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• W2340762786 abstract "A substantial part of mammalian genome (66%–69%) is occupied by repetitive DNA elements (RDEs), which possess a huge variety in terms of structure and origin and provide a wide range of functional elements to eukaryotic genomes (de Koning et al., 2011de Koning A.P. Gu W. Castoe T.A. Batzer M.A. Pollock D.D. PLoS Genet. 2011; 7: e1002384Crossref PubMed Scopus (711) Google Scholar). The physiological relevance, molecular regulation, and the composition of repetitive and heterochromatic parts in mammalian genome are still largely unknown. RDEs can produce in next generation sequencing (NGS) experiments ambiguous reads aligning to multiple locations and are usually eliminated from consideration. This results in a substantial loss of information and persuades to biased conclusions emphasizing euchromatic parts (gene regions) alone. In our 2014 study (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: 23-35Abstract Full Text Full Text PDF PubMed Scopus (103) Google Scholar), we aimed to reveal putative nucleosome binding sites in mammalian sperm genome with due regard to the high probability that nucleosomes might also retain in RDEs. The assumption that the sperm nucleosomes associated to gene promoters as shown in initial studies (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, 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 (506) Google Scholar) represent a small subset of all preserved nucleosomes is supported by elementary arithmetical considerations: human sperm retain reportedly 4.9% of the nucleosome complement of a somatic cell (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). Even if nucleosomes were penetrantly retained in all 25,000–30,000 promoters across 1 kb, this would account for maximum 1% of the haploid genome. The key question here was whether nucleosomes appearing beyond the gene promoters and representing the vast majority of preserved nucleosomes in spermatozoa have a biological relevance. In order to address this question, the alignment setting “-v-0-a” was utilized, which captures every alignment per read and tolerates zero mismatches. Peak calling was an essential step toward identification of sperm-specific enrichments in different RDEs. Peak calling was combined with an approach comparing the number of de facto detected RDEs in peaks with the number of expected at genome-wide random distribution. This combinatorial computational procedure provided substantial evidence that sperm nucleosomes discriminate between different types of RDEs and retain preferentially in LINE1s and SINEs (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: 23-35Abstract Full Text Full Text PDF PubMed Scopus (103) Google Scholar). One possible misinterpretation of the term “repetitive” is the understanding that RDEs of one family or one subtype have completely identical sequences. In fact, e.g., LINEs have the same structure (two open-reading frames flanked by 5′-UTR and target site duplications) but could differ considerably in their sequence and genome origin. LINEs alone comprise five groups, which can be subdivided into 28 clades (Kapitonov et al., 2009Kapitonov V.V. Tempel S. Jurka J. Gene. 2009; 448: 207-213Crossref PubMed Scopus (72) Google Scholar). Therefore, it was relevant for conceptual design to consider that RDEs of same families and subtypes can occur frequently with different slight variations at multiple genome locations. In practice, when applying alignment settings considering one random match of a multi-read, this can lead to a “dilution” or complete “disappearance” of RDE signals alongside the reference genome and can impair the formation of evaluable enrichments (peaks). This was observed in revision process by using the alignment setting “-v-0-b” (each read gets one random best match, zero mismatch tolerance), where we did not detect any significant enrichments for nucleosomal DNA either in heterochromatic or euchromatic regions of sperm chromatin. From our perspective, we do not feel that the results in the Royo et al., 2016Royo H. Stadler M.B. Peters A.H.F.M. Dev. Cell. 2016; 37 (this issue): 98-104Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar Matters Arising refute the findings of 