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Zhang Y, Zou R, Abudureyimu M, Liu Q, Ma J, Xu H, Yu W, Yang J, Jia J, Qian S, Wang H, Yang Y, Wang X, Fan X, Ren J. Mitochondrial aldehyde dehydrogenase rescues against diabetic cardiomyopathy through GSK3β-mediated preservation of mitochondrial integrity and Parkin-mediated mitophagy. J Mol Cell Biol 2024; 15:mjad056. [PMID: 37771085 PMCID: PMC11193060 DOI: 10.1093/jmcb/mjad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 04/19/2023] [Accepted: 09/27/2023] [Indexed: 09/30/2023] Open
Abstract
Mitochondrial aldehyde dehydrogenase (ALDH2) offers proven cardiovascular benefit, although its impact on diabetes remains elusive. This study examined the effects of ALDH2 overexpression and knockout on diabetic cardiomyopathy and the mechanism involved with a focus on mitochondrial integrity. Mice challenged with streptozotocin (STZ, 200 mg/kg, via intraperitoneal injection) exhibited pathological alterations, including reduced respiratory exchange ratio, dampened fractional shortening and ejection fraction, increased left ventricular end-systolic and diastolic diameters, cardiac remodeling, cardiomyocyte contractile anomalies, intracellular Ca2+ defects, myocardial ultrastructural injury, oxidative stress, apoptosis, and mitochondrial damage, which were overtly attenuated or accentuated by ALDH2 overexpression or knockout, respectively. Diabetic patients also exhibited reduced plasma ALDH2 activity, cardiac remodeling, and diastolic dysfunction. In addition, STZ challenge altered expression levels of mitochondrial proteins (PGC-1α and UCP2) and Ca2+ regulatory proteins (SERCA, Na+-Ca2+ exchanger, and phospholamban), dampened autophagy and mitophagy (LC3B ratio, TOM20, Parkin, FUNDC1, and BNIP3), disrupted phosphorylation of Akt, GSK3β, and Foxo3a, and elevated PTEN phosphorylation, most of which were reversed or worsened by ALDH2 overexpression or knockout, respectively. Furthermore, the novel ALDH2 activator torezolid, as well as the classical ALDH2 activator Alda-1, protected against STZ- or high glucose-induced in vivo or in vitro cardiac anomalies, which was nullified by inhibition of Akt, GSK3β, Parkin, or mitochondrial coupling. Our data discerned a vital role for ALDH2 in diabetic cardiomyopathy possibly through regulation of Akt and GSK3β activation, Parkin mitophagy, and mitochondrial function.
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Affiliation(s)
- Yingmei Zhang
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai 710032, China
- National Clinical Research Center for Interventional Medicine, Shanghai 200032, China
| | - Rongjun Zou
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Miyesaier Abudureyimu
- National Clinical Research Center for Interventional Medicine, Shanghai 200032, China
- Cardiovascular Department, Shanghai Xuhui Central Hospital, Fudan University, Shanghai 200031, China
| | - Qiong Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences and Medicine, Northwest University, Xi'an 710069, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, School of Life Sciences and Medicine, Northwest University, Xi'an 710069, China
| | - Jipeng Ma
- Department of Cardiovascular Surgery, Xijing Hospital, Air Force Medical University, Xi'an 710032, China
| | - Haixia Xu
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai 710032, China
- National Clinical Research Center for Interventional Medicine, Shanghai 200032, China
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Wei Yu
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Jian Yang
- Department of Cardiovascular Surgery, Xijing Hospital, Air Force Medical University, Xi'an 710032, China
| | - Jianguo Jia
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai 710032, China
- National Clinical Research Center for Interventional Medicine, Shanghai 200032, China
| | - Sanli Qian
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai 710032, China
- National Clinical Research Center for Interventional Medicine, Shanghai 200032, China
| | - Haichang Wang
- Xi'an International Medical Center Hospital Affiliated to Northwest University, Xi'an 710077, China
| | - Yang Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences and Medicine, Northwest University, Xi'an 710069, China
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, The Affiliated Hospital of Northwest University, School of Life Sciences and Medicine, Northwest University, Xi'an 710069, China
| | - Xin Wang
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9GB, UK
| | - Xiaoping Fan
