#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#
preLekára.sk / Odborné časopisy / PLOS Genetics / 2014 - 12

Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development

English version České info

DNA methylation reprogramming after fertilization is critical for normal mammalian development. Early embryos are sensitive to environmental stresses and a number of reports have pointed out the increased risk of DNA methylation errors associated with assisted reproduction technologies. Therefore, it is very important to understand normal DNA methylation patterns during early human development. Recent reduced representation bisulfite sequencing studies reported partial methylomes of human gametes and early embryos. To provide a more comprehensive view of DNA methylation dynamics during early human development, we report on whole genome bisulfite sequencing of human gametes and blastocysts. We show that the paternal genome is globally demethylated in blastocysts whereas the maternal genome is demethylated to a much lesser extent. We also reveal unique regulation of imprinted differentially methylated regions, gene bodies and repeat sequences during early human development. Our high-resolution methylome maps are essential to understand epigenetic reprogramming by human oocytes and will aid in the preimplantation epigenetic diagnosis of human embryos.

Vyšlo v časopise: Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development. PLoS Genet 10(12): e32767. doi:10.1371/journal.pgen.1004868
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004868

Souhrn

DNA methylation reprogramming after fertilization is critical for normal mammalian development. Early embryos are sensitive to environmental stresses and a number of reports have pointed out the increased risk of DNA methylation errors associated with assisted reproduction technologies. Therefore, it is very important to understand normal DNA methylation patterns during early human development. Recent reduced representation bisulfite sequencing studies reported partial methylomes of human gametes and early embryos. To provide a more comprehensive view of DNA methylation dynamics during early human development, we report on whole genome bisulfite sequencing of human gametes and blastocysts. We show that the paternal genome is globally demethylated in blastocysts whereas the maternal genome is demethylated to a much lesser extent. We also reveal unique regulation of imprinted differentially methylated regions, gene bodies and repeat sequences during early human development. Our high-resolution methylome maps are essential to understand epigenetic reprogramming by human oocytes and will aid in the preimplantation epigenetic diagnosis of human embryos.

Zdroje

1. MesserschmidtDM, KnowlesBB, SolterD (2014) DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev 28 : 812–828.

2. SmithZD, MeissnerA (2013) DNA methylation: roles in mammalian development. Nat Rev Genet 14 : 204–220.

3. SaitouM, KagiwadaS, KurimotoK (2012) Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells. Development 139 : 15–31.

4. SmallwoodSA, TomizawaS, KruegerF, RufN, CarliN, et al. (2011) Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat Genet 43 : 811–814.

5. KobayashiH, SakuraiT, ImaiM, TakahashiN, FukudaA, et al. (2012) Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet 8: e1002440.

6. KohliRM, ZhangY (2013) TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502 : 472–479.

7. GuoH, ZhuP, YanL, LiR, HuB, et al. (2014) The DNA methylation landscape of human early embryos. Nature 511 : 606–610.

8. BeaujeanN, HartshorneG, CavillaJ, TaylorJ, GardnerJ, et al. (2004) Non-conservation of mammalian preimplantation methylation dynamics. Curr Biol 14: R266–267.

9. SmithZD, ChanMM, HummKC, KarnikR, MekhoubadS, et al. (2014) DNA methylation dynamics of the human preimplantation embryo. Nature 511 : 611–615.

10. MiuraF, EnomotoY, DairikiR, ItoT (2012) Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res 40: e136.

11. ShiraneK, TohH, KobayashiH, MiuraF, ChibaH, et al. (2013) Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet 9: e1003439.

12. WangL, ZhangJ, DuanJ, GaoX, ZhuW, et al. (2014) Programming and inheritance of parental DNA methylomes in mammals. Cell 157 : 979–991.

13. MolaroA, HodgesE, FangF, SongQ, McCombieWR, et al. (2011) Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 146 : 1029–1041.

14. Al-KhtibM, BlachereT, GuerinJF, LefevreA (2012) Methylation profile of the promoters of Nanog and Oct4 in ICSI human embryos. Hum Reprod 27 : 2948–2954.

15. DenommeMM, MannMR (2012) Genomic imprints as a model for the analysis of epigenetic stability during assisted reproductive technologies. Reproduction 144 : 393–409.

16. Ferguson-SmithAC (2011) Genomic imprinting: the emergence of an epigenetic paradigm. Nat Rev Genet 12 : 565–575.

17. CourtF, TayamaC, RomanelliV, Martin-TrujilloA, Iglesias-PlatasI, et al. (2014) Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment. Genome Res 24 : 554–569.

