@article{simmers_jima_tsuji_cowley_2023, title={LncRNA Tuna is activated in cadmium-induced placental insufficiency and drives the NRF2-mediated oxidative stress response}, volume={11}, ISSN={["2296-634X"]}, DOI={10.3389/fcell.2023.1151108}, abstractNote={Cadmium (Cd) is a toxic heavy metal found throughout the environment and one of the top ten toxicants of major public health concern identified by the World Health Organization. In utero Cd exposure causes fetal growth restriction, malformation, and spontaneous abortion; however, the mechanisms by which Cd impacts these outcomes are poorly understood. Cd accumulates in the placenta, suggesting that these negative outcomes may be a consequence of disrupted placental function and placental insufficiency. To understand the impact of Cd on gene expression within the placenta, we developed a mouse model of Cd-induced fetal growth restriction through maternal consumption of CdCl2 and performed RNA-seq on control and CdCl2 exposed placentae. The top differentially expressed transcript was the Tcl1 Upstream Neuron-Associated (Tuna) long non-coding RNA, which was upregulated over 25-fold in CdCl2 exposed placentae. Tuna has been shown to be critical for neural stem cell differentiation. However, within the placenta, there is no evidence that Tuna is normally expressed or functional at any developmental stage. To determine the spatial expression of Cd-activated Tuna within the placenta, we used in situ hybridization as well as placental layer-specific RNA isolation and analysis. Both methods confirmed the absence of Tuna expression in control samples and determined that Cd-induced Tuna expression is specific to the junctional zone. Since many lncRNAs regulate gene expression, we hypothesized that Tuna forms part of the mechanism of Cd-induced transcriptomic changes. To test this, we over-expressed Tuna in cultured choriocarcinoma cells and compared gene expression profiles to those of control and CdCl2 exposed cells. We demonstrate significant overlap between genes activated by Tuna overexpression and genes activated by CdCl2 exposure, with enrichment in the NRF2-mediated oxidative stress response. Herein we analyze the NRF2 pathway and show that Tuna increases NRF2/NRF2 both at the transcript and protein levels. Tuna drives increased NRF2 target gene expression, a result that is abrogated with the use of an NRF2 inhibitor, confirming that Tuna activates oxidative stress response genes through this pathway. This work identifies the lncRNA Tuna as a potential novel player in Cd-induced placental insufficiency.}, journal={FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY}, author={Simmers, Mark D. and Jima, Dereje D. and Tsuji, Yoshiaki and Cowley, Michael}, year={2023}, month={Jun} }
 @article{simmers_hudson_baptissart_cowley_2022, title={Epigenetic control of the imprinted growth regulator Cdkn1c in cadmium-induced placental dysfunction}, volume={7}, ISSN={["1559-2308"]}, url={https://doi.org/10.1080/15592294.2022.2088173}, DOI={10.1080/15592294.2022.2088173}, abstractNote={ABSTRACT Cadmium (Cd) is a toxic metal ubiquitous in the environment. In utero, Cd is inefficiently transported to the foetus but causes foetal growth restriction (FGR), likely through impairment of the placenta where Cd accumulates. However, the underlying molecular mechanisms are poorly understood. Cd can modulate the expression of imprinted genes, defined by their transcription from one parental allele, which play critical roles in placental and foetal growth. The expression of imprinted genes is governed by DNA methylation at Imprinting Control Regions (ICRs), which are susceptible to environmental perturbation. The imprinted gene Cdkn1c/CDKN1C is a major regulator of placental development, is implicated in FGR, and shows increased expression in response to Cd exposure in mice. Here, we use a hybrid mouse model of in utero Cd exposure to determine if the increase in placental Cdkn1c expression is caused by changes to ICR DNA methylation and loss of imprinting (LOI). Consistent with prior studies, Cd causes FGR and impacts placental structure and Cdkn1c expression at late gestation. Using polymorphisms to distinguish parental alleles, we demonstrate that increased Cdkn1c expression is not driven by changes to DNA methylation or LOI. We show that Cdkn1c is expressed primarily in the placental labyrinth which is proportionally increased in size in response to Cd. We conclude that the Cd-associated increase in Cdkn1c expression can be fully explained by alterations to placental structure. These results have implications for understanding mechanisms of Cd-induced placental dysfunction and, more broadly, for the study of FGR associated with increased Cdkn1c/CDKN1C expression.}, journal={EPIGENETICS}, author={Simmers, Mark D. and Hudson, Kathleen M. and Baptissart, Marine and Cowley, Michael}, year={2022}, month={Jul} }
