scholarly journals DISRUPTION OF CPG ISLAND-MEDIATED CHROMATIN ARCHITECTURE AND TRANSCRIPTIONAL HOMEOSTASIS DURING AGING

2019 ◽  
Vol 3 (Supplement_1) ◽  
pp. S208-S208
Author(s):  
Samuel Beck ◽  
Junyeong Lee

Abstract Aging causes the global disorganization of nuclear chromatin architecture. In a normal young nucleus, silent heterochromatin is associated with the nuclear lamina layer underlying nuclear envelope, thus spatially separated from euchromatin at the nuclear center. Notably, aging causes the disruption of nuclear lamina and the decondensation of associated heterochromatin. However, it is not clearly understood how these changes of chromatin architectures contribute to age-related diseases. Through large-scale computational analyses, we present that CpG islands (CGIs) give important clues to answering this question. CGIs are DNA elements with high Cytosine-phosphate-Guanine dinucleotide frequencies. In human, about 60% of total genes contain CGIs at their promoters (CGI+ genes) and are broadly expressed throughout the body. The other 40% of genes that do not have CGIs (CGI- genes) exhibit tissue-restricted expression patterns. Our results demonstrate that, in normal young nuclei, only CGI- genes can reside within lamina-associated heterochromatin when transcriptionally inactive, while CGI+ genes associate with nuclear central euchromatin even when they are repressed. In parallel, we show that age-associated heterochromatin decondensation can specifically de-repress tissue-specific CGI- genes leading to their uncontrolled expressions. Our results further demonstrate that global misregulation of CGI- genes increases the noise in gene transcription that, in turn, causes the loss of cellular identities during aging. Taken together, our study establishes critical implication of CGI-mediated chromatin architecture in age-associated degenerative changes and loss of tissue homeostasis.

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. 676-677
Author(s):  
Jun-Yeong Lee ◽  
Ian Davis ◽  
Samuel Beck

Abstract Global disorganization of chromatin architecture, characterized by disrupted nuclear lamina and associated heterochromatin, is commonly observed in various aging contexts, including premature aging diseases, cellular senescence, and normative aging. Although these conserved structural changes have been reported for over two decades, their impact on transcription and contribution to age-related degenerative changes remain unclear. Here we show that genes not associated with CpG islands (CGI- genes), which form heterochromatin when transcriptionally silent, are globally misexpressed in aged nuclei with disrupted chromatin architectures. Our data also show that CGI- gene misexpression is a direct outcome of nuclear architecture disruption. Notably, CGI- gene misexpression explains the molecular basis of various defects observed during aging, including loss of cellular identity and increased noises in transcription. We also show that uncontrolled secretory phenotypes commonly observed during aging are largely attributable to CGI- gene misexpression, which drives disruption of intercellular communication and fuel chronic inflammation in aged tissues. Our large-scale meta-analysis further demonstrates that CGI- gene misexpression is a common feature of mammalian aging and age-associated diseases. Interestingly, CGI- gene misexpression can be suppressed by anti-aging interventions. Our study suggests that age-associated CGI- gene misexpression is a novel biomarker of physiological aging which offers an effective therapeutic target for delaying or ameliorating degenerative changes associated with aging.


2001 ◽  
Vol 11 (5) ◽  
pp. 677-684
Author(s):  
Yutaka Suzuki ◽  
Tatsuhiko Tsunoda ◽  
Jun Sese ◽  
Hirotoshi Taira ◽  
Junko Mizushima-Sugano ◽  
...  

To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumes of genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the “oligo-capping” method. We aligned the mRNA start sites with the genomic sequences and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences were searched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) contained TATA boxes, 872 (85%) contained initiators, 999 (97%) contained GC box, and 663 (64%) contained CAAT box. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced in TATA+/Inr+PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRA gene, and theTM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs.[The nucleotide sequences described in this paper have been deposited in the DDBJ, EMBL, and GenBank data libraries under accession nos.AU098358–AU100608.]


