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Jedynak P, Siroux V, Broséus L, Tost J, Busato F, Gabet S, Thomsen C, Sakhi AK, Sabaredzovic A, Lyon-Caen S, Bayat S, Slama R, Philippat C, Lepeule J. Epigenetic footprints: Investigating placental DNA methylation in the context of prenatal exposure to phenols and phthalates. ENVIRONMENT INTERNATIONAL 2024; 189:108763. [PMID: 38824843 DOI: 10.1016/j.envint.2024.108763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/22/2024] [Accepted: 05/18/2024] [Indexed: 06/04/2024]
Abstract
BACKGROUND Endocrine disrupting compounds (EDCs) such as phthalates and phenols can affect placental functioning and fetal health, potentially via epigenetic modifications. We investigated the associations between pregnancy exposure to synthetic phenols and phthalates estimated from repeated urine sampling and genome wide placental DNA methylation. METHODS The study is based on 387 women with placental DNA methylation assessed with Infinium MethylationEPIC arrays and with 7 phenols, 13 phthalates, and two non-phthalate plasticizer metabolites measured in pools of urine samples collected twice during pregnancy. We conducted an exploratory analysis on individual CpGs (EWAS) and differentially methylated regions (DMRs) as well as a candidate analysis focusing on 20 previously identified CpGs. Sex-stratified analyses were also performed. RESULTS In the exploratory analysis, when both sexes were studied together no association was observed in the EWAS. In the sex-stratified analysis, 114 individual CpGs (68 in males, 46 in females) were differentially methylated, encompassing 74 genes (36 for males and 38 for females). We additionally identified 28 DMRs in the entire cohort, 40 for females and 42 for males. Associations were mostly positive (for DMRs: 93% positive associations in the entire cohort, 60% in the sex-stratified analysis), with the exception of several associations for bisphenols and DINCH metabolites that were negative. Biomarkers associated with most DMRs were parabens, DEHP, and DiNP metabolite concentrations. Some DMRs encompassed imprinted genes including APC (associated with parabens and DiNP metabolites), GNAS (bisphenols), ZIM2;PEG3;MIMT1 (parabens, monoethyl phthalate), and SGCE;PEG10 (parabens, DINCH metabolites). Terms related to adiposity, lipid and glucose metabolism, and cardiovascular function were among the enriched phenotypes associated with differentially methylated CpGs. The candidate analysis identified one CpG mapping to imprinted LGALS8 gene, negatively associated with ethylparaben. CONCLUSIONS By combining improved exposure assessment and extensive placental epigenome coverage, we identified several novel genes associated with the exposure, possibly in a sex-specific manner.
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Affiliation(s)
- Paulina Jedynak
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France; ISGlobal, Barcelona, Spain
| | - Valérie Siroux
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Lucile Broséus
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Stephan Gabet
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France; Univ. Lille, CHU Lille, Institut Pasteur de Lille, ULR 4483-IMPacts de l'Environnement Chimique sur la Santé (IMPECS), 59000 Lille, France
| | - Cathrine Thomsen
- Department of Food Safety, Norwegian Institue of Public Health, Oslo, Norway
| | - Amrit K Sakhi
- Department of Food Safety, Norwegian Institue of Public Health, Oslo, Norway
| | | | - Sarah Lyon-Caen
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Sam Bayat
- Department of Pulmonology and Physiology, CHU Grenoble Alpes, Grenoble, France
| | - Rémy Slama
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Claire Philippat
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France.
| | - Johanna Lepeule
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
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2
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Miller JR, Adjeroh DA. Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq. BMC Bioinformatics 2024; 25:109. [PMID: 38475727 DOI: 10.1186/s12859-024-05728-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Parent-of-origin allele-specific gene expression (ASE) can be detected in interspecies hybrids by virtue of RNA sequence variants between the parental haplotypes. ASE is detectable by differential expression analysis (DEA) applied to the counts of RNA-seq read pairs aligned to parental references, but aligners do not always choose the correct parental reference. RESULTS We used public data for species that are known to hybridize. We measured our ability to assign RNA-seq read pairs to their proper transcriptome or genome references. We tested software packages that assign each read pair to a reference position and found that they often favored the incorrect species reference. To address this problem, we introduce a post process that extracts alignment features and trains a random forest classifier to choose the better alignment. On each simulated hybrid dataset tested, our machine-learning post-processor achieved higher accuracy than the aligner by itself at choosing the correct parent-of-origin per RNA-seq read pair. CONCLUSIONS For the parent-of-origin classification of RNA-seq, machine learning can improve the accuracy of alignment-based methods. This approach could be useful for enhancing ASE detection in interspecies hybrids, though RNA-seq from real hybrids may present challenges not captured by our simulations. We believe this is the first application of machine learning to this problem domain.
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Affiliation(s)
- Jason R Miller
- Department of Computer Science, Mathematics, Engineering, Shepherd University, Shepherdstown, WV, USA.
- EVOGENE, Department of Biosciences, University of Oslo, Oslo, Norway.
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA.
| | - Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, USA
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3
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Jedynak P, Broséus L, Tost J, Busato F, Gabet S, Thomsen C, Sakhi AK, Pin I, Slama R, Lepeule J, Philippat C. Prenatal exposure to triclosan assessed in multiple urine samples and placental DNA methylation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 335:122197. [PMID: 37481027 DOI: 10.1016/j.envpol.2023.122197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
A previous study reported positive associations of maternal urinary concentrations of triclosan, a synthetic phenol with widespread exposure in the general population, with placental DNA methylation of male fetuses. Given the high number of comparisons performed in -omic research, further studies were needed to validate and extend on these findings. Using a cohort of male and female fetuses with repeated maternal urine samples to assess exposure, we studied the associations between triclosan and placental DNA methylation. We assessed triclosan concentrations in two pools of 21 urine samples collected among 395 women from the SEPAGES cohort. We used Infinium Methylation EPIC arrays to measure DNA methylation in placental biopsies collected at delivery. We performed a candidate study restricted to a set of candidate CpGs (n = 500) identified in a previous work as well as an exploratory epigenome-wide association study to investigate the associations between triclosan and differentially methylated probes and regions. Analyses were conducted on the whole population and stratified by child's sex. Mediation analysis was performed to test whether heterogeneity of placental tissue may mediate the observed associations. In the candidate approach, we confirmed 18 triclosan-associated genes when both sexes were considered. After stratification for child's sex, triclosan was associated with 72 genes in females and three in males. Most of the associations were positive and several CpGs mapped to imprinted genes: FBRSL1, KCNQ1, RHOBTB3, and SMOC1. A mediation effect by placental tissue heterogeneity was identified for most of the observed associations. In the exploratory analysis, we identified a few isolated associations in the sex-stratified analysis. In line with a previous study on male placentas, our approach revealed several positive associations between triclosan exposure and placental DNA methylation. Several identified loci mapped to imprinted genes.
