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Mora A, Huang X, Jauhari S, Jiang Q, Li X. Chromatin Hubs: A biological and computational outlook. Comput Struct Biotechnol J 2022; 20:3796-3813. [PMID: 35891791 PMCID: PMC9304431 DOI: 10.1016/j.csbj.2022.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/02/2022] [Accepted: 07/02/2022] [Indexed: 11/20/2022] Open
Abstract
This review discusses our current understanding of chromatin biology and bioinformatics under the unifying concept of “chromatin hubs.” The first part reviews the biology of chromatin hubs, including chromatin–chromatin interaction hubs, chromatin hubs at the nuclear periphery, hubs around macromolecules such as RNA polymerase or lncRNAs, and hubs around nuclear bodies such as the nucleolus or nuclear speckles. The second part reviews existing computational methods, including enhancer–promoter interaction prediction, network analysis, chromatin domain callers, transcription factory predictors, and multi-way interaction analysis. We introduce an integrated model that makes sense of the existing evidence. Understanding chromatin hubs may allow us (i) to explain long-unsolved biological questions such as interaction specificity and redundancy of mechanisms, (ii) to develop more realistic kinetic and functional predictions, and (iii) to explain the etiology of genomic disease.
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Affiliation(s)
- Antonio Mora
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
- Corresponding authors.
| | - Xiaowei Huang
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Shaurya Jauhari
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China
| | - Qin Jiang
- Affiliated Eye Hospital of Nanjing Medical University, Nanjing 210000, PR China
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, and Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, PR China
- Corresponding authors.
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Nguyen NM, Vellichirammal NN, Guda C, Pendyala G. Decoding the Synaptic Proteome with Long-Term Exposure to Midazolam during Early Development. Int J Mol Sci 2022; 23:ijms23084137. [PMID: 35456952 PMCID: PMC9027542 DOI: 10.3390/ijms23084137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 12/05/2022] Open
Abstract
The intensive use of anesthetic and sedative agents in the neonatal intensive care unit (NICU) has raised controversial concerns about the potential neurodevelopmental risks. This study focused on midazolam (MDZ), a common benzodiazepine regularly used as a sedative on neonates in the NICU. Mounting evidence suggests a single exposure to MDZ during the neonatal period leads to learning disturbances. However, a knowledge gap that remains is how long-term exposure to MDZ during very early stages of life impacts synaptic alterations. Using a preclinical rodent model system, we mimicked a dose-escalation regimen on postnatal day 3 (P3) pups until day 21. Next, purified synaptosomes from P21 control and MDZ animals were subjected to quantitative mass-spectrometry-based proteomics, to identify potential proteomic signatures. Further analysis by ClueGO identified enrichment of proteins associated with actin-binding and protein depolymerization process. One potential hit identified was alpha adducin (ADD1), belonging to the family of cytoskeleton proteins, which was upregulated in the MDZ group and whose expression was further validated by Western blot. In summary, this study sheds new information on the long-term exposure of MDZ during the early stages of development impacts synaptic function, which could subsequently perturb neurobehavioral outcomes at later stages of life.
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Affiliation(s)
- Nghi M. Nguyen
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (N.N.V.); (C.G.)
| | - Neetha N. Vellichirammal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (N.N.V.); (C.G.)
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (N.N.V.); (C.G.)
| | - Gurudutt Pendyala
- Department of Anesthesiology, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (N.N.V.); (C.G.)
- Child Health Research Institute, Omaha, NE 68198, USA
- Correspondence: ; Tel.: +1-402-559-8690
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Maung MT, Carlson A, Olea-Flores M, Elkhadragy L, Schachtschneider KM, Navarro-Tito N, Padilla-Benavides T. The molecular and cellular basis of copper dysregulation and its relationship with human pathologies. FASEB J 2021; 35:e21810. [PMID: 34390520 DOI: 10.1096/fj.202100273rr] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/23/2021] [Accepted: 07/07/2021] [Indexed: 12/16/2022]
Abstract
Copper (Cu) is an essential micronutrient required for the activity of redox-active enzymes involved in critical metabolic reactions, signaling pathways, and biological functions. Transporters and chaperones control Cu ion levels and bioavailability to ensure proper subcellular and systemic Cu distribution. Intensive research has focused on understanding how mammalian cells maintain Cu homeostasis, and how molecular signals coordinate Cu acquisition and storage within organs. In humans, mutations of genes that regulate Cu homeostasis or facilitate interactions with Cu ions lead to numerous pathologic conditions. Malfunctions of the Cu+ -transporting ATPases ATP7A and ATP7B cause Menkes disease and Wilson disease, respectively. Additionally, defects in the mitochondrial and cellular distributions and homeostasis of Cu lead to severe neurodegenerative conditions, mitochondrial myopathies, and metabolic diseases. Cu has a dual nature in carcinogenesis as a promotor of tumor growth and an inducer of redox stress in cancer cells. Cu also plays role in cancer treatment as a component of drugs and a regulator of drug sensitivity and uptake. In this review, we provide an overview of the current knowledge of Cu metabolism and transport and its relation to various human pathologies.