 @article{jima_skaar_planchart_motsinger-reif_cevik_park_cowley_wright_house_liu_et al._2022, title={Genomic map of candidate human imprint control regions: the imprintome}, volume={6}, ISSN={["1559-2308"]}, url={https://doi.org/10.1080/15592294.2022.2091815}, DOI={10.1080/15592294.2022.2091815}, abstractNote={ABSTRACT Imprinted genes – critical for growth, metabolism, and neuronal function – are expressed from one parental allele. Parent-of-origin-dependent CpG methylation regulates this expression at imprint control regions (ICRs). Since ICRs are established before tissue specification, these methylation marks are similar across cell types. Thus, they are attractive for investigating the developmental origins of adult diseases using accessible tissues, but remain unknown. We determined genome-wide candidate ICRs in humans by performing whole-genome bisulphite sequencing (WGBS) of DNA derived from the three germ layers and from gametes. We identified 1,488 hemi-methylated candidate ICRs, including 19 of 25 previously characterized ICRs (https://humanicr.org/). Gamete methylation approached 0% or 100% in 332 ICRs (178 paternally and 154 maternally methylated), supporting parent-of-origin-specific methylation, and 65% were in well-described CTCF-binding or DNaseI hypersensitive regions. This draft of the human imprintome will allow for the systematic determination of the role of early-acquired imprinting dysregulation in the pathogenesis of human diseases and developmental and behavioural disorders.}, journal={EPIGENETICS}, author={Jima, Dereje D. and Skaar, David A. and Planchart, Antonio and Motsinger-Reif, Alison and Cevik, Sebnem E. and Park, Sarah S. and Cowley, Michael and Wright, Fred and House, John and Liu, Andy and et al.}, year={2022}, month={Jun} }
 @article{riegl_starnes_jima_baptissart_diehl_belcher_cowley_2022, title={The imprinted gene Zac1 regulates steatosis in developmental cadmium-induced nonalcoholic fatty liver disease}, volume={10}, ISSN={["1096-0929"]}, url={https://doi.org/10.1093/toxsci/kfac106}, DOI={10.1093/toxsci/kfac106}, abstractNote={Abstract}, journal={TOXICOLOGICAL SCIENCES}, author={Riegl, Sierra D. and Starnes, Cassie and Jima, Dereje D. and Baptissart, Marine and Diehl, Anna Mae and Belcher, Scott M. and Cowley, Michael}, year={2022}, month={Oct} }
 @article{baptissart_bradish_jones_walsh_tehrani_marrero-colon_mehta_jima_oh_diehl_et al._2022, title={Zac1 and the Imprinted Gene Network program juvenile NAFLD in response to maternal metabolic syndrome}, volume={2}, ISSN={["1527-3350"]}, url={https://doi.org/10.1002/hep.32363}, DOI={10.1002/hep.32363}, abstractNote={Abstract}, journal={HEPATOLOGY}, author={Baptissart, Marine and Bradish, Christine M. and Jones, Brie S. and Walsh, Evan and Tehrani, Jesse and Marrero-Colon, Vicmarie and Mehta, Sanya and Jima, Dereje D. and Oh, Seh Hoon and Diehl, Anna Mae and et al.}, year={2022}, month={Feb} }
 @article{prickett_montibus_barkas_amante_franco_cowley_puszyk_shannon_irving_madon-simon_et al._2021, title={Imprinted Gene Expression and Function of the Dopa Decarboxylase Gene in the Developing Heart}, volume={9}, ISSN={["2296-634X"]}, url={https://europepmc.org/articles/PMC8258389}, DOI={10.3389/fcell.2021.676543}, abstractNote={Dopa decarboxylase (DDC) synthesizes serotonin in the developing mouse heart where it is encoded by Ddc_exon1a, a tissue-specific paternally expressed imprinted gene. Ddc_exon1a shares an imprinting control region (ICR) with the imprinted, maternally expressed (outside of the central nervous system) Grb10 gene on mouse chromosome 11, but little else is known about the tissue-specific imprinted expression of Ddc_exon1a. Fluorescent immunostaining localizes DDC to the developing myocardium in the pre-natal mouse heart, in a region susceptible to abnormal development and implicated in congenital heart defects in human. Ddc_exon1a and Grb10 are not co-expressed in heart nor in brain where Grb10 is also paternally expressed, despite sharing an ICR, indicating they are mechanistically linked by their shared ICR but not by Grb10 gene expression. Evidence from a Ddc_exon1a gene knockout mouse model suggests that it mediates the growth of the developing myocardium and a thinning of the myocardium is observed in a small number of mutant mice examined, with changes in gene expression detected by microarray analysis. Comparative studies in the human developing heart reveal a paternal expression bias with polymorphic imprinting patterns between individual human hearts at DDC_EXON1a, a finding consistent with other imprinted genes in human.}, journal={FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY}, author={Prickett, Adam R. and Montibus, Bertille and Barkas, Nikolaos and Amante, Samuele M. and Franco, Mauricio M. and Cowley, Michael and Puszyk, William and Shannon, Matthew F. and Irving, Melita D. and Madon-Simon, Marta and et al.}, year={2021}, month={Jun} }
