads to the potential problem of gene dosage imbalances between autosomes and sex chromosomes and also between males and females. To circumvent these imbalances, mammals have developed an elaborate system of dosage compensation that includes both upregulation and repression of the X chromosome. Recent advances have provided insights into the evolutionary history of how both the imprinted and random forms of X chromosome inactivation have come about. Furthermore, our understanding of the epigenetic switch at the X-inactivation center and the molecular aspects of chromosome-wide silencing has greatly improved recently. Here, we review various facets of the ever-expanding field of mammalian dosage compensation and discuss its evolutionary, developmental, and mechanistic components.
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Affiliation(s)
- Bernhard Payer
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
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Zheng YG, Wu J, Chen Z, Goodman M. Chemical regulation of epigenetic modifications: opportunities for new cancer therapy. Med Res Rev 2008; 28:645-87. [PMID: 18271058 DOI: 10.1002/med.20120] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Epigenetics is concerned about heritable changes in gene expression without alteration of the coding sequence. Epigenetic modification of chromatin includes methylation of genomic DNA as well as post-translational modification of chromatin-associated proteins, in particular, histones. The spectrum of histone and non-histone modifications ranges from the addition of relatively small groups such as methyl, acetyl and phosphoryl groups to the attachment of larger moieties such as poly(ADP-ribose) and small proteins ubiquitin or small ubiquitin-like modifier (SUMO). The combinatorial nature of DNA methylation and histone modifications constitutes a significant pathway of epigenetic regulation and considerably extends the information potential of the genetic code. Chromatin modification has emerged as a new fundamental mechanism for gene transcriptional activity control associated with many cellular processes like proliferation, growth, and differentiation. Also it is increasingly recognized that epigenetic modifications constitute important regulatory mechanisms for the pathogenesis of malignant transformations. We review here the recent progress in the development of chemical inhibitors/activators that target different chromatin modifying enzymes. Such potent natural or synthetic modulators can be utilized to establish the quantitative contributions of epigenetic modifications in DNA regulated pathways including transcription, replication, recombination and repair, as well as provide leads for developing new cancer therapeutics.
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Affiliation(s)
- Yujun George Zheng
- Department of Chemistry, Georgia State University, PO Box 4098, Atlanta, Georgia 30302-4098, USA.
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Abstract
Epigenetics are defined, in broad-terms, as alterations in gene expression without changes in DNA sequence. While histone modifications and DNA methylation are two classical means to regulate gene expression, miRNA has also recently been documented to govern gene expression in normal as well as cancer cells. In this review, we will first describe briefly histone modifications, DNA methylation and miRNAs and the functions of these epigenetic marks during different cellular processes involving DNA metabolism. We will then highlight some epigenetic changes in glioblastomas, a malignant form of brain tumor, and potential application of epigenetic means for diagnosis, prognosis, and treatment of gliomas. We expect that novel therapies will be developed to counter epigenetic changes in this deadly disease.
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Affiliation(s)
- Rebecca Burgess
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
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Chookajorn T, Ponsuwanna P, Cui L. Mutually exclusive var gene expression in the malaria parasite: multiple layers of regulation. Trends Parasitol 2008; 24:455-61. [PMID: 18771955 DOI: 10.1016/j.pt.2008.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 07/15/2008] [Accepted: 07/16/2008] [Indexed: 02/05/2023]
Abstract
As a major factor in Plasmodium falciparum malaria pathogenesis, the var gene family has been the focus of extensive research, which has contributed to our current understanding of Plasmodium antigenic variation. In recent years, sophisticated molecular tools have enabled the generation of interesting data regarding the regulation of mutually exclusive var expression. Although their results are still inconclusive, these studies have demonstrated the existence of multiple layers of control over gene activation, silencing, memory and 'counting'. This review attempts to summarize recent findings and dissect the different layers of var regulation.