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Affiliation(s)
- May T Maung
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT, USA
| | - Alyssa Carlson
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT, USA
| | - Monserrat Olea-Flores
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Guerrero, Mexico
| | - Lobna Elkhadragy
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Kyle M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA.,Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Napoleon Navarro-Tito
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Guerrero, Mexico
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Sarin H. Pressure regulated basis for gene transcription by delta-cell micro-compliance modeled in silico: Biphenyl, bisphenol and small molecule ligand models of cell contraction-expansion. PLoS One 2020; 15:e0236446. [PMID: 33021979 PMCID: PMC7537880 DOI: 10.1371/journal.pone.0236446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Molecular diameter, lipophilicity and hydrophilicity exclusion affinity limits exist for small molecule carrier-mediated diffusion or transport through channel pores or interaction with the cell surface glycocalyx. The molecular structure lipophilicity limit for non-specific carrier-mediated transmembrane diffusion through polarity-selective transport channels of the cell membrane is Lexternal structure ∙ Hpolar group-1 of ≥ 1.07. The cell membrane channel pore size is > 0.752 and < 0.758 nm based on a 3-D ellipsoid model (biphenyl), and within the molecular diameter size range 0.744 and 0.762 nm based on a 2-D elliptical model (alkanol). The adjusted van der Waals diameter (vdWD, adj; nm) for the subset of halogenated vapors is predictive of the required MAC for anesthetic potency at an initial (-) Δ Cmicro effect. The molecular structure L ∙ Hpolar group-1 for Neu5Ac is 0.080, and the L ∙ Hpolar group-1 interval range for the cell surface glycocalyx hydrophilicity barrier interaction is 0.101 (Saxitoxin, Stx; Linternal structure ∙ Hpolar group-1) - 0.092 (m-xylenediamine, Lexternal structure · Hpolar group). Differential predictive effective pressure mapping of gene activation or repression reveals that p-dioxin exposure results in activation of AhR-Erβ (Arnt)/Nrf-2, Pparδ, Errγ (LxRα), Dio3 (Dio2) and Trα limbs, and due to high affinity Dio2 and Dio3 (OH-TriCDD, Lext · H-1: 1.91–4.31) exothermy-antagonism (Δ contraction) with high affinity T4/rT3-TRα-mediated agonism (Δ expansion). co-planar PCB metabolite exposure (Lext · H-1: 1.95–3.91) results in activation of AhR (Erα/β)/Nrf2, Rev-Erbβ, Errα, Dio3 (Dio2) and Trα limbs with a Δ Cmicro contraction of 0.89 and Δ Cmicro expansion of 1.05 as compared to p-dioxin. co-, ortho-planar PCB metabolite exposure results in activation of Car/PxR, Pparα (Srebf1,—Lxrβ), Arnt (AhR-Erβ), AR, Dio1 (Dio2) and Trβ limbs with a Δ Cmicro contraction of 0.73 and Δ Cmicro expansion of 1.18 (as compared to p-dioxin). Bisphenol A exposure (Lext struct ∙ H-1: 1.08–1.12, BPA–BPE, Errγ; BPAF, Lext struct ∙ H-1: 1.23, CM Erα, β) results in increased duration at Peff for Timm8b (Peff 0.247) transcription and in indirect activation of the AhR/Nrf-2 hybrid pathway with decreased duration at Peff 0.200 (Nrf1) and increased duration at Peff 0.257 (Dffa). The Bpa/Bpaf convergent pathway Cmicro contraction-expansion response increase in the lower Peff interval is 0.040; in comparison, small molecule hormone Δ Cmicro contraction-expansion response increases in the lower Peff intervals for gene expression ≤ 0.168 (Dex· GR) ≥ 0.156 (Dht · AR), with grade of duration at Peff (min·count) of 1.33x105 (Dex/Cort) and 1.8–2.53x105 (Dht/R1881) as compared to the (-) coupled (+) Δ CmicroPeff to 0.136 (Wnt5a, Esr2) with applied DES (1.86x106). The subtype of trans-differentiated cell as a result of an applied toxin or toxicant is predictable by delta-Cmicro determined by Peff mapping. Study findings offer additional perspective on the basis for pressure regulated gene transcription by alterations in cell micro-compliance (Δ contraction-expansion, Cmicro), and are applicable for the further predictive modeling of gene to gene transcription interactions, and small molecule modulation of cell effective pressure (Peff) and its potential.
