Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome Tanya Vavouri1¤, Ben Lehner1,2* 1 EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Spain, 2 Institucio´ Catalana de Recerca i Estudis Avanc¸ats (ICREA), Centre for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Spain Abstract Chromatin in sperm is different from that in other cells, with most of the genome packaged by protamines not nucleosomes. Nucleosomes are, however, retained at some genomic sites, where they have the potential to transmit paternal epigenetic information. It is not understood how this retention is specified. Here we show that base composition is the major determinant of nucleosome retention in human sperm, predicting retention very well in both genic and non- genic regions of the genome. The retention of nucleosomes at GC-rich sequences with high intrinsic nucleosome affinity accounts for the previously reported retention at transcription start sites and at genes that regulate development. It also means that nucleosomes are retained at the start sites of most housekeeping genes. We also report a striking link between the retention of nucleosomes in sperm and the establishment of DNA methylation-free regions in the early embryo. Taken together, this suggests that paternal nucleosome transmission may facilitate robust gene regulation in the early embryo. We propose that chromatin organization in the male germline, rather than in somatic cells, is the major functional consequence of fine-scale base composition variation in the human genome. The selective pressure driving base composition evolution in mammals could, therefore, be the need to transmit paternal epigenetic information to the zygote. Citation: Vavouri T, Lehner B (2011) Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome. PLoS Genet 7(4): e1002036. doi:10.1371/journal.pgen.1002036 Editor: Jason D. Lieb, The University of North Carolina at Chapel Hill, United States of America Received October 21, 2010; Accepted February 11, 2011; Published April 7, 2011 Copyright: 2011 Vavouri, Lehner. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was funded by a Marie Curie Intra-European fellowship to TV and by an ERC Starting Grant, MICINN, ICREA, AGAUR, ERASysBio+, and the EMBL-CRG Systems Biology Program to BL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: ben.lehner@crg.es ¤ Current address: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Barcelona, Spain Introduction The chromatin of mature sperm differs dramatically from that of other cell types. Most of the sperm genome is packaged by small basic proteins called protamines, with only a few genomic sites remaining bound by nucleosomes [1,2,3,4,5]. This change in DNA packaging takes place towards the end of male germline development in transcriptionally inactive spermatids and results in a highly compact genome that fits in the small volume of the sperm head [2,6]. In contrast to the nucleosome structure that consists of ,147 bp of DNA wrapped around a histone octamer, individual protamine molecules bind one turn of the DNA helix [7]. In mature sperm, protamines compact the genome into large doughnut-shaped toroids, each containing ,50 kbp of the haploid genome [2,8,9]. This compact packaging of the sperm genome is essential for fertility, genome integrity, and early embryonic development [7,10,11,12]. In human sperm about 4% of the genome remains bound by nucleosomes [5]. Sites of nucleosome retention are dispersed along chromosomes but are not random. Instead, they are strikingly consistent among individuals [3,4,13]. Nucleosome retention sites are also enriched in particular genomic regions [13,14,15], and recent genome-wide localization analyses have reported that nucleosomes are preferentially retained in gene promoters and at loci that regulate development [3,5]. However, despite these genome-wide maps, the signals that specify retention sites are unknown. Although they are transcriptionally inactive, mature spermatozoa do contain nucleosomes containing histones marked by post-translational modifications, including both activation (e.g. methylation of histone H3 lysine 4) and repression marks (e.g. tri-methylation of H3 at lysine 27) [3,4,5]. Interestingly, both paternal nucleosomes [16] and histone modifications [17] are transmitted to the early zygote, and so have the potential to propagate paternal epigenetic information to the early embryo [18]. It is thus of great interest to understand how sites of nucleosome retention in sperm are determined, as these sites specify where epigenetic information transfer can potentially occur from the paternal germline to the zygote [19,20,21]. In somatic cells and in lower eukaryotes several important influences on nucleosome occupancy and positioning have been demonstrated. First, many nucleosomes are located ‘statistically’ [22] relative to nucleosomes positioned by transcription and other DNA-binding proteins [23,24,25]. Second, nucleosomes do not bind to all DNA- sequences with equal affinity. Rather, they have clear binding preferences that can be quantified in vitro [25,26,27] and predicted using sequence-based binding models [28,29,30,31,32]. In vitro, nucleosomes bind preferentially to GC-rich DNA [31,32]. GC-rich sequences have increased flexibility that may help the wrapping of DNA around the histone octamer. Further, PLoS Genetics | www.plosgenetics.org 1 April 2011 | Volume 7 | Issue 4 | e1002036