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Affiliation(s)
- Paulina Jedynak
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Lucile Broséus
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Stephan Gabet
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France; University Lille, CHU Lille, Institut Pasteur de Lille, ULR 4483-IMPacts de L'Environnement Chimique sur La Santé (IMPECS), Lille, France
| | - Cathrine Thomsen
- Division of Climate and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Amrit K Sakhi
- Division of Climate and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Isabelle Pin
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France; Pediatric Department, Grenoble Alpes University Hospital, La Tronche, France
| | - Rémy Slama
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Johanna Lepeule
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France.
| | - Claire Philippat
- University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
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4
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Rodriguez-Caro F, Moore EC, Good JM. Evolution of parent-of-origin effects on placental gene expression in house mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554674. [PMID: 37662315 PMCID: PMC10473692 DOI: 10.1101/2023.08.24.554674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The mammalian placenta is a hotspot for the evolution of genomic imprinting, a form of gene regulation that involves the parent-specific epigenetic silencing of one allele. Imprinted genes are central to placental development and are thought to contribute to the evolution of reproductive barriers between species. However, it is unclear how rapidly imprinting evolves or how functional specialization among placental tissues influences the evolution of imprinted expression. We compared parent-of-origin expression bias across functionally distinct placental layers sampled from reciprocal crosses within three closely related lineages of mice ( Mus ). Using genome-wide gene expression and DNA methylation data from fetal and maternal tissues, we developed an analytical strategy to minimize pervasive bias introduced by maternal contamination of placenta samples. We corroborated imprinted expression at 42 known imprinted genes and identified five candidate imprinted genes showing parent-of-origin specific expression and DNA methylation. Paternally-biased expression was enriched in the labyrinth zone, a layer specialized in nutrient transfer, and maternally-biased genes were enriched in the junctional zone, which specializes in modulation of maternal physiology. Differentially methylated regions were predominantly determined through epigenetic modification of the maternal genome and were associated with both maternally- and paternally-biased gene expression. Lastly, comparisons between lineages revealed a small set of co-regulated genes showing rapid divergence in expression levels and imprinted status in the M. m. domesticus lineage. Together, our results reveal important links between core functional elements of placental biology and the evolution of imprinted gene expression among closely related rodent species.
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5
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Huang X, Tang X, Bai X, Li H, Tao H, Wang J, Li Y, Sun Y, Zheng Y, Xu X, Wang L, Ding Y, Lu M, Zhou P, Bo X, Li H, Chen H. dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development. Genome Res 2022; 32:gr.276744.122. [PMID: 35977841 PMCID: PMC9435744 DOI: 10.1101/gr.276744.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/15/2022] [Indexed: 11/24/2022]
Abstract
During early mammalian embryo development, different epigenetic marks undergo reprogramming and play crucial roles in the mediation of gene expression. Currently, several databases provide multi-omics information on early embryos. However, how interconnected epigenetic markers function together to coordinate the expression of the genetic code in a spatiotemporal manner remains difficult to analyze, markedly limiting scientific and clinical research. Here, we present dbEmbryo, an integrated and interactive multi-omics database for human and mouse early embryos. dbEmbryo integrates data on gene expression, DNA methylation, histone modifications, chromatin accessibility, and higher-order chromatin structure profiles for human and mouse early embryos. It incorporates customized analysis tools, such as "multi-omics visualization," "Gene&Peak annotation," "ZGA gene cluster," "cis-regulation," "synergistic regulation," "promoter signal enrichment," and "3D genome." Users can retrieve gene expression and epigenetic profile patterns to analyze synergistic changes across different early embryo developmental stages. We showed the uniqueness of dbEmbryo among extant databases containing data on early embryo development and provided an overview. Using dbEmbryo, we obtained a phase-separated model of transcriptional control during early embryo development. dbEmbryo offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher molecular regulatory mechanisms of human and mouse early embryo development.
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Affiliation(s)
- Xin Huang
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaohan Tang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Xuemei Bai
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Honglei Li
- Beijing Cloudna Technology Company, Limited, Beijing 100029, China
| | - Huan Tao
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Junting Wang
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Yaru Li
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Yu Sun
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Yang Zheng
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Xiang Xu
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Longteng Wang
- Center for Statistical Science, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yang Ding
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Meisong Lu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Pingkun Zhou
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Hao Li
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
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6
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Yang H, Bai D, Li Y, Yu Z, Wang C, Sheng Y, Liu W, Gao S, Zhang Y. Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo. Nat Cell Biol 2022; 24:783-792. [PMID: 35484247 DOI: 10.1038/s41556-022-00900-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 03/16/2022] [Indexed: 12/13/2022]
Abstract
Parental DNA methylation and histone modifications undergo distinct global reprogramming in mammalian pre-implantation embryos, but the landscape of epigenetic crosstalk and its effects on embryogenesis are largely unknown. Here we comprehensively analyse the association between DNA methylation and H3K9me3 reprogramming in mouse pre-implantation embryos and reveal that CpG-rich genomic loci with high H3K9me3 signal and DNA methylation level (CHM) are hotspots of DNA methylation maintenance during pre-implantation embryogenesis. We further profile the allele-specific epigenetic map with unprecedented resolution in gynogenetic and androgenetic embryos, respectively, and identify 1,279 allele-specific CHMs, including 19 known imprinting control regions (ICRs). Our study suggests that 22 ICR-like regions (ICRLRs) may regulate allele-specific transcription similarly to known ICRs, and five of them are confirmed to be important for mouse embryo development. Taken together, our study reveals the widespread existence of allele-specific CHMs and largely extends the scope of allele-specific regulation in mammalian pre-implantation embryos.
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Affiliation(s)
- Hui Yang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Dandan Bai
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Yanhe Li
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Zhaowei Yu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Chenfei Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yifan Sheng
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Wenqiang Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China. .,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China. .,Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China. .,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China. .,Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Yong Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China. .,Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China.
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7
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Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation. Cell Res 2022; 32:801-813. [PMID: 35428874 PMCID: PMC9437020 DOI: 10.1038/s41422-022-00652-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/10/2022] [Indexed: 12/13/2022] Open
Abstract
AbstractChromatin remodeling is essential for epigenome reprogramming after fertilization. However, the underlying mechanisms of chromatin remodeling remain to be explored. Here, we investigated the dynamic changes in nucleosome occupancy and positioning in pronucleus-stage zygotes using ultra low-input MNase-seq. We observed distinct features of inheritance and reconstruction of nucleosome positioning in both paternal and maternal genomes. Genome-wide de novo nucleosome occupancy in the paternal genome was observed as early as 1 h after the injection of sperm into ooplasm. The nucleosome positioning pattern was continually rebuilt to form nucleosome-depleted regions (NDRs) at promoters and transcription factor (TF) binding sites with differential dynamics in paternal and maternal genomes. NDRs formed more quickly on the promoters of genes involved in zygotic genome activation (ZGA), and this formation is closely linked to histone acetylation, but not transcription elongation or DNA replication. Importantly, we found that NDR establishment on the binding motifs of specific TFs might be associated with their potential pioneer functions in ZGA. Further investigations suggested that the predicted factors MLX and RFX1 played important roles in regulating minor and major ZGA, respectively. Our data not only elucidate the nucleosome positioning dynamics in both male and female pronuclei following fertilization, but also provide an efficient method for identifying key transcription regulators during development.
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8
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Sandovici I, Georgopoulou A, Pérez-García V, Hufnagel A, López-Tello J, Lam BYH, Schiefer SN, Gaudreau C, Santos F, Hoelle K, Yeo GSH, Burling K, Reiterer M, Fowden AL, Burton GJ, Branco CM, Sferruzzi-Perri AN, Constância M. The imprinted Igf2-Igf2r axis is critical for matching placental microvasculature expansion to fetal growth. Dev Cell 2022; 57:63-79.e8. [PMID: 34963058 PMCID: PMC8751640 DOI: 10.1016/j.devcel.2021.12.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 09/30/2021] [Accepted: 12/03/2021] [Indexed: 11/21/2022]
Abstract
In all eutherian mammals, growth of the fetus is dependent upon a functional placenta, but whether and how the latter adapts to putative fetal signals is currently unknown. Here, we demonstrate, through fetal, endothelial, hematopoietic, and trophoblast-specific genetic manipulations in the mouse, that endothelial and fetus-derived IGF2 is required for the continuous expansion of the feto-placental microvasculature in late pregnancy. The angiocrine effects of IGF2 on placental microvasculature expansion are mediated, in part, through IGF2R and angiopoietin-Tie2/TEK signaling. Additionally, IGF2 exerts IGF2R-ERK1/2-dependent pro-proliferative and angiogenic effects on primary feto-placental endothelial cells ex vivo. Endothelial and fetus-derived IGF2 also plays an important role in trophoblast morphogenesis, acting through Gcm1 and Synb. Thus, our study reveals a direct role for the imprinted Igf2-Igf2r axis on matching placental development to fetal growth and establishes the principle that hormone-like signals from the fetus play important roles in controlling placental microvasculature and trophoblast morphogenesis.
