scholarly journals Misexpression of genes lacking CpG islands drives degenerative changes during aging

2021 ◽  
Vol 7 (51) ◽  
Author(s):  
Jun-Yeong Lee ◽  
Ian Davis ◽  
Elliot H. H. Youth ◽  
Jonghwan Kim ◽  
Gary Churchill ◽  
...  
Keyword(s):  
Cpg Islands ◽  
Degenerative Changes

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

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. 676-677
Author(s):  
Jun-Yeong Lee ◽  
Ian Davis ◽  
Samuel Beck
Keyword(s):  
Large Scale ◽  
Structural Changes ◽  
Meta Analysis ◽  
Cpg Islands ◽  
Nuclear Architecture ◽  
Nuclear Lamina ◽  
Premature Aging ◽  
Degenerative Changes ◽  
Age Related ◽  
Direct Outcome

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.

Electron Microscopic and Isozyme Study of a Case of Ochronosis

1972 ◽  
Vol 30 ◽  
pp. 88-89
Author(s):  
Jay W. Cha ◽  
Perry J. Melnick
Keyword(s):  
Benzene Ring ◽  
Enzyme System ◽  
Homogentisic Acid ◽  
Degenerative Changes ◽  
Acid Oxidase ◽  
Electron Microscopic ◽  
Tyrosine Metabolism ◽  
Collagenous Tissues

Hereditary ochronosis in very few cases has been examined electron microscopically or histochemically. In this disease homogentisic acid, a normal intermediary of tyrosine metabolism, forms in excessive amounts. This is believed to be due to absence or defective activity of homogentisic acid oxidase, an enzyme system necessary to break the benzene ring and to further break it down to fumaric and acetoacetic acids. Ochronotic pigment, a polymerized form of homogentisic acid, deposits mainly in mesenchymal tissues. There has been a question whether the pigment originates from the collagenous tissues, or deposits passively, where in contrast to melanin it induces degenerative changes.

MR-derived CT-like Images for the Assessment of Acute Vertebral Fractures and Osseous Degenerative Changes in the Thoracolumbar Spine

2020 ◽  
Author(s):  
Benedikt J. Schwaiger ◽  
Charlotte Schneider ◽  
Sophia Kronthaler ◽  
Christoph Böhm ◽  
Julian Zapf ◽  
...  
Keyword(s):  
Vertebral Fractures ◽  
Thoracolumbar Spine ◽  
Degenerative Changes

Testosterone-dependent changes in neurons of hypothalamic arcuate nucleus and reversibility of these changes by modeled male hypogonadism

2017 ◽  
pp. 21-30
Author(s):  
А.В. Дробленков ◽  
Л.Г. Прошина ◽  
Ю.Н. Юхлина ◽  
А.А. Байрамов ◽  
П.Д. Шабанов ◽  
...  
Keyword(s):  
Replacement Therapy ◽  
Nerve Cell ◽  
Arcuate Nucleus ◽  
Degenerative Changes ◽  
Control Group ◽  
Male Hypogonadism ◽  
Nissl Staining ◽  
Neuron Body ◽  
Androgen Synthesis ◽  
Reactive Changes