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Affiliation(s)
- Hemant Sarin
- Freelance Investigator in Translational Science and Medicine, Charleston, West Virginia, United States of America
- * E-mail:
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Singh RK, Saini SK, Prakasam G, Kalairasan P, Bamezai RNK. Role of ectopically expressed mtDNA encoded cytochrome c oxidase subunit I (MT-COI) in tumorigenesis. Mitochondrion 2019; 49:56-65. [PMID: 31299394 DOI: 10.1016/j.mito.2019.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 05/17/2019] [Accepted: 07/03/2019] [Indexed: 11/30/2022]
Abstract
Somatic mutations within mitochondrial DNA (mtDNA) encoded cytochrome c oxidase subunit I (MT-CO1 or MT-COI) are frequent in various cancer types. In addition, perturbation from orchestrated expression of mitochondrial DNA encoded genes is also associated with complex disorders, including cancer. Since codon bias and the mitochondrial translation system restricts functional characterization of over-expressed wild type or mutant mitochondrial DNA encoded genes, the codon optimization and artificial synthesis of entire MT-CO1 allowed us to over-express the wild type and one of its deleterious mutants into the mitochondria of the transfected cells. Ectopically expressed MT-CO1 was observed to efficiently express and localized to mitochondria but showed high level of aggregation under denaturing condition. Over-expression of wild type or mutant variant of MT-CO1 promoted anchorage dependent and independent proliferation potential in in-vitro experiments and introduced the cancer cell metabolic phenotype of high glucose uptake and lactate release. Reactive oxygen species generated in cells over-expressing MT-CO1 variants acted as key effectors mediating differential expression of apoptosis and DNA damage pathway related genes. High ROS generated also down-regulated the expression of global regulators of gene expression, DNMT3A and DNMT3B. The down-regulated expression of DNMTs co-related with differential methylation of the CpG islands in the promoter region of a select set of studied genes, in a manner to promote pro-cancerous phenotype. Apart from assigning the mechanistic role to the MT-CO1 variants and their perturbed expression in cancer development, the present study provides novel insights into the functional role of somatic mutations within MT-CO1 promoting cancer phenotype.
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Affiliation(s)
- Rajnish Kumar Singh
- National Centre of Applied Human Genetics, School of life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Sunil Kumar Saini
- National Centre of Applied Human Genetics, School of life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Gopinath Prakasam
- National Centre of Applied Human Genetics, School of life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ponnuusamy Kalairasan
- National Centre of Applied Human Genetics, School of life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rameshwar N K Bamezai
- National Centre of Applied Human Genetics, School of life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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Chicherin IV, Dashinimaev E, Baleva M, Krasheninnikov I, Levitskii S, Kamenski P. Cytochrome c Oxidase on the Crossroads of Transcriptional Regulation and Bioenergetics. Front Physiol 2019; 10:644. [PMID: 31231235 PMCID: PMC6558401 DOI: 10.3389/fphys.2019.00644] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 05/07/2019] [Indexed: 11/13/2022] Open
Abstract
Mitochondria are the organelles of eukaryotic cells responsible for the ATP production by means of the electron transfer chain (ETC). Its work is under strict genetic control providing the correct assembly of the enzyme complexes and the interface to adapt the energetic demands of the cell to the environment. These mechanisms are particularly developed in the cells with high energy consumption, like neurons and myocytes. This review summarizes several aspects of the involvement of the ETC complexes in the transcriptional control mechanisms of the neurons and other cells. Their influence on the differentiation of neurons is also discussed.
