1
|
Fu B, Ma H, Liu D. Essential roles of the nucleolus during early embryonic development: a regulatory hub for chromatin organization. Open Biol 2024; 14:230358. [PMID: 38689555 PMCID: PMC11065130 DOI: 10.1098/rsob.230358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
The nucleolus is the most prominent liquid droplet-like membrane-less organelle in mammalian cells. Unlike the nucleolus in terminally differentiated somatic cells, those in totipotent cells, such as murine zygotes or two-cell embryos, have a unique nucleolar structure known as nucleolus precursor bodies (NPBs). Previously, it was widely accepted that NPBs in zygotes are simply passive repositories of materials that will be gradually used to construct a fully functional nucleolus after zygotic genome activation (ZGA). However, recent research studies have challenged this simplistic view and demonstrated that functions of the NPBs go beyond ribosome biogenesis. In this review, we provide a snapshot of the functions of NPBs in zygotes and early two-cell embryos in mice. We propose that these membrane-less organelles function as a regulatory hub for chromatin organization. On the one hand, NPBs provide the structural platform for centric and pericentric chromatin remodelling. On the other hand, the dynamic changes in nucleolar structure control the release of the pioneer factors (i.e. double homeobox (Dux)). It appears that during transition from totipotency to pluripotency, decline of totipotency and initiation of fully functional nucleolus formation are not independent events but are interconnected. Consequently, it is reasonable to hypothesize that dissecting more unknown functions of NPBs may shed more light on the enigmas of early embryonic development and may ultimately provide novel approaches to improve reprogramming efficiency.
Collapse
Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry, HeiLongJiang Academy of
Agricultural Sciences, Harbin150086, People's Republic of China
- Key Laboratory of Combining Farming and Animal Husbandry,
Ministry of Agriculture and Rural Affairs, Harbin150086, People's Republic of China
| | - Hong Ma
- Institute of Animal Husbandry, HeiLongJiang Academy of
Agricultural Sciences, Harbin150086, People's Republic of China
- Key Laboratory of Combining Farming and Animal Husbandry,
Ministry of Agriculture and Rural Affairs, Harbin150086, People's Republic of China
| | - Di Liu
- Institute of Animal Husbandry, HeiLongJiang Academy of
Agricultural Sciences, Harbin150086, People's Republic of China
- Key Laboratory of Combining Farming and Animal Husbandry,
Ministry of Agriculture and Rural Affairs, Harbin150086, People's Republic of China
| |
Collapse
|
2
|
Wong CJ, Friedman SD, Snider L, Bennett SR, Jones TI, Jones PL, Shaw DWW, Blemker SS, Riem L, DuCharme O, Lemmers RJFL, van der Maarel SM, Wang LH, Tawil R, Statland JM, Tapscott SJ. Regional and bilateral MRI and gene signatures in facioscapulohumeral dystrophy: implications for clinical trial design and mechanisms of disease progression. Hum Mol Genet 2024; 33:698-708. [PMID: 38268317 PMCID: PMC11000661 DOI: 10.1093/hmg/ddae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/11/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024] Open
Abstract
Identifying the aberrant expression of DUX4 in skeletal muscle as the cause of facioscapulohumeral dystrophy (FSHD) has led to rational therapeutic development and clinical trials. Several studies support the use of MRI characteristics and the expression of DUX4-regulated genes in muscle biopsies as biomarkers of FSHD disease activity and progression. We performed lower-extremity MRI and muscle biopsies in the mid-portion of the tibialis anterior (TA) muscles bilaterally in FSHD subjects and validated our prior reports of the strong association between MRI characteristics and expression of genes regulated by DUX4 and other gene categories associated with FSHD disease activity. We further show that measurements of normalized fat content in the entire TA muscle strongly predict molecular signatures in the mid-portion of the TA, indicating that regional biopsies can accurately measure progression in the whole muscle and providing a strong basis for inclusion of MRI and molecular biomarkers in clinical trial design. An unanticipated finding was the strong correlations of molecular signatures in the bilateral comparisons, including markers of B-cells and other immune cell populations, suggesting that a systemic immune cell infiltration of skeletal muscle might have a role in disease progression.
Collapse
Affiliation(s)
- Chao-Jen Wong
- Division of Human Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, United States
| | - Seth D Friedman
- Department of Radiology, Seattle Children’s Hospital, 4540 Sandpoint Way, Seattle, WA 98105, United States
| | - Lauren Snider
- Division of Human Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, United States
| | - Sean R Bennett
- Division of Human Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, United States
| | - Takako I Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, Reno, NV 89557, United States
| | - Peter L Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, Reno, NV 89557, United States
| | - Dennis W W Shaw
- Department of Radiology, Seattle Children’s Hospital, 4540 Sandpoint Way, Seattle, WA 98105, United States
| | - Silvia S Blemker
- Springbok Analytics, 100 W South St, Charlottesville, VA 22902, United States
| | - Lara Riem
- Springbok Analytics, 100 W South St, Charlottesville, VA 22902, United States
| | - Olivia DuCharme
- Springbok Analytics, 100 W South St, Charlottesville, VA 22902, United States
| | - Richard J F L Lemmers
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Leo H Wang
- Department of Neurology, University of Washington, 1959 NE Pacific St, Seattle, WA 98105, United States
| | - Rabi Tawil
- Department of Neurology, University of Rochester Medical Center, 601 Elm St, Rochester, NY 14642, United States
| | - Jeffrey M Statland
- Department of Neurology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KA 66160, United States
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, United States
- Department of Neurology, University of Washington, 1959 NE Pacific St, Seattle, WA 98105, United States
| |
Collapse
|
3
|
Sun C, Serra C, Kalicharan BH, Harding J, Rao M. Challenges and Considerations of Preclinical Development for iPSC-Based Myogenic Cell Therapy. Cells 2024; 13:596. [PMID: 38607035 PMCID: PMC11011706 DOI: 10.3390/cells13070596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Cell therapies derived from induced pluripotent stem cells (iPSCs) offer a promising avenue in the field of regenerative medicine due to iPSCs' expandability, immune compatibility, and pluripotent potential. An increasing number of preclinical and clinical trials have been carried out, exploring the application of iPSC-based therapies for challenging diseases, such as muscular dystrophies. The unique syncytial nature of skeletal muscle allows stem/progenitor cells to integrate, forming new myonuclei and restoring the expression of genes affected by myopathies. This characteristic makes genome-editing techniques especially attractive in these therapies. With genetic modification and iPSC lineage specification methodologies, immune-compatible healthy iPSC-derived muscle cells can be manufactured to reverse the progression of muscle diseases or facilitate tissue regeneration. Despite this exciting advancement, much of the development of iPSC-based therapies for muscle diseases and tissue regeneration is limited to academic settings, with no successful clinical translation reported. The unknown differentiation process in vivo, potential tumorigenicity, and epigenetic abnormality of transplanted cells are preventing their clinical application. In this review, we give an overview on preclinical development of iPSC-derived myogenic cell transplantation therapies including processes related to iPSC-derived myogenic cells such as differentiation, scaling-up, delivery, and cGMP compliance. And we discuss the potential challenges of each step of clinical translation. Additionally, preclinical model systems for testing myogenic cells intended for clinical applications are described.
Collapse
Affiliation(s)
- Congshan Sun
- Vita Therapeutics, Baltimore, MD 21043, USA (M.R.)
| | - Carlo Serra
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Mahendra Rao
- Vita Therapeutics, Baltimore, MD 21043, USA (M.R.)
| |
Collapse
|
4
|
Butterfield RJ, Dunn DM, Duval B, Moldt S, Weiss RB. Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing. Genome Res 2023; 33:1439-1454. [PMID: 37798116 PMCID: PMC10620044 DOI: 10.1101/gr.277871.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/02/2023] [Indexed: 10/07/2023]
Abstract
Fascioscapulohumeral muscular dystrophy (FSHD) is caused by a unique genetic mechanism that relies on contraction and hypomethylation of the D4Z4 macrosatellite array on the Chromosome 4q telomere allowing ectopic expression of the DUX4 gene in skeletal muscle. Genetic analysis is difficult because of the large size and repetitive nature of the array, a nearly identical array on the 10q telomere, and the presence of divergent D4Z4 arrays scattered throughout the genome. Here, we combine nanopore long-read sequencing with Cas9-targeted enrichment of 4q and 10q D4Z4 arrays for comprehensive genetic analysis including determination of the length of the 4q and 10q D4Z4 arrays with base-pair resolution. In the same assay, we differentiate 4q from 10q telomeric sequences, determine A/B haplotype, identify paralogous D4Z4 sequences elsewhere in the genome, and estimate methylation for all CpGs in the array. Asymmetric, length-dependent methylation gradients were observed in the 4q and 10q D4Z4 arrays that reach a hypermethylation point at approximately 10 D4Z4 repeat units, consistent with the known threshold of pathogenic D4Z4 contractions. High resolution analysis of individual D4Z4 repeat methylation revealed areas of low methylation near the CTCF/insulator region and areas of high methylation immediately preceding the DUX4 transcriptional start site. Within the DUX4 exons, we observed a waxing/waning methylation pattern with a 180-nucleotide periodicity, consistent with phased nucleosomes. Targeted nanopore sequencing complements recently developed molecular combing and optical mapping approaches to genetic analysis for FSHD by adding precision of the length measurement, base-pair resolution sequencing, and quantitative methylation analysis.
Collapse
Affiliation(s)
- Russell J Butterfield
- Department of Pediatrics, University of Utah, Salt Lake City, Utah 84108, USA;
- Department of Neurology, University of Utah, Salt Lake City, Utah 84132, USA
| | - Diane M Dunn
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Brett Duval
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Sarah Moldt
- Department of Pediatrics, University of Utah, Salt Lake City, Utah 84108, USA
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| |
Collapse
|
5
|
Smith CM, Grow EJ, Shadle SC, Cairns BR. Multiple repeat regions within mouse DUX recruit chromatin regulators to facilitate an embryonic gene expression program. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534786. [PMID: 37034731 PMCID: PMC10081216 DOI: 10.1101/2023.03.29.534786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The embryonic transcription factor DUX regulates chromatin opening and gene expression in totipotent cleavage-stage mouse embryos, and its expression in embryonic stem cells promotes their conversion to 2-cell embryo-like cells (2CLCs) with extraembryonic potential. However, little is known regarding which domains within mouse DUX interact with particular chromatin and transcription regulators. Here, we reveal that the C-terminus of mouse DUX contains five uncharacterized ~100 amino acid (aa) repeats followed by an acidic 14 amino acid tail. Unexpectedly, structure-function approaches classify two repeats as 'active' and three as 'inactive' in cleavage/2CLC transcription program enhancement, with differences narrowed to a key 6 amino acid section. Our proximity dependent biotin ligation (BioID) approach identified factors selectively associated with active DUX repeat derivatives (including the 14aa 'tail'), including transcription and chromatin factors such as SWI/SNF (BAF) complex, as well as nucleolar factors that have been previously implicated in regulating the Dux locus. Finally, our mechanistic studies reveal cooperativity between DUX active repeats and the acidic tail in cofactor recruitment, DUX target opening, and transcription. Taken together, we provide several new insights into DUX structure-function, and mechanisms of chromatin and gene regulation.
