Nuclear Architecture Disruption During Aging Causes Misexpression of Genes Lacking CpG Islands

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.

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

Innovation in Aging ◽

10.1093/geroni/igz038.756 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

pp. S208-S208

Author(s):

Samuel Beck ◽

Junyeong Lee

Keyword(s):

Large Scale ◽

Cpg Island ◽

Expression Patterns ◽

Cpg Islands ◽

Nuclear Lamina ◽

The Body ◽

Chromatin Architecture ◽

Age Related ◽

Dna Elements ◽

Computational Analyses

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.

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Nuclear envelope defects cause stem cell dysfunction in premature-aging mice

The Journal of Cell Biology ◽

10.1083/jcb.200801096 ◽

2008 ◽

Vol 181 (1) ◽

pp. 27-35 ◽

Cited By ~ 114

Author(s):

Jesús Espada ◽

Ignacio Varela ◽

Ignacio Flores ◽

Alejandro P. Ugalde ◽

Juan Cadiñanos ◽

...

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Nuclear Envelope ◽

Nuclear Architecture ◽

Nuclear Lamina ◽

Premature Aging ◽

Molecular Signaling ◽

Cell Dysfunction ◽

Age Related ◽

Microphthalmia Transcription Factor

Nuclear lamina alterations occur in physiological aging and in premature aging syndromes. Because aging is also associated with abnormal stem cell homeostasis, we hypothesize that nuclear envelope alterations could have an important impact on stem cell compartments. To evaluate this hypothesis, we examined the number and functional competence of stem cells in Zmpste24-null progeroid mice, which exhibit nuclear lamina defects. We show that Zmpste24 deficiency causes an alteration in the number and proliferative capacity of epidermal stem cells. These changes are associated with an aberrant nuclear architecture of bulge cells and an increase in apoptosis of their supporting cells in the hair bulb region. These alterations are rescued in Zmpste24−/−Lmna+/− mutant mice, which do not manifest progeroid symptoms. We also report that molecular signaling pathways implicated in the regulation of stem cell behavior, such as Wnt and microphthalmia transcription factor, are altered in Zmpste24−/− mice. These findings establish a link between age-related nuclear envelope defects and stem cell dysfunction.

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Abstract 15352: Age-associated Nuclear Remodeling May Contribute to Cardiac Dysfunction

Circulation ◽

10.1161/circ.142.suppl_3.15352 ◽

2020 ◽

Vol 142 (Suppl_3) ◽

Author(s):

Natalie J Kirkland ◽

James D Hocker ◽

Sebastian Preissl ◽

Bing Ren ◽

Rolf Bodmer ◽

...

Keyword(s):

Cardiac Dysfunction ◽

Nuclear Architecture ◽

Nuclear Lamina ◽

Tissue Level ◽

Chromatin Accessibility ◽

Premature Aging ◽

Proper Function ◽

Nuclear Lamins ◽

Age Related ◽

Level Function

Introduction: Cardiac performance depends on proper function of the extracellular matrix, cytoskeleton and nucleus to regulate systolic contraction and diastolic relaxation. As we age, the mechanical properties of these structures change, but their influence on tissue-level function is unclear. Nuclear Lamins (Lam), intermediate filaments that underly the nuclear envelope, change in expression and localization with age, leading to irregularly shaped nuclei. Mutations in LamA/C can cause premature aging and cardiomyopathy but whether Lamin changes with age contribute to cardiac dysfunction is unknown. Hence, we hypothesize that age-associated LamA/C reduction remodels nuclear shape, force propagation, and gene accessibility to reduce cardiac function. Methods: We profiled nuclear morphology and protein expression in hearts from two wildtype Drosophila melanogaster strains for up to 5 weeks, when median survival is less than 50%. We performed live imaging to assess heart performance in wildtype flies and flies with Lamin knock-down using the Gal4-UAS system. To profile chromatin accessibility changes we use an ATAC-seq protocol that we optimized for frozen heart nuclei. Results: Cardiomyocyte nuclei become smaller and more circular with age in contrast to skeletal nuclei across w 1118 and yw wildtype fly strains. Expression of both LamB and LamC ( Drosophila LamA/C) decrease with age and differentially regulate nucleus size and circularity. LamC knockdown, but not LamB, induces contractile dysfunction, measured by fractional shortening, at 1-week, and shortens lifespan. LamB and LamC knockdown also mimicked DNA decondensation observed in aged wildtype flies, suggesting that reduced DNA packaging could result from fewer contacts with the nuclear lamina. Thus, we developed a novel ATAC-seq pipeline that will identify how age-related nuclear architecture may influence the epigenome and contribute to pathogenic heart remodeling. Conclusions: Cardiomyocyte nuclei decrease in size and increase in circularity upon aging as a result of diminished Lamin expression. Loss of Lamin expression induces cardiac dysfunction. Our future work aims to elucidate the mechanism by which nuclear aging contributes to age-related cardiac dysfunction.

