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Johnson GD, Jodar M, Pique-Regi R, Krawetz SA. Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events. Sci Rep 2016; 6:25864. [PMID: 27184706 PMCID: PMC4869110 DOI: 10.1038/srep25864] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/22/2016] [Indexed: 01/08/2023] Open
Abstract
Nuclear remodeling to a condensed state is a hallmark of spermatogenesis. This is achieved by replacement of histones with protamines. Regions retaining nucleosomes may be of functional significance. To determine their potential roles, sperm from wild type and transgenic mice harboring a single copy insert of the human protamine cluster were subjected to Micrococcal Nuclease-seq. CENTIPEDE, a hierarchical Bayesian model, was used to identify multiple spatial patterns, "footprints", of MNase-seq reads along the sperm genome. Regions predicted by CENTIPEDE analysis to be bound by a regulatory factor in sperm were correlated with genomic landmarks and higher order chromatin structure datasets to identify potential roles for these factors in regulating either prior or post spermatogenic, i.e., early embryonic events. This approach linked robust endogenous protamine transcription and transgene suppression to its chromatin environment within topologically associated domains. Of the candidate enhancer-bound regulatory proteins, Ctcf, was associated with chromatin domain boundaries in testes and embryonic stem cells. The continuity of Ctcf binding through the murine germline may permit rapid reconstitution of chromatin organization following fertilization. This likely reflects its preparation for early zygotic genome activation and comparatively accelerated preimplantation embryonic development program observed in mouse as compared to human and bull.
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Affiliation(s)
- Graham D Johnson
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Meritxell Jodar
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
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Johnson GD, Mackie P, Jodar M, Moskovtsev S, Krawetz SA. Chromatin and extracellular vesicle associated sperm RNAs. Nucleic Acids Res 2015; 43:6847-59. [PMID: 26071953 PMCID: PMC4538811 DOI: 10.1093/nar/gkv591] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 05/23/2015] [Indexed: 12/16/2022] Open
Abstract
A diverse pool of RNAs remain encapsulated within the transcriptionally silent spermatozoon despite the dramatic reduction in cellular and nuclear volume following cytoplasm/nucleoplasm expulsion. The impact of this pronounced restructuring on the distribution of transcripts inside the sperm essentially remains unknown. To define their compartmentalization, total RNA >100 nt was extracted from sonicated (SS) mouse spermatozoa and detergent demembranated sucrose gradient fractionated (Cs/Tx) sperm heads. Sperm RNAs predominately localized toward the periphery. The corresponding distribution of transcripts and thus localization and complexity were then inferred by RNA-seq. Interestingly, the number of annotated RNAs in the CsTx sperm heads exhibiting reduced peripheral enrichment was restricted. However this included Cabyr, the calcium-binding tyrosine phosphorylation-regulated protein encoded transcript. It is present in murine zygotes prior to the maternal to the zygotic transition yet absent in oocytes, consistent with the delivery of internally positioned sperm-borne RNAs to the embryo. In comparison, transcripts enriched in sonicated sperm contributed to the mitochondria and exosomes along with several nuclear transcripts including the metastasis associated lung adenocarcinoma transcript 1 (Malat1) and several small nucleolar RNAs. Their preferential peripheral localization suggests that chromatin remodeling during spermiogenesis is not limited to nucleoproteins as part of the nucleoprotein exchange.