Collapse
Affiliation(s)
- Christina M. Smith
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Edward J. Grow
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Green Center for Reproductive Biological Sciences, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sean C. Shadle
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bradley R. Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| |
Collapse
|
6
|
Nip Y, Bennett SR, Smith AA, Jones TI, Jones PL, Tapscott SJ. Human DUX4 and porcine DUXC activate similar early embryonic programs in pig muscle cells: implications for preclinical models of FSHD. Hum Mol Genet 2023; 32:1864-1874. [PMID: 36728804 PMCID: PMC10196675 DOI: 10.1093/hmg/ddad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/10/2023] [Accepted: 01/29/2023] [Indexed: 02/03/2023] Open
Abstract
Human DUX4 and its mouse ortholog Dux are normally expressed in the early embryo-the 4-cell or 2-cell cleavage stage embryo, respectively-and activate a portion of the first wave of zygotic gene expression. DUX4 is epigenetically suppressed in nearly all somatic tissue, whereas facioscapulohumeral dystrophy (FSHD)-causing mutations result in its aberrant expression in skeletal muscle, transcriptional activation of the early embryonic program and subsequent muscle pathology. Although DUX4 and Dux both activate an early totipotent transcriptional program, divergence of their DNA binding domains limits the use of DUX4 expressed in mice as a preclinical model for FSHD. In this study, we identify the porcine DUXC messenger ribonucleic acid expressed in early development and show that both pig DUXC and human DUX4 robustly activate a highly similar early embryonic program in pig muscle cells. These results support further investigation of pig preclinical models for FSHD.
Collapse
Affiliation(s)
- Yee Nip
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sean R Bennett
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Andrew A Smith
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Takako I Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Peter L Jones
- Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Neurology, University of Washington School of Medicine, Seattle, WA 98105, USA
| |
Collapse
|
7
|
Butterfield RJ, Dunn DM, Duval B, Moldt S, Weiss RB. Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.528868. [PMID: 36824722 PMCID: PMC9949141 DOI: 10.1101/2023.02.17.528868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Fascioscapulohumeral muscular dystrophy (FSHD) is caused by a unique genetic mechanism that relies on contraction and hypomethylation of the D4Z4 macrosatellite array on the chromosome 4q telomere allowing ectopic expression of the DUX4 gene in skeletal muscle. Genetic analysis is difficult due to the large size and repetitive nature of the array, a nearly identical array on the 10q telomere, and the presence of divergent D4Z4 arrays scattered throughout the genome. Here, we combine nanopore long-read sequencing with Cas9-targeted enrichment of 4q and 10q D4Z4 arrays for comprehensive genetic analysis including determination of the length of the 4q and 10q D4Z4 arrays with base-pair resolution. In the same assay, we differentiate 4q from 10q telomeric sequences, determine A/B haplotype, identify paralogous D4Z4 sequences elsewhere in the genome, and estimate methylation for all CpGs in the array. Asymmetric, length-dependent methylation gradients were observed in the 4q and 10q D4Z4 arrays that reach a hypermethylation point at approximately 10 D4Z4 repeat units, consistent with the known threshold of pathogenic D4Z4 contractions. High resolution analysis of individual D4Z4 repeat methylation revealed areas of low methylation near the CTCF/insulator region and areas of high methylation immediately preceding the DUX4 transcriptional start site. Within the DUX4 exons, we observed a waxing/waning methylation pattern with a 180-nucleotide periodicity, consistent with phased nucleosomes. Targeted nanopore sequencing complements recently developed molecular combing and optical mapping approaches to genetic analysis for FSHD by adding precision of the length measurement, base-pair resolution sequencing, and quantitative methylation analysis.
Collapse
Affiliation(s)
- Russell J Butterfield
- Department of Pediatrics, University of Utah, Salt Lake City, UT
- Department of Neurology, University of Utah, Salt Lake City, UT
| | - Diane M Dunn
- University of Utah, Department of Human Genetics, Salt Lake City, UT
| | - Brett Duval
- University of Utah, Department of Human Genetics, Salt Lake City, UT
| | - Sarah Moldt
- Department of Pediatrics, University of Utah, Salt Lake City, UT
| | - Robert B Weiss
- University of Utah, Department of Human Genetics, Salt Lake City, UT
| |
Collapse
|
8
|
Wong CJ, Friedman SD, Snider L, Bennett SR, Jones TI, Jones PL, Shaw DWW, Blemker SS, Riem L, DuCharme O, Lemmers RJFL, van der Maarel SRM, Wang LH, Tawil R, Statland JM, Tapscott SJ. Validation of the association between MRI and gene signatures in facioscapulohumeral dystrophy muscle: implications for clinical trial design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529303. [PMID: 36865168 PMCID: PMC9980042 DOI: 10.1101/2023.02.20.529303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Identifying the aberrant expression of DUX4 in skeletal muscle as the cause of facioscapulohumeral dystrophy (FSHD) has led to rational therapeutic development and clinical trials. Several studies support the use of MRI characteristics and the expression of DUX4-regulated genes in muscle biopsies as biomarkers of FSHD disease activity and progression, but reproducibility across studies needs further validation. We performed lower-extremity MRI and muscle biopsies in the mid-portion of the tibialis anterior (TA) muscles bilaterally in FSHD subjects and validated our prior reports of the strong association between MRI characteristics and expression of genes regulated by DUX4 and other gene categories associated with FSHD disease activity. We further show that measurements of normalized fat content in the entire TA muscle strongly predict molecular signatures in the mid-portion of the TA. Together with moderate-to-strong correlations of gene signatures and MRI characteristics between the TA muscles bilaterally, these results suggest a whole muscle model of disease progression and provide a strong basis for inclusion of MRI and molecular biomarkers in clinical trial design.
Collapse
|
9
|
Stage-specific H3K9me3 occupancy ensures retrotransposon silencing in human pre-implantation embryos. Cell Stem Cell 2022; 29:1051-1066.e8. [DOI: 10.1016/j.stem.2022.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/31/2022] [Accepted: 06/01/2022] [Indexed: 12/13/2022]
|
10
|
Himeda CL, Jones PL. FSHD Therapeutic Strategies: What Will It Take to Get to Clinic? J Pers Med 2022; 12:jpm12060865. [PMID: 35743650 PMCID: PMC9225474 DOI: 10.3390/jpm12060865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 12/10/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is arguably one of the most challenging genetic diseases to understand and treat. The disease is caused by epigenetic dysregulation of a macrosatellite repeat, either by contraction of the repeat or by mutations in silencing proteins. Both cases lead to chromatin relaxation and, in the context of a permissive allele, pathogenic misexpression of DUX4 in skeletal muscle. The complex nature of the locus and the fact that FSHD is a toxic, gain-of-function disease present unique challenges for the design of therapeutic strategies. There are three major DUX4-targeting avenues of therapy for FSHD: small molecules, oligonucleotide therapeutics, and CRISPR-based approaches. Here, we evaluate the preclinical progress of each avenue, and discuss efforts being made to overcome major hurdles to translation.
Collapse
|
11
|
Ren W, Gao L, Mou Y, Deng W, Hua J, Yang F. DUX: One Transcription Factor Controls 2-Cell-like Fate. Int J Mol Sci 2022; 23:ijms23042067. [PMID: 35216182 PMCID: PMC8877164 DOI: 10.3390/ijms23042067] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 02/06/2023] Open
Abstract
The double homeobox (Dux) gene, encoding a double homeobox transcription factor, is one of the key drivers of totipotency in mice. Recent studies showed Dux was temporally expressed at the 2-cell stage and acted as a transcriptional activator during zygotic genome activation (ZGA) in embryos. A similar activation occurs in mouse embryonic stem cells, giving rise to 2-cell-like cells (2CLCs). Though the molecular mechanism underlying this expanded 2CLC potency caused by Dux activation has been partially revealed, the regulation mechanisms controlling Dux expression remain elusive. Here, we discuss the latest advancements in the multiple levels of regulation of Dux expression, as well as Dux function in 2CLCs transition, aiming to provide a theoretical framework for understanding the mechanisms that regulate totipotency.
Collapse
Affiliation(s)
- Wei Ren
- College of Veterinary Medicine, Northwest A & F University, Xianyang 712100, China; (W.R.); (L.G.); (Y.M.); (J.H.)
- Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A & F University, Xianyang 712100, China
- College of Innovation and Experiment, Northwest A & F University, Xianyang 712100, China
| | - Leilei Gao
- College of Veterinary Medicine, Northwest A & F University, Xianyang 712100, China; (W.R.); (L.G.); (Y.M.); (J.H.)
- Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A & F University, Xianyang 712100, China
| | - Yaling Mou
- College of Veterinary Medicine, Northwest A & F University, Xianyang 712100, China; (W.R.); (L.G.); (Y.M.); (J.H.)
- Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A & F University, Xianyang 712100, China
| | - Wen Deng
- College of Veterinary Medicine, Northwest A & F University, Xianyang 712100, China; (W.R.); (L.G.); (Y.M.); (J.H.)
- Correspondence: (W.D.); (F.Y.)
| | - Jinlian Hua
- College of Veterinary Medicine, Northwest A & F University, Xianyang 712100, China; (W.R.); (L.G.); (Y.M.); (J.H.)
- Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A & F University, Xianyang 712100, China
| | - Fan Yang
- College of Veterinary Medicine, Northwest A & F University, Xianyang 712100, China; (W.R.); (L.G.); (Y.M.); (J.H.)
- Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A & F University, Xianyang 712100, China
- Correspondence: (W.D.); (F.Y.)
| |
Collapse
|
12
|
The evolution of DUX4 gene regulation and its implication for facioscapulohumeral muscular dystrophy. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166367. [PMID: 35158020 PMCID: PMC9173005 DOI: 10.1016/j.bbadis.2022.166367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 11/22/2022]
Abstract
Double homeobox 4 (DUX4) is an early embryonic transcription factor whose expression in the skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). Despite decades of research, our knowledge of FSHD and DUX4 biology is incomplete, and the disease has currently no cures or targeted therapies. The unusual evolutionary origin of DUX4, its extensive epigenetic and post-transcriptional gene regulation, and various feedback regulatory loops that control its expression and function all contribute to the highly complex nature of FSHD pathogenesis. In this minireview, I synthesize the current state of knowledge in DUX4 and FSHD biology to highlight key areas where further research is needed to better understand DUX4 regulation. I also emphasize post-transcriptional regulation of and by DUX4 via changes in RNA and protein stability that might underlie key features of FSHD pathophysiology. Finally, I discuss the various feedback loops involved in DUX4 regulation and the context-specific consequences of its expression, which could be key to developing novel therapeutic approaches to combat FSHD.