- Department of Cardiovascular Surgery, Guangdong Provincial Hospital of Chinese Medicine, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jun Ren
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai 710032, China
- National Clinical Research Center for Interventional Medicine, Shanghai 200032, China
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Faiq MA, Sengupta T, Nath M, Velpandian T, Saluja D, Dada R, Dada T, Chan KC. Ocular manifestations of central insulin resistance. Neural Regen Res 2022; 18:1139-1146. [PMID: 36255004 PMCID: PMC9827783 DOI: 10.4103/1673-5374.355765] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Central insulin resistance, the diminished cellular sensitivity to insulin in the brain, has been implicated in diabetes mellitus, Alzheimer's disease and other neurological disorders. However, whether and how central insulin resistance plays a role in the eye remains unclear. Here, we performed intracerebroventricular injection of S961, a potent and specific blocker of insulin receptor in adult Wistar rats to test if central insulin resistance leads to pathological changes in ocular structures. 80 mg of S961 was stereotaxically injected into the lateral ventricle of the experimental group twice at 7 days apart, whereas buffer solution was injected to the sham control group. Blood samples, intraocular pressure, trabecular meshwork morphology, ciliary body markers, retinal and optic nerve integrity, and whole genome expression patterns were then evaluated. While neither blood glucose nor serum insulin level was significantly altered in the experimental or control group, we found that injection of S961 but not buffer solution significantly increased intraocular pressure at 14 and 24 days after first injection, along with reduced porosity and aquaporin 4 expression in the trabecular meshwork, and increased tumor necrosis factor α and aquaporin 4 expression in the ciliary body. In the retina, cell density and insulin receptor expression decreased in the retinal ganglion cell layer upon S961 injection. Fundus photography revealed peripapillary atrophy with vascular dysregulation in the experimental group. These retinal changes were accompanied by upregulation of pro-inflammatory and pro-apoptotic genes, downregulation of anti-inflammatory, anti-apoptotic, and neurotrophic genes, as well as dysregulation of genes involved in insulin signaling. Optic nerve histology indicated microglial activation and changes in the expression of glial fibrillary acidic protein, tumor necrosis factor α, and aquaporin 4. Molecular pathway architecture of the retina revealed the three most significant pathways involved being inflammation/cell stress, insulin signaling, and extracellular matrix regulation relevant to neurodegeneration. There was also a multimodal crosstalk between insulin signaling derangement and inflammation-related genes. Taken together, our results indicate that blocking insulin receptor signaling in the central nervous system can lead to trabecular meshwork and ciliary body dysfunction, intraocular pressure elevation, as well as inflammation, glial activation, and apoptosis in the retina and optic nerve. Given that central insulin resistance may lead to neurodegenerative phenotype in the visual system, targeting insulin signaling may hold promise for vision disorders involving the retina and optic nerve.
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Affiliation(s)
- Muneeb A. Faiq
- Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India,Neuroimaging and Visual Science Laboratory, Department of Ophthalmology, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, NY, USA,Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Trina Sengupta
- Dr. Baldev Singh Sleep Laboratory, Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Madhu Nath
- Department of Ocular Pharmacology, Dr. Rajendra Prasad Center for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Thirumurthy Velpandian
- Department of Ocular Pharmacology, Dr. Rajendra Prasad Center for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - Daman Saluja
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Rima Dada
- Laboratory for Molecular Reproduction and Genetics, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
| | - Tanuj Dada
- Dr. Rajendra Prasad Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India,Correspondence to: Tanuj Dada, ; Kevin C. Chan, .
| | - Kevin C. Chan
- Neuroimaging and Visual Science Laboratory, Department of Ophthalmology, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, NY, USA,Correspondence to: Tanuj Dada, ; Kevin C. Chan, .