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Meta-analysis of genome-wide DNA methylation and integrative OMICs in human skeletal muscle

10.1101/2020.09.28.315838 ◽

2020 ◽

Author(s):

S Voisin ◽

M Jacques ◽

S Landen ◽

NR Harvey ◽

LM Haupt ◽

...

Keyword(s):

Skeletal Muscle ◽

Dna Methylation ◽

Large Scale ◽

Human Skeletal Muscle ◽

Meta Analysis ◽

Total N ◽

Age Related ◽

Differentially Methylated Genes ◽

Comprehensive Picture ◽

User Friendly

AbstractKnowledge of age-related DNA methylation changes in skeletal muscle is limited, yet this tissue is severely affected by aging in humans. Using a large-scale epigenome-wide association study (EWAS) meta-analysis of age in human skeletal muscle from 10 studies (total n = 908 human muscle methylomes), we identified 9,986 differentially methylated regions at a stringent false discovery rate < 0.005, spanning 8,748 unique genes, many of which related to skeletal muscle structure and development. We then integrated the DNA methylation results with known transcriptomic and proteomic age-related changes in skeletal muscle, and found that even though most differentially methylated genes are not altered at the mRNA or protein level, they are nonetheless strongly enriched for genes showing age-related differential expression. We provide here the most comprehensive picture of DNA methylation aging in human skeletal muscle, and have made our results available as an open-access, user-friendly, web-based tool called MetaMeth (https://sarah-voisin.shinyapps.io/MetaMeth/).

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Cortical Thickness Trajectories across the Lifespan: Data from 17,075 healthy individuals aged 3-90 years

10.1101/2020.05.05.077834 ◽

2020 ◽

Cited By ~ 2

Author(s):

Sophia Frangou ◽

Amirhossein Modabbernia ◽

Gaelle E Doucet ◽

Efstathios Papachristou ◽

Steven CR Williams ◽

...

Keyword(s):

Cortical Thickness ◽

Large Scale ◽

Meta Analysis ◽

General Pattern ◽

Individual Variability ◽

Anterior Cingulate ◽

Healthy Individuals ◽

Large Scale Analysis ◽

Age Related ◽

Steep Decrease

AbstractDelineating age-related cortical trajectories in healthy individuals is critical given the association of cortical thickness with cognition and behaviour. Previous research has shown that deriving robust estimates of age-related brain morphometric changes requires large-scale studies. In response, we conducted a large-scale analysis of cortical thickness in 17,075 individuals aged 3-90 years by pooling data through the Lifespan Working group of the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) Consortium. We used fractional polynomial (FP) regression to characterize age-related trajectories in cortical thickness, and we computed normalized growth centiles using the parametric Lambda, Mu, and Sigma (LMS) method. Inter-individual variability was estimated using meta-analysis and one-way analysis of variance. Overall, cortical thickness peaked in childhood and had a steep decrease during the first 2-3 decades of life; thereafter, it showed a gradual monotonic decrease which was steeper in men than in women particularly in middle-life. Notable exceptions to this general pattern were entorhinal, temporopolar and anterior cingulate cortices. Inter-individual variability was largest in temporal and frontal regions across the lifespan. Age and its FP combinations explained up to 59% variance in cortical thickness. These results reconcile uncertainties about age-related trajectories of cortical thickness; the centile values provide estimates of normative variance in cortical thickness, and may assist in detecting abnormal deviations in cortical thickness, and associated behavioural, cognitive and clinical outcomes.

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HiPLA: High-throughput imaging Proximity Ligation Assay

10.1101/371062 ◽

2018 ◽

Author(s):

Leonid A. Serebryannyy ◽

Tom Misteli

Keyword(s):

High Throughput ◽

Protein Interactions ◽

Large Scale ◽

Protein Complexes ◽

Nuclear Lamina ◽

Cellular Protein ◽

Premature Aging ◽

Proximity Ligation Assay ◽

Proximity Ligation ◽

High Throughput Imaging

AbstractProtein-protein interactions are essential for cellular structure and function. To delineate how the intricate assembly of protein interactions contribute to cellular processes in health and disease, new methodologies that are both highly sensitive and can be applied at large scale are needed. Here, we develop HiPLA (high-throughput imaging proximity ligation assay), a method that employs the antibody-based proximity ligation assay in a high-throughput imaging screening format to systematically probe protein interactomes. Using HiPLA, we probe the interaction of 60 proteins and associated PTMs with the nuclear lamina in a model of the premature aging disorder Hutchinson-Gilford progeria syndrome (HGPS). We identify a subset of proteins that differentially interact with the nuclear lamina in HGPS. In combination with quantitative indirect immunofluorescence, we find that the majority of differential interactions were accompanied by corresponding changes in expression of the interacting protein. Taken together, HiPLA offers a novel approach to probe cellular protein-protein interaction at a large scale and reveals mechanistic insights into the assembly of protein complexes.

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Meta-Analysis of Grainyhead-Like Dependent Transcriptional Networks: A Roadmap for Identifying Novel Conserved Genetic Pathways

Genes ◽

10.3390/genes10110876 ◽

2019 ◽

Vol 10 (11) ◽

pp. 876

Author(s):

Mathiyalagan ◽

Miles ◽

Anderson ◽

Wilanowski ◽

Grills ◽

...