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Affiliation(s)
- Ivan Vladimirovich Chicherin
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, Russia
| | - Erdem Dashinimaev
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Mariia Baleva
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Igor Krasheninnikov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey Levitskii
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Piotr Kamenski
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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Mintzopoulos D, Gillis TE, Tedford CE, Kaufman MJ. Effects of Near-Infrared Light on Cerebral Bioenergetics Measured with Phosphorus Magnetic Resonance Spectroscopy. Photomed Laser Surg 2017; 35:395-400. [PMID: 28186868 DOI: 10.1089/pho.2016.4238] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE Cerebral photobiomodulation (PBM) improves mood and cognition. Cerebral metabolic enhancement is a mechanism proposed to underlie PBM effects. No PBM studies to date have applied phosphorus magnetic resonance spectroscopy (31P MRS), which can be used to assess metabolic intermediates such as phosphocreatine (PCr) and adenosine triphosphate, the latter of which is elevated by PBM. Accordingly, we used 9.4 Tesla 31P MRS to characterize effects of single and repeat cerebral PBM treatments on metabolism. PBM was delivered to healthy adult beagles in the form of transcranial laser treatment (TLT) at a wavelength of 808 nm, which passes safely through the skull and activates cytochrome C oxidase, a mitochondrial respiratory chain enzyme. METHODS Isoflurane-anesthetized subjects (n = 4) underwent a baseline 31P MRS scan followed by TLT applied sequentially for 2 min each to anterior and posterior cranium midline locations, to irradiate the dorsal cortex. Subjects then underwent 31P MRS scans for 2 h to assess acute TLT effects. After 2 weeks of repeat TLT (3 times/week), subjects were scanned again with 31P MRS to characterize effects of repeat TLT. RESULTS TLT did not induce acute 31P MRS changes over the course of 2 h in either scan session. However, after repeat TLT, the baseline PCr/β-nucleoside triphosphate ratio was higher than the scan 1 baseline (p < 0.0001), an effect attributable to increased PCr level (p < 0.0001). CONCLUSIONS Our findings are consistent with reports that bioenergetic effects of PBM can take several hours to evolve. Thus, in vivo 31P MRS may be useful for characterizing bioenergetic effects of PBM in brain and other tissues.
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Affiliation(s)
| | - Timothy E Gillis
- 1 McLean Imaging Center , McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | | | - Marc J Kaufman
- 1 McLean Imaging Center , McLean Hospital, Harvard Medical School, Belmont, Massachusetts
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Preciados M, Yoo C, Roy D. Estrogenic Endocrine Disrupting Chemicals Influencing NRF1 Regulated Gene Networks in the Development of Complex Human Brain Diseases. Int J Mol Sci 2016; 17:E2086. [PMID: 27983596 PMCID: PMC5187886 DOI: 10.3390/ijms17122086] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/21/2016] [Accepted: 11/29/2016] [Indexed: 12/13/2022] Open
Abstract
During the development of an individual from a single cell to prenatal stages to adolescence to adulthood and through the complete life span, humans are exposed to countless environmental and stochastic factors, including estrogenic endocrine disrupting chemicals. Brain cells and neural circuits are likely to be influenced by estrogenic endocrine disruptors (EEDs) because they strongly dependent on estrogens. In this review, we discuss both environmental, epidemiological, and experimental evidence on brain health with exposure to oral contraceptives, hormonal therapy, and EEDs such as bisphenol-A (BPA), polychlorinated biphenyls (PCBs), phthalates, and metalloestrogens, such as, arsenic, cadmium, and manganese. Also we discuss the brain health effects associated from exposure to EEDs including the promotion of neurodegeneration, protection against neurodegeneration, and involvement in various neurological deficits; changes in rearing behavior, locomotion, anxiety, learning difficulties, memory issues, and neuronal abnormalities. The effects of EEDs on the brain are varied during the entire life span and far-reaching with many different mechanisms. To understand endocrine disrupting chemicals mechanisms, we use bioinformatics, molecular, and epidemiologic approaches. Through those approaches, we learn how the effects of EEDs on the brain go beyond known mechanism to disrupt the circulatory and neural estrogen function and estrogen-mediated signaling. Effects on EEDs-modified estrogen and nuclear respiratory factor 1 (NRF1) signaling genes with exposure to natural estrogen, pharmacological estrogen-ethinyl estradiol, PCBs, phthalates, BPA, and metalloestrogens are presented here. Bioinformatics analysis of gene-EEDs interactions and brain