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Tanave A, Imai Y, Koide T. Nested retrotransposition in the East Asian mouse genome causes the classical nonagouti mutation. Commun Biol 2019; 2:283. [PMID: 31396563 PMCID: PMC6677723 DOI: 10.1038/s42003-019-0539-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 07/10/2019] [Indexed: 01/31/2023] Open
Abstract
Black coat color (nonagouti) is a widespread classical mutation in laboratory mouse strains. The intronic insertion of endogenous retrovirus VL30 in the nonagouti (a) allele of agouti gene was previously reported as the cause of the nonagouti phenotype. Here, we report agouti mouse strains from East Asia that carry the VL30 insertion, indicating that VL30 alone does not cause the nonagouti phenotype. We find that a rare type of endogenous retrovirus, β4, was integrated into the VL30 region at the a allele through nested retrotransposition, causing abnormal splicing. Targeted complete deletion of the β4 element restores agouti gene expression and agouti coat color, whereas deletion of β4 except for a single long terminal repeat results in black-and-tan coat color. Phylogenetic analyses show that the a allele and the β4 retrovirus originated from an East Asian mouse lineage most likely related to Japanese fancy mice. These findings reveal the causal mechanism and historic origin of the classical nonagouti mutation.
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Affiliation(s)
- Akira Tanave
- Mouse Genomics Resource Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540 Japan
- Present Address: Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 1–3 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Yuji Imai
- Mouse Genomics Resource Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540 Japan
| | - Tsuyoshi Koide
- Mouse Genomics Resource Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540 Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540 Japan
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Buckley L, Lacey M, Ehrlich M. Epigenetics of the myotonic dystrophy-associated DMPK gene neighborhood. Epigenomics 2016; 8:13-31. [PMID: 26756355 PMCID: PMC4863877 DOI: 10.2217/epi.15.104] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: Identify epigenetic marks in the vicinity of DMPK (linked to myotonic dystrophy, DM1) that help explain tissue-specific differences in its expression. Materials & methods: At DMPK and its flanking genes (DMWD, SIX5, BHMG1 and RSPH6A), we analyzed many epigenetic and transcription profiles from myoblasts, myotubes, skeletal muscle, heart and 30 nonmuscle samples. Results: In the DMPK gene neighborhood, muscle-associated DNA hypermethylation and hypomethylation, enhancer chromatin, and CTCF binding were seen. Myogenic DMPK hypermethylation correlated with high expression and decreased alternative promoter usage. Testis/sperm hypomethylation of BHMG1 and RSPH6A was associated with testis-specific expression. G-quadruplex (G4) motifs and sperm-specific hypomethylation were found near the DM1-linked CTG repeats within DMPK. Conclusion: Tissue-specific epigenetic features in DMPK and neighboring genes help regulate its expression. G4 motifs in DMPK DNA and RNA might contribute to DM1 pathology.
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Affiliation(s)
- Lauren Buckley
- Human Genetics Program, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michelle Lacey
- Tulane Cancer Center & Department of Mathematics, Tulane University, New Orleans, LA 70112, USA
| | - Melanie Ehrlich
- Human Genetics Program, Center for Bioinformatics & Genomics, Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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Mogessie B, Roth D, Rahil Z, Straube A. A novel isoform of MAP4 organises the paraxial microtubule array required for muscle cell differentiation. eLife 2015; 4:e05697. [PMID: 25898002 PMCID: PMC4423121 DOI: 10.7554/elife.05697] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/19/2015] [Indexed: 12/22/2022] Open
Abstract
The microtubule cytoskeleton is critical for muscle cell differentiation and undergoes reorganisation into an array of paraxial microtubules, which serves as template for contractile sarcomere formation. In this study, we identify a previously uncharacterised isoform of microtubule-associated protein MAP4, oMAP4, as a microtubule organising factor that is crucial for myogenesis. We show that oMAP4 is expressed upon muscle cell differentiation and is the only MAP4 isoform essential for normal progression of the myogenic differentiation programme. Depletion of oMAP4 impairs cell elongation and cell–cell fusion. Most notably, oMAP4 is required for paraxial microtubule organisation in muscle cells and prevents dynein- and kinesin-driven microtubule–microtubule sliding. Purified oMAP4 aligns dynamic microtubules into antiparallel bundles that withstand motor forces in vitro. We propose a model in which the cooperation of dynein-mediated microtubule transport and oMAP4-mediated zippering of microtubules drives formation of a paraxial microtubule array that provides critical support for the polarisation and elongation of myotubes. DOI:http://dx.doi.org/10.7554/eLife.05697.001 Skeletal muscles—which enable animals to move—are made up of large elongated muscle cells that span the entire length of the muscle. These cells contain stacks of structures called sarcomeres that enable the cells