Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

Molaro, Antoine; Hodges, Emily; Fang, Fang; Song, Qiang; McCombie, W. Richard; Hannon, Gregory J.; Smith, Andrew D.

doi:10.1016/j.cell.2011.08.016

Cited by 361 publications

(425 citation statements)

References 64 publications

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“…We computed the methylation level in sperm at each of the identified AMRs using data from a previous study (31). Among the 579 autosomal AMRs common to three out of five uncultured methylomes, 146 were methylated (>50%) in sperm.…”

Section: Genome-wide Amr Identification Predicts Imprinted Genesmentioning

confidence: 99%

Genomic landscape of human allele-specific DNA methylation

Fang

Hodges

Molaro

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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105

121

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DNA methylation mediates imprinted gene expression by passing an epigenomic state across generations and differentially marking specific regulatory regions on maternal and paternal alleles. Imprinting has been tied to the evolution of the placenta in mammals and defects of imprinting have been associated with human diseases. Although recent advances in genome sequencing have revolutionized the study of DNA methylation, existing methylome data remain largely untapped in the study of imprinting. We present a statistical model to describe allele-specific methylation (ASM) in data from high-throughput short-read bisulfite sequencing. Simulation results indicate technical specifications of existing methylome data, such as read length and coverage, are sufficient for fullgenome ASM profiling based on our model. We used our model to analyze methylomes for a diverse set of human cell types, including cultured and uncultured differentiated cells, embryonic stem cells and induced pluripotent stem cells. Regions of ASM identified most consistently across methylomes are tightly connected with known imprinted genes and precisely delineate the boundaries of several known imprinting control regions. Predicted regions of ASM common to multiple cell types frequently mark noncoding RNA promoters and represent promising starting points for targeted validation. More generally, our model provides the analytical complement to cutting-edge experimental technologies for surveying ASM in specific cell types and across species.

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Section: Genome-wide Amr Identification Predicts Imprinted Genesmentioning

confidence: 99%

Genomic landscape of human allele-specific DNA methylation

Fang

Hodges

Molaro

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

105

121

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“…Twenty-one significant clusters of these CpG 'beacons' were determined by permutation and these loci were enriched for neurological disease due to co-location with monogenic neurological and developmental disorders. CpG 'beacons' individually were enriched within SVA repeats, the class that is enriched for sperm hypomethylation from Molaro et al [93]. Furthermore, using primate comparative DNA methylome data, CpG density gain indicated by CpG 'beacons' correlated with reduced methylation in orthologous CGIs in these species over evolutionary time.…”

Section: Clustering Of Species-specific Cpgsmentioning

confidence: 81%

“…Molaro et al investigated the sperm DNA methylome by BiS-seq between human and chimpanzee, and identified extended hypomethylation around CGI regions in comparison to embryonic stem cells, analogous to CGI shore regions [93]. A subsequent tidal reduction in size of these hypomethylated regions was observed with differentiation.…”

Section: Germline Influences On the Evolution Of Dna Methylationmentioning

confidence: 99%

Insights in human epigenomic dynamics through comparative primate analysis

Bell

2016

Genomics

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Epigenomic analysis gives a molecular insight into cell-specific genomic activity. It provides a detailed functional plan to dissect an organism, tissue by tissue.Therefore comparative epigenomics may increase understanding of human-acquired traits, by revealing regulatory changes in systems such as the neurological, musculoskeletal, and immunological.Enhancer loci evolve fast by hijacking elements from other tissues or rewiring and amplifying existing units for human-specific function. Promoters by contrast often require a CpG dense genetic infrastructure. Specific interplay occurs between the two, but also a shared modality of function, with coordination from global chromatin-modifying enzymes. Changes in specific transcription factor binding sites also facilitate the local epigenetic state. In the case of CTCF, these may further influence 3-dimensional structure and interaction.How these mechanistic units are modulated between tissue and species enables more comprehensive understanding of human processes and pathology.With this, precise therapeutic targeting of these epigenetic modifications may become possible.

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“…A correct pattern of DNA methylation is a requirement for fertility, embryo development and viability of the offspring (O'Doherty and McGettigan 2014;Jenkins and Carrell 2012b;Jenkins and Carrell 2012a). With the description of the human sperm methylome, a methylation status at 70 % of genomic CpGs has been considered as "normal" in human sperm (Molaro et al 2011), lower to that observed in zebrafish, with 95% of methylated CpGs (Potok et al 2013). Sperm DNA methylation pattern is close to that observed in embryonic stem cells, showing hypomethylation at developmental promoters (Hammoud et al 2009;Schagdarsurengin et al 2012).…”

Section: The Importance Of Chromatin Methylationmentioning

confidence: 99%

Paternal contribution to development: Sperm genetic damage and repair in fish

et al. 2017

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In this review we provide an overview of the components of the spermatozoa playing an important role in reproductive success beyond fertilization, showing the relationship between the integrity of the diverse elements and the development of a healthy offspring. The present knowledge about fish sperm chromatin organization, epigenetic modifications of DNA and histones and sperm-borne RNAs, essential in controlling embryo development, is summarized, pointing out the possibility of using specific genes or transcripts as biomarkers of sperm quality. Data about commercial species are reported when available and more detailed information about zebrafish sperm is presented.Considering the implications that the integrity of sperm genome and epigenome has on the preservation of a proper genotype and phenotype in the progeny, the methods applied for the study of chromatin damage and for the study of transcriptome are described. Moreover we discuss some injuring agents affecting paternal information, from the presence of contaminants in the aquatic environment, to the reproductive *Manuscript Click here to download Manuscript: Herrez et al revised aquaculture.docx Click here to view linked References practices applied in fish farming. The consequences of fertilizing with damaged spermatozoa, as well as the zygotic ability to repair damage are also reviewed.

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Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

Cited by 361 publications

References 64 publications

Genomic landscape of human allele-specific DNA methylation

Genomic landscape of human allele-specific DNA methylation

Insights in human epigenomic dynamics through comparative primate analysis

Paternal contribution to development: Sperm genetic damage and repair in fish

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