 @article{hudson_shiver_yu_mehta_jima_kane_patisaul_cowley_2021, title={Transcriptomic, proteomic, and metabolomic analyses identify candidate pathways linking maternal cadmium exposure to altered neurodevelopment and behavior}, volume={11}, ISSN={["2045-2322"]}, url={https://europepmc.org/articles/PMC8357970}, DOI={10.1038/s41598-021-95630-2}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Hudson, Kathleen M. and Shiver, Emily and Yu, Jianshi and Mehta, Sanya and Jima, Dereje D. and Kane, Maureen A. and Patisaul, Heather B. and Cowley, Michael}, year={2021}, month={Aug} }
 @article{amante_montibus_cowley_barkas_setiadi_saadeh_giemza_contreras-castillo_fleischanderl_schulz_et al._2020, title={Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing}, volume={48}, ISSN={["1362-4962"]}, url={https://europepmc.org/articles/PMC7470969}, DOI={10.1093/nar/gkaa556}, abstractNote={Abstract}, number={15}, journal={NUCLEIC ACIDS RESEARCH}, author={Amante, Samuele M. and Montibus, Bertille and Cowley, Michael and Barkas, Nikolaos and Setiadi, Jessica and Saadeh, Heba and Giemza, Joanna and Contreras-Castillo, Stephania and Fleischanderl, Karin and Schulz, Reiner and et al.}, year={2020}, month={Sep}, pages={8349–8359} }
 @article{hudson_belcher_cowley_2019, title={Maternal cadmium exposure in the mouse leads to increased heart weight at birth and programs susceptibility to hypertension in adulthood}, volume={9}, ISSN={["2045-2322"]}, url={https://doi.org/10.1038/s41598-019-49807-5}, DOI={10.1038/s41598-019-49807-5}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, publisher={Springer Science and Business Media LLC}, author={Hudson, Kathleen M. and Belcher, Scott M. and Cowley, Michael}, year={2019}, month={Sep} }
 @article{martin_jima_sharp_mccullough_park_gowdy_skaar_cowley_maguire_fuemmeler_et al._2019, title={Maternal pre-pregnancy obesity, offspring cord blood DNA methylation, and offspring cardiometabolic health in early childhood: an epigenome-wide association study}, volume={14}, ISSN={["1559-2308"]}, url={https://doi.org/10.1080/15592294.2019.1581594}, DOI={10.1080/15592294.2019.1581594}, abstractNote={ABSTRACT Pre-pregnancy obesity is an established risk factor for adverse sex-specific cardiometabolic health in offspring. Epigenetic alterations, such as in DNA methylation (DNAm), are a hypothesized link; however, sex-specific epigenomic targets remain unclear. Leveraging data from the Newborn Epigenetics Study (NEST) cohort, linear regression models were used to identify CpG sites in cord blood leukocytes associated with pre-pregnancy obesity in 187 mother-female and 173 mother-male offsprings. DNAm in cord blood was measured using the Illumina HumanMethylation450k BeadChip. Replication analysis was conducted among the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Associations between pre-pregnancy obesity-associated CpG sites and offspring BMI z-score (BMIz) and blood pressure (BP) percentiles at 4–5-years of age were also examined. Maternal pre-pregnacy obesity was associated with 876 CpGs in female and 293 CpGs in male offspring (false discovery rate <5%). Among female offspring, 57 CpG sites, including the top 18, mapped to the TAPBP gene (range of effect estimates: −0.83% decrease to 4.02% increase in methylation). CpG methylation differences in the TAPBP gene were also observed among males (range of effect estimates: −0.30% decrease to 2.59% increase in methylation). While technically validated, none of the TAPBP CpG sites were replicated in ALSPAC. In NEST, methylation differences at CpG sites of the TAPBP gene were associated with BMI z-score (cg23922433 and cg17621507) and systolic BP percentile (cg06230948) in female and systolic (cg06230948) and diastolic (cg03780271) BP percentile in male offspring. Together, these findings suggest sex-specific effects, which, if causal, may explain observed sex-specific effects of maternal obesity.}, number={4}, journal={EPIGENETICS}, author={Martin, Chantel L. and Jima, Dereje and Sharp, Gemma C. and McCullough, Lauren E. and Park, Sarah S. and Gowdy, Kymberly M. and Skaar, David and Cowley, Michael and Maguire, Rachel L. and Fuemmeler, Bernard and et al.}, year={2019}, month={Apr}, pages={325–340} }
