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Bogush N, Tan L, Naib H, Faizullabhoy E, Calvert JW, Iismaa SE, Gupta A, Ramchandran R, Martin DIK, Graham RM, Husain A, Naqvi N. DUSP5 expression in left ventricular cardiomyocytes of young hearts regulates thyroid hormone (T3)-induced proliferative ERK1/2 signaling. Sci Rep 2020; 10:21918. [PMID: 33318551 PMCID: PMC7736286 DOI: 10.1038/s41598-020-78825-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/27/2020] [Indexed: 02/01/2023] Open
Abstract
Cardiomyocytes of newborn mice proliferate after injury or exposure to growth factors. However, these responses are diminished after postnatal day-6 (P6), representing a barrier to building new cardiac muscle in adults. We have previously shown that exogenous thyroid hormone (T3) stimulates cardiomyocyte proliferation in P2 cardiomyocytes, by activating insulin-like growth factor-1 receptor (IGF-1R)-mediated ERK1/2 signaling. But whether exogenous T3 functions as a mitogen in post-P6 murine hearts is not known. Here, we show that exogenous T3 increases the cardiomyocyte endowment of P8 hearts, but the proliferative response is confined to cardiomyocytes of the left ventricular (LV) apex. Exogenous T3 stimulates proliferative ERK1/2 signaling in apical cardiomyocytes, but not in those of the LV base, which is inhibited by expression of the nuclear phospho-ERK1/2-specific dual-specificity phosphatase, DUSP5. Developmentally, between P7 and P14, DUSP5 expression increases in the myocardium from the LV base to its apex; after this period, it is uniformly expressed throughout the LV. In young adult hearts, exogenous T3 increases cardiomyocyte numbers after DUSP5 depletion, which might be useful for eliciting cardiac regeneration.
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Affiliation(s)
- Nikolay Bogush
- Department of Medicine (Cardiology), Emory University School of Medicine, 323 WMRB, 101 Woodruff Circle, Atlanta, GA, 30322, USA
| | - Lin Tan
- Department of Medicine (Cardiology), Emory University School of Medicine, 323 WMRB, 101 Woodruff Circle, Atlanta, GA, 30322, USA
| | - Hussain Naib
- Department of Medicine (Cardiology), Emory University School of Medicine, 323 WMRB, 101 Woodruff Circle, Atlanta, GA, 30322, USA
| | - Ebrahim Faizullabhoy
- Department of Medicine (Cardiology), Emory University School of Medicine, 323 WMRB, 101 Woodruff Circle, Atlanta, GA, 30322, USA
| | - John W Calvert
- Department of Surgery, Carlyle Fraser Heart Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Siiri E Iismaa
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Ankan Gupta
- Developmental Vascular Biology Program, Division of Neonatology, Department of Pediatrics, Department of Obstetrics and Gynecology, Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ramani Ramchandran
- Developmental Vascular Biology Program, Division of Neonatology, Department of Pediatrics, Department of Obstetrics and Gynecology, Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - David I K Martin
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Robert M Graham
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Ahsan Husain
- Department of Medicine (Cardiology), Emory University School of Medicine, 323 WMRB, 101 Woodruff Circle, Atlanta, GA, 30322, USA.
| | - Nawazish Naqvi
- Department of Medicine (Cardiology), Emory University School of Medicine, 323 WMRB, 101 Woodruff Circle, Atlanta, GA, 30322, USA.
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Tan L, Bogush N, Naib H, Perry J, Calvert JW, Martin DIK, Graham RM, Naqvi N, Husain A. Redox activation of JNK2α2 mediates thyroid hormone-stimulated proliferation of neonatal murine cardiomyocytes. Sci Rep 2019; 9:17731. [PMID: 31776360 PMCID: PMC6881338 DOI: 10.1038/s41598-019-53705-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022] Open
Abstract
Mitochondria-generated reactive oxygen species (mROS) are frequently associated with DNA damage and cell cycle arrest, but physiological increases in mROS serve to regulate specific cell functions. T3 is a major regulator of mROS, including hydrogen peroxide (H2O2). Here we show that exogenous thyroid hormone (T3) administration increases cardiomyocyte numbers in neonatal murine hearts. The mechanism involves signaling by mitochondria-generated H2O2 (mH2O2) acting via the redox sensor, peroxiredoxin-1, a thiol peroxidase with high reactivity towards H2O2 that activates c-Jun N-terminal kinase-2α2 (JNK2α2). JNK2α2, a relatively rare member of the JNK family of mitogen-activated protein kinases (MAPK), phosphorylates c-Jun, a component of the activator protein 1 (AP-1) early response transcription factor, resulting in enhanced insulin-like growth factor 1 (IGF-1) expression and activation of proliferative ERK1/2 signaling. This non-canonical mechanism of MAPK activation couples T3 actions on mitochondria to cell cycle activation. Although T3 is regarded as a maturation factor for cardiomyocytes, these studies identify a novel redox pathway that is permissive for T3-mediated cardiomyocyte proliferation—this because of the expression of a pro-proliferative JNK isoform that results in growth factor elaboration and ERK1/2 cell cycle activation.
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Affiliation(s)
- Lin Tan
- Department of Medicine (Cardiology), Emory University School of Medicine, Atlanta, Georgia, USA
| | - Nikolay Bogush
- Department of Medicine (Cardiology), Emory University School of Medicine, Atlanta, Georgia, USA
| | - Hussain Naib
- Department of Medicine (Cardiology), Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jennifer Perry
- Department of Animal Resources, Emory University School of Medicine, Atlanta, Georgia, USA
| | - John W Calvert
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - David I K Martin
- Children's Hospital Oakland Research Institute, Oakland, California, USA
| | - Robert M Graham
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Nawazish Naqvi
- Department of Medicine (Cardiology), Emory University School of Medicine, Atlanta, Georgia, USA.
| | - Ahsan Husain
- Department of Medicine (Cardiology), Emory University School of Medicine, Atlanta, Georgia, USA.
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3
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Chung JE, Magis W, Vu J, Heo SJ, Wartiovaara K, Walters MC, Kurita R, Nakamura Y, Boffelli D, Martin DIK, Corn JE, DeWitt MA. CRISPR-Cas9 interrogation of a putative fetal globin repressor in human erythroid cells. PLoS One 2019; 14:e0208237. [PMID: 30645582 PMCID: PMC6333401 DOI: 10.1371/journal.pone.0208237] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/14/2018] [Indexed: 01/14/2023] Open
Abstract
Sickle Cell Disease and ß-thalassemia, which are caused by defective or deficient adult ß-globin (HBB) respectively, are the most common serious genetic blood diseases in the world. Persistent expression of the fetal ß-like globin, also known as 𝛾-globin, can ameliorate both disorders by serving in place of the adult ß-globin as a part of the fetal hemoglobin tetramer (HbF). Here we use CRISPR-Cas9 gene editing to explore a potential 𝛾-globin silencer region upstream of the δ-globin gene identified by comparison of naturally-occurring deletion mutations associated with up-regulated 𝛾-globin. We find that deletion of a 1.7 kb consensus element or select 350 bp sub-regions from bulk populations of cells increases levels of HbF. Screening of individual sgRNAs in one sub-region revealed three single guides that caused increases in 𝛾-globin expression. Deletion of the 1.7 kb region in HUDEP-2 clonal sublines, and in colonies derived from CD34+ hematopoietic stem/progenitor cells (HSPCs), does not cause significant up-regulation of 𝛾-globin. These data suggest that the 1.7 kb region is not an autonomous 𝛾-globin silencer, and thus by itself is not a suitable therapeutic target for gene editing treatment of ß-hemoglobinopathies.