disease associations identified hundreds of genes that were altered by exposure to estrogen, phthalate, PCBs, BPA or metalloestrogens. Many genes modified by EEDs are common targets of both 17 β-estradiol (E2) and NRF1. Some of these genes are involved with brain diseases, such as Alzheimer's Disease (AD), Parkinson's Disease, Huntington's Disease, Amyotrophic Lateral Sclerosis, Autism Spectrum Disorder, and Brain Neoplasms. For example, the search of enriched pathways showed that top ten E2 interacting genes in AD-APOE, APP, ATP5A1, CALM1, CASP3, GSK3B, IL1B, MAPT, PSEN2 and TNF-underlie the enrichment of the Kyoto Encyclopedia of Genes and Genomes (KEGG) AD pathway. With AD, the six E2-responsive genes are NRF1 target genes: APBB2, DPYSL2, EIF2S1, ENO1, MAPT, and PAXIP1. These genes are also responsive to the following EEDs: ethinyl estradiol (APBB2, DPYSL2, EIF2S1, ENO1, MAPT, and PAXIP1), BPA (APBB2, EIF2S1, ENO1, MAPT, and PAXIP1), dibutyl phthalate (DPYSL2, EIF2S1, and ENO1), diethylhexyl phthalate (DPYSL2 and MAPT). To validate findings from Comparative Toxicogenomics Database (CTD) curated data, we used Bayesian network (BN) analysis on microarray data of AD patients. We observed that both gender and NRF1 were associated with AD. The female NRF1 gene network is completely different from male human AD patients. AD-associated NRF1 target genes-APLP1, APP, GRIN1, GRIN2B, MAPT, PSEN2, PEN2, and IDE-are also regulated by E2. NRF1 regulates targets genes with diverse functions, including cell growth, apoptosis/autophagy, mitochondrial biogenesis, genomic instability, neurogenesis, neuroplasticity, synaptogenesis, and senescence. By activating or repressing the genes involved in cell proliferation, growth suppression, DNA damage/repair, apoptosis/autophagy, angiogenesis, estrogen signaling, neurogenesis, synaptogenesis, and senescence, and inducing a wide range of DNA damage, genomic instability and DNA methylation and transcriptional repression, NRF1 may act as a major regulator of EEDs-induced brain health deficits. In summary, estrogenic endocrine disrupting chemicals-modified genes in brain health deficits are part of both estrogen and NRF1 signaling pathways. Our findings suggest that in addition to estrogen signaling, EEDs influencing NRF1 regulated communities of genes across genomic and epigenomic multiple networks may contribute in the development of complex chronic human brain health disorders.
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Affiliation(s)
- Mark Preciados
- Department of Environmental & Occupational Health, Florida International University, Miami, FL 33199, USA.
| | - Changwon Yoo
- Department of Biostatistics, Florida International University, Miami, FL 33199, USA.
| | - Deodutta Roy
- Department of Environmental & Occupational Health, Florida International University, Miami, FL 33199, USA.
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Nair B, Johar K, Priya A, Wong-Riley MTT. Specificity protein 4 (Sp4) transcriptionally regulates inhibitory GABAergic receptors in neurons. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:1-9. [PMID: 26469128 DOI: 10.1016/j.bbamcr.2015.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/05/2015] [Accepted: 10/10/2015] [Indexed: 10/22/2022]
Abstract
Previous studies in our laboratory have shown that the neuron-specific specificity protein 4 (Sp4) transcriptionally regulates many excitatory neurotransmitter receptor subunit genes, such as those for GluN1, GluN2A, and GluN2B of N-methyl-d-aspartate (NMDA) receptors and Gria2 of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. It also regulates Atp1a1 and Atp1b1 subunit genes of Na(+)/K(+)-ATPase, a major energy-consuming enzyme, as well as all 13 subunits of cytochrome c oxidase (COX), an important energy-generating enzyme. Thus, there is a tight coupling between energy consumption, energy production, and excitatory neuronal activity at the transcriptional level in neurons. The question is whether inhibitory neurotransmitter receptors are also regulated by Sp4. In the present study, we tested our hypothesis that Sp4 regulates receptor subunit genes of a major inhibitory neurotransmitter, GABA, specifically GABAA receptors. By means of multiple approaches, including in silico analysis, electrophoretic mobility shift and supershift assays, real-time quantitative PCR, chromatin immunoprecipitation, promoter mutational analysis, over-expression and shRNA of Sp4, functional assays, and western blots, we found that Sp4 functionally regulates the transcription of Gabra1 (GABAA α1) and Gabra2 (GABAA α2), but not Gabra3 (GABAA α3) subunit genes. The binding sites of Sp4 are conserved among rats, humans, and mice. Thus, our results substantiate our hypothesis that Sp4 plays a key role in regulating the transcription of GABAA receptor subunit genes. They also indicate that Sp4 is in a position to transcriptionally regulate the balance between excitatory and inhibitory neurochemical expressions in neurons.