Collapse
|
13
|
Wong CJ, Whiddon JL, Langford AT, Belleville AE, Tapscott SJ. Canine DUXC: Implications for DUX4 retrotransposition and preclinical models of FSHD. Hum Mol Genet 2021; 31:1694-1704. [PMID: 34888646 DOI: 10.1093/hmg/ddab352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/24/2021] [Accepted: 12/03/2021] [Indexed: 11/15/2022] Open
Abstract
Mis-expression of DUX4 in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). Human DUX4 and mouse Dux are retrogenes derived from retrotransposition of the mRNA from the parental DUXC gene. Primates and rodents have lost the parental DUXC gene and it is unknown whether DUXC had a similar role in driving an early pluripotent transcriptional program. Dogs and other Laurasiatherians have retained DUXC, providing an opportunity to determine the functional similarity to the retrotransposed DUX4 and Dux. Here we identify expression of two isoforms of DUXC mRNA in canine testis tissues, one encoding the canonical double homeodomain protein (DUXC), similar to DUX4/Dux, and a second that includes an in-frame alternative exon that disrupts the conserved amino-acid sequence of the first homeodomain (DUXC-ALT). Expression of DUXC in canine cells induces a pluripotent program similar to DUX4 and Dux, and induces expression of a similar set of retrotransposons of the ERV/MaLR and LINE-1 families, as well as pericentromeric satellite repeats; whereas DUXC-ALT did not robustly activate gene expression in these assays. Important for preclinical models of FSHD, human DUX4 and canine DUXC show higher conservation of their homeodomains and corresponding binding motifs compared to the conservation between human DUX4 and mouse Dux, and human DUX4 activates a highly similar transcriptional program in canine cells. Together, these findings show that retrotransposition resulted in the loss of an alternatively spliced isoform and that DUXC containing mammals might be good candidates for certain pre-clinical models of FSHD.
Collapse
Affiliation(s)
- Chao-Jen Wong
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle WA 98109 USA
| | - Jennifer L Whiddon
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle WA 98109 USA
| | - Ashlee T Langford
- Comparative Medicine, Fred Hutchinson Cancer Research Center, Seattle WA 98109 USA
| | - Andrea E Belleville
- Divisions of Public Health Sciences and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle WA 98109 USA
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle WA 98109 USA.,Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle WA USA
| |
Collapse
|
14
|
Senft AD, Macfarlan TS. Transposable elements shape the evolution of mammalian development. Nat Rev Genet 2021; 22:691-711. [PMID: 34354263 DOI: 10.1038/s41576-021-00385-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Transposable elements (TEs) promote genetic innovation but also threaten genome stability. Despite multiple layers of host defence, TEs actively shape mammalian-specific developmental processes, particularly during pre-implantation and extra-embryonic development and at the maternal-fetal interface. Here, we review how TEs influence mammalian genomes both directly by providing the raw material for genetic change and indirectly via co-evolving TE-binding Krüppel-associated box zinc finger proteins (KRAB-ZFPs). Throughout mammalian evolution, individual activities of ancient TEs were co-opted to enable invasive placentation that characterizes live-born mammals. By contrast, the widespread activity of evolutionarily young TEs may reflect an ongoing co-evolution that continues to impact mammalian development.
Collapse
Affiliation(s)
- Anna D Senft
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
15
|
The Cytogenetics of the Water Buffalo: A Review. Animals (Basel) 2021; 11:ani11113109. [PMID: 34827841 PMCID: PMC8614332 DOI: 10.3390/ani11113109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/17/2022] Open
Abstract
The water buffalo (Bubalus bubalis), also known as the Asian buffalo, is an essential domestic bovid. Indeed, although its world population (~209 million heads) is approximately one-ninth that of cattle, the management of this species involves a larger human population than that involved with raising cattle. Compared with cattle, water buffalo have been understudied for many years, but interest in this species has been increasing, especially considering that the world population of these bovids grows every year-particularly that of the river buffalo. There are two genera of buffalo worldwide: the Syncerus (from the African continent), and the Bubalus (from the southwest Asian continent, Mediterranean area, southern America, and Australia). All species belonging to these two genera have specific chromosome numbers and shapes. Because of such features, the study of chromosomes is a fascinating biological basis for differentiating various species (and hybrids) of buffaloes and characterizing their karyotypes in evolutionary, clinical, and molecular studies. In this review, we report an update on essential cytogenetic studies in which various buffalo species were described from evolutionary, clinical, and molecular perspectives-particularly considering the river buffalo (Bubalus bubalis 2n = 50). In addition, we show new data on swamp buffalo chromosomes.
Collapse
|
16
|
Jia FF, Drew AP, Nicholson GA, Corbett A, Kumar KR. Facioscapulohumeral muscular dystrophy type 2: an update on the clinical, genetic, and molecular findings. Neuromuscul Disord 2021; 31:1101-1112. [PMID: 34711481 DOI: 10.1016/j.nmd.2021.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/01/2021] [Accepted: 09/09/2021] [Indexed: 11/25/2022]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a common genetic disease of the skeletal muscle with a characteristic pattern of weakness. Facioscapulohumeral muscular dystrophy type 2 (FSHD2) accounts for approximately 5% of all cases of FSHD and describes patients without a D4Z4 repeat contraction on chromosome 4. Phenotypically FSHD2 shows virtually no difference from FSHD1 and both forms of FSHD arise via a common downstream mechanism of epigenetic derepression of the transcription factor DUX4 in skeletal muscle cells. This results in expression of DUX4 and target genes leading to skeletal muscle toxicity. Over the past decade, major progress has been made in our understanding of the genetic and epigenetic architecture that underlies FSHD2 pathogenesis, as well as the clinical manifestations and disease progression. These include the finding that FSHD2 is a digenic disease and that mutations in the genes SMCHD1, DNMT3B, and more recently LRIF1, can cause FSHD2. FSHD2 is complex and it is important that clinicians keep abreast of recent developments; this review aims to serve as an update of the clinical, genetic, and molecular research into this condition.
Collapse
Affiliation(s)
- Fangzhi Frank Jia
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia.
| | - Alexander P Drew
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.
| | - Garth Alexander Nicholson
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
| | - Alastair Corbett
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
| | - Kishore Raj Kumar
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia; Sydney Medical School, University of Sydney, Camperdown, New South Wales 2050, Australia.
| |
Collapse
|
17
|
Banerji CRS, Zammit PS. Pathomechanisms and biomarkers in facioscapulohumeral muscular dystrophy: roles of DUX4 and PAX7. EMBO Mol Med 2021; 13:e13695. [PMID: 34151531 PMCID: PMC8350899 DOI: 10.15252/emmm.202013695] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/27/2021] [Accepted: 03/30/2021] [Indexed: 12/29/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is characterised by progressive skeletal muscle weakness and wasting. FSHD is linked to epigenetic derepression of the subtelomeric D4Z4 macrosatellite at chromosome 4q35. Epigenetic derepression permits the distal-most D4Z4 unit to transcribe DUX4, with transcripts stabilised by splicing to a poly(A) signal on permissive 4qA haplotypes. The pioneer transcription factor DUX4 activates target genes that are proposed to drive FSHD pathology. While this toxic gain-of-function model is a satisfying "bottom-up" genotype-to-phenotype link, DUX4 is rarely detectable in muscle and DUX4 target gene expression is inconsistent in patients. A reliable biomarker for FSHD is suppression of a target gene score of PAX7, a master regulator of myogenesis. However, it is unclear how this "top-down" finding links to genomic changes that characterise FSHD and to DUX4. Here, we explore the roles and interactions of DUX4 and PAX7 in FSHD pathology and how the relationship between these two transcription factors deepens understanding via the immune system and muscle regeneration. Considering how FSHD pathomechanisms are represented by "DUX4opathy" models has implications for developing therapies and current clinical trials.
Collapse
Affiliation(s)
| | - Peter S Zammit
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| |
Collapse
|
18
|
Grow EJ, Weaver BD, Smith CM, Guo J, Stein P, Shadle SC, Hendrickson PG, Johnson NE, Butterfield RJ, Menafra R, Kloet SL, van der Maarel SM, Williams CJ, Cairns BR. p53 convergently activates Dux/DUX4 in embryonic stem cells and in facioscapulohumeral muscular dystrophy cell models. Nat Genet 2021; 53:1207-1220. [PMID: 34267371 PMCID: PMC8513633 DOI: 10.1038/s41588-021-00893-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/01/2021] [Indexed: 12/21/2022]
Abstract
In mammalian embryos, proper zygotic genome activation (ZGA) underlies totipotent development. Double homeobox (DUX)-family factors participate in ZGA, and mouse Dux is required for forming cultured two-cell (2C)-like cells. Remarkably, in mouse embryonic stem cells, Dux is activated by the tumor suppressor p53, and Dux expression promotes differentiation into expanded-fate cell types. Long-read sequencing and assembly of the mouse Dux locus reveals its complex chromatin regulation including putative positive and negative feedback loops. We show that the p53-DUX/DUX4 regulatory axis is conserved in humans. Furthermore, we demonstrate that cells derived from patients with facioscapulohumeral muscular dystrophy (FSHD) activate human DUX4 during p53 signaling via a p53-binding site in a primate-specific subtelomeric long terminal repeat (LTR)10C element. In summary, our work shows that p53 activation convergently evolved to couple p53 to Dux/DUX4 activation in embryonic stem cells, embryos and cells from patients with FSHD, potentially uniting the developmental and disease regulation of DUX-family factors and identifying evidence-based therapeutic opportunities for FSHD.
Collapse
Affiliation(s)
- Edward J Grow
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bradley D Weaver
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Christina M Smith
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jingtao Guo
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paula Stein
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Sean C Shadle
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Peter G Hendrickson
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Nicholas E Johnson
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Russell J Butterfield
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Roberta Menafra
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Susan L Kloet
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Carmen J Williams
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.
| |
Collapse
|
19
|
Fu B, Ma H, Liu D. Functions and Regulation of Endogenous Retrovirus Elements during Zygotic Genome Activation: Implications for Improving Somatic Cell Nuclear Transfer Efficiency. Biomolecules 2021; 11:829. [PMID: 34199637 PMCID: PMC8229993 DOI: 10.3390/biom11060829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 12/28/2022] Open
Abstract
Endogenous retroviruses (ERVs), previously viewed as deleterious relics of ancestral retrovirus infections, are silenced in the vast majority of cells to minimize the risk of retrotransposition. Counterintuitively, bursts of ERV transcription usually occur during maternal-to-zygotic transition (MZT) in preimplantation embryos; this is regarded as a major landmark event in the zygotic genome activation (ZGA) process, indicating that ERVs play an active part in ZGA. Evolutionarily, the interaction between ERVs and hosts is mutually beneficial. The endogenization of retrovirus sequences rewires the gene regulatory network during ZGA, and ERV repression may lower germline fitness. Unfortunately, owing to various limitations of somatic cell nuclear transfer (SCNT) technology, both developmental arrest and ZGA abnormalities occur in a high percentage of cloned embryos, accompanied by ERV silencing, which may be caused by the activation failure of upstream ERV inducers. In this review, we discuss the functions and regulation of ERVs during the ZGA process and the feasibility of temporal control over ERVs in cloned embryos via exogenous double homeobox (DUX). We hypothesize that further accurate characterization of the ERV-rewired gene regulatory network during ZGA may provide a novel perspective on the development of preimplantation embryos.
Collapse
Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; (B.F.); (H.M.)
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Hong Ma
- Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; (B.F.); (H.M.)
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Di Liu
- Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; (B.F.); (H.M.)
