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Gene Expression and Chromatin Modification in the Brain

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 November 2021) | Viewed by 41713

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Special Issue Editor

Dr. Subramaniam Jayanthi

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Guest Editor

Molecular Neuropsychiatry Branch, National Institute on Drug Abuse/Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
Interests: substance use disorders; epigenetics; gene expression; high-throughput screening; signaling cascades; neurotoxicity; biomarker discovery

Special Issue Information

Dear Colleagues,

Epigenetic machinery not only modulates gene expression in the brain but also influences processes such as DNA repair, neural development, and activities that completely alter the cellular status. Alterations in post-translational histone modifications and chromatin structure may trigger changes in gene networks that contribute to diverse forms of abnormalities and diseases of the central nervous system (CNS). During the past two decades, many investigators have been actively dissecting the epigenetic landscape using single-gene approaches and genome-wide studies. These approaches have provided key insights into how chromatin regulation controls transcription and consequent brain functions. In this Special Issue, we are inviting articles that focus on recent advances in chromatin modifications and their contributions to understanding the mechanisms that underlie neurodevelopment, aging, and neurodegenerative diseases. Relevant articles will focus on epigenetic alterations including DNA methylation and histone modifications responsible for changes in functional chromatin architecture. Exploring the intricacies of chromatin regulation should help to clarify epigenetic interactions that may lead to the discovery of novel targets for therapeutic interventions that can restore homeostatic brain functions. Writers are encouraged to submit the results of studies using animal models of human diseases. We also encourage the submission of results from diverse human populations that reflect the chromatin remodeling process involved in neuronal activity and brain diseases.

Dr. Subramaniam Jayanthi
Guest Editor

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Keywords

histone modifications
DNA methylation
neurodegeneration
neurodevelopment
neurological disorders
histone deacetylase
epigenetics

Published Papers (12 papers)

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Research

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23 pages, 4197 KiB

Open AccessArticle

Whole Genome DNA Methylation Profiling of D2 Medium Spiny Neurons in Mouse Nucleus Accumbens Using Two Independent Library Preparation Methods

by Yuxiang Li, Haiyang Xu, Javed M. Chitaman and Jian Feng

Genes 2022, 13(2), 306; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13020306 - 06 Feb 2022

Cited by 2 | Viewed by 2781

Abstract

DNA methylation plays essential roles in various cellular processes. Next-generation sequencing has enabled us to study the functional implication of DNA methylation across the whole genome. However, this approach usually requires a substantial amount of genomic DNA, which limits its application to defined cell types within a discrete brain region. Here, we applied two separate protocols, Accel-NGS Methyl-Seq (AM-seq) and Enzymatic Methyl-seq (EM-seq), to profile the methylome of D2 dopamine receptor-expressing medium spiny neurons (D2-MSNs) in mouse nucleus accumbens (NAc). Using 40 ng DNA extracted from FACS-isolated D2-MSNs, we found that both methods yielded comparably high-quality methylome data. Additionally, we identified numerous unmethylated regions (UMRs) as cell type-specific regulatory regions. By comparing the NAc D2-MSN methylome with the published methylomes of mouse prefrontal cortex excitatory neurons and neural progenitor cells (NPCs), we identified numerous differentially methylated CpG and non-CpG regions. Our study not only presents a comparison of these two low-input DNA whole genome methylation profiling protocols, but also provides a resource of DNA methylome of mouse accumbal D2-MSNs, a neuron type that has critical roles in addiction and other neuropsychiatric disorders. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

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12 pages, 1996 KiB

Open AccessArticle

Meta-Analysis of Transcriptome-Wide Association Studies across 13 Brain Tissues Identified Novel Clusters of Genes Associated with Nicotine Addiction

by Zhenyao Ye, Chen Mo, Hongjie Ke, Qi Yan, Chixiang Chen, Peter Kochunov, L. Elliot Hong, Braxton D. Mitchell, Shuo Chen and Tianzhou Ma

Genes 2022, 13(1), 37; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13010037 - 23 Dec 2021