to contract and generate the force required for movement. Cells called myoblasts elongate and fuse together at their tips to make the muscle cells. Within the myoblasts, long filaments called microtubules are arranged in an overlapping linear pattern. The filaments act as a template that helps the sarcomeres to align as the muscle cells form. A family of microtubule-associated proteins (or ‘MAPs’ for short) bind to microtubules and assist in organising the filaments, but it is not clear how they work. Mogessie et al. used microscopy to observe the formation of the microtubule filaments in living myoblasts. The experiments show that the filaments progressively become more ordered as the myoblasts develop into muscle cells. Mogessie et al. identified a new member of the MAP family that is produced in myoblasts as soon as they start to form muscle fibres, and named it oMAP4. The microtubules in cells that make smaller amounts of this protein were more disorganised, and these cells were unable to fuse with each other to form muscle cells. The experiments also found that oMAP4 can create links between different microtubules and act as a brake to prevent the filaments being moved excessively by motor proteins. Therefore, Mogessie et al. suggest that oMAP4 contributes to the formation of a strong and stable arrangement of filaments. This, in turn, allows the muscle cells to become very long. Making more oMAP4 alone is not sufficient to form the elongated muscle cells. Therefore, the next challenge is to understand how other processes—such as the selective stabilisation of some microtubules and the movement of cell materials along the microtubules—cooperate to control muscle fibre formation. DOI:http://dx.doi.org/10.7554/eLife.05697.002
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Affiliation(s)
- Binyam Mogessie
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Daniel Roth
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Zainab Rahil
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Anne Straube
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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Barash Y, Vaquero-Garcia J, González-Vallinas J, Xiong HY, Gao W, Lee LJ, Frey BJ. AVISPA: a web tool for the prediction and analysis of alternative splicing. Genome Biol 2014; 14:R114. [PMID: 24156756 PMCID: PMC4014802 DOI: 10.1186/gb-2013-14-10-r114] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/11/2013] [Indexed: 11/10/2022] Open
Abstract
Transcriptome complexity and its relation to numerous diseases underpins the need to predict in silico splice variants and the regulatory elements that affect them. Building upon our recently described splicing code, we developed AVISPA, a Galaxy-based web tool for splicing prediction and analysis. Given an exon and its proximal sequence, the tool predicts whether the exon is alternatively spliced, displays tissue-dependent splicing patterns, and whether it has associated regulatory elements. We assess AVISPA's accuracy on an independent dataset of tissue-dependent exons, and illustrate how the tool can be applied to analyze a gene of interest. AVISPA is available at http://avispa.biociphers.org.
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Dippold RP, Fisher SA. A bioinformatic and computational study of myosin phosphatase subunit diversity. Am J Physiol Regul Integr Comp Physiol 2014; 307:R256-70. [PMID: 24898838 PMCID: PMC4121627 DOI: 10.1152/ajpregu.00145.2014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 05/25/2014] [Indexed: 01/01/2023]
Abstract
Variability in myosin phosphatase (MP) subunits may provide specificity in signaling pathways that regulate muscle tone. We utilized public databases and computational algorithms to investigate the phylogenetic diversity of MP regulatory (PPP1R12A-C) and inhibitory (PPP1R14A-D) subunits. The comparison of exonic coding sequences and expression data confirmed or refuted the existence of isoforms and their tissue-specific expression in different model organisms. The comparison of intronic and exonic sequences identified potential expressional regulatory elements. As examples, smooth muscle MP regulatory subunit (PPP1R12A) is highly conserved through evolution. Its alternative exon E24 is present in fish through mammals with two invariant features: 1) a reading frame shift generating a premature termination codon and 2) a hexanucleotide sequence adjacent to the 3' splice site hypothesized to be a novel suppressor of exon splicing. A characteristic of the striated muscle MP regulatory subunit (PPP1R12B) locus is numerous and phylogenetically variable transcriptional start sites. In fish this locus only codes for the small (M21) subunit, suggesting the primordial function of this gene. Inhibitory subunits show little intragenic variability; their diversity is thought to have arisen by expansion and tissue-specific expression of different gene family members. We demonstrate differences in the regulatory landscape between smooth muscle enriched (PPP1R14A) and more ubiquitously expressed (PPP1R14B) family members and identify deeply conserved intronic sequence and predicted transcriptional cis-regulatory elements. This bioinformatic and computational study has uncovered a number of attributes of MP subunits that supports selection of ideal model organisms and testing of hypotheses regarding their physiological significance and regulated expression.