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| |
Collapse
|
20
|
Guo SM, Mei NH, Yang J, Zhou LQ. Transcription factor OTX2 silences the expression of cleavage embryo genes and transposable elements. J Reprod Dev 2021; 67:223-228. [PMID: 33896883 PMCID: PMC8238675 DOI: 10.1262/jrd.2021-007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Upon mammalian fertilization, zygotic genome activation (ZGA) and activation of transposable elements (TEs) occur in early embryos to establish totipotency and
support embryogenesis. However, the molecular mechanisms controlling the expression of these genes in mammals remain poorly understood. The 2-cell-like
population of mouse embryonic stem cells (mESCs) mimics cleavage-stage embryos with transient Dux activation. In this study, we demonstrated
that deficiency of the transcription factor OTX2 stimulates the expression of ZGA genes in mESCs. Further analysis revealed that OTX2 is incorporated at
the Dux locus with corepressors for transcriptional inhibition. We also found that OTX2 associates with TEs and silences the subtypes of TEs.
Therefore, OTX2 protein plays an important role in ZGA and TE expression in mESCs to orchestrate the transcriptional network.
Collapse
Affiliation(s)
- Shi-Meng Guo
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430030, China
| | - Ning-Hua Mei
- Reproductive Medical Center, Renmin Hospital of Wuhan University & Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
| | - Jing Yang
- Reproductive Medical Center, Renmin Hospital of Wuhan University & Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
| | - Li-Quan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430030, China
| |
Collapse
|
21
|
Karpukhina A, Tiukacheva E, Dib C, Vassetzky YS. Control of DUX4 Expression in Facioscapulohumeral Muscular Dystrophy and Cancer. Trends Mol Med 2021; 27:588-601. [PMID: 33863674 DOI: 10.1016/j.molmed.2021.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022]
Abstract
DUX4, a gene encoding a transcription factor involved in early embryogenesis, is located within the D4Z4 subtelomeric repeat on chromosome 4q35. In most healthy somatic tissues, DUX4 is heavily repressed by multiple genetic and epigenetic mechanisms, and its aberrant expression is linked to facioscapulohumeral muscular dystrophy (FSHD) where it has been extensively studied. Recently, DUX4 expression has been implicated in oncogenesis, although this is much less explored. In this review, we discuss multiple levels of control of DUX4 expression, including enhancer-promoter interactions, DNA methylation, histone modifications, noncoding RNAs, and telomere positioning effect. We also connect disparate data on intrachromosomal contacts involving DUX4 and emphasize the feedback loops in DUX4 regulation. Finally, we bridge data on DUX4 in FSHD and cancer and discuss prospective approaches for future FSHD therapies and the potential outcomes of DUX4 inhibition in cancer.
Collapse
Affiliation(s)
- Anna Karpukhina
- UMR 9018, CNRS, Université Paris Saclay, Institut Gustave Roussy, Villejuif F-94805, France; Koltzov Institute of Developmental Biology, Moscow 117334, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Eugenia Tiukacheva
- UMR 9018, CNRS, Université Paris Saclay, Institut Gustave Roussy, Villejuif F-94805, France
| | - Carla Dib
- UMR 9018, CNRS, Université Paris Saclay, Institut Gustave Roussy, Villejuif F-94805, France; Stanford University School of Medicine, Stanford, CA 94305-510, USA
| | - Yegor S Vassetzky
- UMR 9018, CNRS, Université Paris Saclay, Institut Gustave Roussy, Villejuif F-94805, France; Koltzov Institute of Developmental Biology, Moscow 117334, Russia.
| |
Collapse
|
22
|
Sugie K, Funaya S, Kawamura M, Nakamura T, Suzuki MG, Aoki F. Expression of Dux family genes in early preimplantation embryos. Sci Rep 2020; 10:19396. [PMID: 33173118 PMCID: PMC7655946 DOI: 10.1038/s41598-020-76538-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022] Open
Abstract
After fertilization, the zygotic genome is activated through two phases, minor zygotic activation (ZGA) and major ZGA.
Recently, it was suggested that DUX is expressed during minor ZGA and activates some genes during major ZGA. However, it has not been proven that Dux is expressed during minor ZGA and functions to activate major ZGA genes, because there are several Dux paralogs that may be expressed in zygotes instead of Dux. In this study, we found that more than a dozen Dux paralogs, as well as Dux, are expressed during minor ZGA. Overexpression of some of these genes induced increased expression of major ZGA genes. These results suggest that multiple Dux paralogs are expressed to ensure a sufficient amount of functional Dux and its paralogs which are generated during a short period of minor ZGA with a low transcriptional activity. The mechanism by which multiple Dux paralogs are expressed is discussed.
Collapse
Affiliation(s)
- Kenta Sugie
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Satoshi Funaya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Machika Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Toshinobu Nakamura
- Department of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan.
| |
Collapse
|
23
|
DeSimone AM, Cohen J, Lek M, Lek A. Cellular and animal models for facioscapulohumeral muscular dystrophy. Dis Model Mech 2020; 13:13/10/dmm046904. [PMID: 33174531 PMCID: PMC7648604 DOI: 10.1242/dmm.046904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is one of the most common forms of muscular dystrophy and presents with weakness of the facial, scapular and humeral muscles, which frequently progresses to the lower limbs and truncal areas, causing profound disability. Myopathy results from epigenetic de-repression of the D4Z4 microsatellite repeat array on chromosome 4, which allows misexpression of the developmentally regulated DUX4 gene. DUX4 is toxic when misexpressed in skeletal muscle and disrupts several cellular pathways, including myogenic differentiation and fusion, which likely underpins pathology. DUX4 and the D4Z4 array are strongly conserved only in primates, making FSHD modeling in non-primate animals difficult. Additionally, its cytotoxicity and unusual mosaic expression pattern further complicate the generation of in vitro and in vivo models of FSHD. However, the pressing need to develop systems to test therapeutic approaches has led to the creation of multiple engineered FSHD models. Owing to the complex genetic, epigenetic and molecular factors underlying FSHD, it is difficult to engineer a system that accurately recapitulates every aspect of the human disease. Nevertheless, the past several years have seen the development of many new disease models, each with their own associated strengths that emphasize different aspects of the disease. Here, we review the wide range of FSHD models, including several in vitro cellular models, and an array of transgenic and xenograft in vivo models, with particular attention to newly developed systems and how they are being used to deepen our understanding of FSHD pathology and to test the efficacy of drug candidates. Summary: Owing to its complex etiology and the toxicity of DUX4, modeling facioscapulohumeral muscular dystrophy (FSHD) is uniquely challenging. Here, we review the approaches that overcame these difficulties to develop highly relevant FSHD models.
Collapse
Affiliation(s)
- Alec M DeSimone
- Yale School of Medicine, Department of Genetics, New Haven, CT 06510, USA
| | - Justin Cohen
- Yale School of Medicine, Department of Genetics, New Haven, CT 06510, USA
| | - Monkol Lek
- Yale School of Medicine, Department of Genetics, New Haven, CT 06510, USA
| | - Angela Lek
- Yale School of Medicine, Department of Genetics, New Haven, CT 06510, USA
| |
Collapse
|
24
|
Karpukhina A, Vassetzky Y. DUX4, a Zygotic Genome Activator, Is Involved in Oncogenesis and Genetic Diseases. Russ J Dev Biol 2020. [DOI: 10.1134/s1062360420030078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
25
|
Le R, Huang Y, Zhao A, Gao S. Lessons from expanded potential of embryonic stem cells: Moving toward totipotency. J Genet Genomics 2020; 47:123-130. [PMID: 32305172 DOI: 10.1016/j.jgg.2020.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 01/20/2020] [Accepted: 02/10/2020] [Indexed: 02/06/2023]
Abstract
Embryonic stem cells possess fascinating capacity of self-renewal and developmental potential, leading to significant progress in understanding the molecular basis of pluripotency, disease modeling, and reprogramming technology. Recently, 2-cell-like embryonic stem cells (ESCs) and expanded potential stem cells or extended pluripotent stem cells (EPSCs) generated from early-cleavage embryos display some features of totipotent embryos. These cell lines provide valuable in vitro models to study underlying principles of totipotency, cell plasticity, and lineage segregation. In this review, we summarize the current progress in this filed and highlight the application potentials of these cells in the future.
Collapse
Affiliation(s)
- Rongrong Le
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yixin Huang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Anqi Zhao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| |
Collapse
|
26
|
Wu E, Vastenhouw NL. From mother to embryo: A molecular perspective on zygotic genome activation. Curr Top Dev Biol 2020; 140:209-254. [PMID: 32591075 DOI: 10.1016/bs.ctdb.2020.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In animals, the early embryo is mostly transcriptionally silent and development is fueled by maternally supplied mRNAs and proteins. These maternal products are important not only for survival, but also to gear up the zygote's genome for activation. Over the last three decades, research with different model organisms and experimental approaches has identified molecular factors and proposed mechanisms for how the embryo transitions from being transcriptionally silent to transcriptionally competent. In this chapter, we discuss the molecular players that shape the molecular landscape of ZGA and provide insights into their mode of action in activating the transcription program in the developing embryo.
Collapse
Affiliation(s)
- Edlyn Wu
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| |
Collapse
|
27
|
De Iaco A, Verp S, Offner S, Grun D, Trono D. DUX is a non-essential synchronizer of zygotic genome activation. Development 2020; 147:dev.177725. [PMID: 31806660 DOI: 10.1242/dev.177725] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022]
Abstract
Some of the earliest transcripts produced in fertilized human and mouse oocytes code for DUX, a double homeodomain protein that promotes embryonic genome activation (EGA). Deleting Dux by genome editing at the one- to two-cell stage in the mouse impairs EGA and blastocyst maturation. Here, we demonstrate that mice carrying homozygous Dux deletions display markedly reduced expression of DUX target genes and defects in both pre- and post-implantation development, with, notably, a disruption of the pace of the first few cell divisions and significant rates of late embryonic mortality. However, some Dux -/- embryos give rise to viable pups, indicating that DUX is important but not strictly essential for embryogenesis.
Collapse
Affiliation(s)
- Alberto De Iaco
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sonia Verp
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Delphine Grun
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| |
Collapse
|
28
|
Zhang W, Chen F, Chen R, Xie D, Yang J, Zhao X, Guo R, Zhang Y, Shen Y, Göke J, Liu L, Lu X. Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes. Nucleic Acids Res 2019; 47:8485-8501. [PMID: 31304534 PMCID: PMC7145578 DOI: 10.1093/nar/gkz594] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 01/09/2023] Open
Abstract
Endogenous retroviruses (ERVs) contribute to ∼10 percent of the mouse genome. They are often silenced in differentiated somatic cells but differentially expressed at various embryonic developmental stages. A minority of mouse embryonic stem cells (ESCs), like 2-cell cleavage embryos, highly express ERV MERVL. However, the role of ERVs and mechanism of their activation in these cells are still poorly understood. In this study, we investigated the regulation and function of the stage-specific expressed ERVs, with a particular focus on the totipotency marker MT2/MERVL. We show that the transcription factor Zscan4c functions as an activator of MT2/MERVL and 2-cell/4-cell embryo genes. Zinc finger domains of Zscan4c play an important role in this process. In addition, Zscan4c interacts with MT2 and regulates MT2-nearby 2-cell/4-cell genes through promoting enhancer activity of MT2. Furthermore, MT2 activation is accompanied by enhanced H3K4me1, H3K27ac, and H3K14ac deposition on MT2. Zscan4c also interacts with GBAF chromatin remodelling complex through SCAN domain to further activate MT2 enhancer activity. Taken together, we delineate a previously unrecognized regulatory axis that Zscan4c interacts with and activates MT2/MERVL loci and their nearby genes through epigenetic regulation.
