Paternal Nucleosomes: Are They Retained in Developmental Promoters or Gene Deserts?
2014; Elsevier BV; Volume: 30; Issue: 1 Linguagem: Inglês
10.1016/j.devcel.2014.06.025
ISSN1878-1551
AutoresMitinori Saitou, Kazuki Kurimoto,
Tópico(s)Renal and related cancers
ResumoNucleosomes retained in spermatozoa may influence development and epigenetic inheritance. In this issue of Developmental Cell, Samans et al., 2014Samans B. Yang Y. Krebs S. Sarode G.V. Blum H. Reichenbach M. Wolf E. Steger K. Dansranjavin T. Schagdarsurengin U. Dev. Cell. 2014; 30 (this issue): 23-35Abstract Full Text Full Text PDF PubMed Scopus (104) Google Scholar and Carone et al., 2014Carone B.R. Hung J.-H. Hainer S.J. Chou M.-T. Carone D.M. Weng Z. Fazzio T.G. Rando O.J. Dev. Cell. 2014; 30 (this issue): 11-22Abstract Full Text Full Text PDF PubMed Scopus (162) Google Scholar provide evidence for the predominant retention of sperm nucleosomes in gene deserts, necessitating a reevaluation of the prevailing notion claiming their enrichment over developmental promoters. Nucleosomes retained in spermatozoa may influence development and epigenetic inheritance. In this issue of Developmental Cell, Samans et al., 2014Samans B. Yang Y. Krebs S. Sarode G.V. Blum H. Reichenbach M. Wolf E. Steger K. Dansranjavin T. Schagdarsurengin U. Dev. Cell. 2014; 30 (this issue): 23-35Abstract Full Text Full Text PDF PubMed Scopus (104) Google Scholar and Carone et al., 2014Carone B.R. Hung J.-H. Hainer S.J. Chou M.-T. Carone D.M. Weng Z. Fazzio T.G. Rando O.J. Dev. Cell. 2014; 30 (this issue): 11-22Abstract Full Text Full Text PDF PubMed Scopus (162) Google Scholar provide evidence for the predominant retention of sperm nucleosomes in gene deserts, necessitating a reevaluation of the prevailing notion claiming their enrichment over developmental promoters. Zygotes with full developmental capacity are formed by the fertilization of an oocyte by a sperm. Recent work has focused intensive investigation on the mechanisms underlying differential contributions by the paternal and maternal haploid genome and epigenome to development and inheritance in mammals. During mammalian spermatogenesis, following meiotic divisions, haploid spermatids condense their nuclei by replacing nucleosomes with small basic arginine-rich proteins called protamines. Although the replacement by protamines occurs in a genome-wide fashion, a certain fraction of nucleosomes remains associated with the sperm genome. These remaining nucleosomes, unlike protamines that are exclusively re-replaced by maternal nucleosomes in the zygotes, may potentially direct certain processes of development and are thus a potential source for epigenetic inheritance through the paternal germline. Therefore, the genomic loci associated with retained nucleosomes in sperm are of great interest. In this issue of Development Cell, two independent studies provide evidence that in mammalian sperm, nucleosomes remain predominantly within distal gene-poor regions and are depleted significantly in promoters of genes for developmental regulators (Samans et al., 2014Samans B. Yang Y. Krebs S. Sarode G.V. Blum H. Reichenbach M. Wolf E. Steger K. Dansranjavin T. Schagdarsurengin U. Dev. Cell. 2014; 30 (this issue): 23-35Abstract Full Text Full Text PDF PubMed Scopus (104) Google Scholar, Carone et al., 2014Carone B.R. Hung J.-H. Hainer S.J. Chou M.