Cited by 2 | Viewed by 3407

Abstract

Genome-wide association studies (GWAS) have identified and reproduced thousands of diseases associated loci, but many of them are not directly interpretable due to the strong linkage disequilibrium among variants. Transcriptome-wide association studies (TWAS) incorporated expression quantitative trait loci (eQTL) cohorts as a reference panel to detect associations with the phenotype at the gene level and have been gaining popularity in recent years. For nicotine addiction, several important susceptible genetic variants were identified by GWAS, but TWAS that detected genes associated with nicotine addiction and unveiled the underlying molecular mechanism were still lacking. In this study, we used eQTL data from the Genotype-Tissue Expression (GTEx) consortium as a reference panel to conduct tissue-specific TWAS on cigarettes per day (CPD) over thirteen brain tissues in two large cohorts: UK Biobank (UKBB; number of participants (N) = 142,202) and the GWAS & Sequencing Consortium of Alcohol and Nicotine use (GSCAN; N = 143,210), then meta-analyzing the results across tissues while considering the heterogeneity across tissues. We identified three major clusters of genes with different meta-patterns across tissues consistent in both cohorts, including homogenous genes associated with CPD in all brain tissues; partially homogeneous genes associated with CPD in cortex, cerebellum, and hippocampus tissues; and, lastly, the tissue-specific genes associated with CPD in only a few specific brain tissues. Downstream enrichment analyses on each gene cluster identified unique biological pathways associated with CPD and provided important biological insights into the regulatory mechanism of nicotine dependence in the brain. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

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10 pages, 723 KiB

Open AccessArticle

Spatial and Temporal Expression of High-Mobility-Group Nucleosome-Binding (HMGN) Genes in Brain Areas Associated with Cognition in Individuals with Down Syndrome

by Alejandra Rodríguez-Ortiz, Julio César Montoya-Villegas, Felipe García-Vallejo and Yecid Mina-Paz

Genes 2021, 12(12), 2000; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12122000 - 17 Dec 2021

Cited by 1 | Viewed by 2265

Abstract

DNA methylation and histone posttranslational modifications are epigenetics processes that contribute to neurophenotype of Down Syndrome (DS). Previous reports present strong evidence that nonhistone high-mobility-group N proteins (HMGN) are epigenetic regulators. They play important functions in various process to maintain homeostasis in the brain. We aimed to analyze the differential expression of five human HMGN genes in some brain structures and age ranks from DS postmortem brain samples. Methodology: We performed a computational analysis of the expression of human HMGN from the data of a DNA microarray experiment (GEO database ID GSE59630). Using the transformed log2 data, we analyzed the differential expression of five HMGN genes in several brain areas associated with cognition in patients with DS. Moreover, using information from different genome databases, we explored the co-expression and protein interactions of HMNGs with the histones of nucleosome core particle and linker H1 histone. Results: We registered that HMGN1 and HMGN5 were significantly overexpressed in the hippocampus and areas of prefrontal cortex including DFC, OFC, and VFC of DS patients. Age-rank comparisons between euploid control and DS individuals showed that HMGN2 and HMGN4 were overexpressed in the DS brain at 16 to 22 gestation weeks. From the BioGRID database, we registered high interaction scores of HMGN2 and HMGN4 with Hist1H1A and Hist1H3A. Conclusions: Overall, our results give strong evidence to propose that DS would be an epigenetics-based aneuploidy. Remodeling brain chromatin by HMGN1 and HMGN5 would be an essential pathway in the modification of brain homeostasis in DS. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

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7 pages, 1754 KiB

Open AccessArticle

Novel In-Frame Deletion in HTRA1 Gene, Responsible for Stroke at a Young Age and Dementia—A Case Study

by Julija Grigaitė, Kamilė Šiaurytė, Eglė Audronytė, Eglė Preikšaitienė, Birutė Burnytė, Erinija Pranckevičienė, Aleksandra Ekkert, Algirdas Utkus and Dalius Jatužis

Genes 2021, 12(12), 1955; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12121955 - 07 Dec 2021

Cited by 4 | Viewed by 2214

Abstract

Biallelic mutations in the high-temperature requirement A serine peptidase 1 (HTRA1) gene are known to cause an extremely rare cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL), which belongs to the group of hereditary cerebral small vessel diseases and is mainly observed in the Japanese population. Even though this pathology is inherited in an autosomal recessive manner, recent studies have described symptomatic carriers with heterozygous HTRA1 mutations who have milder symptoms than patients with biallelic HTRA1 mutations. We present the case of a Lithuanian male patient who had a stroke at the age of 36, experienced several transient ischemic attacks, and developed an early onset, progressing dementia. These clinical symptoms were associated with extensive leukoencephalopathy, lacunar infarcts, and microbleeds based on brain magnetic resonance imaging (MRI). A novel heterozygous in-frame HTRA1 gene deletion (NM_002775.5:c.533_535del; NP_002766.1:p.(Lys178del)) was identified by next generation sequencing. The variant was consistent with the patient’s phenotype, which could not be explained by alternative causes, appeared highly deleterious after in silico analysis, and was not reported in the medical literature or population databases to date. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