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Affiliation(s)
- Rachael P Dippold
- Department of Medicine, Cardiology, University of Maryland Baltimore, Baltimore, Maryland
| | - Steven A Fisher
- Department of Medicine, Cardiology, University of Maryland Baltimore, Baltimore, Maryland
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Qiu H, Gołas A, Grzmil P, Wojnowski L. Lineage-specific duplications of Muroidea Faim and Spag6 genes and atypical accelerated evolution of the parental Spag6 gene. J Mol Evol 2013; 77:119-29. [PMID: 24071998 DOI: 10.1007/s00239-013-9585-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 09/16/2013] [Indexed: 12/01/2022]
Abstract
Gene duplications restricted to single lineage combined with an asymmetric evolution of the resulting genes may play particularly important roles in this lineage's biology. We searched and identified asymmetrical evolution in nine gene families that duplicated exclusively in rodents and are present as single-copies in human, dog, cow, elephant, opossum, chicken, lizard, and Western clawed frog. Among those nine gene families are Fas apoptosis inhibitory molecule (Faim), implicated in apoptosis, and Sperm antigen 6 (Spag6), implicated in sperm mobility. Both genes were duplicated in or before the Muroidea ancestor. Due to the highly asymmetric evolution of the resulting paralogs, the existence of these duplications had been previously overlooked. Interestingly, Spag6, previously regarded and characterized as a single-copy ortholog of human Spag6, turns out to be a Muroidea-specific paralog. Conversely, the newly identified, highly divergent Spag6-BC061194 is in fact the parental gene. In consequence, this gene represents a rare exception from the general rule of rapid evolution of derived rather than parental genes following gene duplication. Unusual genes such as murine Spag6 may help to understand which mechanisms are responsible for this rule.
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Affiliation(s)
- Huan Qiu
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany,
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9
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Ikeda R, Shiura H, Numata K, Sugimoto M, Kondo M, Mise N, Suzuki M, Greally JM, Abe K. Large, male germ cell-specific hypomethylated DNA domains with unique genomic and epigenomic features on the mouse X chromosome. DNA Res 2013; 20:549-65. [PMID: 23861320 PMCID: PMC3859323 DOI: 10.1093/dnares/dst030] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
To understand the epigenetic regulation required for germ cell-specific gene expression in the mouse, we analysed DNA methylation profiles of developing germ cells using a microarray-based assay adapted for a small number of cells. The analysis revealed differentially methylated sites between cell types tested. Here, we focused on a group of genomic sequences hypomethylated specifically in germline cells as candidate regions involved in the epigenetic regulation of germline gene expression. These hypomethylated sequences tend to be clustered, forming large (10 kb to ∼9 Mb) genomic domains, particularly on the X chromosome of male germ cells. Most of these regions, designated here as large hypomethylated domains (LoDs), correspond to segmentally duplicated regions that contain gene families showing germ cell- or testis-specific expression, including cancer testis antigen genes. We found an inverse correlation between DNA methylation level and expression of genes in these domains. Most LoDs appear to be enriched with H3 lysine 9 dimethylation, usually regarded as a repressive histone modification, although some LoD genes can be expressed in male germ cells. It thus appears that such a unique epigenomic state associated with the LoDs may constitute a basis for the specific expression of genes contained in these genomic domains.