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Affiliation(s)
- Jennifer E Chung
- Innovative Genomics Institute, University of California, Berkeley, CA, United States of America
| | - Wendy Magis
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, CA, United States of America
| | - Jonathan Vu
- Innovative Genomics Institute, University of California, Berkeley, CA, United States of America
| | - Seok-Jin Heo
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, CA, United States of America
| | - Kirmo Wartiovaara
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, CA, United States of America.,Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Clinical Genetics, HUSLAB, Helsinki University Central Hospital, Helsinki, Finland
| | - Mark C Walters
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, CA, United States of America.,Blood and Marrow Transplant Program, Division of Hematology, UCSF Benioff Children's Hospital, Oakland, CA, United States of America
| | - Ryo Kurita
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan.,Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, CA, United States of America
| | - David I K Martin
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, CA, United States of America
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, CA, United States of America.,Department of Molecular and Cellular Biology, University of California, Berkeley, CA, United States of America
| | - Mark A DeWitt
- Innovative Genomics Institute, University of California, Berkeley, CA, United States of America
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DeWitt MA, Magis W, Bray NL, Wang T, Berman JR, Urbinati F, Heo SJ, Mitros T, Muñoz DP, Boffelli D, Kohn DB, Walters MC, Carroll D, Martin DIK, Corn JE. Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells. Sci Transl Med 2016; 8:360ra134. [PMID: 27733558 PMCID: PMC5500303 DOI: 10.1126/scitranslmed.aaf9336] [Citation(s) in RCA: 317] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/22/2016] [Indexed: 12/19/2022]
Abstract
Genetic diseases of blood cells are prime candidates for treatment through ex vivo gene editing of CD34+ hematopoietic stem/progenitor cells (HSPCs), and a variety of technologies have been proposed to treat these disorders. Sickle cell disease (SCD) is a recessive genetic disorder caused by a single-nucleotide polymorphism in the β-globin gene (HBB). Sickle hemoglobin damages erythrocytes, causing vasoocclusion, severe pain, progressive organ damage, and premature death. We optimize design and delivery parameters of a ribonucleoprotein (RNP) complex comprising Cas9 protein and unmodified single guide RNA, together with a single-stranded DNA oligonucleotide donor (ssODN), to enable efficient replacement of the SCD mutation in human HSPCs. Corrected HSPCs from SCD patients produced less sickle hemoglobin RNA and protein and correspondingly increased wild-type hemoglobin when differentiated into erythroblasts. When engrafted into immunocompromised mice, ex vivo treated human HSPCs maintain SCD gene edits throughout 16 weeks at a level likely to have clinical benefit. These results demonstrate that an accessible approach combining Cas9 RNP with an ssODN can mediate efficient HSPC genome editing, enables investigator-led exploration of gene editing reagents in primary hematopoietic stem cells, and suggests a path toward the development of new gene editing treatments for SCD and other hematopoietic diseases.
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Affiliation(s)
- Mark A DeWitt
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA. Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wendy Magis
- Children's Hospital Oakland Research Institute, University of California San Francisco (UCSF) Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Nicolas L Bray
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA. Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Tianjiao Wang
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA. Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer R Berman
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, CA 94588, USA
| | - Fabrizia Urbinati
- Departments of Microbiology, Immunology, and Molecular Genetics; Pediatrics; and Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Seok-Jin Heo
- Children's Hospital Oakland Research Institute, University of California San Francisco (UCSF) Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Therese Mitros
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Denise P Muñoz
- Children's Hospital Oakland Research Institute, University of California San Francisco (UCSF) Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, University of California San Francisco (UCSF) Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Donald B Kohn
- Departments of Microbiology, Immunology, and Molecular Genetics; Pediatrics; and Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mark C Walters
- Children's Hospital Oakland Research Institute, University of California San Francisco (UCSF) Benioff Children's Hospital, Oakland, CA 94609, USA. Blood and Marrow Transplant Program, Division of Hematology, UCSF Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Dana Carroll
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA. Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - David I K Martin
- Children's Hospital Oakland Research Institute, University of California San Francisco (UCSF) Benioff Children's Hospital, Oakland, CA 94609, USA.
| | - Jacob E Corn
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA. Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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Cropley JE, Eaton SA, Aiken A, Young PE, Giannoulatou E, Ho JWK, Buckland ME, Keam SP, Hutvagner G, Humphreys DT, Langley KG, Henstridge DC, Martin DIK, Febbraio MA, Suter CM. Male-lineage transmission of an acquired metabolic phenotype induced by grand-paternal obesity. Mol Metab 2016; 5:699-708. [PMID: 27656407 PMCID: PMC5021672 DOI: 10.1016/j.molmet.2016.06.008] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/14/2016] [Accepted: 06/16/2016] [Indexed: 12/22/2022] Open
Abstract
Objective Parental obesity can induce metabolic phenotypes in offspring independent of the inherited DNA sequence. Here we asked whether such non-genetic acquired metabolic traits can be passed on to a second generation that has never been exposed to obesity, even as germ cells. Methods We examined the F1, F2, and F3 a/a offspring derived from F0 matings of obese prediabetic Avy/a sires and lean a/a dams. After F0, only lean a/a mice were used for breeding. Results We found that F1 sons of obese founder males exhibited defects in glucose and lipid metabolism, but only upon a post-weaning dietary challenge. F1 males transmitted these defects to their own male progeny (F2) in the absence of the dietary challenge, but the phenotype was largely attenuated by F3. The sperm of F1 males exhibited changes in the abundance of several small RNA species, including the recently reported diet-responsive tRNA-derived fragments. Conclusions These data indicate that induced metabolic phenotypes may be propagated for a generation beyond any direct exposure to an inducing factor. This non-genetic inheritance likely occurs via the actions of sperm noncoding RNA. Paternal obesity induces latent defects in metabolism in F1 sons. Metabolic disease in F1 sons is exposed by short challenge with a Western diet. F1 sons transmit their phenotype to F2 grandsons in the absence of dietary challenge. F1 sperm exhibit changes to prominent small RNA species.
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Affiliation(s)
- Jennifer E Cropley
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales, Kensington, NSW, 2052, Australia.
| | - Sally A Eaton
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales, Kensington, NSW, 2052, Australia
| | - Alastair Aiken
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Paul E Young
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Eleni Giannoulatou
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Joshua W K Ho
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales, Kensington, NSW, 2052, Australia
| | - Michael E Buckland
- Brain and Mind Research Institute, University of Sydney, Sydney, NSW, 2006, Australia
| | - Simon P Keam
- Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Gyorgy Hutvagner
- Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - David T Humphreys
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia
| | - Katherine G Langley
- Cellular and Molecular Metabolism Laboratory, Baker IDI Diabetes and Heart Research Institute, Melbourne, VIC, 3004, Australia
| | - Darren C Henstridge
- Cellular and Molecular Metabolism Laboratory, Baker IDI Diabetes and Heart Research Institute, Melbourne, VIC, 3004, Australia
| | - David I K Martin
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA
| | - Mark A Febbraio
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Catherine M Suter
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia; Faculty of Medicine, University of New South Wales, Kensington, NSW, 2052, Australia.
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Naqvi N, Singh R, Iismaa SE, Li M, Calvert JW, Martin DIK, Harvey RP, Graham RM, Husain A. Cardiomyocytes Replicate and their Numbers Increase in Young Hearts. Cell 2016; 163:783-4. [PMID: 26544928 DOI: 10.1016/j.cell.2015.10.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nawazish Naqvi
- Department of Medicine, Emory University, Atlanta, Georgia 30322, USA
| | - Reena Singh
- Development and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - Siiri E Iismaa
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - Ming Li
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - John W Calvert
- Department of Surgery, Emory University, Atlanta, Georgia 30322, USA
| | - David I K Martin
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
| | - Richard P Harvey
- Development and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - Robert M Graham
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia.
| | - Ahsan Husain
- Department of Medicine, Emory University, Atlanta, Georgia 30322, USA.
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Yamtich J, Heo SJ, Dhahbi J, Martin DIK, Boffelli D. piRNA-like small RNAs mark extended 3'UTRs present in germ and somatic cells. BMC Genomics 2015; 16:462. [PMID: 26076733 PMCID: PMC4469462 DOI: 10.1186/s12864-015-1662-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/29/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Piwi-interacting RNAs (piRNAs) are a class of small RNAs; distinct types of piRNAs are expressed in the mammalian testis at different stages of development. The function of piRNAs expressed in the adult testis is not well established. We conducted a detailed characterization of piRNAs aligning at or near the 3' UTRs of protein-coding genes in a deep dataset of small RNAs from adult mouse testis. RESULTS We identified 2710 piRNA clusters associated with 3' UTRs, including 1600 that overlapped genes not previously associated with piRNAs. 35% of the clusters extend beyond the annotated transcript; we find that these clusters correspond to, and are likely derived from, novel polyadenylated mRNA isoforms that contain previously unannotated extended 3'UTRs. Extended 3' UTRs, and small RNAs derived from them, are also present in somatic tissues; a subset of these somatic 3'UTR small RNA clusters are absent in mice lacking MIWI2, indicating a role for MIWI2 in the metabolism of somatic small RNAs. CONCLUSIONS The finding that piRNAs are processed from extended 3' UTRs suggests a role for piRNAs in the remodeling of 3' UTRs. The presence of both clusters and extended 3'UTRs in somatic cells, with evidence for involvement of MIWI2, indicates that this pathway is more broadly distributed than currently appreciated.
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Affiliation(s)
- Jennifer Yamtich
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| | - Seok-Jin Heo
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| | - Joseph Dhahbi
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| | - David I K Martin
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
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Abstract
Drosophila melanogaster is often considered to lack genomic 5-methylcytosine (m(5) C), an opinion reinforced by two whole genome bisulfite-sequencing studies that failed to find m(5) C. New evidence, however, indicates that genomic methylation is indeed present in the fly, albeit in small quantities and in unusual patterns. At embryonic stage 5, m(5) C occurs in short strand-specific regions that cover ∼1% of the genome, at tissue levels suggesting a distribution restricted to a subset of nuclei. Its function is not obvious, but methylation in subsets of nuclei would obscure functional associations since transcript levels and epigenetic modifications are assayed in whole embryos. Surprisingly, Mt2, the fly's only candidate DNA methyltransferase, is not necessary for the observed methylation. Full evaluation of the functions of genome methylation in Drosophila must await discovery and experimental inactivation of the DNA methyltransferase, as well as a better understanding of the pattern and developmental regulation of genomic m(5) C.