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19 pages, 24472 KiB

Open AccessArticle

Rhythmic Regulation of DNA Methylation Factors and Core-Clock Genes in Brain Structures Activated by Cocaine or Sucrose: Potential Role of Chromatin Remodeling

by Lamis Saad, Andries Kalsbeek, Jean Zwiller and Patrick Anglard

Genes 2021, 12(8), 1195; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12081195 - 31 Jul 2021

Cited by 1 | Viewed by 2098

Abstract

The circadian system interacts with the mesocorticolimbic reward system to modulate reward and memory in a time-of-day dependent manner. The circadian discrimination of reward, however, remains difficult to address between natural reinforcers and drugs of abuse. Circadian rhythms control cocaine sensitization and conversely cocaine causes long-term alteration in circadian periodicity in part through the serotonergic neurotransmission. Since neural circuits activated by cocaine and natural reinforcers do not completely overlap, we compared the effect of cocaine with that of sucrose, a strong reinforcer in rodents, by using passive chronic administration. The expression of fifteen genes playing a major role in DNA methylation (Dnmts, Tets), circadian rhythms (Clock, Bmal1, Per1/2, Cry1/2, Rev-Erbβ, Dbp1), appetite, and satiety (Orexin, Npy) was analyzed in dopamine projection areas like the prefrontal cortex, the caudate putamen, and the hypothalamus interconnected with the reward system. The corresponding proteins of two genes (Orexin, Per2) were examined by IHC. For many factors controlling biological and cognitive functions, striking opposite responses were found between the two reinforcers, notably for genes controlling DNA methylation/demethylation processes and in global DNA methylation involved in chromatin remodeling. The data are consistent with a repression of critical core-clock genes by cocaine, suggesting that, consequently, both agents differentially modulate day/night cycles. Whether observed cocaine and sucrose-induced changes in DNA methylation in a time dependent manner are long lasting or contribute to the establishment of addiction requires further neuroepigenetic investigation. Understanding the mechanisms dissociating drugs of abuse from natural reinforcers remains a prerequisite for the design of selective therapeutic tools for compulsive behaviors. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

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15 pages, 3729 KiB

Open AccessArticle

Transcriptional Pausing and Activation at Exons-1 and -2, Respectively, Mediate the MGMT Gene Expression in Human Glioblastoma Cells

by Mohammed A. Ibrahim Al-Obaide and Kalkunte S. Srivenugopal

Genes 2021, 12(6), 888; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12060888 - 08 Jun 2021

Cited by 1 | Viewed by 2671

Abstract

Background: The therapeutically important DNA repair gene O⁶-methylguanine DNA methyltransferase (MGMT) is silenced by promoter methylation in human brain cancers. The co-players/regulators associated with this process and the subsequent progression of MGMT gene transcription beyond the non-coding exon 1 are unknown. As a follow-up to our recent finding of a predicted second promoter mapped proximal to the exon 2 [Int. J. Mol. Sci.2021, 22(5), 2492], we addressed its significance in MGMT transcription. Methods: RT-PCR, RT q-PCR, and nuclear run-on transcription assays were performed to compare and contrast the transcription rates of exon 1 and exon 2 of the MGMT gene in glioblastoma cells. Results: Bioinformatic characterization of the predicted MGMT exon 2 promoter showed several consensus TATA box and INR motifs and the absence of CpG islands in contrast to the established TATA-less, CpG-rich, and GAF-bindable exon 1 promoter. RT-PCR showed very weak MGMT-E1 expression in MGMT-proficient SF188 and T98G GBM cells, compared to active transcription of MGMT-E2. In the MGMT-deficient SNB-19 cells, the expression of both exons remained weak. The RT q-PCR revealed that MGMT-E2 and MGMT-E5 expression was about 80- to 175-fold higher than that of E1 in SF188 and T98G cells. Nuclear run-on transcription assays using bromo-uridine immunocapture followed by RT q-PCR confirmed the exceptionally lower and higher transcription rates for MGMT-E1 and MGMT-E2, respectively. Conclusions: The results provide the first evidence for transcriptional pausing at the promoter 1- and non-coding exon 1 junction of the human MGMT gene and its activation/elongation through the protein-coding exons 2 through 5, possibly mediated by a second promoter. The findings offer novel insight into the regulation of MGMT transcription in glioma and other cancer types. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