 @article{cowley_skaar_jima_maguire_hudson_park_sorrow_hoyo_2018, title={Effects of Cadmium Exposure on DNA Methylation at Imprinting Control Regions and Genome-Wide in Mothers and Newborn Children.}, volume={3}, url={http://europepmc.org/abstract/med/29529597}, DOI={10.1289/ehp2085}, abstractNote={Background: Imprinted genes are defined by their preferential expression from one of the two parental alleles. This unique mode of gene expression is dependent on allele-specific DNA methylation profiles established at regulatory sequences called imprinting control regions (ICRs). These loci have been used as biosensors to study how environmental exposures affect methylation and transcription. However, a critical unanswered question is whether they are more, less, or equally sensitive to environmental stressors as the rest of the genome. Objectives: Using cadmium exposure in humans as a model, we aimed to determine the relative sensitivity of ICRs to perturbation of methylation compared to similar, nonimprinted loci in the genome. Methods: We assayed DNA methylation genome-wide using bisulfite sequencing of 19 newborn cord blood and 20 maternal blood samples selected on the basis of maternal blood cadmium levels. Differentially methylated regions (DMRs) associated with cadmium exposure were identified. Results: In newborn cord blood and maternal blood, 641 and 1,945 cadmium-associated DMRs were identified, respectively. DMRs were more common at the 15 maternally methylated ICRs than at similar nonimprinted loci in newborn cord blood (p=5.64×10−8) and maternal blood (p=6.22×10−14), suggesting a higher sensitivity for ICRs to cadmium. Genome-wide, Enrichr analysis indicated that the top three functional categories for genes that overlapped DMRs in maternal blood were body mass index (BMI) (p=2.0×10−5), blood pressure (p=3.8×10−5), and body weight (p=0.0014). In newborn cord blood, the top three functional categories were BMI, atrial fibrillation, and hypertension, although associations were not significant after correction for multiple testing (p=0.098). These findings suggest that epigenetic changes may contribute to the etiology of cadmium-associated diseases. Conclusions: We analyzed cord blood and maternal blood DNA methylation profiles genome-wide at nucleotide resolution in individuals selected for high and low blood cadmium levels in the first trimester. Our findings suggest that ICRs may be hot spots for perturbation by cadmium, motivating further study of these loci to investigate potential mechanisms of cadmium action. https://doi.org/10.1289/EHP2085}, number={3}, journal={Environmental health perspectives}, author={Cowley, M and Skaar, DA and Jima, DD and Maguire, RL and Hudson, KM and Park, SS and Sorrow, P and Hoyo, C}, year={2018}, month={Mar} }
 @article{baptissart_lamb_to_bradish_tehrani_reif_cowley_2018, title={Neonatal mice exposed to a high-fat diet in utero influence the behaviour of their nursing dam}, volume={285}, url={https://doi.org/10.1098/rspb.2018.1237}, DOI={10.1098/rspb.2018.1237}, abstractNote={
            The behaviour of a nursing dam influences the development, physiology, and behaviour of her offspring. Maternal behaviours can be modulated both by environmental factors, including diet, and by physical or behavioural characteristics of the offspring. In most studies of the effects of the environment on maternal behaviour, F
            0
            dams nurse their own F
            1
            offspring. Because the F
            1
            are indirectly exposed to the environmental stressor
            in utero
            in these studies, it is not possible to differentiate between effects on maternal behaviour from direct exposure of the dam and those mediated by changes in the F
            1
            as a consequence of
            in utero
            exposure. In this study, we used a mouse model of high-fat (HF) diet feeding, which has been shown to influence maternal behaviours, combined with cross-fostering to discriminate between these effects. We tested whether the diet of the F
            0
            dam or the exposure experienced by the F
            1
            pups
            in utero
            is the most significant predictor of maternal behaviour. Neither factor significantly influenced pup retrieval behaviours. However, strikingly, F
            1
            in utero
            exposure was a significant predictor of maternal behaviour in the 15 min immediately following pup retrieval while F
            0
            diet had no discernable effect. Our findings suggest that
            in utero
            exposure to HF diet programmes physiological changes in the offspring which influence the maternal behaviours of their dam after birth.
