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Mammalian Genomic Imprinting
Open accessAbstract
Normal mammalian development requires a maternal and paternal contribution, which is attributed to imprinted genes, or genes that are expressed from a single parental allele. Approximately 100 imprinted genes have been reported in mammals thus far. Imprinted genes are controlled by cis-acting regulatory elements, termed imprinting control regions (ICRs), which have parental-specific epigenetic modifications, including DNA methylation. ICRs are methylated by de novo DNA methyltransferases during germline development; these parental-specific modifications must be maintained following fertilization when the genome is extensively reprogrammed. Many imprinted genes reside in ∼1-megabase clusters, with two major mechanisms of imprinting regulation currently recognized, CTCF-dependent insulators and long noncoding RNAs. Unclustered imprinted genes are generally regulated by germline-derived differential promoter methylation. Here, we describe the identification and functions of imprinted genes, cis-acting control sequences, trans-acting factors, and imprinting mechanisms in clusters. Finally, we define questions that require more extensive research.
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“Genomic imprinting hypothetically evolved to control the dosage of developmentally important genes and occurs in about 100 mammalian genes.113”
From Pubertal development and regulation (2016) · cites this paper as [113]
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Dosage compensation of the sex chromosomes and autosomes
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“It should be noted that there are interesting parallels between mechanisms that silence imprinted genes and those that silence genes regulated by X inactivation [62], both types of genes being regulated by cis-acting lncRNAs, histone modifications, DNA methylation, and specific nuclear positioning [63].”
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“Through the use of the de novo DNA methyltransferases DNMT3A and DNMT3B and the accessory protein DNMT3L, ICRs and DMRs are specifically methylated in the male or female germline (Bartolomei and Ferguson-Smith, 2011).”
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BackgroundInfluentialGenome accessibility is widely preserved and locally modulated during mitosisPreprint
Hsiung, C. C. ‐., Morrissey, C. S., Udugama, M., Frank, C. L., Keller, C. A., Baek, S., Giardine, B. M., Crawford, G. E., Sung, M., Hardison, R. C., et al. (2014) · Genome Research · doi:10.1101/gr.180646.114 · Cited by 118
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“Moreover, imprinted genes tend to be clustered such that imprinted regions coordinate multiple adaptive targets relevant to parental conflict of interest (Bartolomei & Ferguson-Smith, 2011).”
BackgroundForging our understanding of lncRNAs in the brain
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“One crucial function of such transcription-dependent DNA methylation is to establish genomic imprints, which are gamete-specific methylation marks that control allele-specific gene expression once passed on to the fertilized embryos (Bartolomei and Ferguson-Smith, 2011).”
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“Thus, alteration in a single region can drive both biallelic expression and silencing of multiple genes (Bartolomei & Ferguson-Smith, 2011).”
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“As expected, the IS is strongly negatively correlated with expression from the ARSE (29) CA5B (29) CA5BP1 (42) DDX3X (51) HUWE1 (13) INE2 (10) KDM6A (22) MED14 (4) PUDP (63) RBMX (0) SMC1A (41) STS (20) TTC3P1 (25) USP9X (34) ZFX (94) CA5BP1 (37) DDX3X (29) HUWE1 (23) INE2 (14) KDM5C (38) KDM6A (16) MED14 (0) MXRA5 (4…”
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“In addition, this is the stage at which imprinted genes are biallelically reprogrammed in each sex such that paternally imprinted genes will become biallelically methylated in spermatogenic cells, while maternally imprinted genes will be biallelically methylated in oogenic cells [111].”
BackgroundQuantitative and functional interrogation of parent-of-origin allelic expression biases in the brain
Perez, J. D., Rubinstein, N. D., Fernandez, D. E., Santoro, S. W., Needleman, L. A., Ho-Shing, O., Choi, J. J., Zirlinger, M., Chen, S., Liu, J. S., et al. (2015) · eLife · doi:10.7554/elife.07860 · Cited by 93
“…genes, monoallelic or parentally biased expression has been shown to be primarily dependent on DNA methylation marks established in one of the parental germ lines, and maintained post-fertilization in the parental alleles of the embryo and mature organism (Bartolomei and Ferguson-Smith, 2011).”