-T. Carone D.M. Weng Z. Fazzio T.G. Rando O.J. Dev. Cell. 2014; 30 (this issue): 11-22Abstract Full Text Full Text PDF PubMed Scopus (162) Google Scholar). These observations apparently contradict a number of previous reports (Table 1). For example, Hammoud et al., 2009Hammoud S.S. Nix D.A. Zhang H. Purwar J. Carrell D.T. Cairns B.R. Nature. 2009; 460: 473-478PubMed Google Scholar reported that the retained nucleosomes in human sperm are significantly enriched at loci of developmental importance, including imprinted gene clusters, microRNA clusters, and HOX gene clusters, and Erkek et al., 2013Erkek S. Hisano M. Liang C.Y. Gill M. Murr R. Dieker J. Schübeler D. van der Vlag J. Stadler M.B. Peters A.H. Nat. Struct. Mol. Biol. 2013; 20: 868-875Crossref PubMed Scopus (243) Google Scholar identified an approximately 10- and 2-fold overrepresentation of retained nucleosomes in mouse sperm at promoter regions and exons, respectively, and underrepresentation at introns and repeat regions. Accordingly, the nucleosome retention highly correlated with the GC content, and the retained nucleosomes exhibited characteristic histone modifications such as histone H3 lysine 4 trimethylation (H3K4me3) and H3K27me3 or histone variants. It is, on the other hand, of note that Brykczynska et al., 2010Brykczynska U. Hisano M. Erkek S. Ramos L. Oakeley E.J. Roloff T.C. Beisel C. Schübeler D. Stadler M.B. Peters A.H. Nat. Struct. Mol. Biol. 2010; 17: 679-687Crossref PubMed Scopus (508) Google Scholar observed a regular distribution of nucleosomes along the entire genome of human sperm with only a slight (2.2-fold) enrichment around the transcriptional start sites (TSSs).Table 1Methods for Mapping Nucleosomes Retained in Mammalian SpermatozoaReferencesSpeciesMethod for Nucleosome CollectionMethod for Mapping on GenomeDistribution of Nucleosome RetentionCrosslinkMNase DigestionCfg after MNase DigestionSize Fractionation by ElectrophoresisZalenskaya et al., 2000Zalenskaya I.A. Bradbury E.M. Zalensky A.O. Biochem. Biophys. Res. Commun. 2000; 279: 213-218Crossref PubMed Scopus (139) Google Scholarhumanno30U per 1 mg of DNA, 37°C for 5–20 min10,000 rpm, 3 minyesSouthern blot for telomeric DNAenriched with telomeric DNA organized into closely spaced nucleosomes with a period of 148 bpHammoud et al., 2009Hammoud S.S. Nix D.A. Zhang H. Purwar J. Carrell D.T. Cairns B.R. Nature. 2009; 460: 473-478PubMed Google Scholarhumanno>10U, 37°C per 40 million cells (partly as in Zalenskaya et al., 2000Zalenskaya I.A. Bradbury E.M. Zalensky A.O. Biochem. Biophys. Res. Commun. 2000; 279: 213-218Crossref PubMed Scopus (139) Google Scholar)yes140–155 bpdeep sequencingenriched at loci of developmental importance, including imprinted gene clusters, microRNA clusters, HOX gene clusters, and promoters of standalone developmental transcription factorsArpanahi et al., 2009Arpanahi A. Brinkworth M. Iles D. Krawetz S.A. Paradowska A. Platts A.E. Saida M. Steger K. Tedder P. Miller D. Genome Res. 2009; 19: 1338-1349Crossref PubMed Scopus (231) Google Scholarhuman, mouseno5U, 37°C for 3 min per 100 million cells5 kg, 10 minnocomparative genome hybridizationassociated with gene regulatory regions, including promoters and CTCF binding sequenceBrykczynska et al., 2010Brykczynska U. Hisano M. Erkek S. Ramos L. Oakeley E.J. Roloff T.C. Beisel C. Schübeler D. Stadler M.B. Peters A.H. Nat. Struct. Mol. Biol. 2010; 17: 679-687Crossref PubMed Scopus (508) Google Scholarhuman, mousenodetailed as in Hisano et al., 2013Hisano M. Erkek S. Dessus-Babus S. Ramos L. Stadler M.B. Peters A.H. Nat. Protoc. 