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Affiliation(s)
- Rieko Ikeda
- 1Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba City, Ibaraki 305-0074, Japan
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10
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van Heesch S, Mokry M, Boskova V, Junker W, Mehon R, Toonen P, de Bruijn E, Shull JD, Aitman TJ, Cuppen E, Guryev V. Systematic biases in DNA copy number originate from isolation procedures. Genome Biol 2013; 14:R33. [PMID: 23618369 PMCID: PMC4054094 DOI: 10.1186/gb-2013-14-4-r33] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 04/24/2013] [Indexed: 11/18/2022] Open
Abstract
Background The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal. Results While GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing. Conclusion These results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses.
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11
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Bidirectional promoters as important drivers for the emergence of species-specific transcripts. PLoS One 2013; 8:e57323. [PMID: 23460838 PMCID: PMC3583895 DOI: 10.1371/journal.pone.0057323] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 01/21/2013] [Indexed: 11/23/2022] Open
Abstract
The diversification of gene functions has been largely attributed to the process of gene duplication. Novel examples of genes originating from previously untranscribed regions have been recently described without regard to a unifying functional mechanism for their emergence. Here we propose a model mechanism that could generate a large number of lineage-specific novel transcripts in vertebrates through the activation of bidirectional transcription from unidirectional promoters. We examined this model in silico using human transcriptomic and genomic data and identified evidence consistent with the emergence of more than 1,000 primate-specific transcripts. These are transcripts with low coding potential and virtually no functional annotation. They initiate at less than 1 kb upstream of an oppositely transcribed conserved protein coding gene, in agreement with the generally accepted definition of bidirectional promoters. We found that the genomic regions upstream of ancestral promoters, where the novel transcripts in our dataset reside, are characterized by preferential accumulation of transposable elements. This enhances the sequence diversity of regions located upstream of ancestral promoters, further highlighting their evolutionary importance for the emergence of transcriptional novelties. By applying a newly developed test for positive selection to transposable element-derived fragments in our set of novel transcripts, we found evidence of adaptive evolution in the human lineage in nearly 3% of the novel transcripts in our dataset. These findings indicate that at least some novel transcripts could become functionally relevant, and thus highlight the evolutionary importance of promoters, through their capacity for bidirectional transcription, for the emergence of novel genes.
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Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R, Pedersen JS. New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res 2011; 21:1929-43. [PMID: 21994249 DOI: 10.1101/gr.112516.110] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Regulatory RNA structures are often members of families with multiple paralogous instances across the genome. Family members share functional and structural properties, which allow them to be studied as a whole, facilitating both bioinformatic and experimental characterization. We have developed a comparative method, EvoFam, for genome-wide identification of families of regulatory RNA structures, based on primary sequence and secondary structure similarity. We apply EvoFam to a 41-way genomic vertebrate alignment. Genome-wide, we identify 220 human, high-confidence families outside protein-coding regions comprising 725 individual structures, including 48 families with known structural RNA elements. Known families identified include both noncoding RNAs, e.g., miRNAs and the recently identified MALAT1/MEN β lincRNA family; and cis-regulatory structures, e.g., iron-responsive elements. We also identify tens of new families supported by strong evolutionary evidence and other statistical evidence, such as GO term enrichments. For some of these, detailed analysis has led to the formulation of specific functional hypotheses. Examples include two hypothesized auto-regulatory feedback mechanisms: one involving six long hairpins in the 3'-UTR of MAT2A, a key metabolic gene that produces the primary human methyl donor S-adenosylmethionine; the other involving a tRNA-like structure in the intron of the tRNA maturation gene POP1. We experimentally validate the predicted MAT2A structures. Finally, we identify potential new regulatory networks, including large families of short hairpins enriched in immunity-related genes, e.g., TNF, FOS, and CTLA4, which include known transcript destabilizing elements. Our findings exemplify the diversity of post-transcriptional regulation and provide a resource for further characterization of new regulatory mechanisms and families of noncoding RNAs.
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Affiliation(s)
- Brian J Parker
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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