Collapse
Affiliation(s)
- Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Fuquan Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Ruiqing Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Dan Xie
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Jiao Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Xin Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Renpeng Guo
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Yongwang Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Yang Shen
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jonathan Göke
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| |
Collapse
|
29
|
Establishment of a novel human CIC-DUX 4 sarcoma cell line, Kitra-SRS, with autocrine IGF-1R activation and metastatic potential to the lungs. Sci Rep 2019; 9:15812. [PMID: 31676869 PMCID: PMC6825133 DOI: 10.1038/s41598-019-52143-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/14/2019] [Indexed: 02/07/2023] Open
Abstract
Approximately 60–70% of EWSR1-negative small blue round cell sarcomas harbour a rearrangement of CIC, most commonly CIC-DUX4. CIC-DUX4 sarcoma (CDS) is an aggressive and often fatal high-grade sarcoma appearing predominantly in children and young adults. Although cell lines and their xenograft models are essential tools for basic research and development of antitumour drugs, few cell lines currently exist for CDS. We successfully established a novel human CDS cell line designated Kitra-SRS and developed orthotopic tumour xenografts in nude mice. The CIC-DUX4 fusion gene in Kitra-SRS cells was generated by t(12;19) complex chromosomal rearrangements with an insertion of a chromosome segment including a DUX4 pseudogene component. Kitra-SRS xenografts were histologically similar to the original tumour and exhibited metastatic potential to the lungs. Kitra-SRS cells displayed autocrine activation of the insulin-like growth factor 1 (IGF-1)/IGF-1 receptor (IGF-1R) pathway. Accordingly, treatment with the IGF-1R inhibitor, linsitinib, attenuated Kitra-SRS cell growth and IGF-1-induced activation of IGF-1R/AKT signalling both in vitro and in vivo. Furthermore, upon screening 1134 FDA-approved drugs, the responses of Kitra-SRS cells to anticancer drugs appeared to reflect those of the primary tumour. Our model will be a useful modality for investigating the molecular pathology and therapy of CDS.
Collapse
|
30
|
Abstract
Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, provides a powerful model of the complex interplay between genetic and epigenetic mechanisms of chromatin regulation. FSHD is caused by dysregulation of a macrosatellite repeat, either by contraction of the repeat or by mutations in silencing proteins. Both cases lead to chromatin relaxation and, in the context of a permissive allele, aberrant expression of the DUX4 gene in skeletal muscle. DUX4 is a pioneer transcription factor that activates a program of gene expression during early human development, after which its expression is silenced in most somatic cells. When misexpressed in FSHD skeletal muscle, the DUX4 program leads to accumulated muscle pathology. Epigenetic regulators of the disease locus represent particularly attractive therapeutic targets for FSHD, as many are not global modifiers of the genome, and altering their expression or activity should allow correction of the underlying defect.
Collapse
MESH Headings
- CRISPR-Cas Systems
- Chromatin/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Human, Pair 4
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Gene Editing
- Genetic Loci
- Genome, Human
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Facioscapulohumeral/classification
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Muscular Dystrophy, Facioscapulohumeral/pathology
- Mutation
- Severity of Illness Index
- DNA Methyltransferase 3B
Collapse
Affiliation(s)
- Charis L Himeda
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
| | - Peter L Jones
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
| |
Collapse
|
31
|
Oliva J, Galasinski S, Richey A, Campbell AE, Meyers MJ, Modi N, Zhong JW, Tawil R, Tapscott SJ, Sverdrup FM. Clinically Advanced p38 Inhibitors Suppress DUX4 Expression in Cellular and Animal Models of Facioscapulohumeral Muscular Dystrophy. J Pharmacol Exp Ther 2019; 370:219-230. [PMID: 31189728 PMCID: PMC6652132 DOI: 10.1124/jpet.119.259663] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 06/10/2019] [Indexed: 11/22/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is characterized by misexpression of the double homeobox 4 (DUX4) developmental transcription factor in mature skeletal muscle, where it is responsible for muscle degeneration. Preventing expression of DUX4 mRNA is a disease-modifying therapeutic strategy with the potential to halt or reverse the course of disease. We previously reported that agonists of the β-2 adrenergic receptor suppress DUX4 expression by activating adenylate cyclase to increase cAMP levels. Efforts to further explore this signaling pathway led to the identification of p38 mitogen-activated protein kinase as a major regulator of DUX4 expression. In vitro experiments demonstrate that clinically advanced p38 inhibitors suppress DUX4 expression in FSHD type 1 and 2 myoblasts and differentiating myocytes in vitro with exquisite potency. Individual small interfering RNA-mediated knockdown of either p38α or p38β suppresses DUX4 expression, demonstrating that each kinase isoform plays a distinct requisite role in activating DUX4 Finally, p38 inhibitors effectively suppress DUX4 expression in a mouse xenograft model of human FSHD gene regulation. These data support the repurposing of existing clinical p38 inhibitors as potential therapeutics for FSHD. The surprise finding that p38α and p38β isoforms each independently contribute to DUX4 expression offers a unique opportunity to explore the utility of p38 isoform-selective inhibitors to balance efficacy and safety in skeletal muscle. We propose p38 inhibition as a disease-modifying therapeutic strategy for FSHD. SIGNIFICANCE STATEMENT: Facioscapulohumeral muscular dystrophy (FSHD) currently has no treatment options. This work provides evidence that repurposing a clinically advanced p38 inhibitor may provide the first disease-modifying drug for FSHD by suppressing toxic DUX4 expression, the root cause of muscle degeneration in this disease.
Collapse
Affiliation(s)
- Jonathan Oliva
- Departments of Biochemistry and Molecular Biology (J.O., A.R., N.M., F.M.S.) and Chemistry (M.J.M.), Saint Louis University, St. Louis, Missouri; Ultragenyx Pharmaceutical Inc., Novato, California (S.G.); Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (A.E.C., J.W.Z., S.J.T.); Department of Neurology, University of Rochester Medical Center, Rochester, New York (R.T.); and Department of Neurology, University of Washington, Seattle, Washington (S.J.T.)
| | - Scott Galasinski
- Departments of Biochemistry and Molecular Biology (J.O., A.R., N.M., F.M.S.) and Chemistry (M.J.M.), Saint Louis University, St. Louis, Missouri; Ultragenyx Pharmaceutical Inc., Novato, California (S.G.); Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (A.E.C., J.W.Z., S.J.T.); Department of Neurology, University of Rochester Medical Center, Rochester, New York (R.T.); and Department of Neurology, University of Washington, Seattle, Washington (S.J.T.)
| | - Amelia Richey
- Departments of Biochemistry and Molecular Biology (J.O., A.R., N.M., F.M.S.) and Chemistry (M.J.M.), Saint Louis University, St. Louis, Missouri; Ultragenyx Pharmaceutical Inc., Novato, California (S.G.); Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (A.E.C., J.W.Z., S.J.T.); Department of Neurology, University of Rochester Medical Center, Rochester, New York (R.T.); and Department of Neurology, University of Washington, Seattle, Washington (S.J.T.)
| | - Amy E Campbell
- Departments of Biochemistry and Molecular Biology (J.O., A.R., N.M., F.M.S.) and Chemistry (M.J.M.), Saint Louis University, St. Louis, Missouri; Ultragenyx Pharmaceutical Inc., Novato, California (S.G.); Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (A.E.C., J.W.Z., S.J.T.); Department of Neurology, University of Rochester Medical Center, Rochester, New York (R.T.); and Department of Neurology, University of Washington, Seattle, Washington (S.J.T.)
| | - Marvin J Meyers
- Departments of Biochemistry and Molecular Biology (J.O., A.R., N.M., F.M.S.) and Chemistry (M.J.M.), Saint Louis University, St. Louis, Missouri; Ultragenyx Pharmaceutical Inc., Novato, California (S.G.); Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (A.E.C., J.W.Z., S.J.T.); Department of Neurology, University of Rochester Medical Center, Rochester, New York (R.T.); and Department of Neurology, University of Washington, Seattle, Washington (S.J.T.)
| | - Neal Modi
- Departments of Biochemistry and Molecular Biology (J.O., A.R., N.M., F.M.S.) and Chemistry (M.J.M.), Saint Louis University, St. Louis, Missouri; Ultragenyx Pharmaceutical Inc., Novato, California (S.G.); Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (A.E.C., J.W.Z., S.J.T.); Department of Neurology, University of Rochester Medical Center, Rochester, New York (R.T.); and Department of Neurology, University of Washington, Seattle, Washington (S.J.T.)
| | - Jun Wen Zhong
- Departments of Biochemistry and Molecular Biology (J.O., A.R., N.M., F.M.S.) and Chemistry (M.J.M.), Saint Louis University, St. Louis, Missouri; Ultragenyx Pharmaceutical Inc., Novato, California (S.G.); Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (A.E.C., J.W.Z., S.J.T.); Department of Neurology, University of Rochester Medical Center, Rochester, New York (R.T.); and Department of Neurology, University of Washington, Seattle, Washington (S.J.T.)
| | - Rabi Tawil
- Departments of Biochemistry and Molecular Biology (J.O., A.R., N.M., F.M.S.) and Chemistry (M.J.M.), Saint Louis University, St. Louis, Missouri; Ultragenyx Pharmaceutical Inc., Novato, California (S.G.); Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (A.E.C., J.W.Z., S.J.T.); Department of Neurology, University of Rochester Medical Center, Rochester, New York (R.T.); and Department of Neurology, University of Washington, Seattle, Washington (S.J.T.)
| | - Stephen J Tapscott
- Departments of Biochemistry and Molecular Biology (J.O., A.R., N.M., F.M.S.) and Chemistry (M.J.M.), Saint Louis University, St. Louis, Missouri; Ultragenyx Pharmaceutical Inc., Novato, California (S.G.); Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (A.E.C., J.W.Z., S.J.T.); Department of Neurology, University of Rochester Medical Center, Rochester, New York (R.T.); and Department of Neurology, University of Washington, Seattle, Washington (S.J.T.)
| | - Francis M Sverdrup
- Departments of Biochemistry and Molecular Biology (J.O., A.R., N.M., F.M.S.) and Chemistry (M.J.M.), Saint Louis University, St. Louis, Missouri; Ultragenyx Pharmaceutical Inc., Novato, California (S.G.); Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington (A.E.C., J.W.Z., S.J.T.); Department of Neurology, University of Rochester Medical Center, Rochester, New York (R.T.); and Department of Neurology, University of Washington, Seattle, Washington (S.J.T.)
| |
Collapse
|
32
|
Campbell AE, Belleville AE, Resnick R, Shadle SC, Tapscott SJ. Facioscapulohumeral dystrophy: activating an early embryonic transcriptional program in human skeletal muscle. Hum Mol Genet 2019; 27:R153-R162. [PMID: 29718206 DOI: 10.1093/hmg/ddy162] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 04/27/2018] [Indexed: 12/12/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is the third most prevalent muscular dystrophy. A progressive disease, it presents clinically as weakness and wasting of the face, shoulder and upper arm muscles, with later involvement of the trunk and lower extremities. FSHD develops through complex genetic and epigenetic events that converge on a common mechanism of toxicity with mis-expression of the transcription factor double homeobox 4 (DUX4). There is currently no treatment available for FSHD. However, the consensus that ectopic DUX4 expression in skeletal muscle is the root cause of FSHD pathophysiology has allowed research efforts to turn toward cultivating a deeper understanding of DUX4 biology and the pathways that underlie FSHD muscle pathology, and to translational studies aimed at developing targeted therapeutics using ever more sophisticated cell and animal-based models of FSHD. This review summarizes recent advances in our understanding of FSHD, including the regulation and activity of DUX4 in its normal developmental roles as well as its pathological contexts. We highlight how these advances raise new questions and challenges for the field as it moves into the next decade of FSHD research.