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Affiliation(s)
- Bindu Nair
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Kaid Johar
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Anusha Priya
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Margaret T T Wong-Riley
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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Jasiewicz A, Rubiś B, Samochowiec J, Małecka I, Suchanecka A, Jabłoński M, Grzywacz A. DAT1 methylation changes in alcohol-dependent individuals vs. controls. J Psychiatr Res 2015; 64:130-3. [PMID: 25862379 DOI: 10.1016/j.jpsychires.2015.03.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 03/13/2015] [Accepted: 03/13/2015] [Indexed: 01/12/2023]
Abstract
INTRODUCTION The dopaminergic system plays a crucial role in the development of alcohol dependence. Regulation of the extracellular dopamine concentration is driven by dopamine transporter. Both, the expression and function of dopamine transporter, are influenced by chronic alcohol intake. Dopamine transporter (DAT) gene is also supposed to be differentially methylated in alcohol-dependent patients than in controls. MATERIAL AND METHODS DNA was extracted from peripheral blood leukocytes. We analyzed the methylation status in 23 CpG islands of DAT gene promoter in alcohol dependent subjects (n = 171) and control (n = 160) group. RESULTS No statistical differences in the general frequency of DAT CpG islands was revealed between patients (altogether 175 methylated islands) and control subjects (170 methylated islands (p = 0.86). However it was revealed that one of analyzed positions is significantly more often methylated in control subjects than in alcohol dependent individuals (p = 0.0296). CONCLUSION Further subsequent studies are necessary to determine whether the methylation change of one (out of 23) CpG site results in DAT expression changes.
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Affiliation(s)
- Andrzej Jasiewicz
- Department of Psychiatry, Pomeranian Medical University, Broniewskiego 26, 71-460 Szczecin, Poland
| | - Błażej Rubiś
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Przybyszewskiego 49, 60-355 Poznan, Poland
| | - Jerzy Samochowiec
- Department of Psychiatry, Pomeranian Medical University, Broniewskiego 26, 71-460 Szczecin, Poland
| | - Iwona Małecka
- Department of Psychiatry, Pomeranian Medical University, Broniewskiego 26, 71-460 Szczecin, Poland
| | - Aleksandra Suchanecka
- Department of Psychiatry, Pomeranian Medical University, Broniewskiego 26, 71-460 Szczecin, Poland
| | - Marcin Jabłoński
- Department of Psychiatry, Pomeranian Medical University, Broniewskiego 26, 71-460 Szczecin, Poland
| | - Anna Grzywacz
- Department of Psychiatry, Pomeranian Medical University, Broniewskiego 26, 71-460 Szczecin, Poland.
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de Paula WBM, Agip ANA, Missirlis F, Ashworth R, Vizcay-Barrena G, Lucas CH, Allen JF. Female and male gamete mitochondria are distinct and complementary in transcription, structure, and genome function. Genome Biol Evol 2014; 5:1969-77. [PMID: 24068653 PMCID: PMC3814205 DOI: 10.1093/gbe/evt147] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Respiratory electron transport in mitochondria is coupled to ATP synthesis while generating mutagenic oxygen free radicals. Mitochondrial DNA mutation then accumulates with age, and may set a limit to the lifespan of individual, multicellular organisms. Why is this mutation not inherited? Here we demonstrate that female gametes—oocytes—have unusually small and simple mitochondria that are suppressed for DNA transcription, electron transport, and free radical production. By contrast, male gametes—sperm—and somatic cells of both sexes transcribe mitochondrial genes for respiratory electron carriers and produce oxygen free radicals. This germ-line division between mitochondria of sperm and egg is observed in both the vinegar fruitfly and the zebrafish—species spanning a major evolutionary divide within the animal kingdom. We interpret these findings as an evidence that oocyte mitochondria serve primarily as genetic templates, giving rise, irreversibly and in each new generation, to the familiar energy-transducing mitochondria of somatic cells and male gametes. Suppressed mitochondrial metabolism in the female germ line may therefore constitute a mechanism for increasing the fidelity of mitochondrial DNA inheritance.