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Affiliation(s)
- Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
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9
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Keam SP, Young PE, McCorkindale AL, Dang THY, Clancy JL, Humphreys DT, Preiss T, Hutvagner G, Martin DIK, Cropley JE, Suter CM. The human Piwi protein Hiwi2 associates with tRNA-derived piRNAs in somatic cells. Nucleic Acids Res 2014; 42:8984-95. [PMID: 25038252 PMCID: PMC4132735 DOI: 10.1093/nar/gku620] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/26/2014] [Accepted: 06/26/2014] [Indexed: 01/31/2023] Open
Abstract
The Piwi-piRNA pathway is active in animal germ cells where its functions are required for germ cell maintenance and gamete differentiation. Piwi proteins and piRNAs have been detected outside germline tissue in multiple phyla, but activity of the pathway in mammalian somatic cells has been little explored. In particular, Piwi expression has been observed in cancer cells, but nothing is known about the piRNA partners or the function of the system in these cells. We have surveyed the expression of the three human Piwi genes, Hiwi, Hili and Hiwi2, in multiple normal tissues and cancer cell lines. We find that Hiwi2 is ubiquitously expressed; in cancer cells the protein is largely restricted to the cytoplasm and is associated with translating ribosomes. Immunoprecipitation of Hiwi2 from MDAMB231 cancer cells enriches for piRNAs that are predominantly derived from processed tRNAs and expressed genes, species which can also be found in adult human testis. Our studies indicate that a Piwi-piRNA pathway is present in human somatic cells, with an uncharacterised function linked to translation. Taking this evidence together with evidence from primitive organisms, we propose that this somatic function of the pathway predates the germline functions of the pathway in modern animals.
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Affiliation(s)
- Simon P Keam
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology Sydney, 235 Jones Street, Ultimo, NSW, 2007, Australia
| | - Paul E Young
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Alexandra L McCorkindale
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Thurston H Y Dang
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Jennifer L Clancy
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - David T Humphreys
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Thomas Preiss
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
| | - Gyorgy Hutvagner
- Faculty of Engineering and Information Technology, Centre of Health Technologies, University of Technology Sydney, 235 Jones Street, Ultimo, NSW, 2007, Australia
| | - David I K Martin
- Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA
| | - Jennifer E Cropley
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia Faculty of Medicine, University of New South Wales, Kensington, 2052, Australia
| | - Catherine M Suter
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia Faculty of Medicine, University of New South Wales, Kensington, 2052, Australia
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10
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Naqvi N, Li M, Calvert JW, Tejada T, Lambert JP, Wu J, Kesteven SH, Holman SR, Matsuda T, Lovelock JD, Howard WW, Iismaa SE, Chan AY, Crawford BH, Wagner MB, Martin DIK, Lefer DJ, Graham RM, Husain A. A proliferative burst during preadolescence establishes the final cardiomyocyte number. Cell 2014; 157:795-807. [PMID: 24813607 DOI: 10.1016/j.cell.2014.03.035] [Citation(s) in RCA: 208] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 01/22/2014] [Accepted: 03/12/2014] [Indexed: 12/11/2022]
Abstract
It is widely believed that perinatal cardiomyocyte terminal differentiation blocks cytokinesis, thereby causing binucleation and limiting regenerative repair after injury. This suggests that heart growth should occur entirely by cardiomyocyte hypertrophy during preadolescence when, in mice, cardiac mass increases many-fold over a few weeks. Here, we show that a thyroid hormone surge activates the IGF-1/IGF-1-R/Akt pathway on postnatal day 15 and initiates a brief but intense proliferative burst of predominantly binuclear cardiomyocytes. This proliferation increases cardiomyocyte numbers by ~40%, causing a major disparity between heart and cardiomyocyte growth. Also, the response to cardiac injury at postnatal day 15 is intermediate between that observed at postnatal days 2 and 21, further suggesting persistence of cardiomyocyte proliferative capacity beyond the perinatal period. If replicated in humans, this may allow novel regenerative therapies for heart diseases.
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Affiliation(s)
- Nawazish Naqvi
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ming Li
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - John W Calvert
- Division of Cardiothoracic Surgery, Department of Surgery, Carlyle Fraser Heart Center, Emory University School of Medicine, Atlanta, GA 30308, USA
| | - Thor Tejada
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jonathan P Lambert
- Division of Cardiothoracic Surgery, Department of Surgery, Carlyle Fraser Heart Center, Emory University School of Medicine, Atlanta, GA 30308, USA
| | - Jianxin Wu
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - Scott H Kesteven
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - Sara R Holman
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - Torahiro Matsuda
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joshua D Lovelock
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Wesley W Howard
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Siiri E Iismaa
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; University of New South Wales, Kensington, NSW 2033, Australia
| | - Andrea Y Chan
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - Brian H Crawford
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Center for Cardiovascular Biology, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Mary B Wagner
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Center for Cardiovascular Biology, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - David I K Martin
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - David J Lefer
- Division of Cardiothoracic Surgery, Department of Surgery, Carlyle Fraser Heart Center, Emory University School of Medicine, Atlanta, GA 30308, USA
| | - Robert M Graham
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; University of New South Wales, Kensington, NSW 2033, Australia.
| | - Ahsan Husain
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA.
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11
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Takayama S, Dhahbi J, Roberts A, Mao G, Heo SJ, Pachter L, Martin DIK, Boffelli D. Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity. Genome Res 2014; 24:821-30. [PMID: 24558263 PMCID: PMC4009611 DOI: 10.1101/gr.162412.113] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cytosine methylation in the genome of Drosophila melanogaster has been elusive and controversial: Its location and function have not been established. We have used a novel and highly sensitive genomewide cytosine methylation assay to detect and map genome methylation in stage 5 Drosophila embryos. The methylation we observe with this method is highly localized and strand asymmetrical, limited to regions covering ∼1% of the genome, dynamic in early embryogenesis, and concentrated in specific 5-base sequence motifs that are CA- and CT-rich but depleted of guanine. Gene body methylation is associated with lower expression, and many genes containing methylated regions have developmental or transcriptional functions. The only known DNA methyltransferase in Drosophila is the DNMT2 homolog MT2, but lines deficient for MT2 retain genomic methylation, implying the presence of a novel methyltransferase. The association of methylation with a lower expression of specific developmental genes at stage 5 raises the possibility that it participates in controlling gene expression during the maternal-zygotic transition.
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Affiliation(s)
- Sachiko Takayama
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
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12
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Jacobs JE, Wagner M, Dhahbi J, Boffelli D, Martin DIK. Deficiency of MIWI2 (Piwil4) induces mouse erythroleukemia cell differentiation, but has no effect on hematopoiesis in vivo. PLoS One 2013; 8:e82573. [PMID: 24376547 PMCID: PMC3871168 DOI: 10.1371/journal.pone.0082573] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/24/2013] [Indexed: 12/12/2022] Open
Abstract
Piwi proteins and their small non-coding RNA partners are involved in the maintenance of stem cell character and genome integrity in the male germ cells of mammals. MIWI2, one of the mouse Piwi-like proteins, is expressed in the prepachytene phase of spermatogenesis during the period of de novo methylation. Absence of this protein leads to meiotic defects and a progressive loss of germ cells. There is an accumulation of evidence that Piwi proteins may be active in hematopoietic tissues. Thus, MIWI2 may have a role in hematopoietic stem and/or progenitor cell self-renewal and differentiation, and defects in MIWI2 may lead to abnormal hematopoiesis. MIWI2 mRNA can be detected in a mouse erythroblast cell line by RNA-seq, and shRNA-mediated knockdown of this mRNA causes the cells to take on characteristics of differentiated erythroid precursors. However, there are no detectable hematopoietic abnormalities in a MIWI2-deficient mouse model. While subtle, non-statistically significant changes were noted in the hematopoietic function of mice without a functional MIWI2 gene when compared to wild type mice, our results show that MIWI2 is not solely necessary for hematopoiesis within the normal life span of a mouse.