Collapse
Affiliation(s)
- Amy E Campbell
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrea E Belleville
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rebecca Resnick
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.,Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Sean C Shadle
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Neurology, University of Washington, Seattle, WA, USA
| |
Collapse
|
33
|
Fu B, Ma H, Liu D. Endogenous Retroviruses Function as Gene Expression Regulatory Elements During Mammalian Pre-implantation Embryo Development. Int J Mol Sci 2019; 20:ijms20030790. [PMID: 30759824 PMCID: PMC6387303 DOI: 10.3390/ijms20030790] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 01/13/2023] Open
Abstract
Pre-implantation embryo development encompasses several key developmental events, especially the activation of zygotic genome activation (ZGA)-related genes. Endogenous retroviruses (ERVs), which are regarded as “deleterious genomic parasites”, were previously considered to be “junk DNA”. However, it is now known that ERVs, with limited conservatism across species, mediate conserved developmental processes (e.g., ZGA). Transcriptional activation of ERVs occurs during the transition from maternal control to zygotic genome control, signifying ZGA. ERVs are versatile participants in rewiring gene expression networks during epigenetic reprogramming. Particularly, a subtle balance exists between ERV activation and ERV repression in host–virus interplay, which leads to stage-specific ERV expression during pre-implantation embryo development. A large portion of somatic cell nuclear transfer (SCNT) embryos display developmental arrest and ZGA failure during pre-implantation embryo development. Furthermore, because of the close relationship between ERV activation and ZGA, exploring the regulatory mechanism underlying ERV activation may also shed more light on the enigma of SCNT embryo development in model animals.
Collapse
Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry Research, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China.
- Key Laboratory of Combine of Planting and Feeding, Ministry of Agriculture of the People's Republic of China, Harbin 150086, China.
| | - Hong Ma
- Institute of Animal Husbandry Research, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China.
- Key Laboratory of Combine of Planting and Feeding, Ministry of Agriculture of the People's Republic of China, Harbin 150086, China.
| | - Di Liu
- Institute of Animal Husbandry Research, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China.
- Key Laboratory of Combine of Planting and Feeding, Ministry of Agriculture of the People's Republic of China, Harbin 150086, China.
| |
Collapse
|
34
|
Oncogenic Amplification of Zygotic Dux Factors in Regenerating p53-Deficient Muscle Stem Cells Defines a Molecular Cancer Subtype. Cell Stem Cell 2018; 23:794-805.e4. [PMID: 30449715 DOI: 10.1016/j.stem.2018.10.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/27/2018] [Accepted: 10/08/2018] [Indexed: 01/09/2023]
Abstract
The identity of tumor-initiating cells in many cancer types is unknown. Tumors often express genes associated with embryonic development, although the contributions of zygotic programs to tumor initiation and formation are poorly understood. Here, we show that regeneration-induced loss of quiescence in p53-deficient muscle stem cells (MuSCs) results in rhabdomyosarcoma formation with 100% penetrance. Genomic analyses of purified tumor cells revealed spontaneous and discrete oncogenic amplifications in MuSCs that drive tumorigenesis, including, but not limited to, the amplification of the cleavage-stage Dux transcription factor (TF) Duxbl. We further found that Dux factors drive an early embryonic gene signature that defines a molecular subtype across a broad range of human cancers. Duxbl initiates tumorigenesis by enforcing a mesenchymal-to-epithelial transition, and targeted inactivation of Duxbl specifically in Duxbl-expressing tumor cells abolishes their expansion. These findings reveal how regeneration and genomic instability can interact to activate zygotic genes that drive tumor initiation and growth.
Collapse
|
35
|
Nimble and Ready to Mingle: Transposon Outbursts of Early Development. Trends Genet 2018; 34:806-820. [DOI: 10.1016/j.tig.2018.06.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/19/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022]
|
36
|
Pfeffer PL. Building Principles for Constructing a Mammalian Blastocyst Embryo. BIOLOGY 2018; 7:biology7030041. [PMID: 30041494 PMCID: PMC6164496 DOI: 10.3390/biology7030041] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 12/16/2022]
Abstract
The self-organisation of a fertilised egg to form a blastocyst structure, which consists of three distinct cell lineages (trophoblast, epiblast and hypoblast) arranged around an off-centre cavity, is unique to mammals. While the starting point (the zygote) and endpoint (the blastocyst) are similar in all mammals, the intervening events have diverged. This review examines and compares the descriptive and functional data surrounding embryonic gene activation, symmetry-breaking, first and second lineage establishment, and fate commitment in a wide range of mammalian orders. The exquisite detail known from mouse embryogenesis, embryonic stem cell studies and the wealth of recent single cell transcriptomic experiments are used to highlight the building principles underlying early mammalian embryonic development.
Collapse
Affiliation(s)
- Peter L Pfeffer
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand.
| |
Collapse
|
37
|
Campbell AE, Shadle SC, Jagannathan S, Lim JW, Resnick R, Tawil R, van der Maarel SM, Tapscott SJ. NuRD and CAF-1-mediated silencing of the D4Z4 array is modulated by DUX4-induced MBD3L proteins. eLife 2018; 7:e31023. [PMID: 29533181 PMCID: PMC5849414 DOI: 10.7554/elife.31023] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 02/05/2018] [Indexed: 12/19/2022] Open
Abstract
The DUX4 transcription factor is encoded by a retrogene embedded in each unit of the D4Z4 macrosatellite repeat. DUX4 is normally expressed in the cleavage-stage embryo, whereas chromatin repression prevents DUX4 expression in most somatic tissues. Failure of this repression causes facioscapulohumeral muscular dystrophy (FSHD) due to mis-expression of DUX4 in skeletal muscle. In this study, we used CRISPR/Cas9 engineered chromatin immunoprecipitation (enChIP) locus-specific proteomics to characterize D4Z4-associated proteins. These and other approaches identified the Nucleosome Remodeling Deacetylase (NuRD) and Chromatin Assembly Factor 1 (CAF-1) complexes as necessary for DUX4 repression in human skeletal muscle cells and induced pluripotent stem (iPS) cells. Furthermore, DUX4-induced expression of MBD3L proteins partly relieved this repression in FSHD muscle cells. Together, these findings identify NuRD and CAF-1 as mediators of DUX4 chromatin repression and suggest a mechanism for the amplification of DUX4 expression in FSHD muscle cells.
Collapse
Affiliation(s)
- Amy E Campbell
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Sean C Shadle
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
- Molecular and Cellular Biology ProgramUniversity of WashingtonSeattleUnited States
| | - Sujatha Jagannathan
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
- Basic Sciences DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
- Computational Biology Program, Public Health Sciences DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Jong-Won Lim
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Rebecca Resnick
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
- Molecular and Cellular Biology ProgramUniversity of WashingtonSeattleUnited States
- Medical Scientist Training ProgramUniversity of WashingtonSeattleUnited States
| | - Rabi Tawil
- Department of NeurologyUniversity of Rochester Medical CenterRochesterUnited States
| | | | - Stephen J Tapscott
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleUnited States
- Department of NeurologyUniversity of WashingtonSeattleUnited States
| |
Collapse
|
38
|
Eidahl JO, Giesige CR, Domire JS, Wallace LM, Fowler AM, Guckes SM, Garwick-Coppens SE, Labhart P, Harper SQ. Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4. Hum Mol Genet 2018; 25:4577-4589. [PMID: 28173143 PMCID: PMC5409219 DOI: 10.1093/hmg/ddw287] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 08/19/2016] [Accepted: 08/25/2016] [Indexed: 01/28/2023] Open
Abstract
D4Z4 repeats are present in at least 11 different mammalian species, including humans and mice. Each repeat contains an open reading frame encoding a double homeodomain (DUX) family transcription factor. Aberrant expression of the D4Z4 ORF called DUX4 is associated with the pathogenesis of Facioscapulohumeral muscular dystrophy (FSHD). DUX4 is toxic to numerous cell types of different species, and over-expression caused dysmorphism and developmental arrest in frogs and zebrafish, embryonic lethality in transgenic mice, and lesions in mouse muscle. Because DUX4 is a primate-specific gene, questions have been raised about the biological relevance of over-expressing it in non-primate models, as DUX4 toxicity could be related to non-specific cellular stress induced by over-expressing a DUX family transcription factor in organisms that did not co-evolve its regulated transcriptional networks. We assessed toxic phenotypes of DUX family genes, including DUX4, DUX1, DUX5, DUXA, DUX4-s, Dux-bl and mouse Dux. We found that DUX proteins were not universally toxic, and only the mouse Dux gene caused similar toxic phenotypes as human DUX4. Using RNA-seq, we found that 80% of genes upregulated by Dux were similarly increased in DUX4-expressing cells. Moreover, 43% of Dux-responsive genes contained ChIP-seq binding sites for both Dux and DUX4, and both proteins had similar consensus binding site sequences. These results suggested DUX4 and Dux may regulate some common pathways, and despite diverging from a common progenitor under different selective pressures for millions of years, the two genes maintain partial functional homology.