2013; 8: 2449-2470Crossref PubMed Scopus (55) Google Scholardetailed as in Hisano et al., 2013Hisano M. Erkek S. Dessus-Babus S. Ramos L. Stadler M.B. Peters A.H. Nat. Protoc. 2013; 8: 2449-2470Crossref PubMed Scopus (55) Google Scholarmononucleosomedeep sequencingregular distribution along genome with modest enrichment around TSSsVavouri and Lehner, 2011Vavouri T. Lehner B. PLoS Genet. 2011; 7: e1002036Crossref PubMed Scopus (77) Google Scholar(using data from Hammoud et al., 2009Hammoud S.S. Nix D.A. Zhang H. Purwar J. Carrell D.T. Cairns B.R. Nature. 2009; 460: 473-478PubMed Google Scholar)predicted by base composition in both genic and nongenic regions (retention at GC-rich sequences)Erkek et al., 2013Erkek S. Hisano M. Liang C.Y. Gill M. Murr R. Dieker J. Schübeler D. van der Vlag J. Stadler M.B. Peters A.H. Nat. Struct. Mol. Biol. 2013; 20: 868-875Crossref PubMed Scopus (243) Google Scholarmouseno15U, 37°C for 5 min per 2 million cells (detailed as in Hisano et al., 2013Hisano M. Erkek S. Dessus-Babus S. Ramos L. Stadler M.B. Peters A.H. Nat. Protoc. 2013; 8: 2449-2470Crossref PubMed Scopus (55) Google Scholar)as in Brykczynska et al., 2010Brykczynska U. Hisano M. Erkek S. Ramos L. Oakeley E.J. Roloff T.C. Beisel C. Schübeler D. Stadler M.B. Peters A.H. Nat. Struct. Mol. Biol. 2010; 17: 679-687Crossref PubMed Scopus (508) Google Scholar (detailed as in Hisano et al., 2013Hisano M. Erkek S. Dessus-Babus S. Ramos L. Stadler M.B. Peters A.H. Nat. Protoc. 2013; 8: 2449-2470Crossref PubMed Scopus (55) Google Scholar)150 bpdeep sequencinghigh enrichment throughout the genome at CpG-rich sequences that lack DNA methylationHisano et al., 2013Hisano M. Erkek S. Dessus-Babus S. Ramos L. Stadler M.B. Peters A.H. Nat. Protoc. 2013; 8: 2449-2470Crossref PubMed Scopus (55) Google Scholarhumanno30U, 37°C for 5 min per 2 million cells17 kg, 10 min, at room temperaturemononucleosomedeep sequencingNAmouseno15U, 37°C for 5 min per 2 million cells17 kg, 10 min, at room temperaturemononucleosomedeep sequencingSamans et al., 2014Samans B. Yang Y. Krebs S. Sarode G.V. Blum H. Reichenbach M. Wolf E. Steger K. Dansranjavin T. Schagdarsurengin U. Dev. Cell. 2014; 30 (this issue): 23-35Abstract Full Text Full Text PDF PubMed Scopus (104) Google Scholarhuman, bullno20U, 37°C per 10 million cells (partly as in Zalenskaya et al., 2000Zalenskaya I.A. Bradbury E.M. Zalensky A.O. Biochem. Biophys. Res. Commun. 2000; 279: 213-218Crossref PubMed Scopus (139) Google Scholar and Hammoud et al., 2009Hammoud S.S. Nix D.A. Zhang H. Purwar J. Carrell D.T. Cairns B.R. Nature. 2009; 460: 473-478PubMed Google Scholar)10,000 rpm146 bpdeep sequencingpredominantly within distal intergenic regions and introns; associated with centromere repeats and retrotransposons; depletion in 5′ UTR, 3′ UTR, TSS, and TTSCarone et al., 2014Carone B.R. Hung J.-H. Hainer S.J. Chou M.-T. Carone D.M. Weng Z. Fazzio T.G. Rando O.J. Dev. Cell. 2014; 30 (this issue): 11-22Abstract Full Text Full Text PDF PubMed Scopus (162) Google Scholarmouse1% formaldehyde, 15 min, 37°C1U–10U, 37°C for 5 min per 100 million cells5 kg, 5 minnodeep sequencing (paired end)preferentially in large gene-poor regions; depletion in promotersmouse1% formaldehyde, 15 min, 37°C10U–50U per cells fewer than 100 millionnonodeep sequencing (paired end)enriched over promotersAbbreviations used are as follows: MNase, micrococcal