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Affiliation(s)
- Ionel Sandovici
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0SW, UK; Wellcome-MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge CB2 0QQ, UK; Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
| | - Aikaterini Georgopoulou
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0SW, UK; Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Vicente Pérez-García
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera, 46012 Valencia, Spain
| | - Antonia Hufnagel
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0SW, UK
| | - Jorge López-Tello
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Brian Y H Lam
- Wellcome-MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Samira N Schiefer
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0SW, UK
| | - Chelsea Gaudreau
- Wellcome-MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Fátima Santos
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Katharina Hoelle
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0SW, UK
| | - Giles S H Yeo
- Wellcome-MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Keith Burling
- Wellcome-MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Moritz Reiterer
- Physiological Laboratory, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Center for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Abigail L Fowden
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Graham J Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Cristina M Branco
- Physiological Laboratory, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Center for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Amanda N Sferruzzi-Perri
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Miguel Constância
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0SW, UK; Wellcome-MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge CB2 0QQ, UK; Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
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9
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Jedynak P, Tost J, Calafat AM, Bourova-Flin E, Busato F, Forhan A, Heude B, Jakobi M, Rousseaux S, Schwartz J, Slama R, Vaiman D, Philippat C, Lepeule J. Pregnancy exposure to synthetic phenols and placental DNA methylation - An epigenome-wide association study in male infants from the EDEN cohort. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118024. [PMID: 34523531 PMCID: PMC8590835 DOI: 10.1016/j.envpol.2021.118024] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 05/14/2023]
Abstract
In utero exposure to environmental chemicals, such as synthetic phenols, may alter DNA methylation in different tissues, including placenta - a critical organ for fetal development. We studied associations between prenatal urinary biomarker concentrations of synthetic phenols and placental DNA methylation. Our study involved 202 mother-son pairs from the French EDEN cohort. Nine phenols were measured in spot urine samples collected between 22 and 29 gestational weeks. We performed DNA methylation analysis of the fetal side of placental tissues using the IlluminaHM450 BeadChips. We evaluated methylation changes of individual CpGs in an adjusted epigenome-wide association study (EWAS) and identified differentially methylated regions (DMRs). We performed mediation analysis to test whether placental tissue heterogeneity mediated the association between urinary phenol concentrations and DNA methylation. We identified 46 significant DMRs (≥5 CpGs) associated with triclosan (37 DMRs), 2,4-dichlorophenol (3), benzophenone-3 (3), methyl- (2) and propylparaben (1). All but 2 DMRs were positively associated with phenol concentrations. Out of the 46 identified DMRs, 7 (6 for triclosan) encompassed imprinted genes (APC, FOXG1, GNAS, GNASAS, MIR886, PEG10, SGCE), which represented a significant enrichment. Other identified DMRs encompassed genes encoding proteins responsible for cell signaling, transmembrane transport, cell adhesion, inflammatory, apoptotic and immunological response, genes encoding transcription factors, histones, tumor suppressors, genes involved in tumorigenesis and several cancer risk biomarkers. Mediation analysis suggested that placental cell heterogeneity may partly explain these associations. This is the first study describing the genome-wide modifications of placental DNA methylation associated with pregnancy exposure to synthetic phenols or their precursors. Our results suggest that cell heterogeneity might mediate the effects of triclosan exposure on placental DNA methylation. Additionally, the enrichment of imprinted genes within the DMRs suggests mechanisms by which certain exposures, mainly to triclosan, could affect fetal development.
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Affiliation(s)
- Paulina Jedynak
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France.
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Antonia M Calafat
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ekaterina Bourova-Flin
- University Grenoble Alpes, Inserm, CNRS, EpiMed Group, Institute for Advanced Biosciences, Grenoble, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Anne Forhan
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004, Paris, France
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004, Paris, France
| | - Milan Jakobi
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Sophie Rousseaux
- University Grenoble Alpes, Inserm, CNRS, EpiMed Group, Institute for Advanced Biosciences, Grenoble, France
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rémy Slama
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Daniel Vaiman
- Genomics, Epigenetics and Physiopathology of Reproduction, Institut Cochin, U1016 Inserm - UMR 8104 CNRS - Paris-Descartes University, Paris, France
| | - Claire Philippat
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Johanna Lepeule
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
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10
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Chenarani N, Emamjomeh A, Allahverdi A, Mirmostafa S, Afsharinia MH, Zahiri J. Bioinformatic tools for DNA methylation and histone modification: A survey. Genomics 2021; 113:1098-1113. [PMID: 33677056 DOI: 10.1016/j.ygeno.2021.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/10/2020] [Accepted: 03/02/2021] [Indexed: 01/19/2023]
Abstract
Epigenetic inheritance occurs due to different mechanisms such as chromatin and histone modifications, DNA methylation and processes mediated by non-coding RNAs. It leads to changes in gene expressions and the emergence of new traits in different organisms in many diseases such as cancer. Recent advances in experimental methods led to the identification of epigenetic target sites in various organisms. Computational approaches have enabled us to analyze mass data produced by these methods. Next-generation sequencing (NGS) methods have been broadly used to identify these target sites and their patterns. By using these patterns, the emergence of diseases could be prognosticated. In this study, target site prediction tools for two major epigenetic mechanisms comprising histone modification and DNA methylation are reviewed. Publicly accessible databases are reviewed as well. Some suggestions regarding the state-of-the-art methods and databases have been made, including examining patterns of epigenetic changes that are important in epigenotypes detection.
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Affiliation(s)
- Nasibeh Chenarani
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Abbasali Emamjomeh
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran; Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Bioinformatics, Faculty of Basic Sciences, University of Zabol, Zabol, Iran.
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - SeyedAli Mirmostafa
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Hossein Afsharinia
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran; Department of Neuroscience, University of California, San Diego, USA.
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11
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Rousseaux S, Seyve E, Chuffart F, Bourova-Flin E, Benmerad M, Charles MA, Forhan A, Heude B, Siroux V, Slama R, Tost J, Vaiman D, Khochbin S, Lepeule J. Immediate and durable effects of maternal tobacco consumption alter placental DNA methylation in enhancer and imprinted gene-containing regions. BMC Med 2020; 18:306. [PMID: 33023569 PMCID: PMC7542140 DOI: 10.1186/s12916-020-01736-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/06/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Although exposure to cigarette smoking during pregnancy has been associated with alterations of DNA methylation in the cord blood or placental cells, whether such exposure before pregnancy could induce epigenetic alterations in the placenta of former smokers has never been investigated. METHODS Our approach combined the analysis of placenta epigenomic (ENCODE) data with newly generated DNA methylation data obtained from 568 pregnant women, the largest cohort to date, either actively smoking during their pregnancy or formerly exposed to tobacco smoking. RESULTS This strategy resulted in several major findings. First, among the 203 differentially methylated regions (DMRs) identified by the epigenome-wide association study, 152 showed "reversible" alterations of DNA methylation, only present in the placenta of current smokers, whereas 26 were also found altered in former smokers, whose placenta had not been exposed directly to cigarette smoking. Although the absolute methylation changes were smaller than those observed in other contexts, such as in some congenital diseases, the observed alterations were consistent within each DMR. This observation was further supported by a demethylation of LINE-1 sequences in the placentas of both current (beta-coefficient (β) (95% confidence interval (CI)), - 0.004 (- 0.008; 0.001)) and former smokers (β (95% CI), - 0.006 (- 0.011; - 0.001)) compared to nonsmokers. Second, the 203 DMRs were enriched in epigenetic marks corresponding to enhancer regions, including monomethylation of lysine 4 and acetylation of lysine 27 of histone H3 (respectively H3K4me1 and H3K27ac). Third, smoking-associated DMRs were also found near and/or overlapping 10 imprinted genes containing regions (corresponding to 16 genes), notably including the NNAT, SGCE/PEG10, and H19/MIR675 loci. CONCLUSIONS Our results pointing towards genomic regions containing the imprinted genes as well as enhancers as preferential targets suggest mechanisms by which tobacco could directly impact the fetus and future child. The persistence of significant DNA methylation changes in the placenta of former smokers supports the hypothesis of an "epigenetic memory" of exposure to cigarette smoking before pregnancy. This observation not only is conceptually revolutionary, but these results also bring crucial information in terms of public health concerning potential long-term detrimental effects of smoking in women.