Collapse
Affiliation(s)
- Jocelyn O Eidahl
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Carlee R Giesige
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Jacqueline S Domire
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Lindsay M Wallace
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Allison M Fowler
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Susan M Guckes
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Sara E Garwick-Coppens
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Scott Q Harper
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, USA,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
39
|
Vanderplanck C, Tassin A, Ansseau E, Charron S, Wauters A, Lancelot C, Vancutsem K, Laoudj-Chenivesse D, Belayew A, Coppée F. Overexpression of the double homeodomain protein DUX4c interferes with myofibrillogenesis and induces clustering of myonuclei. Skelet Muscle 2018; 8:2. [PMID: 29329560 PMCID: PMC5767009 DOI: 10.1186/s13395-017-0148-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/27/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Facioscapulohumeral muscular dystrophy (FSHD) is associated with DNA hypomethylation at the 4q35 D4Z4 repeat array. Both the causal gene DUX4 and its homolog DUX4c are induced. DUX4c is immunodetected in every myonucleus of proliferative cells, while DUX4 is present in only 1/1000 of myonuclei where it initiates a gene deregulation cascade. FSHD primary myoblasts differentiate into either atrophic or disorganized myotubes. DUX4 expression induces atrophic myotubes and associated FSHD markers. Although DUX4 silencing normalizes the FSHD atrophic myotube phenotype, this is not the case for the disorganized phenotype. DUX4c overexpression increases the proliferation rate of human TE671 rhabdomyosarcoma cells and inhibits their differentiation, suggesting a normal role during muscle differentiation. METHODS By gain- and loss-of-function experiments in primary human muscle cells, we studied the DUX4c impact on proliferation, differentiation, myotube morphology, and FSHD markers. RESULTS In primary myoblasts, DUX4c overexpression increased the staining intensity of KI67 (a proliferation marker) in adjacent cells and delayed differentiation. In differentiating cells, DUX4c overexpression led to the expression of some FSHD markers including β-catenin and to the formation of disorganized myotubes presenting large clusters of nuclei and cytoskeletal defects. These were more severe when DUX4c was expressed before the cytoskeleton reorganized and myofibrils assembled. In addition, endogenous DUX4c was detected at a higher level in FSHD myotubes presenting abnormal clusters of nuclei and cytoskeletal disorganization. We found that the disorganized FSHD myotube phenotype could be rescued by silencing of DUX4c, not DUX4. CONCLUSION Excess DUX4c could disturb cytoskeletal organization and nuclear distribution in FSHD myotubes. We suggest that DUX4c up-regulation could contribute to DUX4 toxicity in the muscle fibers by favoring the clustering of myonuclei and therefore facilitating DUX4 diffusion among them. Defining DUX4c functions in the healthy skeletal muscle should help to design new targeted FSHD therapy by DUX4 or DUX4c inhibition without suppressing DUX4c normal function.
Collapse
Affiliation(s)
- Céline Vanderplanck
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Alexandra Tassin
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Eugénie Ansseau
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Sébastien Charron
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Armelle Wauters
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Céline Lancelot
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Kelly Vancutsem
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | | | - Alexandra Belayew
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| | - Frédérique Coppée
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, 6, Avenue du Champs de Mars, B-7000 Mons, Belgium
| |
Collapse
|
40
|
Boers R, Boers J, de Hoon B, Kockx C, Ozgur Z, Molijn A, van IJcken W, Laven J, Gribnau J. Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI. Genome Res 2017; 28:88-99. [PMID: 29222086 PMCID: PMC5749185 DOI: 10.1101/gr.222885.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 10/27/2017] [Indexed: 02/03/2023]
Abstract
DNA methylation is a well-known epigenetic modification that plays a crucial role in gene regulation, but genome-wide analysis of DNA methylation remains technically challenging and costly. DNA methylation-dependent restriction enzymes can be used to restrict CpG methylation analysis to methylated regions of the genome only, which significantly reduces the required sequencing depth and simplifies subsequent bioinformatics analysis. Unfortunately, this approach has been hampered by complete digestion of DNA in CpG methylation-dense regions, resulting in fragments that are too small for accurate mapping. Here, we show that the activity of DNA methylation-dependent enzyme, LpnPI, is blocked by a fragment size smaller than 32 bp. This unique property prevents complete digestion of methylation-dense DNA and allows accurate genome-wide analysis of CpG methylation at single-nucleotide resolution. Methylated DNA sequencing (MeD-seq) of LpnPI digested fragments revealed highly reproducible genome-wide CpG methylation profiles for >50% of all potentially methylated CpGs, at a sequencing depth less than one-tenth required for whole-genome bisulfite sequencing (WGBS). MeD-seq identified a high number of patient and tissue-specific differential methylated regions (DMRs) and revealed that patient-specific DMRs observed in both blood and buccal samples predict DNA methylation in other tissues and organs. We also observed highly variable DNA methylation at gene promoters on the inactive X Chromosome, indicating tissue-specific and interpatient-specific escape of X Chromosome inactivation. These findings highlight the potential of MeD-seq for high-throughput epigenetic profiling.
Collapse
Affiliation(s)
- Ruben Boers
- Department of Developmental Biology, Erasmus MC, 3015 CN Rotterdam, the Netherlands.,Department of Obstetrics and Gynaecology, Erasmus MC, 3015 CE Rotterdam, the Netherlands
| | - Joachim Boers
- Department of Developmental Biology, Erasmus MC, 3015 CN Rotterdam, the Netherlands.,Delft Diagnostic Laboratories, 2288 ER, Rijswijk, the Netherlands
| | - Bas de Hoon
- Department of Developmental Biology, Erasmus MC, 3015 CN Rotterdam, the Netherlands.,Department of Obstetrics and Gynaecology, Erasmus MC, 3015 CE Rotterdam, the Netherlands
| | - Christel Kockx
- Centre for Biomics, Erasmus MC, 3015 CE Rotterdam, the Netherlands
| | - Zeliha Ozgur
- Centre for Biomics, Erasmus MC, 3015 CE Rotterdam, the Netherlands
| | - Anco Molijn
- Delft Diagnostic Laboratories, 2288 ER, Rijswijk, the Netherlands
| | | | - Joop Laven
- Department of Obstetrics and Gynaecology, Erasmus MC, 3015 CE Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, 3015 CN Rotterdam, the Netherlands
| |
Collapse
|
41
|
Conservation and innovation in the DUX4-family gene network. Nat Genet 2017; 49:935-940. [PMID: 28459454 PMCID: PMC5446306 DOI: 10.1038/ng.3846] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 03/22/2017] [Indexed: 12/13/2022]
Abstract
Facioscapulohumeral dystrophy (FSHD; OMIM #158900, #158901) is caused by mis-expression of the DUX4 transcription factor in skeletal muscle1. Animal models of FSHD are hampered by incomplete knowledge of the conservation of the DUX4 transcriptional program in other species2–5. Despite divergence of their binding motifs, both mouse Dux and human DUX4 activate genes associated with cleavage-stage embryos, including MERV-L and ERVL-MaLR retrotransposons, in mouse and human muscle cells respectively. When expressed in mouse cells, human DUX4 maintained modest activation of cleavage-stage genes driven by conventional promoters, but did not activate MERV-L-promoted genes. These findings indicate that the ancestral DUX4-factor regulated genes characteristic of cleavage-stage embryos driven by conventional promoters, whereas divergence of the DUX4/Dux homeodomains correlates with retrotransposon specificity. These results provide insight into how species balance conservation of a core transcriptional program with innovation at retrotransposon promoters and provide a basis for animal models that recreate the FSHD transcriptome.
Collapse
|
42
|
Hendrickson PG, Doráis JA, Grow EJ, Whiddon JL, Lim JW, Wike CL, Weaver BD, Pflueger C, Emery BR, Wilcox AL, Nix DA, Peterson CM, Tapscott SJ, Carrell DT, Cairns BR. Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons. Nat Genet 2017; 49:925-934. [PMID: 28459457 PMCID: PMC5703070 DOI: 10.1038/ng.3844] [Citation(s) in RCA: 473] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 03/21/2017] [Indexed: 12/13/2022]
Abstract
To better understand transcriptional regulation during human oogenesis and pre-implantation development, we defined stage-specific transcription, which revealed the cleavage stage as highly distinctive. Here, we present multiple lines of evidence that a eutherian-specific, multi-copy retrogene, DUX4, encodes a transcription factor which activates hundreds of endogenous genes (e.g. ZSCAN4, ZFP352, KDM4E) and retroviral elements (MERVL/HERVL-family) that defines the cleavage-specific transcriptional programs in mouse and human. Remarkably, mouse Dux expression is both necessary and sufficient to convert mouse embryonic stem cells into two-cell embryo-like (‘2C-like’) cells, measured here by the reactivation of ‘2C’ genes and repeat elements, the loss of POU5F1 protein and chromocenters, and by the conversion of the chromatin landscape (assessed by ATAC-seq) to a state strongly resembling mouse two-cell embryos. Taken together, we propose mouse DUX and human DUX4 as major drivers of the cleavage/‘2C’ state.
Collapse
Affiliation(s)
- Peter G Hendrickson
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| | - Jessie A Doráis
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA.,Departments of Obstetrics and Gynecology, and Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Edward J Grow
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| | - Jennifer L Whiddon
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jong-Won Lim
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Candice L Wike
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| | - Bradley D Weaver
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| | - Christian Pflueger
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| | - Benjamin R Emery
- Departments of Obstetrics and Gynecology, and Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Aaron L Wilcox
- Departments of Obstetrics and Gynecology, and Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - David A Nix
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| | - C Matthew Peterson
- Departments of Obstetrics and Gynecology, and Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Douglas T Carrell
- Departments of Obstetrics and Gynecology, and Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Bradley R Cairns
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| |
Collapse
|
43
|
De Iaco A, Planet E, Coluccio A, Verp S, Duc J, Trono D. DUX-family transcription factors regulate zygotic genome activation in placental mammals. Nat Genet 2017; 49:941-945. [PMID: 28459456 PMCID: PMC5446900 DOI: 10.1038/ng.3858] [Citation(s) in RCA: 375] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/07/2017] [Indexed: 12/22/2022]
Abstract
In animal embryos, transcription is mostly silent for several cell divisions, until the release of the first major wave of embryonic transcripts through so-called zygotic genome activation (ZGA). Maternally provided ZGA-triggering factors have been identified in Drosophila melanogaster and Danio rerio, but their mammalian homologs are still undefined. Here, we provide evidence that the DUX family of transcription factors is essential to this process in mice and potentially in humans. First, human DUX4 and mouse Dux are both expressed before ZGA in their respective species. Second, both orthologous proteins bind the promoters of ZGA-associated genes and activate their transcription. Third, Dux knockout in mouse embryonic stem cells (mESCs) prevents the cells from cycling through a 2-cell-like state. Finally, zygotic depletion of Dux leads to impaired early embryonic development and defective ZGA. We conclude that DUX-family proteins are key inducers of zygotic genome activation in placental mammals.
Collapse
Affiliation(s)
- Alberto De Iaco
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Andrea Coluccio
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sonia Verp
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| |
Collapse
|
44
|
Jones TI, Parilla M, Jones PL. Transgenic Drosophila for Investigating DUX4 and FRG1, Two Genes Associated with Facioscapulohumeral Muscular Dystrophy (FSHD). PLoS One 2016; 11:e0150938. [PMID: 26942723 PMCID: PMC4778869 DOI: 10.1371/journal.pone.0150938] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 02/22/2016] [Indexed: 11/19/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is typically an adult onset dominant myopathy. Epigenetic changes in the chromosome 4q35 region linked to both forms of FSHD lead to a relaxation of repression and increased somatic expression of DUX4-fl (DUX4-full length), the pathogenic alternative splicing isoform of the DUX4 gene. DUX4-fl encodes a transcription factor expressed in healthy testis and pluripotent stem cells; however, in FSHD, increased levels of DUX4-fl in myogenic cells lead to aberrant regulation of target genes. DUX4-fl has proven difficult to study in vivo; thus, little is known about its normal and pathogenic roles. The endogenous expression of DUX4-fl in FSHD-derived human muscle and myogenic cells is extremely low, exogenous expression of DUX4-fl in somatic cells rapidly induces cytotoxicity, and, due in part to the lack of conservation beyond primate lineages, viable animal models based on DUX4-fl have been difficult to generate. By contrast, the FRG1 (FSHD region gene 1), which is linked to FSHD, is evolutionarily conserved from invertebrates to humans, and has been studied in several model organisms. FRG1 expression is critical for the development of musculature and vasculature, and overexpression of FRG1 produces a myopathic phenotype, yet the normal and pathological functions of FRG1 are not well understood. Interestingly, DUX4 and FRG1 were recently linked when the latter was identified as a direct transcriptional target of DUX4-FL. To better understand the pathways affected in FSHD by DUX4-fl and FRG1, we generated transgenic lines of Drosophila expressing either gene under control of the UAS/GAL4 binary system. Utilizing these lines, we generated screenable phenotypes recapitulating certain known consequences of DUX4-fl or FRG1 overexpression. These transgenic Drosophila lines provide resources to dissect the pathways affected by DUX4-fl or FRG1 in a genetically tractable organism and may provide insight into both muscle development and pathogenic mechanisms in FSHD.