18. LiX, ItoM, ZhouF, YoungsonN, ZuoX, et al. (2008) A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. Dev Cell 15 : 547–557.

19. Bourc'hisD, XuGL, LinCS, BollmanB, BestorTH (2001) Dnmt3L and the establishment of maternal genomic imprints. Science 294 : 2536–2539.

20. HuntrissJ, HinkinsM, OliverB, HarrisSE, BeazleyJC, et al. (2004) Expression of mRNAs for DNA methyltransferases and methyl-CpG-binding proteins in the human female germ line, preimplantation embryos, and embryonic stem cells. Mol Reprod Dev 67 : 323–336.

21. SmithZD, ChanMM, MikkelsenTS, GuH, GnirkeA, et al. (2012) A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature 484 : 339–344.

22. WangH, XingJ, GroverD, HedgesDJ, HanK, et al. (2005) SVA elements: a hominid-specific retroposon family. J Mol Biol 354 : 994–1007.

23. LaniaL, Di CristofanoA, StrazzulloM, PengueG, MajelloB, et al. (1992) Structural and functional organization of the human endogenous retroviral ERV9 sequences. Virology 191 : 464–468.

24. SchuelerMG, SullivanBA (2006) Structural and functional dynamics of human centromeric chromatin. Annu Rev Genomics Hum Genet 7 : 301–313.

25. GopalakrishnanS, SullivanBA, TrazziS, Della ValleG, RobertsonKD (2009) DNMT3B interacts with constitutive centromere protein CENP-C to modulate DNA methylation and the histone code at centromeric regions. Hum Mol Genet 18 : 3178–3193.

26. XueZ, HuangK, CaiC, CaiL, JiangCY, et al. (2013) Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature 500 : 593–597.

27. KobayashiH, YanagisawaE, SakashitaA, SugawaraN, KumakuraS, et al. (2013) Epigenetic and transcriptional features of the novel human imprinted lncRNA GPR1AS suggest it is a functional ortholog to mouse Zdbf2linc. Epigenetics 8 : 635–645.

28. ProudhonC, DuffieR, AjjanS, CowleyM, IranzoJ, et al. (2012) Protection against de novo methylation is instrumental in maintaining parent-of-origin methylation inherited from the gametes. Mol Cell 47 : 909–920.

29. HirasawaR, ChibaH, KanedaM, TajimaS, LiE, et al. (2008) Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation imprints during preimplantation development. Genes Dev 22 : 1607–1616.

30. YamagataK, YamazakiT, MikiH, OgonukiN, InoueK, et al. (2007) Centromeric DNA hypomethylation as an epigenetic signature discriminates between germ and somatic cell lineages. Dev Biol 312 : 419–426.

31. UedaY, OkanoM, WilliamsC, ChenT, GeorgopoulosK, et al. (2006) Roles for Dnmt3b in mammalian development: a mouse model for the ICF syndrome. Development 133 : 1183–1192.

32. HancksDC, KazazianHHJr (2010) SVA retrotransposons: Evolution and genetic instability. Semin Cancer Biol 20 : 234–245.

33. ChandlerVL (2010) Paramutation's properties and puzzles. Science 330 : 628–629.

34. van MontfoortAP, HanssenLL, de SutterP, VivilleS, GeraedtsJP, et al. (2012) Assisted reproduction treatment and epigenetic inheritance. Hum Reprod Update 18 : 171–197.

35. HiuraH, OkaeH, MiyauchiN, SatoF, SatoA, et al. (2012) Characterization of DNA methylation errors in patients with imprinting disorders conceived by assisted reproduction technologies. Hum Reprod 27 : 2541–2548.

36. HardyK, HandysideAH, WinstonRM (1989) The human blastocyst: cell number, death and allocation during late preimplantation development in vitro. Development 107 : 597–604.

37. UshijimaC, KumasakoY, KihailePE, HirotsuruK, UtsunomiyaT (2000) Analysis of chromosomal abnormalities in human spermatozoa using multi-colour fluorescence in-situ hybridization. Hum Reprod 15 : 1107–1111.

38. BahnakBR, WuQY, CoulombelL, DrouetL, Kerbiriou-NabiasD, et al. (1988) A simple and efficient method for isolating high molecular weight DNA from mammalian sperm. Nucleic Acids Res 16 : 1208.