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Affiliation(s)
- Sophie Rousseaux
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | - Emie Seyve
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | - Florent Chuffart
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | | | - Meriem Benmerad
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | - Marie-Aline Charles
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | - Anne Forhan
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | - Valérie Siroux
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | - Remy Slama
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, Evry, France
| | - Daniel Vaiman
- Genomics, Epigenetics and Physiopathology of Reproduction, Institut Cochin, U1016 Inserm - UMR 8104 CNRS - Paris-Descartes University, Paris, France
| | - Saadi Khochbin
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | - Johanna Lepeule
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France.
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12
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Hitchcock TJ, Paracchini S, Gardner A. Genomic Imprinting As a Window into Human Language Evolution. Bioessays 2020; 41:e1800212. [PMID: 31132171 DOI: 10.1002/bies.201800212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/22/2019] [Indexed: 01/20/2023]
Abstract
Humans spend large portions of their time and energy talking to one another, yet it remains unclear whether this activity is primarily selfish or altruistic. Here, it is shown how parent-of-origin specific gene expression-or "genomic imprinting"-may provide an answer to this question. First, it is shown why, regarding language, only altruistic or selfish scenarios are expected. Second, it is pointed out that an individual's maternal-origin and paternal-origin genes may have different evolutionary interests regarding investment into language, and that this intragenomic conflict may drive genomic imprinting which-as the direction of imprint depends upon whether investment into language is relatively selfish or altruistic-may be used to discriminate between these two possibilities. Third, predictions concerning the impact of various mutations and epimutations at imprinted loci on language pathologies are derived. In doing so, a framework is developed that highlights avenues for using intragenomic conflicts to investigate the evolutionary drivers of language.
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Affiliation(s)
- Thomas J Hitchcock
- School of Biology, University of St Andrews, Dyers Brae, St Andrews, KY16 9TH, UK
| | - Silvia Paracchini
- School of Medicine, University of St Andrews, North Haugh, St Andrews, KY16 9TF, UK
| | - Andy Gardner
- School of Biology, University of St Andrews, Dyers Brae, St Andrews, KY16 9TH, UK
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13
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Xu Y, Wu T, Li F, Dong Q, Wang J, Shang D, Xu Y, Zhang C, Dou Y, Hu C, Yang H, Zheng X, Zhang Y, Wang L, Li X. Identification and comprehensive characterization of lncRNAs with copy number variations and their driving transcriptional perturbed subpathways reveal functional significance for cancer. Brief Bioinform 2019; 21:2153-2166. [PMID: 31792500 DOI: 10.1093/bib/bbz113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/17/2022] Open
Abstract
Numerous studies have shown that copy number variation (CNV) in lncRNA regions play critical roles in the initiation and progression of cancer. However, our knowledge about their functionalities is still limited. Here, we firstly provided a computational method to identify lncRNAs with copy number variation (lncRNAs-CNV) and their driving transcriptional perturbed subpathways by integrating multidimensional omics data of cancer. The high reliability and accuracy of our method have been demonstrated. Then, the method was applied to 14 cancer types, and a comprehensive characterization and analysis was performed. LncRNAs-CNV had high specificity in cancers, and those with high CNV level may perturb broad biological functions. Some core subpathways and cancer hallmarks widely perturbed by lncRNAs-CNV were revealed. Moreover, subpathways highlighted the functional diversity of lncRNAs-CNV in various cancers. Survival analysis indicated that functional lncRNAs-CNV could be candidate prognostic biomarkers for clinical applications, such as ST7-AS1, CDKN2B-AS1 and EGFR-AS1. In addition, cascade responses and a functional crosstalk model among lncRNAs-CNV, impacted genes, driving subpathways and cancer hallmarks were proposed for understanding the driving mechanism of lncRNAs-CNV. Finally, we developed a user-friendly web interface-LncCASE (http://bio-bigdata.hrbmu.edu.cn/LncCASE/) for exploring lncRNAs-CNV and their driving subpathways in various cancer types. Our study identified and systematically characterized lncRNAs-CNV and their driving subpathways and presented valuable resources for investigating the functionalities of non-coding variations and the mechanisms of tumorigenesis.
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Affiliation(s)
- Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tan Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Qun Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jingwen Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Desi Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yingqi Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yiying Dou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Congxue Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Haixiu Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xuan Zheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital, Harbin Medical University, Harbin 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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14
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da Silva Francisco Junior R, Dos Santos Ferreira C, Santos E Silva JC, Terra Machado D, Côrtes Martins Y, Ramos V, Simões Carnivali G, Garcia AB, Medina-Acosta E. Pervasive Inter-Individual Variation in Allele-Specific Expression in Monozygotic Twins. Front Genet 2019; 10:1178. [PMID: 31850058 PMCID: PMC6887657 DOI: 10.3389/fgene.2019.01178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/24/2019] [Indexed: 01/19/2023] Open
Abstract
Despite being developed from one zygote, heterokaryotypic monozygotic (MZ) co-twins exhibit discordant karyotypes. Epigenomic studies in biological samples from heterokaryotypic MZ co-twins are of the most significant value for assessing the effects on gene- and allele-specific expression of an extranumerary chromosomal copy or structural chromosomal disparities in otherwise nearly identical germline genetic contributions. Here, we use RNA-Seq data from existing repositories to establish within-pair correlations for the breadth and magnitude of allele-specific expression (ASE) in heterokaryotypic MZ co-twins discordant for trisomy 21 and maternal 21q inheritance, as well as homokaryotypic co-twins. We show that there is a genome-wide disparity at ASE sites between the heterokaryotypic MZ co-twins. Although most of the disparity corresponds to changes in the magnitude of biallelic imbalance, ASE sites switching from either strictly monoallelic to biallelic imbalance or the reverse occur in few genes that are known or predicted to be imprinted, subject to X-chromosome inactivation or A-to-I(G) RNA edited. We also uncovered comparable ASE differences between homokaryotypic MZ twins. The extent of ASE discordance in MZ twins (2.7%) was about 10-fold lower than the expected between pairs of unrelated, non-twin males or females. The results indicate that the observed within-pair dissimilarities in breadth and magnitude of ASE sites in the heterokaryotypic MZ co-twins could not solely be attributable to the aneuploidy and the missing allelic heritability at 21q.
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Affiliation(s)
| | - Cristina Dos Santos Ferreira
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Juan Carlo Santos E Silva
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Douglas Terra Machado
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Yasmmin Côrtes Martins
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Victor Ramos
- Department of Genetics, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Gustavo Simões Carnivali
- Department of Computational Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Beatriz Garcia
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Enrique Medina-Acosta
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
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15
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Zhu J, Su M, Gu Y, Zhang X, Lv W, Zhang S, Sun Z, Lu H, Zhang Y. Development of a method for identifying and functionally analyzing allele-specific DNA methylation based on BS-seq data. Epigenomics 2019; 11:1679-1692. [PMID: 31701777 DOI: 10.2217/epi-2019-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To comprehensively identify allele-specific DNA methylation (ASM) at the genome-wide level. Methods: Here, we propose a new method, called GeneASM, to identify ASM using high-throughput bisulfite sequencing data in the absence of haplotype information. Results: A total of 2194 allele-specific DNA methylated genes were identified in the GM12878 lymphocyte lineage using GeneASM. These genes are mainly enriched in cell cytoplasm function, subcellular component movement or cellular linkages. GM12878 methylated DNA immunoprecipitation sequencing, and methylation sensitive restriction enzyme sequencing data were used to evaluate ASM. The relationship between ASM and disease was further analyzed using the The Cancer Genome Atlas (TCGA) data of lung adenocarcinoma (LUAD), and whole genome bisulfite sequencing data. Conclusion: GeneASM, which recognizes ASM by high-throughput bisulfite sequencing and heterozygous single-nucleotide polymorphisms, provides new perspective for studying genomic imprinting.