Collapse
Affiliation(s)
- Takako I. Jones
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School Worcester, Massachusetts, United States of America
- The Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Megan Parilla
- The Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Peter L. Jones
- The Department of Cell and Developmental Biology, University of Massachusetts Medical School Worcester, Massachusetts, United States of America
- The Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| |
Collapse
|
45
|
Bürglin TR, Affolter M. Homeodomain proteins: an update. Chromosoma 2015; 125:497-521. [PMID: 26464018 PMCID: PMC4901127 DOI: 10.1007/s00412-015-0543-8] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/20/2015] [Accepted: 09/21/2015] [Indexed: 12/17/2022]
Abstract
Here, we provide an update of our review on homeobox genes that we wrote together with Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have become possible due to genome sequencing projects. Using the 103 Drosophila homeobox genes as example, we present an updated classification. In animals, there are 16 major classes, ANTP, PRD, PRD-LIKE, POU, HNF, CUT (with four subclasses: ONECUT, CUX, SATB, and CMP), LIM, ZF, CERS, PROS, SIX/SO, plus the TALE superclass with the classes IRO, MKX, TGIF, PBC, and MEIS. In plants, there are 11 major classes, i.e., HD-ZIP (with four subclasses: I to IV), WOX, NDX, PHD, PLINC, LD, DDT, SAWADEE, PINTOX, and the two TALE classes KNOX and BEL. Most of these classes encode additional domains apart from the homeodomain. Numerous insights have been obtained in the last two decades into how homeodomain proteins bind to DNA and increase their specificity by interacting with other proteins to regulate cell- and tissue-specific gene expression. Not only protein-DNA base pair contacts are important for proper target selection; recent experiments also reveal that the shape of the DNA plays a role in specificity. Using selected examples, we highlight different mechanisms of homeodomain protein-DNA interaction. The PRD class of homeobox genes was of special interest to Walter Gehring in the last two decades. The PRD class comprises six families in Bilateria, and tinkers with four different motifs, i.e., the PAIRED domain, the Groucho-interacting motif EH1 (aka Octapeptide or TN), the homeodomain, and the OAR motif. Homologs of the co-repressor protein Groucho are also present in plants (TOPLESS), where they have been shown to interact with small amphipathic motives (EAR), and in yeast (TUP1), where we find an EH1-like motif in MATα2.
Collapse
Affiliation(s)
- Thomas R. Bürglin
- />Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
- />Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Markus Affolter
- />Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| |
Collapse
|
46
|
Wilming LG, Boychenko V, Harrow JL. Comprehensive comparative homeobox gene annotation in human and mouse. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav091. [PMID: 26412852 PMCID: PMC4584094 DOI: 10.1093/database/bav091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 08/31/2015] [Indexed: 11/14/2022]
Abstract
Homeobox genes are a group of genes coding for transcription factors with a DNA-binding helix-turn-helix structure called a homeodomain and which play a crucial role in pattern formation during embryogenesis. Many homeobox genes are located in clusters and some of these, most notably the HOX genes, are known to have antisense or opposite strand long non-coding RNA (lncRNA) genes that play a regulatory role. Because automated annotation of both gene clusters and non-coding genes is fraught with difficulty (over-prediction, under-prediction, inaccurate transcript structures), we set out to manually annotate all homeobox genes in the mouse and human genomes. This includes all supported splice variants, pseudogenes and both antisense and flanking lncRNAs. One of the areas where manual annotation has a significant advantage is the annotation of duplicated gene clusters. After comprehensive annotation of all homeobox genes and their antisense genes in human and in mouse, we found some discrepancies with the current gene set in RefSeq regarding exact gene structures and coding versus pseudogene locus biotype. We also identified previously un-annotated pseudogenes in the DUX, Rhox and Obox gene clusters, which helped us re-evaluate and update the gene nomenclature in these regions. We found that human homeobox genes are enriched in antisense lncRNA loci, some of which are known to play a role in gene or gene cluster regulation, compared to their mouse orthologues. Of the annotated set of 241 human protein-coding homeobox genes, 98 have an antisense locus (41%) while of the 277 orthologous mouse genes, only 62 protein coding gene have an antisense locus (22%), based on publicly available transcriptional evidence.
Collapse
Affiliation(s)
- Laurens G Wilming
- HAVANA Group, Informatics Department, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Veronika Boychenko
- HAVANA Group, Informatics Department, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jennifer L Harrow
- HAVANA Group, Informatics Department, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| |
Collapse
|
47
|
|
48
|
Hewitt JE. Loss of epigenetic silencing of the DUX4 transcription factor gene in facioscapulohumeral muscular dystrophy. Hum Mol Genet 2015; 24:R17-23. [PMID: 26113644 DOI: 10.1093/hmg/ddv237] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 06/18/2015] [Indexed: 02/07/2023] Open
Abstract
Current genetic and molecular evidence best supports an epigenetic mechanism for facioscapulohumeral muscular dystrophy (FSHD), whereby de-repression of the D4Z4 macrosatellite array leads to aberrant expression of the DUX4 transcription factor in skeletal muscle. This de-repression is triggered by either array contraction or (more rarely) by mutation of the SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1) gene. Activation of DUX4 targets, including germline genes and several mammalian retrotransposons, then drives pathogenesis. A direct role for DUX4 mRNA in suppression of nonsense-mediated decay pathways has recently been demonstrated and may also contribute to muscle pathology. Loss of D4Z4 repression in FSHD is observed as hypomethylation of the array accompanied by loss of repressive chromatin marks. The molecular mechanisms of D4Z4 repression are poorly understood, but recent data have identified an Argonaute (AGO)-dependent siRNA pathway. Targeting this pathway by exogenous siRNAs could be a therapeutic strategy for FSHD.
Collapse
Affiliation(s)
- Jane E Hewitt
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| |
Collapse
|
49
|
Himeda CL, Jones TI, Jones PL. Facioscapulohumeral muscular dystrophy as a model for epigenetic regulation and disease. Antioxid Redox Signal 2015; 22:1463-82. [PMID: 25336259 PMCID: PMC4432493 DOI: 10.1089/ars.2014.6090] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SIGNIFICANCE Aberrant epigenetic regulation is an integral aspect of many diseases and complex disorders. Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, is caused by disrupted genetic and epigenetic regulation of a macrosatellite repeat. FSHD provides a powerful model to investigate disease-relevant epigenetic modifiers and general mechanisms of epigenetic regulation that govern gene expression. RECENT ADVANCES In the context of a genetically permissive allele, the one aspect of FSHD that is consistent across all known cases is the aberrant epigenetic state of the disease locus. In addition, certain mutations in the chromatin regulator SMCHD1 (structural maintenance of chromosomes hinge-domain protein 1) are sufficient to cause FSHD2 and enhance disease severity in FSHD1. Thus, there are multiple pathways to generate the epigenetic dysregulation required for FSHD. CRITICAL ISSUES Why do some individuals with the genetic requirements for FSHD develop disease pathology, while others remain asymptomatic? Similarly, disease progression is highly variable among individuals. What are the relative contributions of genetic background and environmental factors in determining disease manifestation, progression, and severity in FSHD? What is the interplay between epigenetic factors regulating the disease locus and which, if any, are viable therapeutic targets? FUTURE DIRECTIONS Epigenetic regulation represents a potentially powerful therapeutic target for FSHD. Determining the epigenetic signatures that are predictive of disease severity and identifying the spectrum of disease modifiers in FSHD are vital to the development of effective therapies.
Collapse
Affiliation(s)
- Charis L Himeda
- The Wellstone Program and the Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School , Worcester, Massachusetts
| | | | | |
Collapse
|
50
|
Himeda CL, Debarnot C, Homma S, Beermann ML, Miller JB, Jones PL, Jones TI. Myogenic enhancers regulate expression of the facioscapulohumeral muscular dystrophy-associated DUX4 gene. Mol Cell Biol 2014; 34:1942-55. [PMID: 24636994 PMCID: PMC4019064 DOI: 10.1128/mcb.00149-14] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/12/2014] [Accepted: 03/11/2014] [Indexed: 11/20/2022] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is linked to epigenetic dysregulation of the chromosome 4q35 D4Z4 macrosatellite. However, this does not account for the tissue specificity of FSHD pathology, which requires stable expression of an alternative full-length mRNA splice form of DUX4 (DUX4-fl) from the D4Z4 array in skeletal muscle. Here, we describe the identification of two enhancers, DUX4 myogenic enhancer 1 (DME1) and DME2 which activate DUX4-fl expression in skeletal myocytes but not fibroblasts. Analysis of the chromatin revealed histone modifications and RNA polymerase II occupancy consistent with DME1 and DME2 being functional enhancers. Chromosome conformation capture analysis confirmed association of DME1 and DME2 with the DUX4 promoter in vivo. The strong interaction between DME2 and the DUX4 promoter in both FSHD and unaffected primary myocytes was greatly reduced in fibroblasts, suggesting a muscle-specific interaction. Nucleosome occupancy and methylome sequencing analysis indicated that in most FSHD myocytes, both enhancers are associated with nucleosomes but have hypomethylated DNA, consistent with a permissive transcriptional state, sporadic occupancy, and the observed DUX4 expression in rare myonuclei. Our data support a model in which these myogenic enhancers associate with the DUX4 promoter in skeletal myocytes and activate transcription when epigenetically derepressed in FSHD, resulting in the pathological misexpression of DUX4-fl.
Collapse
Affiliation(s)
- Charis L. Himeda
- Wellstone Program, Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Céline Debarnot
- Ecole Supérieure de Biotechnologie Strasbourg, Illkirch, France
| | - Sachiko Homma
- Neuromuscular Biology and Disease Group, Departments of Neurology and Physiology Biophysics, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Mary Lou Beermann
- Neuromuscular Biology and Disease Group, Departments of Neurology and Physiology Biophysics, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Jeffrey B. Miller
- Neuromuscular Biology and Disease Group, Departments of Neurology and Physiology Biophysics, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Peter L. Jones
- Wellstone Program, Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Takako I. Jones
- Wellstone Program, Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| |
Collapse
|