Author(s):  
Yener N. Yeni ◽  
Roger R. Zauel

Cortical bone tissue quality is imperative in maintaining the mechanical competence of whole bones, particularly at sites of overuse and age-related fragility fractures where a considerable cortical bone component is present. (Note that cortical bone tissue is more than 80% of the bone in the body [1].)


2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Xin Du ◽  
Leng Han ◽  
An-Yuan Guo ◽  
Zhongming Zhao

CpG islands are typically located in the 5′end of genes and considered as gene markers because they play important roles in gene regulation via epigenetic change. In this study, we compared the features of CpG islands identified by several major algorithms by setting the parameter cutoff values in order to obtain a similar number of CpG islands in a genome. This approach allows us to systematically compare the methylation and gene expression patterns in the identified CpG islands. We found that Takai and Jones’ algorithm tends to identify longer CpG islands but with weaker CpG island features (e.g., lower GC content and lower ratio of the observed over expected CpGs) and higher methylation level. Conversely, the CpG clusters identified by Hackenberg et al.’s algorithm using stringent criteria are shorter and have stronger features and lower methylation level. In addition, we used the genome-wide base-resolution methylation profile in two cell lines to show that genes with a lower methylation level at the promoter-associated CpG islands tend to express in more tissues and have stronger expression. Our results validated that the DNA methylation of promoter-associated CpG islands suppresses gene expression at the genome level.


2019 ◽  
Author(s):  
Mizanur Rahman ◽  
Hunter Edwards ◽  
Nikolajs Birze ◽  
Rebecca Gabrilska ◽  
Kendra P. Rumbaugh ◽  
...  

AbstractCaenorhabditis elegans is a powerful animal model in aging research. Standard longevity assays on agar plates involve the tedious task of picking and transferring animals to prevent younger progeny from contaminating age-synchronized adult populations. Large-scale studies employ progeny-blocking drugs or sterile mutants to avoid progeny contamination, but such manipulations change adult physiology and alter the influence of reproduction on normal aging. Moreover, for some agar growth-based technology platforms, such as automated lifespan machines, reagents such as food or drugs cannot be readily added/removed after initiation of the study. Current microfluidic approaches are well-suited to address these limitations, but in their liquid-based environments animals swim rather than crawl, introducing swim-induced stress in the lifespan analysis. Here we report a simple microfluidic device that we call NemaLife that features: 1) an optimized micropillar arena in which animals can crawl, 2) sieve channels that separate progeny and prevent the loss of adults from the arena during culture maintenance, and 3) ports which allow rapid accessibility to feed the adult-only population and introduce reagents as needed. Culture maintenance and liquid manipulation are performed with simple hand-held syringes to facilitate integration of our technology into general laboratory protocols. Additionally, device geometry and feeding protocols were designed to emulate the body gait, locomotion, and lifespan of animals reared on agar. We validated our approach with longevity analyses of classical aging mutants (daf-2, age-1, eat-2, and daf-16) and animals subjected to RNAi knockdown of age-related genes (age-1 and daf-16). We also showed that healthspan measures such as pharyngeal pumping and tap-induced stimulated reversals can be scored across the lifespan. Overall, the capacity to generate reliable lifespan and physiological data from the NemaLife chip underscores the potential of this device to accelerate healthspan and lifespan investigations in C. elegans.