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Affiliation(s)
- Jiang Zhu
- School of Life Science & Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, PR China
| | - Mu Su
- Medical Laboratory Technology College, Daqing Branch of Harbin Medical University, Daqing, Heilongjiang, 163319, PR China
| | - Yue Gu
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 51000, PR China
| | - Xingda Zhang
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, PR China
| | - Wenhua Lv
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 51000, PR China
| | - Shumei Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 51000, PR China
| | - Zhongyi Sun
- Medical Laboratory Technology College, Daqing Branch of Harbin Medical University, Daqing, Heilongjiang, 163319, PR China
| | - Haibo Lu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150081, PR China
| | - Yan Zhang
- Medical Laboratory Technology College, Daqing Branch of Harbin Medical University, Daqing, Heilongjiang, 163319, PR China.,Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, 150040, PR China
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16
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Karami K, Zerehdaran S, Javadmanesh A, Shariati MM, Fallahi H. Characterization of bovine (Bos taurus) imprinted genes from genomic to amino acid attributes by data mining approaches. PLoS One 2019; 14:e0217813. [PMID: 31170205 PMCID: PMC6553745 DOI: 10.1371/journal.pone.0217813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 05/21/2019] [Indexed: 01/05/2023] Open
Abstract
Genomic imprinting results in monoallelic expression of genes in mammals and flowering plants. Understanding the function of imprinted genes improves our knowledge of the regulatory processes in the genome. In this study, we have employed classification and clustering algorithms with attribute weighting to specify the unique attributes of both imprinted (monoallelic) and biallelic expressed genes. We have obtained characteristics of 22 known monoallelically expressed (imprinted) and 8 biallelic expressed genes that have been experimentally validated alongside 208 randomly selected genes in bovine (Bos taurus). Attribute weighting methods and various supervised and unsupervised algorithms in machine learning were applied. Unique characteristics were discovered and used to distinguish mono and biallelic expressed genes from each other in bovine. To obtain the accuracy of classification, 10-fold cross-validation with concerning each combination of attribute weighting (feature selection) and machine learning algorithms, was used. Our approach was able to accurately predict mono and biallelic genes using the genomics and proteomics attributes.
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Affiliation(s)
- Keyvan Karami
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Saeed Zerehdaran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
- * E-mail:
| | - Ali Javadmanesh
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Mahdi Shariati
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
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17
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Hu B, Zheng L, Long C, Song M, Li T, Yang L, Zuo Y. EmExplorer: a database for exploring time activation of gene expression in mammalian embryos. Open Biol 2019; 9:190054. [PMID: 31164042 PMCID: PMC6597754 DOI: 10.1098/rsob.190054] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Understanding early development offers a striking opportunity to investigate genetic disease, stem cell and assisted reproductive technology. Recent advances in high-throughput sequencing technology have led to the rising influx of omics data, which have rapidly boosted our understanding of mammalian developmental mechanisms. Here, we review the database EmExplorer (a database for exploring time activation of gene expression in mammalian embryos), which systematically organizes the genes from development-related pathways, and which we have already established and continue to update it. The current version of EmExplorer incorporates over 26 000 genes obtained from 306 functional pathways in five species. The function annotations of development-related genes were also integrated into EmExplorer. To facilitate data extraction, the database also contains the following information. (i) The dynamic expression values for each development stage are matched to the corresponding genes. (ii) A two-layer search tool which supports multi-option searching, such as by official symbol, pathway name and function annotation. The returned entries can directly link to the analysis results for the corresponding gene or pathway in the analysis module. (iii) The analysis module provides different gene comparisons at the multi-species level and functional pathway level, which shows the species specificity and stage specificity at the gene or pathway level. (iv) The analysis based on the hypergeometric distribution test reveals the enrichment of gene functions at a particular stage of one organism's pathway. (v) The browser is designed for users with ambiguous searching goals and greatly helps new users to get a general idea of the contents of the database. (vi) The experimentally validated pathways are manually curated and shown on the home page. EmExplorer will be helpful for elucidating early developmental mechanisms and exploring time activation genes. EmExplorer is freely available at http://bioinfor.imu.edu.cn/emexplorer.
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Affiliation(s)
- Bosu Hu
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
| | - Lei Zheng
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
| | - Chunshen Long
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
| | - Mingmin Song
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
| | - Tao Li
- 2 College of Life Sciences, Inner Mongolia Agricultural University , Hohhot 010018 , People's Republic of China
| | - Lei Yang
- 3 College of Bioinformatics Science and Technology, Harbin Medical University , Harbin 150081 , People's Republic of China
| | - Yongchun Zuo
- 1 State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University , Hohhot 010070 , People's Republic of China
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18
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Karami K, Zerehdaran S, Javadmanesh A, Shariati MM. Assessment of maternal and parent of origin effects in genetic variation of economic traits in Iranian native fowl. Br Poult Sci 2019; 60:486-492. [PMID: 31132866 DOI: 10.1080/00071668.2019.1621987] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
1. The objective of the study was to investigate the influence of maternal and parent of origin effects (POE) on genetic variation of Iranian native fowl on economic traits. 2. Studied traits were body weights at birth (BW0), at eight (BW8) and 12 weeks of age (BW12), age (ASM) and weight at sexual maturity (WSM), egg number (EN) and average egg weight (AEW). 3. Several models, including additive, maternal additive genetics, permanent environmental effects and POE were compared using Wombat software. Bayesian Information Criterion (BIC) was used to identify the best model for each trait. The chance of reranking of birds between models was investigated using Spearman correlation and Wilcoxon rank test. 4. Based on the best model, direct heritability estimates for BW0, BW8, BW12, ASM, WSM, EN and AEW traits were 0.05, 0.21, 0.23, 0.30, 0.39, 0.22 and 0.38, respectively. Proportion of variance due to paternal POE for BW8 was 4% and proportion of variance due to maternal POE for BW12 was 5%. 5. Estimated maternal heritability for BW0 was 0.30 and for BW8 and BW12 were 0.00 and 0.01, respectively, which shows that maternal heritability was reduced by age. 6. Based on the results, considering POE for BW8 and BW12 and maternal genetic effects for BW0 improved the accuracy of estimations and avoid reranking of birds for these traits.