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Affiliation(s)
- Wilson B M de Paula
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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Priya A, Johar K, Nair B, Wong-Riley MTT. Specificity protein 4 (Sp4) regulates the transcription of AMPA receptor subunit GluA2 (Gria2). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1196-206. [PMID: 24576410 DOI: 10.1016/j.bbamcr.2014.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 11/24/2022]
Abstract
The alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are important glutamatergic receptors mediating fast excitatory synaptic transmission in the brain. The regulation of the four subunits of AMPA receptors, GluA1-4, is poorly understood. Excitatory synaptic transmission is highly energy-demanding, and this energy is derived mainly from the oxidative pathway. Recently, we found that specificity factor regulates all subunits of cytochrome c oxidase (COX), a critical energy-generating enzyme. COX is also regulated by nuclear respiratory factor 1 (NRF-1), which transcriptionally controls the Gria2 (GluA2) gene of AMPA receptors. The goal of the present study was to test our hypothesis that Sp-factors (Sp1, Sp3, and/or Sp4) also regulate AMPA subunit genes. If so, we wish to determine if Sp-factors and NRF-1 function via a complementary, concurrent and parallel, or a combination of complementary and concurrent/parallel mechanism. By means of multiple approaches, including electrophoretic mobility shift and supershift assays, chromatin immunoprecipitation, promoter mutations, real-time quantitative PCR, and western blot analysis, we found that Sp4, but not Sp1 or Sp3, regulates the Gria2, but not Gria1, 3, or 4, subunit gene of the AMPA receptor in a concurrent and parallel manner with NRF-1. Thus, Sp4 and NRF-1 both mediate the tight coupling between neuronal activity and energy metabolism at the transcriptional level.
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Affiliation(s)
- Anusha Priya
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Kaid Johar
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Bindu Nair
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Margaret T T Wong-Riley
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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Johar K, Priya A, Wong-Riley MTT. Regulation of Na(+)/K(+)-ATPase by neuron-specific transcription factor Sp4: implication in the tight coupling of energy production, neuronal activity and energy consumption in neurons. Eur J Neurosci 2013; 39:566-78. [PMID: 24219545 DOI: 10.1111/ejn.12415] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 12/24/2022]
Abstract
A major source of energy demand in neurons is the Na(+)/K(+)-ATPase pump that restores the ionic gradient across the plasma membrane subsequent to depolarizing neuronal activity. The energy comes primarily from mitochondrial oxidative metabolism, of which cytochrome c oxidase (COX) is a key enzyme. Recently, we found that all 13 subunits of COX are regulated by specificity (Sp) factors, and that the neuron-specific Sp4, but not Sp1 or Sp3, regulates the expression of key glutamatergic receptor subunits as well. The present study sought to test our hypothesis that Sp4 also regulates Na(+)/K(+)-ATPase subunit genes in neurons. By means of multiple approaches, including in silico analysis, electrophoretic mobility shift and supershift assays, chromatin immunoprecipitation, promoter mutational analysis, over-expression, and RNA interference studies, we found that Sp4, with minor contributions from Sp1 and Sp3, functionally regulate the Atp1a1, Atp1a3, and Atp1b1 subunit genes of Na(+)/K(+)-ATPase in neurons. Transcripts of all three genes were up-regulated by depolarizing KCl stimulation and down-regulated by the impulse blocker tetrodotoxin (TTX), indicating that their expression was activity-dependent. Silencing of Sp4 blocked the up-regulation of these genes induced by KCl, whereas over-expression of Sp4 rescued them from TTX-induced suppression. The effect of silencing or over-expressing Sp4 on primary neurons was much greater than those of Sp1 or Sp3. The binding sites of Sp factors on these genes are conserved among mice, rats and humans. Thus, Sp4 plays an important role in the transcriptional coupling of energy generation and energy consumption in neurons.