BackgroundThe Interplay between DNA Methylation, Folate and Neurocognitive Development
Irwin, R. E., Pentieva, K. D., Cassidy, T., Lees‐Murdock, D. J., McLaughlin, M., Prasad, G., McNulty, H., & Walsh, C. P. (2016) · Epigenomics · doi:10.2217/epi-2016-0003 · Cited by 98
Adhami, H. A., Evano, B., Digarcher, A. L., Gueydan, C., Dubois, E., Parrinello, H., Dantec, C., Bouschet, T., Varrault, A., & Journot, L. (2015) · Genome Research · doi:10.1101/gr.175919.114 · Cited by 92
Epigenetics and phenotypic variability: some interesting insights from birds
Frésard, L., Morisson, M., Brun, J. M. J. M., Collin, A., Pain, B., Minvielle, F., & Frédérique Pitel, A. (2013) · Genetics Selection Evolution · doi:10.1186/1297-9686-45-16 · Cited by 97
“As recently reviewed, these signatures need to differentiate paternal and maternal inherited chromosomes in order to influence transcription, and to be transmitted through generations [67].”
BackgroundBeygo, J., Citro, V., Sparago, A., Crescenzo, A. D., Cerrato, F., Heitmann, M., Rademacher, K., Guala, A., Enklaar, T., Anichini, C., et al. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds465 · Cited by 89
“Histone modifications likely contribute to the establishment and/or maintenance of the differential expression of the imprinted genes on the parental alleles (4,5).”
BackgroundUsing next-generation RNA sequencing to identify imprinted genes
Wang, X., & Clark, A. G. (2014) · Heredity · doi:10.1038/hdy.2014.18 · Cited by 89
“In some cases, the deviation from 50%:50% is dependent on the parent of origin, such as genomic imprinting (Reik and Walter, 2001; Barlow, 2011; Bartolomei and Ferguson-Smith, 2011) and imprinted X chromosome inactivation (Wake et al., 1976; Huynh and Lee, 2001; Xue et al., 2002; Dindot et al.,…”
BackgroundTargeted DNA methylation in human cells using engineered dCas9-methyltransferases
Xiong, T., Meister, G. E., Workman, R. E., Kato, N. C., Spellberg, M. J., Türker, F., Timp, W., Ostermeier, M., & Novina, C. D. (2017) · Scientific Reports · doi:10.1038/s41598-017-06757-0 · Cited by 88
“(4) Off-target DNA methylation occurs with dCas9 bound at the intended site, and methylation at off-target sites is proportional to a site’s proximity to the target site, which would be dependent on plasmid 3D topology in the cell.”
BackgroundRatajczak, M. Z. (2012) · Folia Histochemica et Cytobiologica · doi:10.5603/fhc.2012.0026 · Cited by 88
“Imprinting at the Igf2-H19 locus is one of the major factors preventing parthenogenetic development in mammals, and the biological importance of this locus is demonstrated by the additional steps necessary for the creation of viable bimaternal mice derived from two female sets of chromosomes [1–4].”
BackgroundInfluentialPlacental expression profile of imprinted genes impacts birth weight
Deyssenroth, M. A., Green, B. B., Armstrong, D. A., Sharp, A. J., Lambertini, L., Marsit, C. J., & Chen, J. (2015) · Epigenetics · doi:10.1080/15592294.2015.1073881 · Cited by 86
“These genes represent a subset of loci that are monoallelically expressed in a parent-of-origin manner and are predominately active in the placenta during fetal development.(5) Early studies delineating the function of imprinted genes indicated a trend in which paternally expressed genes are involved in processes that…”
BackgroundDNA methylation in human sperm: a systematic review
Åsenius, F., Danson, A. F., & Marzi, S. J. (2020) · Human Reproduction Update · doi:10.1093/humupd/dmaa025 · Cited by 86
Dynamics of DNA Methylation in Aging and Alzheimer's Disease
Irier, H. A., & Jin, P. (2012) · DNA and Cell Biology · doi:10.1089/dna.2011.1565 · Cited by 85
“Together with histone modifications, the 5mC modulates epigenetic processes, such as gene silencing via CpG islands (CGIs) (Sharma et al., 2010), and is involved in genomic imprinting (Bird, 2002; Yasukochi et al., 2010; Bartolomei and Ferguson-Smith, 2011).”