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Affiliation(s)
- K Karami
- Department of Animal Science, Ferdowsi University of Mashhad , Mashhad , Iran
| | - S Zerehdaran
- Department of Animal Science, Ferdowsi University of Mashhad , Mashhad , Iran
| | - A Javadmanesh
- Department of Animal Science, Ferdowsi University of Mashhad , Mashhad , Iran
| | - M M Shariati
- Department of Animal Science, Ferdowsi University of Mashhad , Mashhad , Iran
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19
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Tissue-Specific Monoallelic Expression of Bovine AXL is Associated with DNA Methylation of Promoter DMR. Biochem Genet 2019; 57:801-812. [PMID: 31073794 DOI: 10.1007/s10528-019-09925-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 05/02/2019] [Indexed: 12/31/2022]
Abstract
The AXL protein is a receptor tyrosine kinase and is often implicated in proliferation, migration and therapy resistance in various cancers. The AXL gene in humans is maternally expressed and paternally imprinted with differentially methylated regions (DMR) surrounding the promoter region. However, the imprinting status and epigenetic regulation of AXL gene in cattle remain unclear. Therefore, we explored the molecular structure along with the patterns of allelic expression and DNA methylation of the bovine AXL gene. First, the complete cDNA sequence of bovine AXL was gathered by Sanger method, from transcripts obtained from RT-PCR, 5' and 3' -RACE. In silico BLAST alignments showed that the longest mRNA sequence of bovine AXL consists of 19 exons and encodes a protein of 887 amino acids. We further analyzed the allelic expression of bovine AXL by employing single-nucleotide polymorphism (SNP)-based sequencing method. A SNP site (GenBank Accession no: rs210020651) found in exon 7 allowed us to distinguish the two parental alleles. Monoallelic expression of AXL was observed in four adult bovine tissues (heart, liver, spleen and fat), while biallelic expression was found in the other adult tissues such as the lung, kidney, muscle, brain and placenta. To determine whether the DNA methylation played a role in the tissue-specific imprinting of bovine AXL, we performed bisulfite sequencing of two regions: region 1 was a CpG island (CGI) in AXL promoter, mapping to 643 bp upstream of the transcription start site of AXL 5'-v1 transcripts, while region two was homologous to the region of human AXL DMR, with 10 CpG sites overlapping the first translation start site (TSS1) of bovine AXL. In region 2, DNA from both monoallelic and biallelic expressed tissues were mostly found to be completely unmethylated. However, tissue-specific differential methylation patterns were found in monoallelic expressed tissues such as the heart and liver while hypomethylation was noted in the promoter CpG island in biallelic expressed tissues such as the lung. These observations demonstrated that the tissue-specific monoallelic expression of bovine AXL is dependent on the DNA methylation of its promoter region.
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20
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Duan J(E, Zhang M, Flock K, Seesi SA, Mandoiu I, Jones A, Johnson E, Pillai S, Hoffman M, McFadden K, Jiang H, Reed S, Govoni K, Zinn S, Jiang Z, Tian X(C. Effects of maternal nutrition on the expression of genomic imprinted genes in ovine fetuses. Epigenetics 2018; 13:793-807. [PMID: 30051747 PMCID: PMC6224220 DOI: 10.1080/15592294.2018.1503489] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/04/2018] [Accepted: 07/15/2018] [Indexed: 12/27/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon of differential allelic expression based on parental origin. To date, 263 imprinted genes have been identified among all investigated mammalian species. However, only 21 have been described in sheep, of which 11 are annotated in the current ovine genome. Here, we aim to i) use DNA/RNA high throughput sequencing to identify new monoallelically expressed and imprinted genes in day 135 ovine fetuses and ii) determine whether maternal diet (100%, 60%, or 140% of National Research Council Total Digestible Nutrients) influences expression of imprinted genes. We also reported strategies to solve technical challenges in the data analysis pipeline. We identified 80 monoallelically expressed, 13 new putative imprinted genes, and five known imprinted genes in sheep using the 263 genes stated above as a guide. Sanger sequencing confirmed allelic expression of seven genes, CASD1, COPG2, DIRAS3, INPP5F, PLAGL1, PPP1R9A, and SLC22A18. Among the 13 putative imprinted genes, five were localized in the known sheep imprinting domains of MEST on chromosome 4, DLK1/GTL2 on chromosome 18 and KCNQ1 on chromosome 21, and three were in a novel sheep imprinted cluster on chromosome 4, known in other species as PEG10/SGCE. The expression of DIRAS3, IGF2, PHLDA2, and SLC22A18 was altered by maternal diet, albeit without allelic expression reversal. Together, our results expanded the list of sheep imprinted genes to 34 and demonstrated that while the expression levels of four imprinted genes were changed by maternal diet, the allelic expression patterns were un-changed for all imprinted genes studied.
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Affiliation(s)
| | - Mingyuan Zhang
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Kaleigh Flock
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Sahar Al Seesi
- Department of Computer Science, University of Connecticut, Storrs, CT, USA
| | - Ion Mandoiu
- Department of Computer Science, University of Connecticut, Storrs, CT, USA
| | - Amanda Jones
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Elizabeth Johnson
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Sambhu Pillai
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Maria Hoffman
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Katelyn McFadden
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Hesheng Jiang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Sarah Reed
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Kristen Govoni
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Steve Zinn
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Zongliang Jiang
- School of Animal Science, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
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21
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Castillo J, Jodar M, Oliva R. The contribution of human sperm proteins to the development and epigenome of the preimplantation embryo. Hum Reprod Update 2018; 24:535-555. [DOI: 10.1093/humupd/dmy017] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/25/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Judit Castillo
- Molecular Biology of Reproduction and Development Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Faculty of Medicine, University of Barcelona, Casanova, Barcelona, Spain
| | - Meritxell Jodar
- Molecular Biology of Reproduction and Development Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Faculty of Medicine, University of Barcelona, Casanova, Barcelona, Spain
| | - Rafael Oliva
- Molecular Biology of Reproduction and Development Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Faculty of Medicine, University of Barcelona, Casanova, Barcelona, Spain
- Biochemistry and Molecular Genetics Service, Hospital Clínic, Villarroel, Barcelona, Spain
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22
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Xu D, Zhang C, Li J, Wang G, Chen W, Li D, Li S. Polymorphic Imprinting of SLC38A4 Gene in Bovine Placenta. Biochem Genet 2018; 56:639-649. [PMID: 29785670 DOI: 10.1007/s10528-018-9866-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/18/2018] [Indexed: 01/20/2023]
Abstract
Imprinted genes are characterized by monoallelic expression that is dependent on parental origin. Comparative analysis of imprinted genes between species is a powerful tool for understanding the biological significance of genomic imprinting. The slc38a4 gene encodes a neutral amino acid transporter and is identified as imprinted in mice. In this study, the imprinting status of SLC38A4 was assessed in bovine adult tissues and placenta using a polymorphism-based approach. Results indicate that SLC38A4 is not imprinted in eight adult bovine tissues including heart, liver, spleen, lung, kidney, muscle, fat, and brain. It was interesting to note that SLC38A4 showed polymorphic status in five heterogeneous placentas, with three exhibiting paternal monoallelic expression and two exhibiting biallelic expression. Monoallelic expression of imprinted genes is generally associated with allele-specific differentially methylation regions (DMRs) of CpG islands (CGIs)-encompassed promoter; therefore, the DNA methylation statuses of three CGIs in the SLC38A4 promoter and exon 1 region were tested in three placentas (two exhibiting paternal monoallelic and one showing biallelic expression of SLC38A4) and their corresponding paternal sperms. Unexpectedly, extreme hypomethylation (< 3%) of the DNA was observed in all the three detected placentas and their corresponding paternal sperms. The absence of DMR in bovine SLC38A4 promoter region implied that DNA methylation of these three CGIs does not directly or indirectly affect the polymorphic imprinting of SLC38A4 in bovine placenta. This suggested other epigenetic features other than DNA methylation are needed in regulating the imprinting of bovine SLC38A4, which is different from that of mouse with respect to a DMR existence at the mouse's slc38a4 promoter region. Although further work is needed, this first characterization of polymorphic imprinting status of SLC38A4 in cattle placenta provides valuable information on investigating the genomic imprinting phenomenon itself.
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Affiliation(s)
- Da Xu
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - Cui Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - Junliang Li
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - Guannan Wang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - Weina Chen
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China.,College of Chinese Medicine, Hebei University, Baoding, 071000, China
| | - Dongjie Li
- College of Life Science and Life Engineering, Hebei Science and Technology University, Shijiazhuang, 050018, China
| | - Shijie Li
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China.