          }, number={1891}, journal={Proceedings of the Royal Society B: Biological Sciences}, publisher={The Royal Society}, author={Baptissart, Marine and Lamb, Harold E. and To, Kimberly and Bradish, Christine and Tehrani, Jesse and Reif, David and Cowley, Michael}, year={2018}, month={Nov}, pages={20181237} }
 @misc{patten_cowley_oakey_feil_2016, title={Regulatory links between imprinted genes: Evolutionary predictions and consequences}, volume={283}, number={1824}, journal={Proceedings of the Royal Society of London. Series B}, author={Patten, M. M. and Cowley, M. and Oakey, R. J. and Feil, R.}, year={2016} }
 @article{patten_cowley_oakey_feil_2016, title={Regulatory links between imprinted genes: evolutionary predictions and consequences.}, volume={283}, url={http://europepmc.org/abstract/med/26842569}, DOI={10.1098/rspb.2015.2760}, abstractNote={Genomic imprinting is essential for development and growth and plays diverse roles in physiology and behaviour. Imprinted genes have traditionally been studied in isolation or in clusters with respect tocis-acting modes of gene regulation, both from a mechanistic and evolutionary point of view. Recent studies in mammals, however, reveal that imprinted genes are often co-regulated and are part of a gene network involved in the control of cellular proliferation and differentiation. Moreover, a subset of imprinted genes actsin transon the expression of other imprinted genes. Numerous studies have modulated levels of imprinted gene expression to explore phenotypic and gene regulatory consequences. Increasingly, the applied genome-wide approaches highlight how perturbation of one imprinted gene may affect other maternally or paternally expressed genes. Here, we discuss these novel findings and consider evolutionary theories that offer a rationale for such intricate interactions among imprinted genes. An evolutionary view of thesetrans-regulatory effects provides a novel interpretation of the logic of gene networks within species and has implications for the origin of reproductive isolation between species.}, number={1824}, journal={Biological sciences}, author={Patten, MM and Cowley, M and Oakey, RJ and Feil, R}, year={2016}, month={Feb} }
 @article{wolf_cowley_ward_2015, title={Coadaptation between Mother and Offspring: Why Not?}, volume={13}, ISSN={["1545-7885"]}, url={http://europepmc.org/abstract/med/25786111}, DOI={10.1371/journal.pbio.1002085}, abstractNote={A Formal Comment has challenged the interpretation of a study into an imprinted gene, maintaining that conflict, rather than mother-offspring co-adaptation, provides a better mechanistic explanation. Here authors of the original Research Article reply.}, number={3}, journal={PLOS BIOLOGY}, author={Wolf, Jason B. and Cowley, Michael and Ward, Andrew}, year={2015}, month={Mar} }
 @article{madon-simon_cowley_garfield_moorwood_ward_2014, title={Antagonistic roles in fetal development and adult physiology for the oppositely imprinted Grb10 and Dlk1 genes.}, volume={12}, url={http://europepmc.org/abstract/med/25551289}, DOI={10.1186/s12915-014-0099-8}, abstractNote={Despite being a fundamental biological problem the control of body size and proportions during development remains poorly understood, although it is accepted that the insulin-like growth factor (IGF) pathway has a central role in growth regulation, probably in all animals. The involvement of imprinted genes has also attracted much attention, not least because two of the earliest discovered were shown to be oppositely imprinted and antagonistic in their regulation of growth. The Igf2 gene encodes a paternally expressed ligand that promotes growth, while maternally expressed Igf2r encodes a cell surface receptor that restricts growth by sequestering Igf2 and targeting it for lysosomal degradation. There are now over 150 imprinted genes known in mammals, but no other clear examples of antagonistic gene pairs have been identified. The delta-like 1 gene (Dlk1) encodes a putative ligand that promotes fetal growth and in adults restricts adipose deposition. Conversely, Grb10 encodes an intracellular signalling adaptor protein that, when expressed from the maternal allele, acts to restrict fetal growth and is permissive for adipose deposition in adulthood. Here, using knockout mice, we present genetic and physiological evidence that these two factors exert their opposite effects on growth and physiology through a common signalling pathway. The major effects are on body size (particularly growth during early life), lean:adipose proportions, glucose regulated metabolism and lipid storage in the liver. A biochemical pathway linking the two cell signalling factors remains to be defined. We propose that Dlk1 and Grb10 define a mammalian growth axis that is separate from the IGF pathway, yet also features an antagonistic imprinted gene pair.}, journal={BMC biology}, author={Madon-Simon, M and Cowley, M and Garfield, AS and Moorwood, K and Ward, A}, year={2014}, month={Dec}, pages={771,} }