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Affiliation(s)
- Thanat Chookajorn
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
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18
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Developmental and epigenetic regulation of the human TLR3 gene. Mol Immunol 2008; 46:27-36. [PMID: 18715647 DOI: 10.1016/j.molimm.2008.06.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Revised: 06/17/2008] [Accepted: 06/19/2008] [Indexed: 02/02/2023]
Abstract
The receptor encoded by the human TLR3 gene recognizes double-strand RNAs (dsRNAs) associated with viral infection. TLR3 expression is strongly activated upon differentiation of monocytes to dendritic cells, and can be further stimulated by the dsRNA analog polyinosine:polycytosine (PI:C). We report evidence for developmental regulation of the TLR3 gene. In dendritic cells derived from cord blood, both differentiation- and PI:C-associated TLR3 transcriptional activation are impaired as compared to cells from adults. Consistent with relative expression patterns, chromatin states and remodeling differ between newborn and adult samples. TLR3 expression in newborn dendritic cells exhibits heterocellularity and allelic imbalance (skewing), features characteristic of cis-acting epigenetic control. These findings reveal a new source for variability in innate immune system function and provide a model for further study of perinatal epigenetic transitions during development.
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Angelopoulou R, Lavranos G, Manolakou P. Regulatory RNAs and chromatin modification in dosage compensation: a continuous path from flies to humans? Reprod Biol Endocrinol 2008; 6:12. [PMID: 18355403 PMCID: PMC2324084 DOI: 10.1186/1477-7827-6-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 03/20/2008] [Indexed: 11/20/2022] Open
Abstract
Chromosomal sex determination is a widely distributed strategy in nature. In the most classic scenario, one sex is characterized by a homologue pair of sex chromosomes, while the other includes two morphologically and functionally distinct gonosomes. In mammalian diploid cells, the female is characterized by the presence of two identical X chromosomes, while the male features an XY pair, with the Y bearing the major genetic determinant of sex, i.e. the SRY gene. In other species, such as the fruitfly, sex is determined by the ratio of autosomes to X chromosomes. Regardless of the exact mechanism, however, all these animals would exhibit a sex-specific gene expression inequality, due to the different number of X chromosomes, a phenomenon inhibited by a series of genetic and epigenetic regulatory events described as "dosage compensation". Since adequate available data is currently restricted to worms, flies and mammals, while for other groups of animals, such as reptiles, fish and birds it is very limited, it is not yet clear whether this is an evolutionary conserved mechanism. However certain striking similarities have already been observed among evolutionary distant species, such as Drosophila melanogaster and Mus musculus. These mainly refer to a) the need for a counting mechanism, to determine the chromosomal content of the cell, i.e. the ratio of autosomes to gonosomes (a process well understood in flies, but still hypothesized in mammals), b) the implication of non-translated, sex-specific, regulatory RNAs (roX and Xist, respectively) as key elements in this process and the location of similar mediators in the Z chromosome of chicken c) the inclusion of a chromatin modification epigenetic final step, which ensures that gene expression remains stably regulated throughout the affected area of the gonosome. This review summarizes these points and proposes a possible role for comparative genetics, as they seem to constitute proof of maintained cell economy (by using the same basic regulatory elements in various different scenarios) throughout numerous centuries of evolutionary history.
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Affiliation(s)
- Roxani Angelopoulou
- Department of Histology-Embryology, Medical School, Athens University, Greece
| | - Giagkos Lavranos
- Department of Histology-Embryology, Medical School, Athens University, Greece
| | - Panagiota Manolakou
- Department of Histology-Embryology, Medical School, Athens University, Greece
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20
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Wutz A, Gribnau J. X inactivation Xplained. Curr Opin Genet Dev 2007; 17:387-93. [PMID: 17869504 DOI: 10.1016/j.gde.2007.08.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 08/01/2007] [Accepted: 08/02/2007] [Indexed: 11/21/2022]
Abstract
Random inactivation of one of the two female X chromosomes establishes dosage compensation between XY males and XX females in placental mammals. X inactivation is controlled by the X inactivation center (Xic). Recent advances in genome sequencing show that the Xic has evolved from an ancestral vertebrate gene cluster in placental mammals and has undergone separate rearrangements in marsupials. The Xic ensures that all but one X chromosome per diploid genome are inactivated. Which chromosome remains active is randomly chosen. Pairing of Xic loci on the two X chromosomes and alternate states of the X chromosomes before inactivation have recently been implicated in the mechanism of random choice. Chromosome-wide silencing is then initiated by the noncoding Xist RNA, which evolved with the mammalian Xic and covers the inactive X chromosome.
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Affiliation(s)
- Anton Wutz
- Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria.
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