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: 23-35Abstract Full Text Full Text PDF PubMed Scopus (103) Google Scholar. Simulated reads representing a random unspecific DNA pool were aligned to the human genome, and peaks were identified as performed in 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: 23-35Abstract Full Text Full Text PDF PubMed Scopus (103) Google Scholar using MACS with parameters “–nomodel–nolambda–shiftsize=75–bw140–gsize=3e9–tsize=50–keep-dup=1” (Table S1 in Royo et al., 2016Royo H. Stadler M.B. Peters A.H.F.M. Dev. Cell. 2016; 37 (this issue): 98-104Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar). Concerning this, the authors state in the abstract “we observed comparable artificial enrichments at repetitive sequences when aligning simulated reads of uniform genome coverage.” We took the peak calling data of the simulated DNA from Table S1 (Royo et al., 2016Royo H. Stadler M.B. Peters A.H.F.M. Dev. Cell. 2016; 37 (this issue): 98-104Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar), analyzed in detail the frequency (percentage) of RDEs in peaks by RepeatMasker (50% overlap; https://data.mendeley.com/datasets/kg3v5zcwvm/1), and compared it to sperm data presented in (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: 23-35Abstract Full Text Full Text PDF PubMed Scopus (103) Google Scholar). We found completely different profiles in all given repeat families: e.g., LINE1 80.9% (in sperm: 22.6%), SINE 7.9% (in sperm: 68%), which does not support the statement of Matters Arising. It confirms rather our data that sperm nucleosomal DNA has a specific RDE profile completely different from an unspecific simulated DNA of uniform genome coverage. The majority of analyses presented by Royo et al., 2016Royo H. Stadler M.B. Peters A.H.F.M. Dev. Cell. 2016; 37 (this issue): 98-104Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar (except peak calling data for simulated DNA) refer to read alignments without peak calling. Total read counts for RDEs in sperm MNase DNA (Micrococcus Nuclease treated DNA) were compared to those in ENCODE control samples (somatic cell DNAs) using “-v-0-m100” (one alignment per read) and log2 (Figure S2 in Royo et al., 2016Royo H. Stadler M.B. Peters A.H.F.M. Dev. Cell. 2016; 37 (this issue): 98-104Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar). Concerning this, Royo et al. state “Neither SINE, LINE1 nor centromere repeats differ more than two-fold between sperm MNase and ENCODE control samples.” Total read counts alone, e.g., SINEs and LINEs, are limited in validity since they do not consider the diversity of read sequences and the putative genome origins of reads within these RDE families. Corresponding to Samans et al., specific peaks evaluated for sperm MNase sample were two-fold enriched for SINEs (33.9% versus 68% of total RDEs) and 1.3-fold for LINE1s (17.9% versus 22.6% of total RDEs) (first values refer to values expected at random distribution). The obvious difference regarding RDE profiles between sperm MNase DNA and unspecific simulated DNA after peak calling (see above) demonstrates that a comparison of read counts alone (sperm MNase versus ENCODE DNAs) is insufficient in this context. Notably, Royo et al. found that sperm MNase DNA consists of 50% RDEs (ca. 47% unique and 3% non-unique mapping, Figure 1B) and that sperm MNase DNA consists of even more RDEs (Figure S2, similar to levels in somatic cells for LINE1, SINE, etc., i.e., in total 66%–69%; de Koning et al., 2011de Koning A.P. Gu W. Castoe T.A. Batzer M.A. Pollock D.D. PLoS Genet. 2011; 7: e1002384Crossref PubMed Scopus (711) Google Scholar). These do not contradict our results, predicating that the majority of sperm nucleosomes retain in RDEs. It can be reasonably assumed that substitutions in RDEs decrease (as shown for LINE1s in Figures 3 and S3, Royo et al., 2016Royo H. Stadler M.B. Peters A.H.F.M. Dev. Cell. 2016; 37 (this issue): 98-104Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar) and mismatch tolerance values in alignment settings increase (Table 2) the alignment counts. This could be expected for nearly all types of RDEs. Without further specifications regarding inter- and intra-diversities in RDE families, these analyses are only imperfectly applicable as