Keyword(s):

Transcription Factors ◽

Large Scale ◽

Target Genes ◽

Meta Analysis ◽

Genetic Disorder ◽

Neural Tube Closure ◽

Transcriptional Networks ◽

Zebrafish Model ◽

Age Related ◽

Epithelial Development

: The Drosophila grainyhead (grh) and vertebrate Grainyhead-like (Grhl) transcription factors are among the most critical genes for epithelial development, maintenance and homeostasis, and are remarkably well conserved from fungi to humans. Mutations affecting grh/Grhl function lead to a myriad of developmental and adult onset epithelial disease, such as aberrant skin barrier formation, facial/palatal clefting, impaired neural tube closure, age-related hearing loss, ectodermal dysplasia, and importantly, cancers of epithelial origin. Recently, mutations in the family member GRHL3 have been shown to lead to both syndromic and non-syndromic facial and palatal clefting in humans, particularly the genetic disorder Van Der Woude Syndrome (VWS), as well as spina bifida, whereas mutations in mammalian Grhl2 lead to exencephaly and facial clefting. As transcription factors, Grhl proteins bind to and activate (or repress) a substantial number of target genes that regulate and drive a cascade of transcriptional networks. A multitude of large-scale datasets have been generated to explore the grh/Grhl-dependent transcriptome, following ablation or mis-regulation of grh/Grhl-function. Here, we have performed a meta-analysis of all 41 currently published grh and Grhl RNA-SEQ, and microarray datasets, in order to identify and characterise the transcriptional networks controlled by grh/Grhl genes across disparate biological contexts. Moreover, we have also cross-referenced our results with published ChIP and ChIP-SEQ datasets, in order to determine which of the critical effector genes are likely to be direct grh/Grhl targets, based on genomic occupancy by grh/Grhl genes. Lastly, to interrogate the predictive strength of our approach, we experimentally validated the expression of the top 10 candidate grhl target genes in epithelial development, in a zebrafish model lacking grhl3, and found that orthologues of seven of these (cldn23, ppl, prom2, ocln, slc6a19, aldh1a3, and sod3) were significantly down-regulated at 48 hours post-fertilisation. Therefore, our study provides a strong predictive resource for the identification of putative grh/grhl effector target genes.

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Epigenetic aging of classical monocytes from healthy individuals

10.1101/2020.05.10.087023 ◽

2020 ◽

Author(s):

Irina Shchukina ◽

Juhi Bagaitkar ◽

Oleg Shpynov ◽

Ekaterina Loginicheva ◽

Sofia Porter ◽

...

Keyword(s):

Dna Methylation ◽

Large Scale ◽

Healthy Aging ◽

Cpg Islands ◽

Blood Protein ◽

Older Individuals ◽

Total Blood ◽

Age Related ◽

The Impact ◽

Classical Monocytes

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.

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Comprehensive characterization of neutrophil genome topology

10.1101/100198 ◽

2017 ◽

Author(s):

Yina Zhu ◽

Ke Gong ◽

Matthew Denholtz ◽

Vivek Chandra ◽

Mark P. Kamps ◽

...

Keyword(s):

Large Scale ◽

Nuclear Architecture ◽

Nuclear Lamina ◽

Population Based ◽

Receptor Expression ◽

Lamin B ◽

Topologically Associating Domains ◽

Lamin B Receptor ◽

Genomic Regions ◽

Neutrophil Differentiation

Neutrophils are responsible for the first line of defense against invading pathogens. Their nuclei are uniquely structured as multiple lobes that establish a highly constrained nuclear environment. Here we found that neutrophil differentiation was not associated with large-scale changes in the number and sizes of topologically associating domains. However, neutrophil genomes were enriched for long-range genomic interactions that spanned multiple topologically associating domains. Population-based simulation of spherical and toroid genomes revealed declining radii of gyration for neutrophil chromosomes. We found that neutrophil genomes were highly enriched for heterochromatic genomic interactions across vast genomic distances, a process named super-contraction. Super-contraction involved genomic regions located in the heterochromatic compartment in both progenitors and neutrophils or genomic regions that switched from the euchromatic to the heterochromatic compartment during neutrophil differentiation. Super-contraction was accompanied by the repositioning of centromeres, pericentromeres and Long-Interspersed Nuclear Elements (LINEs) to the neutrophil nuclear lamina. We found that Lamin-B Receptor expression was required to attach centromeric and pericentromeric repeats but not LINE-1 elements to the lamina. Differentiating neutrophils also repositioned ribosomal DNA and mini-nucleoli to the lamina: a process that was closely associated with sharply reduced ribosomal RNA expression. We propose that large-scale chromatin reorganization involving super-contraction and recruitment of heterochromatin and nucleoli to the nuclear lamina facilitate the folding of the neutrophil genome into a confined geometry imposed by a multi–lobed nuclear architecture.

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