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23
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Kotler J, Haig D. The tempo of human childhood: a maternal foot on the accelerator, a paternal foot on the brake. Evol Anthropol 2018; 27:80-91. [PMID: 29575348 PMCID: PMC5947556 DOI: 10.1002/evan.21579] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/08/2018] [Accepted: 01/18/2018] [Indexed: 12/21/2022]
Abstract
Relative to the life history of other great apes, that of humans is characterized by early weaning and short interbirth intervals (IBIs). We propose that in modern humans, birth until adrenarche, or the rise in adrenal androgens, developmentally corresponds to the period from birth until weaning in great apes and ancestral hominins. According to this hypothesis, humans achieved short IBIs by subdividing ancestral infancy into a nurseling phase, during which offspring fed at the breast, and a weanling phase, during which offspring fed specially prepared foods. Imprinted genes influence the timing of human weaning and adrenarche, with paternally expressed genes promoting delays in childhood maturation and maternally expressed genes promoting accelerated maturation. These observations suggest that the tempo of human development has been shaped by consequences for the fitness of kin, with faster development increasing maternal fitness at a cost to child fitness. The effects of imprinted genes suggest that the duration of the juvenile period (adrenarche until puberty) has also been shaped by evolutionary conflicts within the family.
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Affiliation(s)
| | - David Haig
- Harvard University, Department of Organismic & Evolutionary Biology
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24
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de Sá Machado Araújo G, da Silva Francisco Junior R, Dos Santos Ferreira C, Mozer Rodrigues PT, Terra Machado D, Louvain de Souza T, Teixeira de Souza J, Figueiredo Osorio da Silva C, Alves da Silva AF, Andrade CCF, da Silva AT, Ramos V, Garcia AB, Machado FB, Medina-Acosta E. Maternal 5 mCpG Imprints at the PARD6G-AS1 and GCSAML Differentially Methylated Regions Are Decoupled From Parent-of-Origin Expression Effects in Multiple Human Tissues. Front Genet 2018; 9:36. [PMID: 29545821 PMCID: PMC5838017 DOI: 10.3389/fgene.2018.00036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/29/2018] [Indexed: 11/13/2022] Open
Abstract
A hallmark of imprinted genes in mammals is the occurrence of parent-of-origin-dependent asymmetry of DNA cytosine methylation (5mC) of alleles at CpG islands (CGIs) in their promoter regions. This 5mCpG asymmetry between the parental alleles creates allele-specific imprinted differentially methylated regions (iDMRs). iDMRs are often coupled to the transcriptional repression of the methylated allele and the activation of the unmethylated allele in a tissue-specific, developmental-stage-specific and/or isoform-specific fashion. iDMRs function as regulatory platforms, built through the recruitment of chemical modifications to histones to achieve differential, parent-of-origin-dependent chromatin segmentation states. Here, we used a comparative computational data mining approach to identify 125 novel constitutive candidate iDMRs that integrate the maximal number of allele-specific methylation region records overlapping CGIs in human methylomes. Twenty-nine candidate iDMRs display gametic 5mCpG asymmetry, and another 96 are candidate secondary iDMRs. We established the maternal origin of the 5mCpG imprints of one gametic (PARD6G-AS1) and one secondary (GCSAML) iDMRs. We also found a constitutively hemimethylated, nonimprinted domain at the PWWP2AP1 promoter CGI with oocyte-derived methylation asymmetry. Given that the 5mCpG level at the iDMRs is not a sufficient criterion to predict active or silent locus states and that iDMRs can regulate genes from a distance of more than 1 Mb, we used RNA-Seq experiments from the Genotype-Tissue Expression project and public archives to assess the transcriptional expression profiles of SNPs across 4.6 Mb spans around the novel maternal iDMRs. We showed that PARD6G-AS1 and GCSAML are expressed biallelically in multiple tissues. We found evidence of tissue-specific monoallelic expression of ZNF124 and OR2L13, located 363 kb upstream and 419 kb downstream, respectively, of the GCSAML iDMR. We hypothesize that the GCSAML iDMR regulates the tissue-specific, monoallelic expression of ZNF124 but not of OR2L13. We annotated the non-coding epigenomic marks in the two maternal iDMRs using data from the Roadmap Epigenomics project and showed that the PARD6G-AS1 and GCSAML iDMRs achieve contrasting activation and repression chromatin segmentations. Lastly, we found that the maternal 5mCpG imprints are perturbed in several hematopoietic cancers. We conclude that the maternal 5mCpG imprints at PARD6G-AS1 and GCSAML iDMRs are decoupled from parent-of-origin transcriptional expression effects in multiple tissues.
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Affiliation(s)
- Graziela de Sá Machado Araújo
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Ronaldo da Silva Francisco Junior
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Cristina Dos Santos Ferreira
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Pedro Thyago Mozer Rodrigues
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Douglas Terra Machado
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thais Louvain de Souza
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Faculdade de Medicina de Campos, Campos dos Goytacazes, Brazil
| | - Jozimara Teixeira de Souza
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Cleiton Figueiredo Osorio da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Antônio Francisco Alves da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Claudia Caixeta Franco Andrade
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Faculdade Metropolitana São Carlos, Bom Jesus do Itabapoana, Brazil
| | - Alan Tardin da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Victor Ramos
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Ana Beatriz Garcia
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Filipe Brum Machado
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Enrique Medina-Acosta
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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25
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De Donato M, Hussain T, Rodulfo H, Peters SO, Imumorin IG, Thomas BN. Conservation of Repeats at the Mammalian KCNQ1OT1-CDKN1C Region Suggests a Role in Genomic Imprinting. Evol Bioinform Online 2017; 13:1176934317715238. [PMID: 28659711 PMCID: PMC5476424 DOI: 10.1177/1176934317715238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/23/2017] [Indexed: 12/19/2022] Open
Abstract
KCNQ1OT1 is located in the region with the highest number of genes showing genomic imprinting, but the mechanisms controlling the genes under its influence have not been fully elucidated. Therefore, we conducted a comparative analysis of the KCNQ1/KCNQ1OT1-CDKN1C region to study its conservation across the best assembled eutherian mammalian genomes sequenced to date and analyzed potential elements that may be implicated in the control of genomic imprinting in this region. The genomic features in these regions from human, mouse, cattle, and dog show a higher number of genes and CpG islands (detected using cpgplot from EMBOSS), but lower number of repetitive elements (including short interspersed nuclear elements and long interspersed nuclear elements), compared with their whole chromosomes (detected by RepeatMasker). The KCNQ1OT1-CDKN1C region contains the highest number of conserved noncoding sequences (CNS) among mammals, where we found 16 regions containing about 38 different highly conserved repetitive elements (using mVista), such as LINE1 elements: L1M4, L1MB7, HAL1, L1M4a, L1Med, and an LTR element: MLT1H. From these elements, we found 74 CNS showing high sequence identity (>70%) between human, cattle, and mouse, from which we identified 13 motifs (using Multiple Em for Motif Elicitation/Motif Alignment and Search Tool) with a significant probability of occurrence, 3 of which were the most frequent and were used to find transcription factor-binding sites. We detected several transcription factors (using JASPAR suite) from the families SOX, FOX, and GATA. A phylogenetic analysis of these CNS from human, marmoset, mouse, rat, cattle, dog, horse, and elephant shows branches with high levels of support and very similar phylogenetic relationships among these groups, confirming previous reports. Our results suggest that functional DNA elements identified by comparative genomics in a region densely populated with imprinted mammalian genes may be related to the regulation of imprinted gene expression.