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MESH Headings
- Aging/pathology
- Animals
- Argonaute Proteins/deficiency
- Argonaute Proteins/metabolism
- Blood Cells/metabolism
- Cell Differentiation
- Cell Line, Tumor
- Gene Knockdown Techniques
- Hematopoiesis
- Hemoglobins/metabolism
- Leukemia, Erythroblastic, Acute/genetics
- Leukemia, Erythroblastic, Acute/pathology
- Mice, Inbred C57BL
- Organ Specificity/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/metabolism
- Sequence Analysis, RNA
- Spleen/metabolism
- Whole-Body Irradiation
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Affiliation(s)
- James E. Jacobs
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
- * E-mail:
| | - Mark Wagner
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Joseph Dhahbi
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - David I. K. Martin
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
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13
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Dhahbi JM, Spindler SR, Atamna H, Boffelli D, Mote P, Martin DIK. 5′-YRNA fragments derived by processing of transcripts from specific YRNA genes and pseudogenes are abundant in human serum and plasma. Physiol Genomics 2013; 45:990-8. [DOI: 10.1152/physiolgenomics.00129.2013] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Small noncoding RNAs carry out a variety of functions in eukaryotic cells, and in multiple species they can travel between cells, thus serving as signaling molecules. In mammals multiple small RNAs have been found to circulate in the blood, although in most cases the targets of these RNAs, and even their functions, are not well understood. YRNAs are small (84–112 nt) RNAs with poorly characterized functions, best known because they make up part of the Ro ribonucleoprotein autoantigens in connective tissue diseases. In surveying small RNAs present in the serum of healthy adult humans, we have found YRNA fragments of lengths 27 nt and 30–33 nt, derived from the 5′-ends of specific YRNAs and generated by cleavage within a predicted internal loop. Many of the YRNAs from which these fragments are derived were previously annotated only as pseudogenes, or predicted informatically. These 5′-YRNA fragments make up a large proportion of all small RNAs (including miRNAs) present in human serum. They are also present in plasma, are not present in exosomes or microvesicles, and circulate as part of a complex with a mass between 100 and 300 kDa. Mouse serum contains far fewer 5′-YRNA fragments, possibly reflecting the much greater copy number of YRNA genes and pseudogenes in humans. The function of the 5′-YRNA fragments is at present unknown, but the processing and secretion of specific YRNAs to produce 5′-end fragments that circulate in stable complexes are consistent with a signaling function.
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Affiliation(s)
- Joseph M. Dhahbi
- Department of Biochemistry, University of California at Riverside, Riverside, California
| | - Stephen R. Spindler
- Department of Biochemistry, University of California at Riverside, Riverside, California
| | - Hani Atamna
- Department of Basic Sciences, Neuroscience, The Commonwealth Medical College, Scranton, Pennsylvania
| | - Dario Boffelli
- Center for Genetics, Childrens Hospital Oakland Research Institute, Oakland, California
| | - Patricia Mote
- Department of Biochemistry, University of California at Riverside, Riverside, California
| | - David I. K. Martin
- Center for Genetics, Childrens Hospital Oakland Research Institute, Oakland, California
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14
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Suter CM, Boffelli D, Martin DIK. A role for epigenetic inheritance in modern evolutionary theory? A comment in response to Dickins and Rahman. Proc Biol Sci 2013; 280:20130903; discussion 20131820. [PMID: 24089330 DOI: 10.1098/rspb.2013.0903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Catherine M Suter
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, , 405 Liverpool Street, Darlinghurst, New South Wales 2010, Australia, Center for Genetics, Children's Hospital Oakland Research Institute, , 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA
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15
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Dhahbi JM, Spindler SR, Atamna H, Yamakawa A, Guerrero N, Boffelli D, Mote P, Martin DIK. Deep sequencing identifies circulating mouse miRNAs that are functionally implicated in manifestations of aging and responsive to calorie restriction. Aging (Albany NY) 2013; 5:130-41. [PMID: 23470454 PMCID: PMC3616200 DOI: 10.18632/aging.100540] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) function to modulate gene expression, and through this property they regulate a broad spectrum of cellular processes. They can circulate in blood and thereby mediate cell-to-cell communication. Aging involves changes in many cellular processes that are potentially regulated by miRNAs, and some evidence has implicated circulating miRNAs in the aging process. In order to initiate a comprehensive assessment of the role of circulating miRNAs in aging, we have used deep sequencing to characterize circulating miRNAs in the serum of young mice, old mice, and old mice maintained on calorie restriction (CR). Deep sequencing identifies a set of novel miRNAs, and also accurately measures all known miRNAs present in serum. This analysis demonstrates that the levels of many miRNAs circulating in the mouse are increased with age, and that the increases can be antagonized by CR. The genes targeted by this set of age-modulated miRNAs are predicted to regulate biological processes directly relevant to the manifestations of aging including metabolic changes, and the miRNAs themselves have been linked to diseases associated with old age. This finding implicates circulating miRNAs in the aging process, raising questions about their tissues of origin, their cellular targets, and their functional role in metabolic changes that occur with aging.
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Affiliation(s)
- Joseph M Dhahbi
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521, USA.
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16
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Dhahbi JM, Spindler SR, Atamna H, Yamakawa A, Boffelli D, Mote P, Martin DIK. 5' tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction. BMC Genomics 2013; 14:298. [PMID: 23638709 PMCID: PMC3654920 DOI: 10.1186/1471-2164-14-298] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 04/26/2013] [Indexed: 11/10/2022] Open
Abstract
Background Small RNAs complex with proteins to mediate a variety of functions in animals and plants. Some small RNAs, particularly miRNAs, circulate in mammalian blood and may carry out a signaling function by entering target cells and modulating gene expression. The subject of this study is a set of circulating 30–33 nt RNAs that are processed derivatives of the 5′ ends of a small subset of tRNA genes, and closely resemble cellular tRNA derivatives (tRFs, tiRNAs, half-tRNAs, 5′ tRNA halves) previously shown to inhibit translation initiation in response to stress in cultured cells. Results In sequencing small RNAs extracted from mouse serum, we identified abundant 5′ tRNA halves derived from a small subset of tRNAs, implying that they are produced by tRNA type-specific biogenesis and/or release. The 5′ tRNA halves are not in exosomes or microvesicles, but circulate as particles of 100–300 kDa. The size of these particles suggest that the 5′ tRNA halves are a component of a macromolecular complex; this is supported by the loss of 5′ tRNA halves from serum or plasma treated with EDTA, a chelating agent, but their retention in plasma anticoagulated with heparin or citrate. A survey of somatic tissues reveals that 5′ tRNA halves are concentrated within blood cells and hematopoietic tissues, but scant in other tissues, suggesting that they may be produced by blood cells. Serum levels of specific subtypes of 5′ tRNA halves change markedly with age, either up or down, and these changes can be prevented by calorie restriction. Conclusions We demonstrate that 5′ tRNA halves circulate in the blood in a stable form, most likely as part of a nucleoprotein complex, and their serum levels are subject to regulation by age and calorie restriction. They may be produced by blood cells, but their cellular targets are not yet known. The characteristics of these circulating molecules, and their known function in suppression of translation initiation, suggest that they are a novel form of signaling molecule.
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Affiliation(s)
- Joseph M Dhahbi
- Department of Biochemistry, University of California at Riverside, Riverside, CA 92521, USA.
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17
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Li CCY, Young PE, Maloney CA, Eaton SA, Cowley MJ, Buckland ME, Preiss T, Henstridge DC, Cooney GJ, Febbraio MA, Martin DIK, Cropley JE, Suter CM. Maternal obesity and diabetes induces latent metabolic defects and widespread epigenetic changes in isogenic mice. Epigenetics 2013; 8:602-11. [PMID: 23764993 PMCID: PMC3857340 DOI: 10.4161/epi.24656] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Intrauterine nutrition can program metabolism, creating stable changes in physiology that may have significant health consequences. The mechanism underlying these changes is widely assumed to involve epigenetic changes to the expression of metabolic genes, but evidence supporting this idea is limited. Here we have performed the first study of the epigenomic consequences of exposure to maternal obesity and diabetes. We used a mouse model of natural-onset obesity that allows comparison of genetically identical mice whose mothers were either obese and diabetic or lean with a normal metabolism. We find that the offspring of obese mothers have a latent metabolic phenotype that is unmasked by exposure to a Western-style diet, resulting in glucose intolerance, insulin resistance and hepatic steatosis. The offspring show changes in hepatic gene expression and widespread but subtle alterations in cytosine methylation. Contrary to expectation, these molecular changes do not point to metabolic pathways but instead reside in broadly developmental ontologies. We propose that, rather than being adaptive, these changes may simply produce an inappropriate response to suboptimal environments; maladaptive phenotypes may be avoidable if postnatal nutrition is carefully controlled.
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Affiliation(s)
- Cheryl C Y Li
- Molecular Genetics Division; Victor Chang Cardiac Research Institute; Darlinghurst, NSW Australia
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18
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Abstract
Multiple epigenetic states can be associated with the same genome, and transmitted through the germline for generations, to create the phenomenon of epigenetic inheritance. This form of inheritance is mediated by complex and highly diverse components of the chromosome that associate with DNA, control its transcription, and are inherited alongside it. But, how extensive, and how stable, is the information carried in the germline by the epigenome? Several known examples of epigenetic inheritance demonstrate that it has the ability to create selectable traits, and thus to mediate Darwinian evolution. Here we discuss the possibility that epigenetic inheritance is responsible for some stable characteristics of species, focusing on a recent comparison of the human and chimpanzee methylomes which reveals that somatic methylation states are related to methylation states in the germline. Interpretation of this finding highlights the potential significance of germline epigenetic states, as well as the challenge of investigating a form of inheritance with complex and unfamiliar rules.