 @article{cowley_garfield_madon-simon_charalambous_clarkson_smalley_kendrick_isles_parry_carney_et al._2014, title={Developmental programming mediated by complementary roles of imprinted Grb10 in mother and pup.}, volume={12}, url={http://europepmc.org/abstract/med/24586114}, DOI={10.1371/journal.pbio.1001799}, abstractNote={A mouse genetic study reveals that a single gene acting in both mother and offspring has a central role in the uniquely mammalian phenomenon of nutrient provisioning through the placenta and the mammary gland.}, number={2}, journal={PLoS biology}, author={Cowley, M and Garfield, AS and Madon-Simon, M and Charalambous, M and Clarkson, RW and Smalley, MJ and Kendrick, H and Isles, AR and Parry, AJ and Carney, S and et al.}, year={2014}, month={Feb}, pages={1001799,} }
 @article{cowley_oakey_2013, title={Transposable elements re-wire and fine-tune the transcriptome.}, volume={9}, url={http://europepmc.org/abstract/med/23358118}, DOI={10.1371/journal.pgen.1003234}, abstractNote={What good are transposable elements (TEs)? Although their activity can be harmful to host genomes and can cause disease, they nevertheless represent an important source of genetic variation that has helped shape genomes. In this review, we examine the impact of TEs, collectively referred to as the mobilome, on the transcriptome. We explore how TEs—particularly retrotransposons—contribute to transcript diversity and consider their potential significance as a source of small RNAs that regulate host gene transcription. We also discuss a critical role for the mobilome in engineering transcriptional networks, permitting coordinated gene expression, and facilitating the evolution of novel physiological processes.}, number={1}, author={Cowley, M and Oakey, RJ}, year={2013}, pages={1003234} }
 @article{böhm_cowley_oakey_schulz_wood_2012, title={Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus.}, volume={40}, url={http://europepmc.org/abstract/med/22790983}, DOI={10.1093/nar/gks654}, abstractNote={Alternative polyadenylation increases transcriptome diversity by generating multiple transcript isoforms from a single gene. It is thought that this process can be subject to epigenetic regulation, but few specific examples of this have been reported. We previously showed that the Mcts2/H13 locus is subject to genomic imprinting and that alternative polyadenylation of H13 transcripts occurs in an allele-specific manner, regulated by epigenetic mechanisms. Here, we demonstrate that allele-specific polyadenylation occurs at another imprinted locus with similar features. Nap1l5 is a retrogene expressed from the paternally inherited allele, is situated within an intron of a ‘host’ gene Herc3, and overlaps a CpG island that is differentially methylated between the parental alleles. In mouse brain, internal Herc3 polyadenylation sites upstream of Nap1l5 are used on the paternally derived chromosome, from which Nap1l5 is expressed, whereas a downstream site is used more frequently on the maternally derived chromosome. Ablating DNA methylation on the maternal allele at the Nap1l5 promoter increases the use of an internal Herc3 polyadenylation site and alters exon splicing. These changes demonstrate the influence of epigenetic mechanisms in regulating Herc3 alternative mRNA processing. Internal Herc3 polyadenylation correlates with expression levels of Nap1l5, suggesting a possible role for transcriptional interference. Similar mechanisms may regulate alternative polyadenylation elsewhere in the genome.}, number={18}, author={Böhm, S and Cowley, M and Oakey, RJ and Schulz, R and Wood, AJ}, year={2012}, month={Oct}, pages={8917–8926} }
 @article{proudhon_duffié_ajjan_cowley_iranzo_carbajosa_saadeh_holland_oakey_rakyan_et al._2012, title={Protection against De Novo Methylation Is Instrumental in Maintaining Parent-of-Origin Methylation Inherited from the Gametes}, volume={47}, ISSN={1097-2765}, url={http://dx.doi.org/10.1016/j.molcel.2012.07.010}, DOI={10.1016/j.molcel.2012.07.010}, abstractNote={Identifying loci with parental differences in DNA methylation is key to unraveling parent-of-origin phenotypes. By conducting a MeDIP-Seq screen in maternal-methylation free postimplantation mouse embryos (Dnmt3L-/+), we demonstrate that maternal-specific methylation exists very scarcely at midgestation. We reveal two forms of oocyte-specific methylation inheritance: limited to preimplantation, or with longer duration, i.e. maternally imprinted loci. Transient and imprinted maternal germline DMRs (gDMRs) are indistinguishable in gametes and preimplantation embryos, however, de novo methylation of paternal alleles at implantation delineates their fates and acts as a major leveling factor of parent-inherited differences. We characterize two new imprinted gDMRs, at the Cdh15 and AK008011 loci, with tissue-specific imprinting loss, again by paternal methylation gain. Protection against demethylation after fertilization has been emphasized as instrumental in maintaining parent-of-origin methylation inherited from the gametes. Here we provide evidence that protection against de novo methylation acts as an equal major pivot, at implantation and throughout life.}, number={6}, journal={Molecular Cell}, publisher={Elsevier BV}, author={Proudhon, Charlotte and Duffié, Rachel and Ajjan, Sophie and Cowley, Michael and Iranzo, Julian and Carbajosa, Guillermo and Saadeh, Heba and Holland, Michelle L. and Oakey, Rebecca J. and Rakyan, Vardhman K. and et al.}, year={2012}, month={Sep}, pages={909–920} }
