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Dissecting the Mechanism of Nucleosome Retention in Mouse Spermatozoa

Final Report Summary - NUCLEOSOME RETENTION (Dissecting the Mechanism of Nucleosome Retention in Mouse Spermatozoa)

Studies in mammalian models and in human suggest that environmental conditions (nutrition, pollutants, parental care during early postnatal life, etc) can affect the development and fitness of the offspring. The epigenetic mechanisms underlying transmission of such traits are largely unknown, but DNA methylation, RNA and nucleosomes have been proposed as mediators of such inheritance. In the male germline, most nucleosomes are removed from the paternal genome and replaced by transition proteins (TNP) then protamines (PRM) in sperm. Two independent groups of epigeneticists (Hammound et al., 2009, Nature), including my host group (Erkek et al., 2013, Nat. Struct. Mol. Biol.; Brykczynska et al., 2010, Nat. Struct. Mol. Biol.), showed that the small fraction of nucleosomes that are retained in sperm of mice and human are preferentially located at gene regulatory regions of the genome, namely CpG island (CGI). This work suggests that nucleosomes retained in spermatozoa could serve as a vector for epigenetic inheritance and thereby influence development of the offspring.

These findings have recently been challenged by two independent studies using similar experimental approaches, claiming that in sperm of human, mouse and bovine, nucleosomes remain predominantly within distal gene-poor regions, and are depleted significantly in regulatory regions (Samans et al., 2014, Dev Cell; Carone et al., 2014, Dev Cell). This lead to an immediate need to re-assess nucleosome occupancy in mammalian spermatozoa.

We reanalyzed the raw sequencing data of nucleosome-associated DNA isolated by Samans and co-workers from human and bovine sperm. We were unable to reproduce the findings by Samans et al.. We could show that the enrichments reported at repeat sequences are artefactual and result from redundant use of reads with multiple mapping positions in the genome. Therefore the main conclusions of the article by Samans et al. are confounded by an inappropriate computational methodology used to analyze the primary data. Our work was published in Developmental cell:
Alternative Computational Analysis Shows No Evidence for Nucleosome Enrichment at Repetitive Sequences in Mammalian Spermatozoa
Royo H, Stadler MB, Peters AHFM
Dev Cell. 2016 Apr 4;37(1):98-104

A major objective of the project in terms of personal development and career was my training in computational biology. The FMI and my host group provided me with a unique opportunity to be trained in computational biology during my fellowship. I made use of this new skill in several collaborations, that resulted in the publication of three studies.

In a collaboration with Dr James Turner from the Crick’s Institute in London, we published two research articles about the specificity of the X chromosome transcriptional regulation.
Non-Canonical and Sexually Dimorphic X Dosage Compensation States in the Mouse and Human Germline.
Sangrithi MN, Royo H, Mahadevaiah SK, Ojarikre O, Bhaw L, Sesay A, Peters AHFM, Stadler M, Turner JM.
Dev Cell. 2017 Feb 6;40(3):289-301
Silencing of X-Linked MicroRNAs by Meiotic Sex Chromosome Inactivation.
Royo H, Seitz H, ElInati E, Peters AHFM, Stadler MB, Turner JM.
PLoS Genet. 2015 Oct 28;11(10):e1005461

In a joint work with the Schwaller group in Basel, we addressed the general question of the impact of cellular origin on acute myeloid leukemia (AML) using mouse genetics.
MLL-AF9 Expression in Hematopoietic Stem Cells Drives a Highly Invasive AML Expressing EMT-Related Genes Linked to Poor Outcome.
Stavropoulou V, Kaspar S, Brault L, Sanders MA, Juge S, Morettini S, Tzankov A, Iacovino M, Lau IJ, Milne TA, Royo H, Kyba M, Valk PJ, Peters AHFM, Schwaller J.
Cancer Cell. 2016 Jul 11;30(1):43-58

In conclusion, in line with our proposal, our work helped resolving confusion in the field of nucleosome retention during spermiogenesis, and set the ground for orthogonal experimental techniques to map nucleosomes in mouse sperm. Insights into the mechanism of nucleosome retention during spermatogenesis lays the foundations for further functional studies in paternal epigenetic inheritance. In addition, the personal and technical skills acquired during my training provided me with the opportunity to get involved in several collaborative projects, in the area of sex chromosome regulation and animal models for acute myeloid leukemia.

From a personal development point of you, thanks to my in-depth training in bioinformatics during my IEF fellowship, I could develop into a computational biologist expert in chromatin biology and epigenomics, and I have the great privilege to have been offered a permanent position in my host group and institute as a Research Associate in Computational Biology.