nuclease; Cfg, centrifugation; U, unit; TSS, transcription start site; TTS, transcription termination site; NA, not applicable. Open table in a new tab Abbreviations used are as follows: MNase, micrococcal nuclease; Cfg, centrifugation; U, unit; TSS, transcription start site; TTS, transcription termination site; NA, not applicable. Samans et al., 2014Samans B. Yang Y. Krebs S. Sarode G.V. Blum H. Reichenbach M. Wolf E. Steger K. Dansranjavin T. Schagdarsurengin U. Dev. Cell. 2014; 30 (this issue): 23-35Abstract Full Text Full Text PDF PubMed Scopus (104) Google Scholar isolated nucleosome-associated chromatin in human and bovine sperm according to a protocol by Hammoud et al., 2009Hammoud S.S. Nix D.A. Zhang H. Purwar J. Carrell D.T. Cairns B.R. Nature. 2009; 460: 473-478PubMed Google Scholar (Table 1) and analyzed the purified 146 bp mononucleosomal DNA sequence released by micrococcal nuclease (MNase) treatment by high-throughput sequencing. They showed that, on average, 2.9% and 13.4% of the human and bovine paternal genomes, respectively, retain nucleosomal chromatin, and these nucleosomal-binding sites appear to be rather evenly scattered. Further analysis indicated that the major portion of the nucleosomal-binding sites (93% in human and 85% in bulls) is in repetitive DNA sequences—including centromere repeats, short interspersed nuclear element (SINE), and long interspersed nuclear element 1 (LINE1)—and the majority of nucleosomal binding sites (56.4% in human and 80.2% in bulls) were enriched in distal intergenic regions. Among the well-known functional elements, nucleosomes were significantly depleted in exons, 5′ UTR, 3′ UTR, and promoters. This appears to be discordant with the observations that 76% of the top 9,841 histone-enriched regions intersect genic regions (Hammoud et al., 2009Hammoud S.S. Nix D.A. Zhang H. Purwar J. Carrell D.T. Cairns B.R. Nature. 2009; 460: 473-478PubMed Google Scholar) and that retained nucleosomes in mouse sperm are overrepresented by approximately 10- and 2-fold at promoter regions and exons, respectively (Erkek et al., 2013Erkek S. Hisano M. Liang C.Y. Gill M. Murr R. Dieker J. Schübeler D. van der Vlag J. Stadler M.B. Peters A.H. Nat. Struct. Mol. Biol. 2013; 20: 868-875Crossref PubMed Scopus (243) Google Scholar). Samans et al., 2014Samans B. Yang Y. Krebs S. Sarode G.V. Blum H. Reichenbach M. Wolf E. Steger K. Dansranjavin T. Schagdarsurengin U. Dev. Cell. 2014; 30 (this issue): 23-35Abstract Full Text Full Text PDF PubMed Scopus (104) Google Scholar showed that in intragenic areas (−3 kb promoter and gene body), 66.1% and 74.7% of human and bovine genes, respectively, retain nucleosomes. Overlapping human and bovine genes with nucleosome-preserving promoters were enriched in factors for RNA and protein processing. In contrast, 33.9% and 25.3% of human and bovine genes, respectively, were nucleosome free in the entire promoter and gene body; strikingly, a large number of these genes encoded developmental regulators, a finding that was in stark opposition to previous reports (Hammoud et al., 2009Hammoud S.S. Nix D.A. Zhang H. Purwar J. Carrell D.T. Cairns B.R. Nature. 2009; 460: 473-478PubMed Google Scholar). Most typically, all HOX clusters were depleted in nucleosomes. The finding that promoters preserving the nucleosomes were enriched in factors for RNA and protein processing relevant for gene expression in preimplantation development, but not in developmental regulators such as the HOX genes that mainly function in postimplantation development, would actually seem quite reasonable, considering the extensive epigenetic reprogramming associated with preimplantation development. The observations by Carone et al., 2014Carone B.R. Hung J.