2000 ◽  
Vol 113 (22) ◽  
pp. 3887-3888
Author(s):  
B. Malfoy

Current Topics in Microbiology and Immunology. Vol. 249: DNA Methylation and Cancer edited by P. A. Jones and P. K. Vogt Springer-Verlag (2000) pp. 170. ISBN 3–540-66608-7 75.50/$129.00 After a long period of relative confidentiality, the DNA methylation field has become a major research domain over the last few years. In this context, the importance of DNA methylation in human cancer has only become apparent over the last 5 to10 years. This small book (9 articles) provides a comprehensive overview of the main data and, more interestingly, presents the new concepts emerging from the recent extensive work, essentially performed over 2–3 years. The article written by B. Hendrich and A. Bird gives an overview of our current knowledge about the proteins implicated in DNA methylation, including DNA-methyltransferases and methylated-DNA-binding-proteins. It should be noted that the discovery of several of these proteins is a direct consequence of the human genome sequencing program, since they were first found ‘in silico’ by searching the databases. The specific properties of each of these partners of DNA methylation are beginning to be identified. Their implication in the regulation of histone acetylation suggests some possible mechanisms for regulation of gene expression. These models take into account, in particular, the remodeling of the chromatin structure. The value of mouse models in the understanding of the role of these proteins is discussed by P. W. Laird in another article. The present limitations of these approaches, essentially due to the non-viability of homozygous mutant mice for the main DNA-methyltransferase (Dnmt1) could be passed in the near future by the generation of conditional knockouts. Three articles by J. G. Herman and S. B. Baylin, M. F. Chan, G. Liang and P. A. Jones and J. P. Issa focus on the role of CpG island methylation in cancer and aging. These small stretches of DNA are frequently located around the transcription-start sites of approximately half of all human genes. For virtually all of these genes, with the exception of genes of the inactive X chromosome and some imprinted genes, these regions are maintained free of methylation in normal cells regardless of whether these genes are transcribed. It has been recognized that the CpG islands of a growing number of genes, either known to be involved in carcinogenesis (p16, E-cadherin, hMLH1,.) or candidate tumor supressor genes (p15, GST-Π,.) are methylated in many types of human cancer. The implication of the hypermethylation of CpG islands in tumor progression is discussed in its various aspects. In particular, the article by Chan et al. highlights the necessity to not oversimplify the relationships between methylation/inactivation and demethylation/activation. Moreover, extending his work on cancer, J. P. Issa shows that specific genes are affected by age-related methylation (EGFR, ER,.) and that such hypermethylation has disastrous consequences for the integrity of aged tissues. The article of A. P. Feinberg covers another area in this field and discusses the role of DNA methylation in imprinting and proposes a model for a role for the of loss of imprinting in cancer. Two articles investigate the action of tumor causing agents: the exogenous carcinogens and the Epstein-Barr virus (EBV). G. P. Pfeifer, M. S. Tang and M. F. Denissenko present the now well known effect of the deamination of methylcytosine on the formation of mutations. However, they insist on the finding that cytosine methylation can increase the rates of mutation by enhancing the binding of chemical carcinogens to DNA. This mechanisms is likely to have important implications for both chemical and ultra violet light induced carcinogenesis. K. D. Robertson summarize his work on the consequences of the inactivation of EBV genes on the virus' life cycle. The use of demethylating agents, like azacytidine, for reactivation of Cp-derived antigens, which could result in specific immune recognition of the tumor, is an interesting idea; however, as analyzed by M. (ABSTRACT TRUNCATED)


2001 ◽  
Vol 15 (2) ◽  
pp. 338-348 ◽  
Author(s):  
John Newell-Price ◽  
Peter King ◽  
Adrian J. L. Clark

Abstract Ectopic secretion of ACTH, from sites such as small cell lung cancer (SCLC), results in severe Cushing’s syndrome. ACTH is cleaved from POMC. The syndrome may occur when the highly tissue-specific promoter of the human POMC gene (POMC) is activated. The mechanism of activation is not fully understood. This promoter is embedded within a defined CpG island, and CpG islands are usually considered to be unmethylated in all tissues. We demonstrate that much of this CpG island is methylated in normal nonexpressing tissues, in contrast to somatically expressed CpG island promoters reported to date, and is specifically unmethylated in expressing tissues, tumors, and the POMC-expressing DMS-79 SCLC cell line. A narrow 100-bp region is free of methylation in all tissues. E2F factors binding to the upstream domain IV region of the promoter have been shown to be involved in the expression of POMC in SCLC. We show that these sites are methylated in normal nonexpressing tissues, which will prevent binding of E2F, but are unmethylated in expressing tissue. Methylation in vitro is sufficient for silencing of expression, which is not reversed by treatment with Trichostatin A, suggesting that inhibition of expression may be mediated by means other than recruitment of histone deacetylase activity. The DMS-79 cells lack POMC demethylating activity, implying that the methylation and expression patterns are likely to be set early or before neoplastic transformation, and that targeted de novo methylation might be a potential therapeutic strategy.