BackgroundAberrant DNA methylation reprogramming in bovine SCNT preimplantation embryos
Zhang, S., Chen, X., Wang, F., An, X., Tang, B., Zhang, X., Sun, L., & Li, Z. (2016) · Scientific Reports · doi:10.1038/srep30345 · Cited by 84
Paternal impact on the life course development of obesity and type 2 diabetes in the offspring
Sharp, G. C., & Lawlor, D. A. (2019) · Diabetologia · doi:10.1007/s00125-019-4919-9 · Cited by 85
Noncanonical Genomic Imprinting Effects in Offspring
Bonthuis, P. J., Huang, W.-C., Hörndli, C. S., Ferris, E., Cheng, T., & Gregg, C. J. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.07.017 · Cited by 81
Genomic Imprinting in the Arabidopsis Embryo Is Partly Regulated by PRC2
Raissig, M. T., Bemer, M., Baroux, C., & Grossniklaus, U. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003862 · Cited by 84
“To our knowledge mRNAs can only be transported symplastically via plasmodesmata [47].”
BackgroundInfluentialCharacters, functions and clinical perspectives of long non-coding RNAs
Wu, R., Su, Y., Wu, H., Dai, Y., Zhao, M., & Lu, Q. (2016) · Molecular Genetics and Genomics · doi:10.1007/s00438-016-1179-y · Cited by 87
Epigenetic legacy of parental experiences: Dynamic and interactive pathways to inheritance
Champagne, F. A. (2016) · Development and Psychopathology · doi:10.1017/s0954579416000808 · Cited by 81
“Though most genes display biallelic expression, imprinted genes are characterized by monoallelic expression patterns due to epigenetic silencing of either the paternal or the maternal allele (Bartolomei & Ferguson-Smith, 2011; Keverne, 2009; see Figure 2).”
BackgroundDarbandi, M., Darbandi, S., Agarwal, A. K., Baskaran, S., Dutta, S., Sengupta, P., Khorshid, H. R. K., Esteves, S. C., Gilany, K., Hedayati, M., et al. (2018) · Journal of Assisted Reproduction and Genetics · doi:10.1007/s10815-018-1350-y · Cited by 80
Maternal H3K27me3-dependent autosomal and X chromosome imprinting
Chen, Z., & Zhang, Y. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0245-9 · Cited by 76
DNA methylation in spermatozoa as a prospective marker in andrology
Kläver, R., Tüttelmann, F., Bleiziffer, A., Haaf, T., Kliesch, S., & Gromoll, J. (2013) · Andrology · doi:10.1111/j.2047-2927.2013.00118.x · Cited by 79
“This ensures the maintenance of their germ line-specific DNA methylation patterns and a parent-of-origin specific gene expression which plays an important role in embryonic development (Trasler, 2009; Bartolomei & Ferguson-Smith, 2011; Jenkins & Carrell, 2011).”
BackgroundLiao, J., Chen, B., Zhu, Z., Du, C., Gao, S., Zhao, G., Zhao, P., Wang, Y., Wang, A., Schwartz, Z., et al. (2023) · Genes & Diseases · doi:10.1016/j.gendis.2023.02.008 · Cited by 76
“The 30 enhancer has a more robust effect on the expression of H19 since H19 has a stronger promoter in this area than Igf2 and is physically closer to the 30 enhancer.(41,48,67,73) On the other hand, tissue-specific and parent-of-origin enhancers were also identified and proved to regulate the expression of Igf2-H19(4…”
BackgroundThe effects of superovulation and reproductive aging on the epigenome of the oocyte and embryo
Marshall, K. L., & Rivera, R. M. (2017) · Molecular Reproduction and Development · doi:10.1002/mrd.22951 · Cited by 83
“Genomic imprinting refers to the mechanism that drives parent-specific, monoallelic expression of a subset of genes in mammals (Bartolomei & Ferguson-Smith, 2011).”
BackgroundCowley, M., Skaar, D. A., Jima, D. D., Maguire, R. L., Hudson, K. M., Park, S. S., Sorrow, P., & Hoyo, C. (2018) · Environmental Health Perspectives · doi:10.1289/ehp2085 · Cited by 78
Ciccarone, F., Klinger, F. G., Catizone, A., Calabrese, R., Zampieri, M., Bacalini, M. G., Felici, M. D., & Caiafa, P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046927 · Cited by 78
“Although paternal pronucleus and PGCs seem to share similar active demethylating mechanisms [11,12], the outcome of these processes is quite different on imprinted loci [2,16].”
