Epigenetic memory articles within Nature Communications

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  • Article
    | Open Access

    The dietary factors causing varying intergenerational responses are not fully identified. Here, the authors show that the relative proportion of protein, fats, and carbohydrates in paternal diets before conception differentially influences the phenotype of the next-generation offspring on energy metabolism and behaviour.

    • Angela Jane Crean
    • , Alistair McNair Senior
    •  & Stephen James Simpson

  • Article
    | Open Access

    The brushtail possum is a treasured Australian marsupial, but also a harmful pest introduced into New Zealand. Here, using functional genomics and a new chromosome-level genome assembly of New Zealand possums, Bond et al. quantify their genome admixture and identify unique parent-specific and weaning associated gene expression.

    • Donna M. Bond
    • , Oscar Ortega-Recalde
    •  & Timothy A. Hore

  • Article
    | Open Access

    How much the environment influences inherited adaptive traits is debated and challenging to demonstrate in mammals. Here the authors performed a multigeneration study that failed to morphologically replicate enhanced wound healing response following ancestral liver injury in rats. However, heritable transcriptional effects suggest transmission at the molecular level, albeit of unclear functional relevance.

    • Johanna Beil
    • , Juliane Perner
    •  & Rémi Terranova

  • Article
    | Open Access

    Here the authors question the prevalent view of DNA methylation as a stably inherited epigenetic mark, revealing that the existing model does not apply when considering genomic loci that are intermediately methylated.

    • Amir D. Hay
    • , Noah J. Kessler
    •  & Anne C. Ferguson-Smith

  • Article
    | Open Access

    Most transcription factors detach from chromatin during mitosis, but some are retained and bookmark genomic sites. Here, the authors show that GATA2-mediated mitotic bookmarking is critical for definitive haematopoiesis.

    • Rita Silvério-Alves
    • , Ilia Kurochkin
    •  & Carlos-Filipe Pereira

  • Article
    | Open Access

    The balance of stem cell maintenance, differentiation, and programmed death is critical for proper development. Here they show that SNIP1 is critical for stem cell survival and differentiation in the developing brain where it acts downstream of TGFb and NFkB and regulates PRC2 activities for governing cell fates.

    • Yurika Matsui
    • , Mohamed Nadhir Djekidel
    •  & Jamy C. Peng

  • Perspective
    | Open Access

    Increasing evidence suggests parental environmental stressors can influence offspring health and disease outcomes. In this perspective, the authors provide an update of the paternal epigenetic inheritance field and propose links between paternally transmitted epigenetic influences and functional changes to the embryo.

    • Ariane Lismer
    •  & Sarah Kimmins

  • Article
    | Open Access

    Developmental plasticity allows organisms to match traits to their environment, however, there are few known molecular mechanisms underlying such plasticity. Here, the authors show that feeding morphs in adult Pristionchus nematodes are set during a critical window in juveniles and identify H4K5/12ac as the environmental information carrier.

    • Michael S. Werner
    • , Tobias Loschko
    •  & Ralf J. Sommer

  • Article
    | Open Access

    Anti-folate drugs, such as methotrexate, have been largely prohibited for pregnant women because of the teratogenic effect on their descendant. Here, the authors report a intergenerational mechanism by why paternal methotrexate exposure causes craniofacial defects on their offspring.

    • Nagif Alata Jimenez
    • , Mauricio Castellano
    •  & Pablo H. Strobl-Mazzulla

  • Article
    | Open Access

    Here the authors investigate whether for imprinted genes the parent-of-origin of the expressed allele or rather appropriate gene dosage is more important for normal development. Using the differentially methylated region of Dlk1-Dio3 gene involved in imprinting, they show that correct parent-of-origin imprinting pattern is secondary to balanced gene dosage.

    • Ariella Weinberg-Shukron
    • , Raz Ben-Yair
    •  & Yonatan Stelzer

  • Article
    | Open Access

    Parents transmit both genetic and epigenetic information to their offspring, with maternal effect genes being critical regulators of the offspring epigenome. Here they show that maternally deposited SMCHD1 has long-lasting effects on Hox gene expression and vertebral patterning during post-implantation development.