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Affiliation(s)
- Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
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19
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Carbone L, Harris RA, Mootnick AR, Milosavljevic A, Martin DIK, Rocchi M, Capozzi O, Archidiacono N, Konkel MK, Walker JA, Batzer MA, de Jong PJ. Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons. Genome Biol Evol 2012; 4:648-58. [PMID: 22593550 PMCID: PMC3606032 DOI: 10.1093/gbe/evs048] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Gibbons (Hylobatidae) shared a common ancestor with the other hominoids only 15–18 million years ago. Nevertheless, gibbons show very distinctive features that include heavily rearranged chromosomes. Previous observations indicate that this phenomenon may be linked to the attenuated epigenetic repression of transposable elements (TEs) in gibbon species. Here we describe the massive expansion of a repeat in almost all the centromeres of the eastern hoolock gibbon (Hoolock leuconedys). We discovered that this repeat is a new composite TE originating from the combination of portions of three other elements (L1ME5, AluSz6, and SVA_A) and thus named it LAVA. We determined that this repeat is found in all the gibbons but does not occur in other hominoids. Detailed investigation of 46 different LAVA elements revealed that the majority of them have target site duplications (TSDs) and a poly-A tail, suggesting that they have been retrotransposing in the gibbon genome. Although we did not find a direct correlation between the emergence of LAVA elements and human–gibbon synteny breakpoints, this new composite transposable element is another mark of the great plasticity of the gibbon genome. Moreover, the centromeric expansion of LAVA insertions in the hoolock closely resembles the massive centromeric expansion of the KERV-1 retroelement reported for wallaby (marsupial) interspecific hybrids. The similarity between the two phenomena is consistent with the hypothesis that evolution of the gibbons is characterized by defects in epigenetic repression of TEs, perhaps triggered by interspecific hybridization.
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Affiliation(s)
- Lucia Carbone
- Children's Hospital Oakland Research Institute, Oakland, CA, USA.
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20
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Cropley JE, Dang THY, Martin DIK, Suter CM. The penetrance of an epigenetic trait in mice is progressively yet reversibly increased by selection and environment. Proc Biol Sci 2012; 279:2347-53. [PMID: 22319121 DOI: 10.1098/rspb.2011.2646] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Natural selection acts on variation that is typically assumed to be genetic in origin. But epigenetic mechanisms, which are interposed between the genome and its environment, can create diversity independently of genetic variation. Epigenetic states can respond to environmental cues, and can be heritable, thus providing a means by which environmentally responsive phenotypes might be selectable independent of genotype. Here, we have tested the possibility that environment and selection can act together to increase the penetrance of an epigenetically determined phenotype. We used isogenic A(vy) mice, in which the epigenetic state of the A(vy) allele is sensitive to dietary methyl donors. By combining methyl donor supplementation with selection for a silent A(vy) allele, we progressively increased the prevalence of the associated phenotype in the population over five generations. After withdrawal of the dietary supplement, the shift persisted for one generation but was lost in subsequent generations. Our data provide the first demonstration that selection for a purely epigenetic trait can result in cumulative germline effects in mammals. These results present an alternative to the paradigm that natural selection acts only on genetic variation, and suggest that epigenetic changes could underlie rapid adaptation of species in response to natural environmental fluctuations.
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Affiliation(s)
- Jennifer E Cropley
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
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21
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Dhahbi JM, Atamna H, Boffelli D, Martin DIK, Spindler SR. mRNA-Seq reveals complex patterns of gene regulation and expression in the mouse skeletal muscle transcriptome associated with calorie restriction. Physiol Genomics 2012; 44:331-44. [PMID: 22274562 DOI: 10.1152/physiolgenomics.00129.2011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Sarcopenia is an age-associated loss of skeletal muscle mass and strength that increases the risk of disability. Calorie restriction (CR), the consumption of fewer calories while maintaining adequate nutrition, mitigates sarcopenia and many other age-related diseases. To identify potential mechanisms by which CR preserves skeletal muscle integrity during aging, we used mRNA-Seq for deep characterization of gene regulation and mRNA abundance in skeletal muscle of old mice compared with old mice subjected to CR. mRNA-Seq revealed complex CR-associated changes in expression of mRNA isoforms, many of which occur without a change in total message abundance and thus would not be detected by methods other than mRNA-Seq. Functional annotation of differentially expressed genes reveals CR-associated upregulation of pathways involved in energy metabolism and lipid biosynthesis, and downregulation of pathways mediating protein breakdown and oxidative stress, consistent with earlier microarray-based studies. CR-associated changes not noted in previous studies involved downregulation of genes controlling actin cytoskeletal structures and muscle development. These CR-associated changes reflect generally healthier muscle, consistent with CR's mitigation of sarcopenia. mRNA-Seq generates a rich picture of the changes in gene expression associated with CR, and may facilitate identification of genes that are primary mediators of CR's effects.
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Affiliation(s)
- Joseph M Dhahbi
- Department of Biochemistry, University of California at Riverside, 92521, USA.
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22
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Meacham F, Boffelli D, Dhahbi J, Martin DIK, Singer M, Pachter L. Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics 2011; 12:451. [PMID: 22099972 PMCID: PMC3295828 DOI: 10.1186/1471-2105-12-451] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 11/21/2011] [Indexed: 12/21/2022] Open
Abstract
Background A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads. The implications of such errors are application specific, ranging from minor informatics nuisances to major problems affecting biological inferences. Recently developed "next-gen" sequencing technologies have greatly reduced the cost of sequencing, but have been shown to be more error prone than previous technologies. Both position specific (depending on the location in the read) and sequence specific (depending on the sequence in the read) errors have been identified in Illumina and Life Technology sequencing platforms. We describe a new type of systematic error that manifests as statistically unlikely accumulations of errors at specific genome (or transcriptome) locations. Results We characterize and describe systematic errors using overlapping paired reads from high-coverage data. We show that such errors occur in approximately 1 in 1000 base pairs, and that they are highly replicable across experiments. We identify motifs that are frequent at systematic error sites, and describe a classifier that distinguishes heterozygous sites from systematic error. Our classifier is designed to accommodate data from experiments in which the allele frequencies at heterozygous sites are not necessarily 0.5 (such as in the case of RNA-Seq), and can be used with single-end datasets. Conclusions Systematic errors can easily be mistaken for heterozygous sites in individuals, or for SNPs in population analyses. Systematic errors are particularly problematic in low coverage experiments, or in estimates of allele-specific expression from RNA-Seq data. Our characterization of systematic error has allowed us to develop a program, called SysCall, for identifying and correcting such errors. We conclude that correction of systematic errors is important to consider in the design and interpretation of high-throughput sequencing experiments.
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Affiliation(s)
- Frazer Meacham
- Department of Mathematics, University of California, Berkeley, 970 Evans Hall #3840, Berkeley, CA 94720, USA
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23
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Dhahbi JM, Atamna H, Boffelli D, Magis W, Spindler SR, Martin DIK. Deep sequencing reveals novel microRNAs and regulation of microRNA expression during cell senescence. PLoS One 2011; 6:e20509. [PMID: 21637828 PMCID: PMC3102725 DOI: 10.1371/journal.pone.0020509] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 04/29/2011] [Indexed: 11/19/2022] Open
Abstract
In cell senescence, cultured cells cease proliferating and acquire aberrant gene expression patterns. MicroRNAs (miRNAs) modulate gene expression through translational repression or mRNA degradation and have been implicated in senescence. We used deep sequencing to carry out a comprehensive survey of miRNA expression and involvement in cell senescence. Informatic analysis of small RNA sequence datasets from young and senescent IMR90 human fibroblasts identifies many miRNAs that are regulated (either up or down) with cell senescence. Comparison with mRNA expression profiles reveals potential mRNA targets of these senescence-regulated miRNAs. The target mRNAs are enriched for genes involved in biological processes associated with cell senescence. This result greatly extends existing information on the role of miRNAs in cell senescence and is consistent with miRNAs having a causal role in the process.