2020 ◽  
Author(s):  
Irina Shchukina ◽  
Juhi Bagaitkar ◽  
Oleg Shpynov ◽  
Ekaterina Loginicheva ◽  
Sofia Porter ◽  
...  

ABSTRACTThe impact of healthy aging on molecular programming of immune cells is poorly understood. Here, we report comprehensive characterization of healthy aging in human classical monocytes, with a focus on epigenomic, transcriptomic, and proteomic alterations, as well as the corresponding proteomic and metabolomic data for plasma, using healthy cohorts of 20 young and 20 older individuals (~27 and ~64 years old on average). For each individual, we performed eRRBS-based DNA methylation profiling, which allowed us to identify a set of age-associated differentially methylated regions (DMRs) – a novel, cell-type specific signature of aging in DNA methylome. Optimized ultra-low-input ChIP-seq (ULI-ChIP-seq) data acquisition and analysis pipelines applied to 5 chromatin marks for each individual revealed lack of large-scale age-associated changes in chromatin modifications and allowed us to link hypo- and hypermethylated DMRs to distinct chromatin modification patterns. Specifically, hypermethylation events were associated with H3K27me3 in the CpG islands near promoters of lowly-expressed genes, while hypomethylated DMRs were enriched in H3K4me1 marked regions and associated with normal pattern of expression. Furthermore, hypo- and hypermethylated DMRs followed distinct functional and genetic association patterns. Hypomethylation events were associated with age-related increase of expression of the corresponding genes, providing a link between DNA methylation and age-associated transcriptional changes in primary human cells. Furthermore, these locations were also enriched in genetic regions associated by GWAS with asthma, total blood protein, hemoglobin levels and MS. On the other side, acceleration of epigenetic age in HIV and asthma stems only from changes in hypermethylated DMRs but not from hypomethylated loci.


2020 ◽  
Author(s):  
Alireza Delfarah ◽  
DongQing Zheng ◽  
James H. Joly ◽  
Jesse Yang ◽  
Nicholas A. Graham

AbstractSenescent cells promote chronic inflammation and age-related disease through secretion of cytokines and other inflammatory proteins. As such, the development of senolytic drugs that specifically eliminate senescent cells is an area of great therapeutic promise. One limitation to the identification of senolytic drugs has been the lack of robust biomarkers that predict toxicity in senescent cells. Here, we used mass spectrometry-based proteomics to identify senescence biomarkers in primary human mammary epithelial cells (HMECs), a model system for aging. By integrating proteomic data from replicative senescence, immortalization by telomerase reactivation, and drug-induced senescence, we identified a robust HMEC proteomic signature of senescence consisting of 57 upregulated and 29 downregulated proteins. This senescence signature identified both known senescence biomarkers, including downregulation of the nuclear lamina protein lamin-B1 (LMNB1), as well as novel biomarkers such as upregulation of the β-galactoside-binding protein galectin-7 (LGALS7). Then, we integrated our proteomic signature of senescence with large-scale drug screening databases to predict that EGFR inhibitors, MEK inhibitors, and the tyrosine kinase inhibitor dasatinib are senolytic in HMEC. Experimental validation demonstrated that the EGFR inhibitors dacomitinib and sapitinib, in addition to dasatinib, induce death in senescent but not proliferating HMECs. Taken together, our results support that the combination of quantitative proteomics and public drug screening databases is a powerful approach to identify senescence biomarkers and novel senolytic compounds.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3281-3281
Author(s):  
Yongxian Hu ◽  
Yanjun Gu ◽  
Lixia Sheng ◽  
Kangni Wu ◽  
Jimin Shi ◽  
...  