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Affiliation(s)
- Graham D Johnson
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Paula Mackie
- CReATe Fertility Centre, Toronto, ON, M5G 1N8, Canada
| | - Meritxell Jodar
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA Department of Obstetrics and Gynaecology, University of Toronto, ON, M5G 1E2, Canada
| | - Sergey Moskovtsev
- CReATe Fertility Centre, Toronto, ON, M5G 1N8, Canada Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA Department of Obstetrics and Gynaecology, University of Toronto, ON, M5G 1E2, Canada
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Sendler E, Johnson GD, Mao S, Goodrich RJ, Diamond MP, Hauser R, Krawetz SA. Stability, delivery and functions of human sperm RNAs at fertilization. Nucleic Acids Res 2013; 41:4104-17. [PMID: 23471003 PMCID: PMC3627604 DOI: 10.1093/nar/gkt132] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Increasing attention has focused on the significance of RNA in sperm, in light of its contribution to the birth and long-term health of a child, role in sperm function and diagnostic potential. As the composition of sperm RNA is in flux, assigning specific roles to individual RNAs presents a significant challenge. For the first time RNA-seq was used to characterize the population of coding and non-coding transcripts in human sperm. Examining RNA representation as a function of multiple methods of library preparation revealed unique features indicative of very specific and stage-dependent maturation and regulation of sperm RNA, illuminating their various transitional roles. Correlation of sperm transcript abundance with epigenetic marks suggested roles for these elements in the pre- and post-fertilization genome. Several classes of non-coding RNAs including lncRNAs, CARs, pri-miRNAs, novel elements and mRNAs have been identified which, based on factors including relative abundance, integrity in sperm, available knockout data of embryonic effect and presence or absence in the unfertilized human oocyte, are likely to be essential male factors critical to early post-fertilization development. The diverse and unique attributes of sperm transcripts that were revealed provides the first detailed analysis of the biology and anticipated clinical significance of spermatozoal RNAs.
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Affiliation(s)
- Edward Sendler
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Mao S, Souza AL, Goodrich RJ, Krawetz SA. Identification of artifactual microarray probe signals constantly present in multiple sample types. Biotechniques 2012; 53:91-8. [PMID: 23030061 DOI: 10.2144/0000113903] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 07/10/2012] [Indexed: 11/23/2022] Open
Abstract
The detection, identification, and quantitation of transcripts have evolved from simple Northern analysis, cDNA cloning, and sequencing to RT-PCR, microarrays, and now digital gene expression using ultra-high-throughput RNA sequencing (RNA-Seq). During the course of our studies we observed that some microarray probes show very high signal intensity values yet are discordant when compared with RNA-Seq. A total of 99 probes from approximately 30,000 were identified as consistently discordant in four human tissues or cell lines. Interestingly, this set of discordant probes appears array-dependent. Among the 99 probes identified, 70 constantly exhibited a high signal in all 713 available samples surveyed using the Illumina HumanHT-12v4 platform. Some were discordant with additional probes that annotated the same genes. Absence of a number of these transcripts was confirmed by quantitative RT-PCR (qRT-PCR). Our findings suggest that one must be cautious, as some array probes do not capture the level of the target.
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Affiliation(s)
- Shihong Mao
- Center for Molecular Medicine and Genetics, Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
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Johnson GD, Lalancette C, Linnemann AK, Leduc F, Boissonneault G, Krawetz SA. The sperm nucleus: chromatin, RNA, and the nuclear matrix. Reproduction 2011; 141:21-36. [PMID: 20876223 PMCID: PMC5358669 DOI: 10.1530/rep-10-0322] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Within the sperm nucleus, the paternal genome remains functionally inert and protected following protamination. This is marked by a structural morphogenesis that is heralded by a striking reduction in nuclear volume. Despite these changes, both human and mouse spermatozoa maintain low levels of nucleosomes that appear non-randomly distributed throughout the genome. These regions may be necessary for organizing higher order genomic structure through interactions with the nuclear matrix. The promoters of this transcriptionally quiescent genome are differentially marked by modified histones that may poise downstream epigenetic effects. This notion is supported by increasing evidence that the embryo inherits these differing levels of chromatin organization. In concert with the suite of RNAs retained in the mature sperm, they may synergistically interact to direct early embryonic gene expression. Irrespective, these features reflect the transcriptional history of spermatogenic differentiation. As such, they may soon be utilized as clinical markers of male fertility. In this review, we explore and discuss how this may be orchestrated.
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Affiliation(s)
- Graham D. Johnson
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
| | - Claudia Lalancette
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
- Department of Obstetrics and Gynecology, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
| | - Amelia K. Linnemann
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
| | - Frédéric Leduc
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - Guylain Boissonneault
- Department of Biochemistry, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | - Stephen A. Krawetz
- The Center for Molecular Medicine and Genetics, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
- Department of Obstetrics and Gynecology, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
- Institute for Scientific Computing, Wayne State University of Medicine, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201
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