    • Natalia Benetti
    • , Quentin Gouil
    •  & Marnie E. Blewitt

  • Article
    | Open Access

    Hox genes are known to control anteroposterior patterning, including the vertebrate spine. Here Xue et al. show that maternal Smchd1 regulates Hox expression in an epigenetic manner, and that wild type offspring from heterozygous mothers show skeletal homeotic transformations as a result of this dysregulation.

    • Shifeng Xue
    • , Thanh Thao Nguyen Ly
    •  & Bruno Reversade

  • Article
    | Open Access

    Cloutier et al. discover that human embryonic stem cells (hESCs) cultured with media containing inhibitors of GSK3 proteins undergo erosion of X-chromosome inactivation, which equalizes X-linked gene expression between females and males. The findings inform the faithful culture of hESCs.

    • Marissa Cloutier
    • , Surinder Kumar
    •  & Sundeep Kalantry

  • Article
    | Open Access

    Here the authors show that a high-fat diet in pregnant mice can release silencing of the imprinted Dlk1 locus in multiple generations of offspring. They found that this occurs via changes in microRNA expression at the locus of interest, as well as transcriptional changes across the genome, in the developing oocytes.

    • Mathew Van de Pette
    • , Andrew Dimond
    •  & Amanda G. Fisher

  • Article
    | Open Access

    The concerted dynamics of X-chromosome upregulation and X-chromosome inactivation, which collectively balance X-chromosome expression, are not well understood. Using allelic single-cell genomics, the authors characterize the dynamics of X-chromosome upregulation and inactivation along mouse embryonic and stem cell development, calling to question keys aspects of the established model of mammalian dosage compensation.

    • Antonio Lentini
    • , Huaitao Cheng
    •  & Björn Reinius

  • Article
    | Open Access

    Tracheobronchopathia osteoplastica (TO), is an underreported affliction characterized by squamous metaplasia and heterotopic bone formation in trachea and bronchi. Here the authors apply functional, as well as genome-wide transcriptional and epigenetic profiling to identify airway basal cells dysfunction underlying TO.

    • Yue Hong
    • , Shan Shan
    •  & Tao Ren

  • Article
    | Open Access

    Using quantitative imaging and monitoring transcription in living embryos, Bellec et al., provide evidence that the pioneer factor GAF acts as a stable mitotic bookmarker during early Drosophila development.

    • Maëlle Bellec
    • , Jérémy Dufourt
    •  & Mounia Lagha

  • Article
    | Open Access

    Cranial neural crest generates a wide diversity of cell types. Here the authors perform single-cell profiling of neural crest to identify key enhancers and transcription factors for cell fate competency, thus revealing progressive acquisition of fate potential.

    • Peter Fabian
    • , Kuo-Chang Tseng
    •  & J. Gage Crump

  • Article
    | Open Access

    During embryogenesis, the genome becomes transcriptionally active in a process known as zygotic genome activation (ZGA); how ZGA is initiated is still an open question. Here the authors show histone variant H2A.Z deposition precedes RNA polymerase II binding on chromatin, before ZGA. H2A.Z loss causes transcriptional downregulation of ZGA genes and leads to changes in the 3D genome organization.

    • Dafne Ibarra-Morales
    • , Michael Rauer
    •  & Nicola Iovino

  • Article
    | Open Access

    While inductive signals controlling germline specification are well characterized, the intrinsic factors that allow epiblast cells to respond to such signals remain largely unknown. Here the authors use in vitro differentiated primordial germ cells to show that partial retention of histone H3K4 monomethylation within relevant enhancers is important for germline competence and specification.

    • Tore Bleckwehl
    • , Giuliano Crispatzu
    •  & Álvaro Rada-Iglesias

  • Article
    | Open Access

    In most mammals, imprinted genes contain epigenetic marks that differ in each parental genome and control their parent-of-origin-specific expression. Here, the authors map imprinted genes in mouse preimplantation embryos and find that imprinted gene expression in blastocysts is mainly dependent on Polycomb-mediated H3K27me3-associated gene silencing.