-H. Hainer S.J. Chou M.-T. Carone D.M. Weng Z. Fazzio T.G. Rando O.J. Dev. Cell. 2014; 30 (this issue): 11-22Abstract Full Text Full Text PDF PubMed Scopus (162) Google Scholar are in good agreement with those by Samans et al., 2014Samans B. Yang Y. Krebs S. Sarode G.V. Blum H. Reichenbach M. Wolf E. Steger K. Dansranjavin T. Schagdarsurengin U. Dev. Cell. 2014; 30 (this issue): 23-35Abstract Full Text Full Text PDF PubMed Scopus (104) Google Scholar. Utilizing a recently developed protocol for nucleosome mapping (Table 1), they characterized the chromatin structure of mouse embryonic stem cells (mESCs) and sperm. The chromatin organizations of mESCs revealed by Carone et al., 2014Carone B.R. Hung J.-H. Hainer S.J. Chou M.-T. Carone D.M. Weng Z. Fazzio T.G. Rando O.J. Dev. Cell. 2014; 30 (this issue): 11-22Abstract Full Text Full Text PDF PubMed Scopus (162) Google Scholar were highly consistent with those identified by previous studies, demonstrating the validity of the authors' methodology. They found that the nucleosomes in mouse sperm are variably distributed along the chromosomes and appear to be preferentially retained in gene-poor regions: the number of nucleosome-length fragments for a given region is strongly anticorrelated with the number of genes in that region. Accordingly, the data from Carone et al., 2014Carone B.R. Hung J.-H. Hainer S.J. Chou M.-T. Carone D.M. Weng Z. Fazzio T.G. Rando O.J. Dev. Cell. 2014; 30 (this issue): 11-22Abstract Full Text Full Text PDF PubMed Scopus (162) Google Scholar showed that sperm nucleosomes are generally depleted from promoters, including developmental promoters such as the Hox promoters. They also went on to show by immunofluorescence analysis that histones H4 and TH2B were predominantly localized in the central DAPI-dense chromocenter occupied by repeat elements, but not in the peripheral area where the CpG-rich fraction of the genome associated with developmental promoters is considered to be concentrated, a finding consistent with previous cytological analyses (Meyer-Ficca et al., 2013Meyer-Ficca M.L. Lonchar J.D. Ihara M. Bader J.J. Meyer R.G. Chromosoma. 2013; 122: 319-335Crossref PubMed Scopus (20) Google Scholar). Why were such contradictory observations made by different groups? Carone et al., 2014Carone B.R. Hung J.-H. Hainer S.J. Chou M.-T. Carone D.M. Weng Z. Fazzio T.G. Rando O.J. Dev. Cell. 2014; 30 (this issue): 11-22Abstract Full Text Full Text PDF PubMed Scopus (162) Google Scholar reasoned that the discrepancies between these studies might result from differences in the extent of MNase digestion of the isolated sperm genome. They obtained the above results using formaldehyde crosslinking and minimal MNase digestion; only after formaldehyde crosslinking and MNase digestion as extensive as that employed by Hammoud et al., 2009Hammoud S.S. Nix D.A. Zhang H. Purwar J. Carrell D.T. Cairns B.R. Nature. 2009; 460: 473-478PubMed Google Scholar did they recover mononucleosomes enriched over promoters of developmental regulators (Table 1). Carone et al., 2014Carone B.R. Hung J.-H. Hainer S.J. Chou M.