39. KruegerF, AndrewsSR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27 : 1571–1572.

40. Huang daW, ShermanBT, LempickiRA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4 : 44–57.

41. BensonG (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27 : 573–580.

42. BaileyTL (2011) DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27 : 1653–1659.

43. YanL, YangM, GuoH, YangL, WuJ, et al. (2013) Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol 20 : 1131–1139.

44. FangF, HodgesE, MolaroA, DeanM, HannonGJ, et al. (2012) Genomic landscape of human allele-specific DNA methylation. Proc Natl Acad Sci U S A 109 : 7332–7337.

45. DasR, LeeYK, StrogantsevR, JinS, LimYC, et al. (2013) DNMT1 and AIM1 Imprinting in human placenta revealed through a genome-wide screen for allele-specific DNA methylation. BMC Genomics 14 : 685.

Štítky
Genetika Reprodukčná medicína
Článek Stratification by Smoking Status Reveals an Association of Genotype with Body Mass Index in Never Smokers
Článek Genome Wide Meta-analysis Highlights the Role of Genetic Variation in in the Regulation of Circulating Serum Chemerin
Článek Occupancy of Mitochondrial Single-Stranded DNA Binding Protein Supports the Strand Displacement Mode of DNA Replication
Článek Distinct Genealogies for Plasmids and Chromosome
Článek Large-scale Metabolomic Profiling Identifies Novel Biomarkers for Incident Coronary Heart Disease
Článek Non-coding RNAs Prevent the Binding of the MSL-complex to Heterochromatic Regions
Článek Plasmid Flux in ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences
Článek Epigenome-Guided Analysis of the Transcriptome of Plaque Macrophages during Atherosclerosis Regression Reveals Activation of the Wnt Signaling Pathway
Článek The Inventiveness of Nature: An Interview with Werner Arber
Článek Mediation Analysis Demonstrates That -eQTLs Are Often Explained by -Mediation: A Genome-Wide Analysis among 1,800 South Asians
Článek Generation of Antigenic Diversity in by Structured Rearrangement of Genes During Mitosis
Článek A Massively Parallel Pipeline to Clone DNA Variants and Examine Molecular Phenotypes of Human Disease Mutations
Článek Genetic Analysis of the Cardiac Methylome at Single Nucleotide Resolution in a Model of Human Cardiovascular Disease
Článek Genetic Analysis of Circadian Responses to Low Frequency Electromagnetic Fields in
Článek The Dissection of Meiotic Chromosome Movement in Mice Using an Electroporation Technique
Článek Altered Chromatin Occupancy of Master Regulators Underlies Evolutionary Divergence in the Transcriptional Landscape of Erythroid Differentiation
Článek Syd/JIP3 and JNK Signaling Are Required for Myonuclear Positioning and Muscle Function
Článek Notch Signaling Mediates the Age-Associated Decrease in Adhesion of Germline Stem Cells to the Niche
Článek Mutation of Leads to Blurred Tonotopic Organization of Central Auditory Circuits in Mice
Článek The IKAROS Interaction with a Complex Including Chromatin Remodeling and Transcription Elongation Activities Is Required for Hematopoiesis
Článek RAN-Binding Protein 9 is Involved in Alternative Splicing and is Critical for Male Germ Cell Development and Male Fertility
Článek Enhanced Longevity by Ibuprofen, Conserved in Multiple Species, Occurs in Yeast through Inhibition of Tryptophan Import
Článek Phosphorylation of Mitochondrial Polyubiquitin by PINK1 Promotes Parkin Mitochondrial Tethering
Článek Recurrent Loss of Specific Introns during Angiosperm Evolution
Článek Natural Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality
Článek SEEDSTICK is a Master Regulator of Development and Metabolism in the Arabidopsis Seed Coat
Článek Overlapping and Non-overlapping Functions of Condensins I and II in Neural Stem Cell Divisions
Článek Unisexual Reproduction Drives Meiotic Recombination and Phenotypic and Karyotypic Plasticity in
Článek Tetraspanin (TSP-17) Protects Dopaminergic Neurons against 6-OHDA-Induced Neurodegeneration in
Článek ABA-Mediated ROS in Mitochondria Regulate Root Meristem Activity by Controlling Expression in
Článek Mutations in Global Regulators Lead to Metabolic Selection during Adaptation to Complex Environments
Článek Global Analysis of Photosynthesis Transcriptional Regulatory Networks
Článek Mucolipin Co-deficiency Causes Accelerated Endolysosomal Vacuolation of Enterocytes and Failure-to-Thrive from Birth to Weaning