 @article{cowley_oakey_2012, title={Resetting for the Next Generation}, volume={48}, ISSN={1097-2765}, url={http://dx.doi.org/10.1016/j.molcel.2012.12.007}, DOI={10.1016/j.molcel.2012.12.007}, abstractNote={In this issue of Molecular Cell, Seisenberger et al. (2012) refine DNA methylation mapping to interrogate the epigenetic reprogramming of primordial germ cells, defining the timings of methylation loss, linking to pluripotency, and identifying potential routes to transgenerational epigenetic inheritance.}, number={6}, journal={Molecular Cell}, publisher={Elsevier BV}, author={Cowley, Michael and Oakey, Rebecca J.}, year={2012}, month={Dec}, pages={819–821} }
 @article{garfield_cowley_smith_moorwood_stewart-cox_gilroy_baker_xia_dalley_hurst_et al._2011, title={Distinct physiological and behavioural functions for parental alleles of imprinted Grb10}, volume={469}, ISSN={0028-0836 1476-4687}, url={http://dx.doi.org/10.1038/nature09651}, DOI={10.1038/nature09651}, abstractNote={Imprinted genes, defined by their preferential expression of a single parental allele, represent a subset of the mammalian genome and often have key roles in embryonic development, but also postnatal functions including energy homeostasis and behaviour. When the two parental alleles are unequally represented within a social group (when there is sex bias in dispersal and/or variance in reproductive success), imprinted genes may evolve to modulate social behaviour, although so far no such instance is known. Predominantly expressed from the maternal allele during embryogenesis, Grb10 encodes an intracellular adaptor protein that can interact with several receptor tyrosine kinases and downstream signalling molecules. Here we demonstrate that within the brain Grb10 is expressed from the paternal allele from fetal life into adulthood and that ablation of this expression engenders increased social dominance specifically among other aspects of social behaviour, a finding supported by the observed increase in allogrooming by paternal Grb10-deficient animals. Grb10 is, therefore, the first example of an imprinted gene that regulates social behaviour. It is also currently alone in exhibiting imprinted expression from each of the parental alleles in a tissue-specific manner, as loss of the peripherally expressed maternal allele leads to significant fetal and placental overgrowth. Thus Grb10 is, so far, a unique imprinted gene, able to influence distinct physiological processes, fetal growth and adult behaviour, owing to actions of the two parental alleles in different tissues.}, number={7331}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Garfield, Alastair S. and Cowley, Michael and Smith, Florentia M. and Moorwood, Kim and Stewart-Cox, Joanne E. and Gilroy, Kerry and Baker, Sian and Xia, Jing and Dalley, Jeffrey W. and Hurst, Laurence D. and et al.}, year={2011}, month={Jan}, pages={534–538} }
 @article{arnaud_bourc'his_camprubi_cowley_feil_frost_guillaumet-adkins_iglesias_martin-trujillo_monk_et al._2011, title={Human imprinted retrogenes exhibit non-canonical imprint chromatin signatures and reside in non-imprinted host genes.}, volume={39}, url={http://europepmc.org/abstract/med/21300645}, DOI={10.1093/nar/gkq1230}, abstractNote={Imprinted retrotransposed genes share a common genomic organization including a promoter-associated differentially methylated region (DMR) and a position within the intron of a multi-exonic ‘host’ gene. In the mouse, at least one transcript of the host gene is also subject to genomic imprinting. Human retrogene orthologues are imprinted and we reveal that human host genes are not imprinted. This coincides with genomic rearrangements that occurred during primate evolution, which increase the separation between the retrogene DMRs and the host genes. To address the mechanisms governing imprinted retrogene expression, histone modifications were assayed at the DMRs. For the mouse retrogenes, the active mark H3K4me2 was associated with the unmethylated paternal allele, while the methylated maternal allele was enriched in repressive marks including H3K9me3 and H4K20me3. Two human retrogenes showed monoallelic enrichment of active, but not of repressive marks suggesting a partial uncoupling of the relationship between DNA methylation and repressive histone methylation, possibly due to the smaller size and lower CpG density of these DMRs. Finally, we show that the genes immediately flanking the host genes in mouse and human are biallelically expressed in a range of tissues, suggesting that these loci are distinct from large imprinted clusters.}, number={11}, journal={Nucleic acids research}, author={Arnaud, P and Bourc'his, D and Camprubi, C and Cowley, M and Feil, R and Frost, JM and Guillaumet-Adkins, A and Iglesias, Platas I and Martin-Trujillo, A and Monk, D and et al.}, year={2011}, month={Jun}, pages={4577–4586} }