Актуальность. Значение недостаточности тестостерона для структурного гомеостазиса нейронов, регулирующих выработку гонадотропин-рилизинг гормона (ГнРГ) и синтезирующих данный гормон, мало изучены. Цель. Установить реактивные изменения, количество рецепторов к андрогенам (АР) и особенности их распределения в нейронах медиального аркуатного ядра гипоталамуса (МАЯ) при экспериментальном гипогонадизме, а также обратимость этих изменений после восстановительной терапии тестостероном. Методы. У самцов крыс Вистар (16 особей) моделировали гипогонадизм путем удаления одной гонады на 2-3 день постнатальной жизни и исследовали гистологические срезы каудальной части МАЯ у молодых животных (4 мес.) при отсутствии и осуществлении заместительной терапии. Контрольную группу составляли интактные самцы аналогичного возраста (8 особей). В середине левосторонней части МАЯ на площади 0,01 мм определяли реактивные изменения клеток и площадь тел малоизмененных нейронов (после окрашивания срезов методом Ниссля), а также число и долю тел нервных клеток, различавшихся по степени экспрессии АР. Результаты. Установлено, что нейроны МАЯ содержат большое количество АР, распределенных в различных частях их тела. При гипогонадизме происходит перераспределение АР и снижение степени их экспрессии (количества). Сгущение АР в области оболочки ядра и плазмолеммы, образование конгломератов в ядре и цитоплазме было характерно для нейронов с умеренной экспрессией. В цитоплазме и в области плазматической мембраны рецепторы отсутствовали у клеток со слабой и очень низкой экспрессией. Снижение степени экспрессии АР при гипогонадизме сопряжено с уменьшением площади тела и гибелью части нейронов. Заключение. Выявленные дегенеративные тестостерон-зависимые изменения нейронов МАЯ, которые синтезируют ГнРГ или пептиды, влияющие на его выработку, могут обусловить уменьшение высвобождения гонадолиберина, вторичное снижение синтеза андрогенов и реализацию морфофункциональных проявлений его вторичного дефицита. Заместительная терапия частично компенсирует дегенеративные изменения нейронов, восстанавливает интенсивность экспрессии АР, однако не влияет на процесс гибели нервных клеток. Background. Importance of testosterone deficiency for structural homeostasis of the neurons regulating production of gonadotropin-releasing hormone (GnRH) and synthesizing this hormone is insufficiently understood. Aim. To determine reactive changes, quantity of androgens receptors (AR), and features of their distribution in neurons of hypothalamic medial arcuate nucleus (MAN) in experimental hypogonadism and reversibility of these changes by restorative therapy with testosterone. Methods. Hypogonadism was modeled in 16 Wistar rats by removing one gonad on postnatal days 2-3, and histological sections of caudal MAN were examined in young, 4-month old animals with and without a replacement therapy. The control group consisted of 8 age-matched intact males. Cell reactive changes, areas of slightly changed neuron bodies (Nissl staining of sections), and the number and proportion of nerve cell bodies differing in the degree of AR expression were determined in the middle left-sided part of MAN, on an area of 0.01 mm. Results. MAN neurons contained a large quantity of AR distributed in different parts of the neuron body. In hypogonadism, AR redistributed and their expression (quantity) decreased. Condensation of AR in the region of nucleo- and plasmolemma and formation of conglomerates in the nucleus and cytoplasm were characteristic of neurons with moderate expression. In the regions of cytoplasm and plasma membrane, the receptors were absent in cells with low and very low expression. The reduced AR expression in hypogonadism was associated with a decreased neuron body area and death of a part of neurons. Conclusions. The identified degenerative changes in the testosterone-dependent neuronal MAN that synthesize GnRH or peptides affecting the GnRH production may decrease the release of GnRH, cause a secondary decrease in the androgen synthesis, and mediate morphological and functional manifestations of GnRH secondary deficit. The replacement therapy partially compensated for degenerative changes in neurons and restored the intensity of AR expression, however, it did not influence the process of nerve cell death.

An Unbiased Predictive Model to Detect DNA Methylation Propensity of CpG Islands in the Human Genome

2020 ◽  
Vol 15 ◽  
Author(s):  
Dicle Yalcin ◽  
Hasan H. Otu
Keyword(s):  
Model Building ◽  
De Novo ◽  
Cpg Islands ◽  
Treatment Strategies ◽  
Area Under The Curve ◽  
Global Methylation ◽  
Sequence Features ◽  
A Genome ◽  
Combined Features ◽  
Epigenetic Repression

Background: Epigenetic repression mechanisms play an important role in gene regulation, specifically in cancer development. In many cases, a CpG island’s (CGI) susceptibility or resistance to methylation are shown to be contributed by local DNA sequence features. Objective: To develop unbiased machine learning models–individually and combined for different biological features–that predict the methylation propensity of a CGI. Methods: We developed our model consisting of CGI sequence features on a dataset of 75 sequences (28 prone, 47 resistant) representing a genome-wide methylation structure. We tested our model on two independent datasets that are chromosome (132 sequences) and disease (70 sequences) specific. Results: We provided improvements in prediction accuracy over previous models. Our results indicate that combined features better predict the methylation propensity of a CGI (area under the curve (AUC) ~0.81). Our global methylation classifier performs well on independent datasets reaching an AUC of ~0.82 for the complete model and an AUC of ~0.88 for the model using select sequences that better represent their classes in the training set. We report certain de novo motifs and transcription factor binding site (TFBS) motifs that are consistently better in separating prone and resistant CGIs. Conclusion: Predictive models for the methylation propensity of CGIs lead to a better understanding of disease mechanisms and can be used to classify genes based on their tendency to contain methylation prone CGIs, which may lead to preventative treatment strategies. MATLAB and Python™ scripts used for model building, prediction, and downstream analyses are available at https://github.com/dicleyalcin/methylProp_predictor.

CpGIScan: An Ultrafast Tool for CpG Islands Identification from Genome Sequence

2017 ◽  
Vol 12 (2) ◽  
pp. 181-184 ◽  
Author(s):  
Zhenxin Fan ◽  
Bisong Yue ◽  
Xiuyue Zhang ◽  
Lianming Du ◽  
Zuoyi Jian
Keyword(s):  
Genome Sequence ◽  
Cpg Islands
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