Abstract Abstract 3281 Regulatory γδT cells (γδTregs) are capable of suppressing T-cell activation and proliferation (Rita et al Journal of immunology 2009). Our previous studies demonstrated the immunosuppressive features of γδTregs and further supported the use of γδTregs as a promising therapeutic strategy for the adoptive immunotherapy of allograft rejection, post-transplantation graft-versus-host disease (GVHD) and autoimmune diseases (Hu et al ASH abstract 2011). To this end, large-scale, efficient expansion of γδTregs represents a fundamentally important prerequisite for their clinical application. Here we explored the efficacy of decitabine (a DNA hypomethylating agent) for the generation of functional γδTregs and its underlying mechanisms. Human peripheral blood mononuclear cells (PBMCs) were cultured with interleukin (IL)-2, IL-15, TGF-β1 and zoledronic acid (ZOL). Decitabine was added to aliquots of PBMCs. Frequency and absolute number of γδTregs were investigated by flow cytometry (FACS) and trypan blue live-cell counts after cultivation. Our results showed a higher frequency (61.9±10.3% versus 38.4±7.8%, p<0.01) and absolute number of γδTregs [(3.1±0.1)×106 versus (5.9±0.2)×106, p<0.01] were seen in cells treated with decitabine plus ZOL/IL-2/IL-15/TGF-β1 (referred to as decitabine-induced γδTregs below) than in cell without decitabine induction (referred to as common γδTregs) as shown in Fig. 1. These data demonstrated that decitabine and ZOL/cytokines synergized to induce stable γδTregs via improved Foxp3 expression. Next we analyzed the underlying mechanisms of decitabine on γδTreg induction. Genomic DNA was isolated from γδTregs sorted by FACS. The Foxp3 gene methyaltion status of upstream enhancer CpG islands from −5995 to −5778 and from −5031 to −4792, proximal promoter CpG island from -139 to -15 and non-coding DNA sequence 3 (CNS3) CpG island from 3748 to 3971 was analyzed by bisulfite sequencing. We found decitabine-induced γδTregs displayed efficient CpG demethylation of the upstream enhancer from −5031 to −4792, and of CNS3 from 3748 to 3971, but no differences were detected in the other CpG islands investigated in contrast to common γδTregs (Fig. 2A). We subsequently investigated if DNA demethylation of CpG islands could influence upstream enhancer or CNS3 activity to promote Foxp3 transcription. The upstream enhancer from −5031 to −4792 and CNS3 from 3748 to 3971 were methylated using SssI (CpG) methylase, and methylated or unmethylated sequences were inserted into demethylated pFoxP3Pro, respectively. Vectors were added to γδT cells and electroporated using the T-023 program of the Nucleofector. Dual fluorescence-based transient reporter assays showed an obvious reduction in luciferase activity after methylation of both CpG islands, but not with the demethylated CpG islands (Fig. 2B), indicating that demethylation of the upstream enhancer and CNS3 can promote Foxp3 expression via increased enhancer activity. Transcription factors (TF) play important roles in gene expression. To test whether decitabine enhanced specific TFs expression to influence γδTreg induction, we performed TF CHIP assays in FACS-sorted common γδTregs versus decitabine-induced γδTregs. The expression levels of 245 TFs were evaluated and the result showed that NF-κb expression in decitabine-induced γδTregs was up-regulated 50 times in contrast to that in common γδTregs. NF-κb up-regulation was further comfirmed by western blot analysis from 6 different healthy volunteers. Finally, We evaluated the immunosuppressive function of the enriched γδTregs on Carboxyfluorescein Diacetate (CFSE)-labeled hPBMC proliferation and activation stimulated with anti-CD3/anti-CD28 monoclonal antibodies for 5 days in vitro. As shown in Fig. 3, both common γδTregs and decitabine-induced γδTregs exerted dose-dependent suppression of proliferation, but decitabine-induced γδTregs had a greater suppressive effect than common γδTregs. In conclusion, these data demonstrate for the first time that decitabine facilitates the generation of functional γδTregs via foxp3 gene demethylation and NF-κb up-regulation. Futhermore, our results lay the foundation for large-scale availability of induced γδTregs for potential clinical applications, and reveal novel targets for regulating Foxp3 expression in γδT cells. Disclosures: No relevant conflicts of interest to declare.


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