-T. Carone D.M. Weng Z. Fazzio T.G. Rando O.J. Dev. Cell. 2014; 30 (this issue): 11-22Abstract Full Text Full Text PDF PubMed Scopus (162) Google Scholar therefore concluded that among all nucleosomes retained in sperm, those retained at developmental promoters are a specific, more-stable subset highly resistant to MNase digestion. The proposed stability of the nucleosomes associated with developmental regulators may be linked with their modification states or their variant histone compositions (Brykczynska et al., 2010Brykczynska U. Hisano M. Erkek S. Ramos L. Oakeley E.J. Roloff T.C. Beisel C. Schübeler D. Stadler M.B. Peters A.H. Nat. Struct. Mol. Biol. 2010; 17: 679-687Crossref PubMed Scopus (508) Google Scholar, Erkek et al., 2013Erkek S. Hisano M. Liang C.Y. Gill M. Murr R. Dieker J. Schübeler D. van der Vlag J. Stadler M.B. Peters A.H. Nat. Struct. Mol. Biol. 2013; 20: 868-875Crossref PubMed Scopus (243) Google Scholar, Hammoud et al., 2009Hammoud S.S. Nix D.A. Zhang H. Purwar J. Carrell D.T. Cairns B.R. Nature. 2009; 460: 473-478PubMed Google Scholar), an interesting possibility that warrants further investigation. However, it is important to note that Samans et al., 2014Samans B. Yang Y. Krebs S. Sarode G.V. Blum H. Reichenbach M. Wolf E. Steger K. Dansranjavin T. Schagdarsurengin U. Dev. Cell. 2014; 30 (this issue): 23-35Abstract Full Text Full Text PDF PubMed Scopus (104) Google Scholar used a protocol essentially identical to that of Hammoud et al., 2009Hammoud S.S. Nix D.A. Zhang H. Purwar J. Carrell D.T. Cairns B.R. Nature. 2009; 460: 473-478PubMed Google Scholar (Table 1) but obtained an apparently contradictory outcome. At the present time, it is difficult to ascribe the reported discrepancies to a specific cause, but nonetheless it appears true that the isolation of retained sperm nucleosomes by MNase digestion involves delicate procedures that can easily lead to variable consequences depending on how precisely each experimental step is performed. More precise knowledge of the genome-wide distribution of the nucleosomes retained in mammalian spermatozoa would provide an important basis for our understanding of the mechanism of both development and epigenetic reprogramming and inheritance. Further explorations will be needed to reach a definitive consensus as to the genome-wide localization of sperm nucleosomes and their modification and/or variant states, which in turn will help to clarify their functional significance. High-Resolution Mapping of Chromatin Packaging in Mouse Embryonic Stem Cells and SpermCarone et al.Developmental CellJuly 3, 2014In BriefSequencing a wide size range of nuclease-protected DNA fragments provides an atlas of DNA-binding factors, including nucleosomes and TFs, in murine ESCs and sperm. Sperm histone retention primarily occurs in gene deserts rather than at promoters, and evidence is provided for CTCF binding to the genome in mature sperm. Full-Text PDF Open ArchiveUniformity of Nucleosome Preservation Pattern in Mammalian Sperm and Its Connection to Repetitive DNA ElementsSamans et al.Developmental CellJuly 3, 2014In BriefThe study demonstrates concordantly in human and bovine the uniformity of the nucleosome-preservation pattern in sperm in a genome-wide manner. A potential role in preimplantation development is suggested for sperm-derived nucleosomes frequently detected in centromere repeats, LINE1 and SINE, and predominantly in genes relevant for RNA and protein processing. Full-Text PDF Open Archive
Referência(s)