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Affiliation(s)
- Joseph M. Dhahbi
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
- Department of Biochemistry, University of California Riverside, Riverside, California, United States of America
- * E-mail: (JMD); (HA); (DIKM)
| | - Hani Atamna
- Department of Basic Sciences, Neuroscience, The Commonwealth Medical College, Scranton, Pennsylvania, United States of America
- * E-mail: (JMD); (HA); (DIKM)
| | - Dario Boffelli
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Wendy Magis
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Stephen R. Spindler
- Department of Biochemistry, University of California Riverside, Riverside, California, United States of America
| | - David I. K. Martin
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
- * E-mail: (JMD); (HA); (DIKM)
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Li CCY, Cropley JE, Cowley MJ, Preiss T, Martin DIK, Suter CM. A sustained dietary change increases epigenetic variation in isogenic mice. PLoS Genet 2011; 7:e1001380. [PMID: 21541011 PMCID: PMC3080854 DOI: 10.1371/journal.pgen.1001380] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 03/21/2011] [Indexed: 02/07/2023] Open
Abstract
Epigenetic changes can be induced by adverse environmental exposures, such as
nutritional imbalance, but little is known about the nature or extent of these
changes. Here we have explored the epigenomic effects of a sustained nutritional
change, excess dietary methyl donors, by assessing genomic CpG methylation
patterns in isogenic mice exposed for one or six generations. We find stochastic
variation in methylation levels at many loci; exposure to methyl donors
increases the magnitude of this variation and the number of variable loci.
Several gene ontology categories are significantly overrepresented in genes
proximal to these methylation-variable loci, suggesting that certain pathways
are susceptible to environmental influence on their epigenetic states. Long-term
exposure to the diet (six generations) results in a larger number of loci
exhibiting epigenetic variability, suggesting that some of the induced changes
are heritable. This finding presents the possibility that epigenetic variation
within populations can be induced by environmental change, providing a vehicle
for disease predisposition and possibly a substrate for natural selection. Epigenetic changes to gene expression that do not involve changes to DNA sequence
can be influenced by the environment and provide one candidate mechanism by
which early nutrition can influence adult disease risk. Here, we examined
epigenetic changes across the genome in response to short- and long-term
exposure to a dietary supplement in genetically identical mice. We find that the
supplement induces small but widespread epigenetic changes in exposed mice.
These changes increase the epigenetic variability among exposed mice, and this
effect is magnified in mice exposed long-term. The epigenetic changes are
overrepresented in gene functions involved in cell and organ development and in
gene expression. Our data is consistent with the external environment having
pervasive effects on the epigenome and suggests that some genetic pathways may
be more susceptible to environmental influence than others.
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Affiliation(s)
- Cheryl C. Y. Li
- Victor Chang Cardiac Research Institute,
University of New South Wales, Sydney, Australia
- Faculty of Medicine, University of New South
Wales, Sydney, Australia
| | - Jennifer E. Cropley
- Victor Chang Cardiac Research Institute,
University of New South Wales, Sydney, Australia
- Faculty of Medicine, University of New South
Wales, Sydney, Australia
| | - Mark J. Cowley
- Peter Wills Bioinformatics Centre, Garvan
Institute of Medical Research, Sydney, Australia
- Cancer Research Program, Garvan Institute of
Medical Research, Sydney, Australia
| | - Thomas Preiss
- Victor Chang Cardiac Research Institute,
University of New South Wales, Sydney, Australia
- Faculty of Medicine, University of New South
Wales, Sydney, Australia
- Faculty of Science, University of New South
Wales, Sydney, Australia
| | - David I. K. Martin
- Children's Hospital Oakland Research
Institute, Oakland, California, United States of America
| | - Catherine M. Suter
- Victor Chang Cardiac Research Institute,
University of New South Wales, Sydney, Australia
- Faculty of Medicine, University of New South
Wales, Sydney, Australia
- * E-mail:
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Singer M, Boffelli D, Dhahbi J, Schönhuth A, Schroth GP, Martin DIK, Pachter L. MetMap enables genome-scale Methyltyping for determining methylation states in populations. PLoS Comput Biol 2010; 6:e1000888. [PMID: 20856582 PMCID: PMC2924245 DOI: 10.1371/journal.pcbi.1000888] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 07/15/2010] [Indexed: 12/17/2022] Open
Abstract
The ability to assay genome-scale methylation patterns using high-throughput sequencing makes it possible to carry out association studies to determine the relationship between epigenetic variation and phenotype. While bisulfite sequencing can determine a methylome at high resolution, cost inhibits its use in comparative and population studies. MethylSeq, based on sequencing of fragment ends produced by a methylation-sensitive restriction enzyme, is a method for methyltyping (survey of methylation states) and is a site-specific and cost-effective alternative to whole-genome bisulfite sequencing. Despite its advantages, the use of MethylSeq has been restricted by biases in MethylSeq data that complicate the determination of methyltypes. Here we introduce a statistical method, MetMap, that produces corrected site-specific methylation states from MethylSeq experiments and annotates unmethylated islands across the genome. MetMap integrates genome sequence information with experimental data, in a statistically sound and cohesive Bayesian Network. It infers the extent of methylation at individual CGs and across regions, and serves as a framework for comparative methylation analysis within and among species. We validated MetMap's inferences with direct bisulfite sequencing, showing that the methylation status of sites and islands is accurately inferred. We used MetMap to analyze MethylSeq data from four human neutrophil samples, identifying novel, highly unmethylated islands that are invisible to sequence-based annotation strategies. The combination of MethylSeq and MetMap is a powerful and cost-effective tool for determining genome-scale methyltypes suitable for comparative and association studies.
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Affiliation(s)
- Meromit Singer
- Computer Science Division, University of California at Berkeley, Berkeley, California, United States of America
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Joseph Dhahbi
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Alexander Schönhuth
- Department of Mathematics, University of California at Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, United States of America
| | | | - David I. K. Martin
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Lior Pachter
- Department of Mathematics, University of California at Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, United States of America
- * E-mail:
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Cropley JE, Suter CM, Beckman KB, Martin DIK. CpG methylation of a silent controlling element in the murine Avy allele is incomplete and unresponsive to methyl donor supplementation. PLoS One 2010; 5:e9055. [PMID: 20140227 PMCID: PMC2816220 DOI: 10.1371/journal.pone.0009055] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 11/18/2009] [Indexed: 11/18/2022] Open
Abstract
Background The viable yellow allele of agouti (Avy) is remarkable for its unstable and partially heritable epigenetic state, which produces wide variation in phenotypes of isogenic mice. In the Avy allele an inserted intracisternal A particle (IAP) acts as a controlling element which deregulates expression of agouti by transcription from the LTR of the IAP; the phenotypic state has been linked to CpG methylation of the LTR. Phenotypic variation between Avy mice indicates that the epigenetic state of the IAP is unstable in the germline. Principal Findings We have made a detailed examination of somatic methylation of the IAP using bisulphite allelic sequencing, and find that the promoter is incompletely methylated even when it is transcriptionally silent. In utero exposure to supplementary methyl donors, which alters the spectrum of Avy phenotypes, does not increase the density of CpG methylation in the silent LTR. Conclusions Our findings suggest that, contrary to previous supposition, methyl donor supplementation acts through an indirect mechanism to silence Avy. The incomplete cytosine methylation we observe at the somatically silent Avy allele may reflect its unstable germline state, and the influence of epigenetic modifications underlying CpG methylation.
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Affiliation(s)
- Jennifer E. Cropley
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Catherine M. Suter
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Kensington, New South Wales, Australia
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Kenneth B. Beckman
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - David I. K. Martin
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
- * E-mail:
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Beilharz TH, Humphreys DT, Clancy JL, Thermann R, Martin DIK, Hentze MW, Preiss T. microRNA-mediated messenger RNA deadenylation contributes to translational repression in mammalian cells. PLoS One 2009; 4:e6783. [PMID: 19710908 PMCID: PMC2728509 DOI: 10.1371/journal.pone.0006783] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 07/24/2009] [Indexed: 12/11/2022] Open
Abstract
Animal microRNAs (miRNAs) typically regulate gene expression by binding to partially complementary target sites in the 3' untranslated region (UTR) of messenger RNA (mRNA) reducing its translation and stability. They also commonly induce shortening of the mRNA 3' poly(A) tail, which contributes to their mRNA decay promoting function. The relationship between miRNA-mediated deadenylation and translational repression has been less clear. Using transfection of reporter constructs carrying three imperfectly matching let-7 target sites in the 3' UTR into mammalian cells we observe rapid target mRNA deadenylation that precedes measureable translational repression by endogenous let-7 miRNA. Depleting cells of the argonaute co-factors RCK or TNRC6A can impair let-7-mediated repression despite ongoing mRNA deadenylation, indicating that deadenylation alone is not sufficient to effect full repression. Nevertheless, the magnitude of translational repression by let-7 is diminished when the target reporter lacks a poly(A) tail. Employing an antisense strategy to block deadenylation of target mRNA with poly(A) tail also partially impairs translational repression. On the one hand, these experiments confirm that tail removal by deadenylation is not strictly required for translational repression. On the other hand they show directly that deadenylation can augment miRNA-mediated translational repression in mammalian cells beyond stimulating mRNA decay. Taken together with published work, these results suggest a dual role of deadenylation in miRNA function: it contributes to translational repression as well as mRNA decay and is thus critically involved in establishing the quantitatively appropriate physiological response to miRNAs.