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Review

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27 pages, 986 KiB

Open AccessReview

Sex Differences in Psychostimulant Abuse: Implications for Estrogen Receptors and Histone Deacetylases

by Oscar V. Torres

Genes 2022, 13(5), 892; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13050892 - 17 May 2022

Cited by 6 | Viewed by 2676

Abstract

Substance abuse is a chronic pathological disorder that negatively affects many health and neurological processes. A growing body of literature has revealed gender differences in substance use. Compared to men, women display distinct drug-use phenotypes accompanied by recovery and rehabilitation disparities. These observations have led to the notion that sex-dependent susceptibilities exist along the progression to addiction. Within this scope, neuroadaptations following psychostimulant exposure are thought to be distinct for each sex. This review summarizes clinical findings and animal research reporting sex differences in the subjective and behavioral responses to cocaine, methamphetamine, and nicotine. This discussion is followed by an examination of epigenetic and molecular alterations implicated in the addiction process. Special consideration is given to histone deacetylases and estrogen receptor-mediated gene expression. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

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15 pages, 300 KiB

Open AccessEditor’s ChoiceReview

Ischemic Stroke Genetics: What Is New and How to Apply It in Clinical Practice?

by Aleksandra Ekkert, Aleksandra Šliachtenko, Julija Grigaitė, Birutė Burnytė, Algirdas Utkus and Dalius Jatužis

Genes 2022, 13(1), 48; https://0-doi-org.brum.beds.ac.uk/10.3390/genes13010048 - 24 Dec 2021

Cited by 26 | Viewed by 7675

Abstract

The etiology of ischemic stroke is multifactorial. Although receiving less emphasis, genetic causes make a significant contribution to ischemic stroke genesis, especially in early-onset stroke. Several stroke classification systems based on genetic information corresponding to various stroke phenotypes were proposed. Twin and family history studies, as well as candidate gene approach, are common methods to discover genetic causes of stroke, however, both have their own limitations. Genome-wide association studies and next generation sequencing are more efficient, promising and increasingly used for daily diagnostics. Some monogenic disorders, despite covering only about 7% of stroke etiology, may cause well-known clinical manifestations that include stroke. Polygenic disorders are more frequent, causing about 38% of all ischemic strokes, and their identification is a rapidly developing field of modern stroke genetics. Current advances in human genetics provide opportunity for personalized prevention of stroke and novel treatment possibilities. Genetic risk scores (GRS) and extended polygenic risk scores (PRS) estimate cumulative contribution of known genetic factors to a specific outcome of stroke. Combining those scores with clinical information and risk factor profiles might result in better primary stroke prevention. Some authors encourage the use of stroke gene panels for stroke risk evaluation and further stroke research. Moreover, new biomarkers for stroke genetic causes and novel targets for gene therapy are on the horizon. In this article, we summarize the latest evidence and perspectives of ischemic stroke genetics that could be of interest to the practitioner and useful for day-to-day clinical work. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

27 pages, 986 KiB

Open AccessReview

Epigenetic Regulatory Dynamics in Models of Methamphetamine-Use Disorder

by Subramaniam Jayanthi, Michael T. McCoy and Jean Lud Cadet

Genes 2021, 12(10), 1614; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12101614 - 14 Oct 2021

Cited by 10 | Viewed by 3015

Abstract

Methamphetamine (METH)-use disorder (MUD) is a very serious, potentially lethal, biopsychosocial disease. Exposure to METH causes long-term changes to brain regions involved in reward processing and motivation, leading vulnerable individuals to engage in pathological drug-seeking and drug-taking behavior that can remain a lifelong struggle. It is crucial to elucidate underlying mechanisms by which exposure to METH leads to molecular neuroadaptive changes at transcriptional and translational levels. Changes in gene expression are controlled by post-translational modifications via chromatin remodeling. This review article focuses on the brain-region specific combinatorial or distinct epigenetic modifications that lead to METH-induced changes in gene expression. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

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27 pages, 1095 KiB

Open AccessReview

Epigenetic Regulation of Circadian Clocks and Its Involvement in Drug Addiction

by Lamis Saad, Jean Zwiller, Andries Kalsbeek and Patrick Anglard

Genes 2021, 12(8), 1263; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12081263 - 19 Aug 2021