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Affiliation(s)
- Marcos De Donato
- Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.,Escuela de Bioingenierias, Tecnologico de Monterrey, Campus Querétaro, Santiago de Querétaro, Mexico
| | - Tanveer Hussain
- Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.,Department Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Hectorina Rodulfo
- Escuela de Bioingenierias, Tecnologico de Monterrey, Campus Querétaro, Santiago de Querétaro, Mexico
| | - Sunday O Peters
- Department of Animal Science, Berry College, Mount Berry, GA, USA
| | - Ikhide G Imumorin
- Animal Genetics and Genomics Laboratory, Office of International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.,African Institute for Biosciences Research and Training, Ibadan, Nigeria.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bolaji N Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, USA
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26
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Liu H, Li S, Wang X, Zhu J, Wei Y, Wang Y, Wen Y, Wang L, Huang Y, Zhang B, Shang S, Zhang Y. DNA methylation dynamics: identification and functional annotation. Brief Funct Genomics 2016; 15:470-484. [PMID: 27515490 DOI: 10.1093/bfgp/elw029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is an epigenetic modification of cytosines that undergoes dynamic changes in a temporal, spatial and cell-type-specific manner. Recent advances in technology have permitted the profiling of high-throughput methylomes in large numbers of biological samples. Various computational tools have been developed to identify and analyze DNA methylation dynamics in a variety of critical biological processes. As DNA methylation is becoming increasingly viewed as a dynamic process, the mechanisms governing DNA methylation dynamics and its roles in the transcriptional regulatory network are of great interest. It has been reported that DNA methylation dynamics plays essential roles in multiple biological processes, including development and cancer. As a functional event, the dynamics of DNA methylation have become increasingly relevant to many researchers. Here, we review state-of-the-art advances at three levels (genome-wide identification, regulatory mechanism investigation and the functional annotation) in the field of DNA methylation dynamics, as well as the future perspective of DNA methylation dynamics.
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27
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Liu H, Liu X, Zhang S, Lv J, Li S, Shang S, Jia S, Wei Y, Wang F, Su J, Wu Q, Zhang Y. Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes. Nucleic Acids Res 2015; 44:75-94. [PMID: 26635396 PMCID: PMC4705665 DOI: 10.1093/nar/gkv1332] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 11/17/2015] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is a key epigenetic mark that is critical for gene regulation in multicellular eukaryotes. Although various human cell types may have the same genome, these cells have different methylomes. The systematic identification and characterization of methylation marks across cell types are crucial to understand the complex regulatory network for cell fate determination. In this study, we proposed an entropy-based framework termed SMART to integrate the whole genome bisulfite sequencing methylomes across 42 human tissues/cells and identified 757 887 genome segments. Nearly 75% of the segments showed uniform methylation across all cell types. From the remaining 25% of the segments, we identified cell type-specific hypo/hypermethylation marks that were specifically hypo/hypermethylated in a minority of cell types using a statistical approach and presented an atlas of the human methylation marks. Further analysis revealed that the cell type-specific hypomethylation marks were enriched through H3K27ac and transcription factor binding sites in cell type-specific manner. In particular, we observed that the cell type-specific hypomethylation marks are associated with the cell type-specific super-enhancers that drive the expression of cell identity genes. This framework provides a complementary, functional annotation of the human genome and helps to elucidate the critical features and functions of cell type-specific hypomethylation.
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Affiliation(s)
- Hongbo Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xiaojuan Liu
- Department of Rehabilitation, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Shumei Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jie Lv
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Song Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shanshan Jia
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yanjun Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Fang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jianzhong Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150001, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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Nguyen CM, Liao W. Genomic imprinting in psoriasis and atopic dermatitis: A review. J Dermatol Sci 2015; 80:89-93. [PMID: 26341698 DOI: 10.1016/j.jdermsci.2015.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 08/13/2015] [Accepted: 08/20/2015] [Indexed: 02/02/2023]
Abstract
Genomic imprinting is a genetic process where only one allele of a particular gene is expressed in a parent-of-origin dependent manner. Epigenetic changes in the DNA, such as methylation or acetylation of histones, are primarily thought to be responsible for silencing of the imprinted allele. Recently, global CpG methylation changes have been identified in psoriatic skin in comparison to normal skin, particularly near genes known to be upregulated in psoriasis such as KYNU, OAS2, and SERPINB3. Furthermore, imprinting has been associated with multi-chromosomal human disease, including diabetes and multiple sclerosis. This paper is the first to review the clinical and genetic evidence that exists in the literature for the association between imprinting and general skin disorders, including atopic dermatitis and psoriatic disease. Atopy was found to have evidence of imprinting on chromosomes 6, 11, 14, and 13. The β subunit of the IgE receptor on chromosome 11q12-13 may be imprinted. Psoriatic disease may be related to imprinting effects on chromosome 6 for psoriasis and 16 for psoriatic arthritis.
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Affiliation(s)
- Catherine M Nguyen
- University of California, Irvine School of Medicine, 1001 Health Sciences Rd, Irvine, CA, 92617, United States.
| | - Wilson Liao
- University of California, San Francisco School of Medicine, 2340 Sutter St, Box 0808, San Francisco, CA 94143, United States
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29
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O'Doherty AM, MacHugh DE, Spillane C, Magee DA. Genomic imprinting effects on complex traits in domesticated animal species. Front Genet 2015; 6:156. [PMID: 25964798 PMCID: PMC4408863 DOI: 10.3389/fgene.2015.00156] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 04/06/2015] [Indexed: 11/13/2022] Open
Abstract
Monoallelically expressed genes that exert their phenotypic effect in a parent-of-origin specific manner are considered to be subject to genomic imprinting, the most well understood form of epigenetic regulation of gene expression in mammals. The observed differences in allele specific gene expression for imprinted genes are not attributable to differences in DNA sequence information, but to specific chemical modifications of DNA and chromatin proteins. Since the discovery of genomic imprinting some three decades ago, over 100 imprinted mammalian genes have been identified and considerable advances have been made in uncovering the molecular mechanisms regulating imprinted gene expression. While most genomic imprinting studies have focused on mouse models and human biomedical disorders, recent work has highlighted the contributions of imprinted genes to complex trait variation in domestic livestock species. Consequently, greater understanding of genomic imprinting and its effect on agriculturally important traits is predicted to have major implications for the future of animal breeding and husbandry. In this review, we discuss genomic imprinting in mammals with particular emphasis on domestic livestock species and consider how this information can be used in animal breeding research and genetic improvement programs.
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Affiliation(s)
- Alan M O'Doherty
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Ireland
| | - David E MacHugh
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Ireland ; Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, National University of Ireland Galway, Galway Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield Ireland ; Department of Animal Science, University of Connecticut, Storrs, CT USA
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30
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Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development. Mol Genet Genomics 2014; 290:685-97. [DOI: 10.1007/s00438-014-0952-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 11/10/2014] [Indexed: 12/20/2022]
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31
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Lv J, Huang Z, Liu H, Liu H, Cui W, Li B, He H, Guo J, Liu Q, Zhang Y, Wu Q. Identification and characterization of long intergenic non-coding RNAs related to mouse liver development. Mol Genet Genomics 2014; 289:1225-35. [PMID: 25012394 DOI: 10.1007/s00438-014-0882-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 06/20/2014] [Indexed: 01/23/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been studied extensively over the last few years. Liver is an important organ that plays a crucial role in glucose metabolism and homeostasis; however, there are few reports of the identification and functional characterization of lncRNAs with important roles in liver development. Therefore, it is necessary to systematically identify lncRNAs that are involved in liver development. In this paper, we assembled the transcriptome using published RNA-seq data across three mouse liver developmental stages and identified 4,882 putative long intergenic non-coding RNAs (lincRNAs) expressed in at least one of the investigated stages. Combining these with Ensembl lincRNAs, we established a reference catalog of 6,602 transcribed lincRNAs in the mouse liver. We then analyzed all the lincRNAs in this reference catalog systematically and revealed that liver lincRNAs carry different genomic signatures from protein-coding genes, while the putative lincRNAs are generally comparable with known Ensembl lincRNAs. In addition, putative lincRNAs are functionally associated with essential biological processes, including RNA splicing, protein localization and fatty acid metabolic process, implying that they may play an important role in regulating liver development. The validation of selected lincRNAs that are specifically expressed in developing liver tissues further suggested the effectiveness of our approach. Our study shows that lincRNAs that are differentially expressed during three liver developmental stages could have important regulatory roles in liver development. The identified putative lincRNAs are a valuable resource for further functional studies.
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Affiliation(s)
- Jie Lv
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150001, China
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