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Affiliation(s)
- Traude H. Beilharz
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- School of Biotechnology & Biomolecular Sciences and St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - David T. Humphreys
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Jennifer L. Clancy
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Rolf Thermann
- European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg, Germany
| | - David I. K. Martin
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Matthias W. Hentze
- European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg, Germany
| | - Thomas Preiss
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
- School of Biotechnology & Biomolecular Sciences and St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail:
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Abstract
Epigenetic modifications provide all multicellular organisms with a system of gene regulation that allows clonally heritable yet reversible alterations in gene transcription. Errors in this complex system can give rise to abnormal gene silencing, termed 'epimutation'; importantly, this can occur in the absence of any underlying genetic defect. Epimutations are commonly somatic events, and are particularly prevalent in tumors, but we and others have shown that epimutation can also arise in the germline, giving rise to soma-wide transcriptional silencing of a gene. A germline epimutation can mimic the effect of an inactivating mutation, and in doing so, can phenocopy a genetic disease. In this article, we will review the recent findings with germline epimutation at the tumor suppressor gene MLH1, discuss the possible etiology of this phenomenon, and the implications of germline epimutation in humans.
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Affiliation(s)
- Jennifer E Cropley
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, Australia
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29
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Affiliation(s)
- David I K Martin
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia.
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Li M, Naqvi N, Yahiro E, Liu K, Powell PC, Bradley WE, Martin DIK, Graham RM, Dell'Italia LJ, Husain A. c-kit is required for cardiomyocyte terminal differentiation. Circ Res 2008; 102:677-85. [PMID: 18258857 DOI: 10.1161/circresaha.107.161737] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
c-kit, the transmembrane tyrosine kinase receptor for stem cell factor, is required for melanocyte and mast cell development, hematopoiesis, and differentiation of spermatogonial stem cells. We show here that in the heart, c-kit is expressed not only by cardiac stem cells but also by cardiomyocytes, commencing immediately after birth and terminating a few days later, coincident with the onset of cardiomyocyte terminal differentiation. To examine the function of c-kit in cardiomyocyte terminal differentiation, we used compound heterozygous mice carrying the W (null) and W(v) (dominant negative) mutations of c-kit. In vivo, adult W/W(v) cardiomyocytes are phenotypically indistinguishable from their wild-type counterparts. After acute pressure overload adult W/W(v) cardiomyocytes reenter the cell cycle and proliferate, leading to left ventricular growth; furthermore in transgenic mice with cardiomyocyte-restricted overexpression of the dominant negative W(v) mutant, pressure overload causes cardiomyocytes to reenter the cell cycle. In contrast, in wild-type mice left ventricular growth after pressure overload results mainly from cardiomyocyte hypertrophy. Importantly, W/W(v) mice with pressure overload-induced cardiomyocyte hyperplasia had improved left ventricular function and survival. In W/W(v) mice, c-kit dysfunction also resulted in an approximately 14-fold decrease (P<0.01) in the number of c-kit(+)/GATA4(+) cardiac progenitors. These findings identify novel functions for c-kit: promotion of cardiac stem cell differentiation and regulation of cardiomyocyte terminal differentiation.
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Affiliation(s)
- Ming Li
- Departments of Physiology and Biophysics, University of Alabama at Birmingham, AL 35294, USA
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Hsu M, Mabaera R, Lowrey CH, Martin DIK, Fiering S. CpG hypomethylation in a large domain encompassing the embryonic beta-like globin genes in primitive erythrocytes. Mol Cell Biol 2007; 27:5047-54. [PMID: 17452448 PMCID: PMC1951500 DOI: 10.1128/mcb.02234-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is little evidence addressing the role of CpG methylation in transcriptional control of genes that do not contain CpG islands. This is reflected in the ongoing debate about whether CpG methylation merely suppresses retroelements or if it also plays a role in developmental and tissue-specific gene regulation. The genes of the beta-globin locus are an important model of mammalian developmental gene regulation and do not contain CpG islands. We have analyzed the methylation status of regions in the murine beta-like globin locus in uncultured primitive and definitive erythroblasts and other cultured primary and transformed cell types. A large ( approximately 20-kb) domain is hypomethylated only in primitive erythroid cells; it extends from the region just past the locus control region to before beta-major and encompasses the embryonic genes Ey, beta h1, and beta h0. Even retrotransposons in this region are hypomethylated in primitive erythroid cells. The existence of this large developmentally regulated domain of hypomethylation supports a mechanistic role for DNA methylation in developmental regulation of globin genes.
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Affiliation(s)
- Mei Hsu
- Department of Microbiology and Immunology, Dartmouth Medical School, Hanover, New Hampshire, USA
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34
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Abstract
Persons who have hypermethylation of one allele of MLH1 in somatic cells throughout the body (a germ-line epimutation) have a predisposition for the development of cancer in a pattern typical of hereditary nonpolyposis colorectal cancer. By studying the families of two such persons, we found evidence that the epimutation was transmitted from a mother to her son but was erased in his spermatozoa. The affected maternal allele was inherited by three other siblings from these two families, but in those offspring the allele had reverted to the normal active state. These findings demonstrate a novel pattern of inheritance of cancer susceptibility and are consistent with transgenerational epigenetic inheritance.
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Affiliation(s)
- Megan P Hitchins
- Department of Medical Oncology, St. Vincent's Hospital, Sydney, Australia
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35
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Cropley JE, Suter CM, Beckman KB, Martin DIK. Germ-line epigenetic modification of the murine A vy allele by nutritional supplementation. Proc Natl Acad Sci U S A 2006; 103:17308-12. [PMID: 17101998 PMCID: PMC1838538 DOI: 10.1073/pnas.0607090103] [Citation(s) in RCA: 323] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Environmental effects on phenotype can be mediated by epigenetic modifications. The epigenetic state of the murine A vy allele is highly variable, and determines phenotypic effects that vary in a mosaic spectrum that can be shifted by in utero exposure to methyl donor supplementation. We have asked if methyl donor supplementation affects the germ-line epigenetic state of the A vy allele. We find that the somatic epigenetic state of A vy is affected by in utero methyl donor supplementation only when the allele is paternally contributed. Exposure to methyl donor supplementation during midgestation shifts A vy phenotypes not only in the mice exposed as fetuses, but in their offspring. This finding indicates that methyl donors can change the epigenetic state of the A vy allele in the germ line, and that the altered state is retained through the epigenetic resetting that takes place in gametogenesis and embryogenesis. Thus a mother's diet may have an enduring influence on succeeding generations, independent of later changes in diet. Although other reports have suggested such heritable epigenetic changes, this study demonstrates that a specific mammalian gene can be subjected to germ-line epigenetic change.
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Affiliation(s)
- Jennifer E. Cropley
- *Victor Chang Cardiac Research Institute, 384 Victoria Street, Darlinghurst 2010, Sydney, Australia
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Junior Way, Oakland, CA 94609
| | - Catherine M. Suter
- *Victor Chang Cardiac Research Institute, 384 Victoria Street, Darlinghurst 2010, Sydney, Australia
- Faculty of Medicine, University of New South Wales, Anzac Parade, Kensington 2033, Sydney, Australia; and
| | - Kenneth B. Beckman
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Junior Way, Oakland, CA 94609
| | - David I. K. Martin
- *Victor Chang Cardiac Research Institute, 384 Victoria Street, Darlinghurst 2010, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences and
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Junior Way, Oakland, CA 94609
- To whom correspondence should be addressed. E-mail:
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Abstract
Epigenetic modifications of DNA produce reversible and clonally heritable alterations in transcription state. Errors in the elaborate apparatus of epigenetic silencing possessed by higher eukaryotes can lead to "epimutation," abnormal silencing of a gene. It was supposed that an epimutation in the germline would produce a phenotype equivalent to that resulting from an inactivating germline mutation in the same gene. In testing this hypothesis individuals were identified in whom one allele of the gene encoding the DNA mismatch repair protein MLH1 is epigenetically silenced throughout the soma (implying a germline event). These individuals fit the clinical criteria for hereditary nonpolyposis colorectal cancer, which is usually produced by germline mutation of MLH1. None of the affected individuals have any genetic abnormality that would explain the presence of the epimutation. Thus, an epimutation can phenocopy a genetic disease; this innate epigenetic defect is not necessarily the result of anything other than chance. Epigenetic phenomena tend to be stochastic, reversible, and mosaic; the occurrence and inheritance of epimutations are likely to have rules completely different from those of Mendelian genetics. The application of this principle to the thalassemias is discussed.
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Affiliation(s)
- David I K Martin
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.