    • Laura Santini
    • , Florian Halbritter
    •  & Martin Leeb

  • Article
    | Open Access

    Abnormal folate metabolism in mice results in transgenerational epigenetic inheritance of congenital malformations. Here, the authors provide evidence that defective folate metabolism causes germline epigenetic instability and observe multigenerational misexpression of Hira in embryos, implicating Hira transcript levels as a biomarker of maternal phenotypic inheritance.

    • Georgina E. T. Blake
    • , Xiaohui Zhao
    •  & Erica D. Watson

  • Article
    | Open Access

    DNA methylation targets CpG island promoters of germline genes to repress their expression in mouse somatic cells. Here the authors show that a transcription factor E2F6 is required to target CpG island DNA methylation and epigenetic silencing to germline genes during early mouse development.

    • Thomas Dahlet
    • , Matthias Truss
    •  & Michael Weber

  • Article
    | Open Access

    Piwi deficiency results in sterility and is associated with transposon expression and genomic instability. Here the authors show that sterility of C. elegans Piwi prg-1 mutant is not associated with transposon-induced DNA damage but is associated with and is phenocopied by dysfunction of germ granules.

    • Maya Spichal
    • , Bree Heestand
    •  & Shawn Ahmed

  • Article
    | Open Access

    Polycomb (PcG) and Trithorax (TrxG) group regulate several hundred target genes with important roles in development and disease. Here the authors combine experiment and theory to provide evidence that the Polycomb/Trithorax system has the potential for a rich repertoire of regulatory modes beyond simple epigenetic memory.

    • Jeannette Reinig
    • , Frank Ruge
    •  & Leonie Ringrose

  • Article
    | Open Access

    Preimplantation embryos undergo extensive transcriptomic and epigenomic remodeling. Here the authors assay open chromatin in bovine oocytes, embryos, and embryonic stem cells, and compare the transcriptomes and epigenomes of cattle, human and mouse embryos, revealing species-specific regulation of genome activation.

    • Michelle M. Halstead
    • , Xin Ma
    •  & Pablo J. Ross

  • Article
    | Open Access

    Evidence for transgenerational inheritance of epigenetic information in vertebrates is scarce. Here the authors report that homozygous dnmt1 mutant zebrafish are essentially normal, with the exception of impaired lymphopoiesis, with impaired larval (but not adult) T cell development being transmitted to subsequent generations by genotypically wildtype fish.

    • Norimasa Iwanami
    • , Divine-Fondzenyuy Lawir
    •  & Thomas Boehm

  • Article
    | Open Access

    Evidence for sperm small noncoding RNA-mediated intergenerational transmission implies communication from responsive somatic cells to sperm. Here, authors show that epididymal cells alter extracellular vesicle cargo after stress exposure, to impact offspring neurodevelopment and stress reactivity.

    • Jennifer C. Chan
    • , Christopher P. Morgan
    •  & Tracy L. Bale

  • Article
    | Open Access

    Use of Assisted Reproductive Technologies (ART) is increasing globally but their impact on long term health remains unclear. Here the authors show that ART-conceived individuals show variation in epigenetic profile at birth that largely resolves by adulthood, with no evidence of an impact on long term outcomes.

    • Boris Novakovic
    • , Sharon Lewis
    •  & Richard Saffery

  • Article
    | Open Access

    Germline cells transfer genetic information to offspring, and in zebrafish, drive sex determination. Here the authors report that, unlike mammals, the germline of zebrafish does not undergo genome-wide DNA methylation erasure, while amplifying and demethylating sex-linked rDNA during feminisation.

    • Oscar Ortega-Recalde
    • , Robert C. Day
    •  & Timothy A. Hore

  • Article
    | Open Access

    Germ cells are the means of transferring genetic information to the next generation. Here the authors characterise the DNA methylomes of zebrafish primordial germ cells and find that, unlike mammals, the zebrafish germ cells do not undergo genome-wide DNA demethylation but rather retain paternal DNA methylation patterns

    • Ksenia Skvortsova
    • , Katsiaryna Tarbashevich
    •  & Ozren Bogdanovic

  • Article
    | Open Access

    Mesenchymal stem cells derived from dental pulp (DP-MSCs) differ in oncogenesic and developmental potential compared to those from bone marrow. Here, the authors show that decreased DNA methylation and histone H3K9Me2 enrichment along with higher PTEN activation in DP-MSCs promotes osteogenesis and reduces oncogenesis.