an argument. Lastly, the realistic number of single alpha satellites at centromeres is difficult to determine, since centromere repeats are highly repetitive and serried located. Certainly, this could lead to an underrepresentation of centromeric repeats in the reference Hg19-genome. The simulated DNA has per se no enrichments at centromere repeats and accordingly does not show considerable “peaks” (Figure 2, Royo et al., 2016Royo H. Stadler M.B. Peters A.H.F.M. Dev. Cell. 2016; 37 (this issue): 98-104Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar). In contrast, ENCODE control DNA (non-simulated genuine DNA) will expectedly have a high number of centromeric repeats and produce peaks as shown in Figure 2. The sperm MNase DNA exhibits at centromeres a profile similar to ENCODE DNA and thus should be also enriched with centromeric repeats. However, the underrepresentation of centromeric repeats in Hg19-genome can’t be taken as a reason for peaks in sperm MNase sample, as many independent techniques confirm the presence of nucleosomes in pericentric sperm heterochromatin (see below). Although maturing, bioinformatical processing of NGS data still has its limitations. Also the MNase procedure in sperm seems to be critical for final results. We do agree with Royo et al. that “orthogonal experimental approaches that are not subject to similar technical challenges are required” to clarify whether sperm nucleosomes are present in LINE1s, SINEs, and centromere repeats. A number of independent studies have already demonstrated in human and mice that nucleosomes occur in mature sperm mainly over repeat elements. Small-scale cloning of DNA released by nuclease digestion of sperm revealed primarily LINEs and SINEs (Pittoggi et al., 1999Pittoggi C. Renzi L. Zaccagnini G. Cimini D. Degrassi F. Giordano R. Magnano A.R. Lorenzini R. Lavia P. Spadafora C. J. Cell Sci. 1999; 112: 3537-3548PubMed Google Scholar) and pericentric repeats (Govin et al., 2007Govin J. Escoffier E. Rousseaux S. Kuhn L. Ferro M. Thévenon J. Catena R. Davidson I. Garin J. Khochbin S. Caron C. J. Cell Biol. 2007; 176: 283-294Crossref PubMed Scopus (221) Google Scholar). Immunostaining and Fluorescence in-situ hybridization (FISH) studies revealed co-localization of sperm histones with the repeat-enriched constitutive heterochromatin (Govin et al., 2007Govin J. Escoffier E. Rousseaux S. Kuhn L. Ferro M. Thévenon J. Catena R. Davidson I. Garin J. Khochbin S. Caron C. J. Cell Biol. 2007; 176: 283-294Crossref PubMed Scopus (221) Google Scholar, van der Heijden et al., 2006van der Heijden G.W. Derijck A.A. Ramos L. Giele M. van der Vlag J. de Boer P. Dev. Biol. 2006; 298: 458-469Crossref PubMed Scopus (146) Google Scholar, 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, 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: 11-22Abstract Full Text Full Text PDF PubMed Scopus (161) Google Scholar, van de Werken et al., 2014van de Werken C. van der Heijden G.W. Eleveld C. Teeuwssen M. Albert M. Baarends W.M. Laven J.S. Peters A.H. Baart E.B. Nat. Commun. 2014; 5: 5868Crossref PubMed Scopus (76) Google Scholar). Moreover, genome-wide analysis of the entire nucleosomal MNase digestion ladder localized the majority of sperm nucleosomes in gene deserts, i.e., mostly in heterochromatin (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: 11-22Abstract Full Text Full Text PDF PubMed Scopus (161) Google Scholar). Alternative Computational Analysis Shows No Evidence for Nucleosome Enrichment at Repetitive Sequences in Mammalian SpermatozoaRoyo et al.Developmental CellApril 04, 2016In BriefSamans et al. (2014) reported presence of nucleosomes at repetitive LINE-1, SINE, and centromeric sequences in human and bovine spermatozoa. Royo et al. provide evidence through reanalysis that observed repetitive sequence nucleosomal enrichments result from inappropriate computational analyses making redundant use of sequencing reads that map to multiple genomic locations. Full-Text PDF Open Archive" @default.
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• W2340762786 title "The Rationale of the Inevitable, or Why Is the Consideration of Repetitive DNA Elements Indispensable in Studies of Sperm Nucleosomes" @default.
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