Článek Controlling Pre-leukemic Thymocyte Self-Renewal
Článek How Malaria Parasites Avoid Running Out of Ammo
Článek Echoes of the Past: Hereditarianism and
Článek Deep Reads: Strands in the History of Molecular Genetics
Článek Keep on Laying Eggs Mama, RNAi My Reproductive Aging Blues Away
Článek Analysis of a Plant Complex Resistance Gene Locus Underlying Immune-Related Hybrid Incompatibility and Its Occurrence in Nature
Článek Epistatic Adaptive Evolution of Human Color Vision
Článek Increased and Imbalanced dNTP Pools Symmetrically Promote Both Leading and Lagging Strand Replication Infidelity
Článek Genetic Basis of Haloperidol Resistance in Is Complex and Dose Dependent
Článek Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer
Článek The Evolution of Sex Ratio Distorter Suppression Affects a 25 cM Genomic Region in the Butterfly
Článek is Required for Adult Maintenance of Dopaminergic Neurons in the Ventral Substantia Nigra
Článek PRL1, an RNA-Binding Protein, Positively Regulates the Accumulation of miRNAs and siRNAs in Arabidopsis
Článek Genetic Control of Contagious Asexuality in the Pea Aphid
Článek Early Mesozoic Coexistence of Amniotes and Hepadnaviridae
Článek Local and Systemic Regulation of Plant Root System Architecture and Symbiotic Nodulation by a Receptor-Like Kinase
Článek Gene Pathways That Delay Reproductive Senescence
Článek The Evolution of Fungal Metabolic Pathways
Článek Maf1 Is a Novel Target of PTEN and PI3K Signaling That Negatively Regulates Oncogenesis and Lipid Metabolism
Článek Formation of Linear Amplicons with Inverted Duplications in Requires the MRE11 Nuclease
Článek Identification of Rare Causal Variants in Sequence-Based Studies: Methods and Applications to , a Gene Involved in Cohen Syndrome and Autism
Článek Rrp12 and the Exportin Crm1 Participate in Late Assembly Events in the Nucleolus during 40S Ribosomal Subunit Biogenesis
Článek The Mutations in the ATP-Binding Groove of the Rad3/XPD Helicase Lead to -Cockayne Syndrome-Like Phenotypes
Článek Topoisomerase I Plays a Critical Role in Suppressing Genome Instability at a Highly Transcribed G-Quadruplex-Forming Sequence
Článek A Cbx8-Containing Polycomb Complex Facilitates the Transition to Gene Activation during ES Cell Differentiation
Článek Transcriptional Frameshifting Rescues Type VI Secretion by the Production of Two Length Variants from the Prematurely Interrupted Gene
Článek Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize
Článek Genome-Wide Analysis of -Regulated and Phased Small RNAs Underscores the Importance of the ta-siRNA Pathway to Maize Development
Článek Dissemination of Cephalosporin Resistance Genes between Strains from Farm Animals and Humans by Specific Plasmid Lineages
Článek The Tau Tubulin Kinases TTBK1/2 Promote Accumulation of Pathological TDP-43
Článek Germline Signals Deploy NHR-49 to Modulate Fatty-Acid β-Oxidation and Desaturation in Somatic Tissues of
Článek Microevolution of in Macrophages Restores Filamentation in a Nonfilamentous Mutant
Článek Vangl2-Regulated Polarisation of Second Heart Field-Derived Cells Is Required for Outflow Tract Lengthening during Cardiac Development
Článek Chondrocytes Transdifferentiate into Osteoblasts in Endochondral Bone during Development, Postnatal Growth and Fracture Healing in Mice
Článek A ABC Transporter Regulates Lifespan
Článek RA and FGF Signalling Are Required in the Zebrafish Otic Vesicle to Pattern and Maintain Ventral Otic Identities
Článek , and Reprogram Thymocytes into Self-Renewing Cells
Článek The miR9863 Family Regulates Distinct Alleles in Barley to Attenuate NLR Receptor-Triggered Disease Resistance and Cell-Death Signaling
Článek Detection of Pleiotropy through a Phenome-Wide Association Study (PheWAS) of Epidemiologic Data as Part of the Environmental Architecture for Genes Linked to Environment (EAGLE) Study
Článek Extensive Copy-Number Variation of Young Genes across Stickleback Populations
Článek The and Genetic Modules Interact to Regulate Ciliogenesis and Ciliary Microtubule Patterning in
Článek Analysis of the Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood
Článok vyšiel v časopise

PLOS Genetics

2014 Číslo 12
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

nový kurz
Autori: doc. MUDr. David Zemánek, Ph.D., MUDr. Anna Chaloupka, Ph.D.
Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#