    • Wen-Ching Shen
    • , Yung-Chih Lai
    •  & Shih-Chieh Hung

  • Article
    | Open Access

    Human induced pluripotent stem cells (hiPSCs) generate all cell types in the body, but different lines can differ in their potential. Here, the authors determine that higher endogenous levels of SALL3 in hiPSCs lead to ectoderm differentiation bias and reduced mesoderm/endoderm due to DNMT3B mediated DNA methylation.

    • Takuya Kuroda
    • , Satoshi Yasuda
    •  & Yoji Sato

  • Article
    | Open Access

    Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to promote gene silencing. Here the authors use reversible tethering of Polycomb proteins to ectopic sites in mouse ESCs and find that canonical but not variant PRC1 can trigger sequence-independent propagation of Polycomb-mediated transcriptional repression.

    • Hagar F. Moussa
    • , Daniel Bsteh
    •  & Oliver Bell

  • Article
    | Open Access

    PWWP domains of DNMT3A and DNMT3B are proposed to interact with H3K36me3. Here the authors present a mouse model carrying a D329A point mutation in the DNMT3A PWWP domain and find this causes dominant postnatal growth retardation, with aberrant progressive gain of DNA methylation across domains marked by H3K27me3 in adult tissues.

    • Gintarė Sendžikaitė
    • , Courtney W. Hanna
    •  & Gavin Kelsey

  • Article
    | Open Access

    The mechanisms of paternal epigenetic inheritance and its influence on offspring are still poorly understood. Here the authors provide evidence that in C. elegans, sperm-inherited chromatin states influence transcription and cell identity in the germ cells of offspring.

    • Kiyomi Raye Kaneshiro
    • , Andreas Rechtsteiner
    •  & Susan Strome

  • Article
    | Open Access

    The inactive X chromosome (Xi) has an atypical structure, with global loss of TADs, A/B compartments and formation of mega-domains. Here the authors show that the non-canonical SMC family protein, SmcHD1, important for developmental gene silencing on Xi, antagonises TAD formation and compartmentalization on the Xi in a transcription independent way.

    • Michal R. Gdula
    • , Tatyana B. Nesterova
    •  & Neil Brockdorff

  • Article
    | Open Access

    HMGN1 and HMGN2 are ubiquitous nucleosome binding proteins. Here the authors provide evidence that HMGN proteins preferentially localize to chromatin regulatory sites to modulate the plasticity of the epigenetic landscape, proposing that HGMNs stabilize, rather than determine, cell identity.

    • Bing He
    • , Tao Deng
    •  & Michael Bustin

  • Article
    | Open Access

    In vitro culture has detrimental effects on transcriptomes and epigenetic programming of zygotes. Here the authors use microfluidic technology to co-culture bovine oviduct epithelial cells with zygotes and show that the transcriptomes and global methylation patterns of these zygotes are more similar to in vivo zygotes than to conventionally cultured zygotes.

    • Marcia A. M. M. Ferraz
    • , Hoon Suk Rho
    •  & Bart M. Gadella

  • Article
    | Open Access

    Paternal contributions to epigenetic inheritance via nucleosomes are poorly understood, as sperm in many organisms replace the majority of nucleosomes with protamines. Here the authors provide evidence that Caenorhabditis elegans sperm retain histone packaging of the genome and provide a histone-based epigenetic memory that is important for germ cell development in offspring.

    • Tomoko M. Tabuchi
    • , Andreas Rechtsteiner
    •  & Susan Strome

  • Article
    | Open Access

    Loss of Polycomb repressive complex 1 (PRC1) proteins usually results in both chromatin unfolding and ectopic transcription. Here, the authors analyze the temporal function of two PRC1 proteins during Drosophila embryogenesis and provide evidence that PRC1 maintains gene silencing by folding chromatin domains.

    • Thierry Cheutin
    •  & Giacomo Cavalli

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