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37
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Humphreys DT, Westman BJ, Martin DIK, Preiss T. MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function. Proc Natl Acad Sci U S A 2005; 102:16961-6. [PMID: 16287976 PMCID: PMC1287990 DOI: 10.1073/pnas.0506482102] [Citation(s) in RCA: 439] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) repress translation of target mRNAs by interaction with partially mismatched sequences in their 3' UTR. The mechanism by which they act on translation has remained largely obscure. We examined the translation of mRNAs containing four partially mismatched miRNA-binding sites in the 3' UTR in HeLa cells cotransfected with a cognate miRNA. The mRNAs were prepared by in vitro transcription and were engineered to employ different modes of translation initiation. We find that the 5' cap structure and the 3' poly(A) tail are each necessary but not sufficient for full miRNA-mediated repression of mRNA translation. Replacing the cap structure with an internal ribosome entry site from either the cricket paralysis virus or the encephalomyocarditis virus impairs miRNA-mediated repression. Collectively, these results demonstrate that miRNAs interfere with the initiation step of translation and implicate the cap-binding protein eukaryotic initiation factor 4E as a molecular target.
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Affiliation(s)
- David T Humphreys
- Molecular Genetics Program, Victor Chang Cardiac Research Institute (VCCRI), 384 Victoria Street, Darlinghurst (Sydney) NSW 2010, Australia
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38
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Lu DP, Read RL, Humphreys DT, Battah FM, Martin DIK, Rasko JEJ. PCR-based expression analysis and identification of microRNAs. J RNAi Gene Silencing 2005; 1:44-9. [PMID: 19771204 PMCID: PMC2737195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Revised: 06/16/2005] [Accepted: 06/16/2005] [Indexed: 11/01/2022]
Abstract
microRNAs (miRNAs) are small RNAs that regulate translation and hence control a variety of cellular processes in metazoans. The quantitation and identification of miRNAs has been hampered by their small size and low abundance. Here we describe two robust PCR-based assays of miRNA expression based on the original cloning strategy. The non-quantitative PCR method allows detection and identification of miRNAs and we utilise this method in the discovery of a new miRNA (miR-532) in retinoic acid differentiated P19 cells. The second and quantitative method (QM-RT-PCR) is simple and accurate, and uses commonly available technology. Of particular interest is the specificity of this PCR-based technology compared to hybridisation-based methods including arrays and northern blotting. Here we have shown that a single base pair mismatch in the priming sequence results in a two order of magnitude reduction in the amplification of let-7f. These streamlined methods will complement previously described methods and will facilitate analysis of miRNA expression in rare cell populations where the amount of RNA is limited.
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Affiliation(s)
- David P Lu
- Gene and Stem Cell Therapy, Centenary Institute of Cancer Medicine and Cell Biology, University of Sydney, Locked Bag No 6, Newtown 2042, Australia
| | - Rebecca L Read
- Gene and Stem Cell Therapy, Centenary Institute of Cancer Medicine and Cell Biology, University of Sydney, Locked Bag No 6, Newtown 2042, Australia
| | | | - Fiona M Battah
- Gene and Stem Cell Therapy, Centenary Institute of Cancer Medicine and Cell Biology, University of Sydney, Locked Bag No 6, Newtown 2042, Australia
| | | | - John E J Rasko
- Gene and Stem Cell Therapy, Centenary Institute of Cancer Medicine and Cell Biology, University of Sydney, Locked Bag No 6, Newtown 2042, Australia,Sydney Cancer Centre, Royal Prince Alfred Hospital, Sydney, Australia,Correspondence to: John EJ Rasko, , Tel: +612 95656156, Fax: +612 95656101
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Suter CM, Martin DIK, Ward RL. Germline epimutation of MLH1 in individuals with multiple cancers. Nat Genet 2004; 36:497-501. [PMID: 15064764 DOI: 10.1038/ng1342] [Citation(s) in RCA: 314] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Accepted: 03/11/2004] [Indexed: 12/12/2022]
Abstract
Epigenetic silencing can mimic genetic mutation by abolishing expression of a gene. We hypothesized that an epimutation could occur in any gene as a germline event that predisposes to disease and looked for examples in tumor suppressor genes in individuals with cancer. Here we report two individuals with soma-wide, allele-specific and mosaic hypermethylation of the DNA mismatch repair gene MLH1. Both individuals lack evidence of genetic mutation in any mismatch repair gene but have had multiple primary tumors that show mismatch repair deficiency, and both meet clinical criteria for hereditary nonpolyposis colorectal cancer. The epimutation was also present in spermatozoa of one of the individuals, indicating a germline defect and the potential for transmission to offspring. Germline epimutation provides a mechanism for phenocopying of genetic disease. The mosaicism and nonmendelian inheritance that are characteristic of epigenetic states could produce patterns of disease risk that resemble those of polygenic or complex traits.
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Affiliation(s)
- Catherine M Suter
- Department of Medical Oncology, St Vincent's Hospital, Sydney, New South Wales, Australia
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40
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Abstract
Epigenetic silencing can mimic genetic mutation by abolishing expression of a gene. We hypothesized that an epimutation could occur in any gene as a germline event that predisposes to disease and looked for examples in tumor suppressor genes in individuals with cancer. Here we report two individuals with soma-wide, allele-specific and mosaic hypermethylation of the DNA mismatch repair gene MLH1. Both individuals lack evidence of genetic mutation in any mismatch repair gene but have had multiple primary tumors that show mismatch repair deficiency, and both meet clinical criteria for hereditary nonpolyposis colorectal cancer. The epimutation was also present in spermatozoa of one of the individuals, indicating a germline defect and the potential for transmission to offspring. Germline epimutation provides a mechanism for phenocopying of genetic disease. The mosaicism and nonmendelian inheritance that are characteristic of epigenetic states could produce patterns of disease risk that resemble those of polygenic or complex traits.
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Affiliation(s)
- Catherine M Suter
- Department of Medical Oncology, St Vincent's Hospital, Sydney, New South Wales, Australia
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41
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Sutter NB, Scalzo D, Fiering S, Groudine M, Martin DIK. Chromatin insulation by a transcriptional activator. Proc Natl Acad Sci U S A 2003; 100:1105-10. [PMID: 12547916 PMCID: PMC298734 DOI: 10.1073/pnas.242732999] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2002] [Indexed: 11/18/2022] Open
Abstract
In eukaryotic genomes, transcriptionally active regions are interspersed with silent chromatin that may repress genes in its vicinity. Chromatin insulators are elements that can shield a locus from repressive effects of flanking chromatin. Few such elements have been characterized in higher eukaryotes, but transcriptional activating elements are an invariant feature of active loci and have been shown to suppress transgene silencing. Hence, we have assessed the ability of a transcriptional activator to cause chromatin insulation, i.e., to relieve position effects at transgene integration sites in cultured cells. The transgene contained a series of binding sites for the metal-inducible transcriptional activator MTF, linked to a GFP reporter. Clones carrying single integrated transgenes were derived without selection for expression, and in most clones the transgene was silent. Induction of MTF resulted in transition of the transgene from the silent to the active state, prolongation of the active state, and a marked narrowing of the range of expression levels at different genomic sites. At one genomic site, prolonged induction of MTF resulted in suppression of transgene silencing that persisted after withdrawal of the induction stimulus. These results are consistent with MTF acting as a chromatin insulator and imply that transcriptional activating elements can insulate active loci against chromatin repression.
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Affiliation(s)
- Nathan B Sutter
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Eszterhas SK, Bouhassira EE, Martin DIK, Fiering S. Transcriptional interference by independently regulated genes occurs in any relative arrangement of the genes and is influenced by chromosomal integration position. Mol Cell Biol 2002; 22:469-79. [PMID: 11756543 PMCID: PMC139736 DOI: 10.1128/mcb.22.2.469-479.2002] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional interference is the influence, generally suppressive, of one active transcriptional unit on another unit linked in cis. Its wide occurrence in experimental systems suggests that it may also influence transcription in many loci, but little is known about its precise nature or underlying mechanisms. Here we report a study of the interaction of two nearly identical transcription units juxtaposed in various arrangements. Each reporter gene in the constructs has its own promoter and enhancer and a strong polyadenylation signal. We used recombinase-mediated cassette exchange (RMCE) to insert the constructs into previously tagged genomic sites in cultured cells. This strategy also allows the constructs to be assessed in both orientations with respect to flanking chromatin. In each of the possible arrangements (tandem, divergent, and convergent), the presence of two genes strongly suppresses expression of both genes compared to that of an identical single gene at the same integration site. The suppression is most severe with the convergent arrangement and least severe in total with the divergent arrangement, while the tandem arrangement is most strongly influenced by the integration site and the genes' orientation within the site. These results suggest that transcriptional interference could underlie some position effects and contribute to the regulation of genes in complex loci.
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Affiliation(s)
- Susan K Eszterhas
- Department of Microbiology and Immunology, Dartmouth Medical School, Lebanon, New Hampshire 03756, USA
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