Cited by 7 | Viewed by 4915

Abstract

Based on studies describing an increased prevalence of addictive behaviours in several rare sleep disorders and shift workers, a relationship between circadian rhythms and addiction has been hinted for more than a decade. Although circadian rhythm alterations and molecular mechanisms associated with neuropsychiatric conditions are an area of active investigation, success is limited so far, and further investigations are required. Thus, even though compelling evidence connects the circadian clock to addictive behaviour and vice-versa, yet the functional mechanism behind this interaction remains largely unknown. At the molecular level, multiple mechanisms have been proposed to link the circadian timing system to addiction. The molecular mechanism of the circadian clock consists of a transcriptional/translational feedback system, with several regulatory loops, that are also intricately regulated at the epigenetic level. Interestingly, the epigenetic landscape shows profound changes in the addictive brain, with significant alterations in histone modification, DNA methylation, and small regulatory RNAs. The combination of these two observations raises the possibility that epigenetic regulation is a common plot linking the circadian clocks with addiction, though very little evidence has been reported to date. This review provides an elaborate overview of the circadian system and its involvement in addiction, and we hypothesise a possible connection at the epigenetic level that could further link them. Therefore, we think this review may further improve our understanding of the etiology or/and pathology of psychiatric disorders related to drug addiction. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

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21 pages, 2640 KiB

Open AccessReview

Epigenetic Alterations in Prescription Opioid Misuse: New Strategies for Precision Pain Management

by Maria Carla Gerra, Cristina Dallabona and Lars Arendt-Nielsen

Genes 2021, 12(8), 1226; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12081226 - 10 Aug 2021

Cited by 7 | Viewed by 3121

Abstract

Prescription opioids are used for some chronic pain conditions. However, generally, long-term therapy has unwanted side effects which may trigger addiction, overdose, and eventually cause deaths. Opioid addiction and chronic pain conditions have both been associated with evidence of genetic and epigenetic alterations. Despite intense research interest, many questions about the contribution of epigenetic changes to this typology of addiction vulnerability and development remain unanswered. The aim of this review was to summarize the epigenetic modifications detected in specific tissues or brain areas and associated with opioid prescription and misuse in patients who have initiated prescribed opioid management for chronic non-cancer pain. The review considers the effects of opioid exposure on the epigenome in central and peripheral tissues in animal models and human subjects and highlights the mechanisms in which opioid epigenetics may be involved. This will improve our current understanding, provide the basis for targeted, personalized pain management, and thus balance opioid risks and benefits in managing chronic pain. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

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Graphical abstract

22 pages, 760 KiB

Open AccessReview

The Role of Preclinical Models in Creatine Transporter Deficiency: Neurobiological Mechanisms, Biomarkers and Therapeutic Development

by Elsa Ghirardini, Francesco Calugi, Giulia Sagona, Federica Di Vetta, Martina Palma, Roberta Battini, Giovanni Cioni, Tommaso Pizzorusso and Laura Baroncelli

Genes 2021, 12(8), 1123; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12081123 - 24 Jul 2021

Cited by 8 | Viewed by 3466

Abstract

Creatine (Cr) Transporter Deficiency (CTD) is an X-linked metabolic disorder, mostly caused by missense mutations in the SLC6A8 gene and presenting with intellectual disability, autistic behavior, and epilepsy. There is no effective treatment for CTD and patients need lifelong assistance. Thus, the research of novel intervention strategies is a major scientific challenge. Animal models are an excellent tool to dissect the disease pathogenetic mechanisms and drive the preclinical development of therapeutics. This review illustrates the current knowledge about Cr metabolism and CTD clinical aspects, with a focus on mainstay diagnostic and therapeutic options. Then, we discuss the rodent models of CTD characterized in the last decade, comparing the phenotypes expressed within clinically relevant domains and the timeline of symptom development. This analysis highlights that animals with the ubiquitous deletion/mutation of SLC6A8 genes well recapitulate the early onset and the complex pathological phenotype of the human condition. Thus, they should represent the preferred model for preclinical efficacy studies. On the other hand, brain- and cell-specific conditional mutants are ideal for understanding the basis of CTD at a cellular and molecular level. Finally, we explain how CTD models might provide novel insight about the pathogenesis of other disorders, including cancer. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

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