 @article{chahal_cowley_mccole_oakey_saadat_schulz_de_2011, title={Short interspersed element (SINE) depletion and long interspersed element (LINE) abundance are not features universally required for imprinting.}, volume={6}, url={http://europepmc.org/abstract/med/21533089}, DOI={10.1371/journal.pone.0018953}, abstractNote={Genomic imprinting is a form of gene dosage regulation in which a gene is expressed from only one of the alleles, in a manner dependent on the parent of origin. The mechanisms governing imprinted gene expression have been investigated in detail and have greatly contributed to our understanding of genome regulation in general. Both DNA sequence features, such as CpG islands, and epigenetic features, such as DNA methylation and non-coding RNAs, play important roles in achieving imprinted expression. However, the relative importance of these factors varies depending on the locus in question. Defining the minimal features that are absolutely required for imprinting would help us to understand how imprinting has evolved mechanistically. Imprinted retrogenes are a subset of imprinted loci that are relatively simple in their genomic organisation, being distinct from large imprinting clusters, and have the potential to be used as tools to address this question. Here, we compare the repeat element content of imprinted retrogene loci with non-imprinted controls that have a similar locus organisation. We observe no significant differences that are conserved between mouse and human, suggesting that the paucity of SINEs and relative abundance of LINEs at imprinted loci reported by others is not a sequence feature universally required for imprinting.}, number={4}, journal={PloS one}, author={Chahal, M and Cowley, M and McCole, RB and Oakey, RJ and Saadat, G and Schulz, R and de, Burca A}, year={2011}, pages={18953} }
 @article{charalambous_cowley_geoghegan_smith_radford_marlow_graham_hurst_ward_2010, title={Maternally-inherited Grb10 reduces placental size and efficiency}, volume={337}, ISSN={0012-1606}, url={http://dx.doi.org/10.1016/j.ydbio.2009.10.011}, DOI={10.1016/j.ydbio.2009.10.011}, abstractNote={The control of foetal growth is poorly understood and yet it is critically important that at birth the body has attained appropriate size and proportions. Growth and survival of the mammalian foetus is dependent upon a functional placenta throughout most of gestation. A few genes are known that influence both foetal and placental growth and might therefore coordinate growth of the conceptus, including the imprinted Igf2 and Grb10 genes. Grb10 encodes a signalling adapter protein, is expressed predominantly from the maternally-inherited allele and acts to restrict foetal and placental growth. Here, we show that following disruption of the maternal allele in mice, the labyrinthine volume was increased in a manner consistent with a cell-autonomous function of Grb10 and the enlarged placenta was more efficient in supporting foetal growth. Thus, Grb10 is the first example of a gene that acts to limit placental size and efficiency. In addition, we found that females inheriting a mutant Grb10 allele from their mother had larger litters and smaller offspring than those inheriting a mutant allele from their father. This grandparental effect suggests Grb10 can influence reproductive strategy through the allocation of maternal resources such that offspring number is offset against size.}, number={1}, journal={Developmental Biology}, publisher={Elsevier BV}, author={Charalambous, Marika and Cowley, Michael and Geoghegan, Fleur and Smith, Florentia M. and Radford, Elizabeth J. and Marlow, Benjamin P. and Graham, Christopher F. and Hurst, Laurence D. and Ward, Andrew}, year={2010}, month={Jan}, pages={1–8} }
 @article{cowley_oakey_2010, title={Retrotransposition and genomic imprinting.}, volume={9}, url={http://europepmc.org/abstract/med/20591835}, DOI={10.1093/bfgp/elq015}, abstractNote={Studies of large imprinted clusters, such as the Gnas locus, have revealed much about the significance of DNA methylation, transcription and other factors in the establishment and maintenance of imprinted gene expression. However, the complexity of such loci can make manipulating them and interpreting the results challenging. We review here a distinct class of imprinted genes, which have arisen by retrotransposition, and which have the potential to be used as models for the dissection of the fundamental features and mechanisms required for imprinting. They are also of interest in their own right, generating diversity in the transcriptome and providing raw material upon which selection can act.}, number={4}, author={Cowley, M and Oakey, RJ}, year={2010}, month={Jul}, pages={340–346} }