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Affiliation(s)
- Kaid Johar
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
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Johar K, Priya A, Dhar S, Liu Q, Wong-Riley MTT. Neuron-specific specificity protein 4 bigenomically regulates the transcription of all mitochondria- and nucleus-encoded cytochrome c oxidase subunit genes in neurons. J Neurochem 2013; 127:496-508. [PMID: 24032355 DOI: 10.1111/jnc.12433] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 08/20/2013] [Accepted: 08/21/2013] [Indexed: 12/20/2022]
Abstract
Neurons are highly dependent on oxidative metabolism for their energy supply, and cytochrome c oxidase (COX) is a key energy-generating enzyme in the mitochondria. A unique feature of COX is that it is one of only four proteins in mammalian cells that are bigenomically regulated. Of its thirteen subunits, three are encoded in the mitochondrial genome and ten are nuclear-encoded on nine different chromosomes. The mechanism of regulating this multisubunit, bigenomic enzyme poses a distinct challenge. In recent years, we found that nuclear respiratory factors 1 and 2 (NRF-1 and NRF-2) mediate such bigenomic coordination. The latest candidate is the specificity factor (Sp) family of proteins. In N2a cells, we found that Sp1 regulates all 13 COX subunits. However, we discovered recently that in primary neurons, it is Sp4 and not Sp1 that regulates some of the key glutamatergic receptor subunit genes. The question naturally arises as to the role of Sp4 in regulating COX in primary neurons. The present study utilized multiple approaches, including chromatin immunoprecipitation, promoter mutational analysis, knockdown and over-expression of Sp4, as well as functional assays to document that Sp4 indeed functionally regulate all 13 subunits of COX as well as mitochondrial transcription factors A and B. The present study discovered that among the specificity family of transcription factors, it is the less known neuron-specific Sp4 that regulates the expression of all 13 subunits of mitochondrial cytochrome c oxidase (COX) enzyme in primary neurons. Sp4 also regulates the three mitochondrial transcription factors (TFAM, TFB1M, and TFB2M) and a COX assembly protein SURF-1 in primary neurons.
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Affiliation(s)
- Kaid Johar
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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15
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Priya A, Johar K, Wong-Riley MTT. Specificity protein 4 functionally regulates the transcription of NMDA receptor subunits GluN1, GluN2A, and GluN2B. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1833:2745-2756. [PMID: 23871830 DOI: 10.1016/j.bbamcr.2013.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/03/2013] [Accepted: 07/08/2013] [Indexed: 10/26/2022]
Abstract
N-Methyl-d-aspartate (NMDA) receptors are major glutamatergic receptors involved in most excitatory neurotransmission in the brain. The transcriptional regulation of NMDA receptors is not fully understood. Previously, we found that the GluN1 and GluN2B subunits of the NMDA receptor are regulated by nuclear respiratory factors 1 and 2 (NRF-1 and NRF-2). NRF-1 and NRF-2 also regulate all 13 subunits of cytochrome c oxidase (COX), a critical energy-generating enzyme, thereby coupling neuronal activity and energy metabolism at the transcriptional level. Specificity protein (Sp) is a family of transcription factors that bind to GC-rich regions, with Sp1, Sp3, and Sp4 all binding to the same cis- motifs. Sp1 and Sp3 are ubiquitously expressed, whereas Sp4 expression is restricted to neurons and testicular cells. Recently, we found that the Sp1 factor regulates all subunits of COX. The goal of the present study was to test our hypothesis that the Sp factors also regulate specific subunits of NMDA receptors, and that they function with NRF-1 and NRF-2 via one of three mechanisms: complementary, concurrent and parallel, or a combination of complementary and concurrent/parallel. By means of multiple approaches we found that Sp4 functionally regulated GluN1, GluN2A, and GluN2B, but not GluN2C. On the other hand, Sp1 and Sp3 did not regulate these subunits as previously thought. Our data suggest that Sp4 operates in a complementary and concurrent/parallel manner with NRF-1 and NRF-2 to mediate the tight coupling between energy metabolism and neuronal activity at the molecular level.
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Affiliation(s)
- Anusha Priya
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Kaid Johar
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Margaret T T Wong-Riley
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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