BackgroundDNMT1, DNMT3A and DNMT3B proteins are differently expressed in mouse oocytes and early embryos
Uysal, F., Öztürk, S., & Akkoyunlu, G. (2017) · Journal of Molecular Histology · doi:10.1007/s10735-017-9739-y · Cited by 71
Conservation through the lens of (mal)adaptation: Concepts and meta‐analysis
Derry, A. M., Fraser, D. J., Brady, S. P., Astorg, L., Lawrence, E. R., Martin, G. K., Matte, J. O., Dastis, J. O. N., Paccard, A., Barrett, R. D. H., et al. (2019) · Evolutionary Applications · doi:10.1111/eva.12791 · Cited by 71
Reshaping the transcriptional frontier: Epigenetics and somatic cell nuclear transfer
Long, C. R., Westhusin, M. E., & Golding, M. C. (2013) · Molecular Reproduction and Development · doi:10.1002/mrd.22271 · Cited by 75
Russo, S., Calzari, L., Mussa, A., Mainini, E., Cassina, M., Candia, S. D., Clementi, M., Guzzetti, S., Tabano, S. M., Miozzo, M. R., et al. (2016) · Clinical Epigenetics · doi:10.1186/s13148-016-0183-8 · Cited by 70
“5 chromosomal region contains two clusters of imprinted genes, the monoallelic expression of which is independently regulated by cis-acting differentially methylated regions (DMRs) or imprinting control centers (ICR), ICR1 (alias H19/IGF2:IG-DMR) and ICR2 (alias KCNQ1OT1:TSS-DMR), corresponding to sequences methylated…”
BackgroundGlobal assessment of imprinted gene expression in the bovine conceptus by next generation sequencing
Chen, Z., Hagen, D. E., Wang, J., Elsik, C. G., Ji, T., Siqueira, L. G. B., Hansen, P. J., & Rivera, R. M. (2016) · Epigenetics · doi:10.1080/15592294.2016.1184805 · Cited by 69
“Most imprinted genes are organized in clusters and are regulated by cluster-specific DNA elements termed imprinting control regions (ICRs).(1) ICRs are marked with DNA methylation and histone posttranslational modifications in a sex-specific manner during gametogenesis.”
BackgroundInfluentialDNA methylomes of bovine gametes and in vivo produced preimplantation embryos
Jiang, Z., Lin, J., Dong, H., Zheng, X., Marjani, S. L., Duan, J. E., Ouyang, Z., Chen, J., & Tian, X. (2018) · Biology of Reproduction · doi:10.1093/biolre/ioy138 · Cited by 67
Cheng, K., Fu, X.-W., Zhang, R.-N., Jia, G., Hou, Y., & Zhu, S. (2014) · Fertility and Sterility · doi:10.1016/j.fertnstert.2014.06.037 · Cited by 69
Metadata
- Authors
- Bartolomei, M. S., & Ferguson-Smith, A. C.
- Affiliations
- University of Pennsylvania (US)
- ORCID
- Bartolomei, M. S.
- Venue
- Cold Spring Harbor Perspectives in Biology
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-05-16
- Volume
- 3
- Issue
- 7
- Pages
- a002592-a002592
- ISSN
- 1943-0264 (ISSN-L)
- PMC
- PMC3119911
- OpenAlex
- W2129246334
- Cited by
- 518
- References
- 109
- Citations by year
- 2026: 14 · 2025: 17 · 2024: 23 · 2023: 21 · 2022: 22 · 2021: 34 · 2020: 32 · 2019: 47 · 2018: 42 · 2017: 44 · 2016: 47 · 2015: 44 · 2014: 36 · 2013: 49 · 2012: 41
- Type
- posted content
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Cold Spring Harbor Perspectives in Biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust
- U.S. Public Health Service
- Medical Research Council
- Biotechnology and Biological Sciences Research Council
- National Institute of General Medical Sciences (GM-51279, R01GM051279, R37GM051279)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD42026, R01HD042026)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- genomic imprinting, imprinted genes, imprinting control regions, DNA methylation, cis-regulatory elements, long non-coding RNA, imprinted gene clusters, germ cell development, trans-acting factors
- MeSH terms
- Animals, Female, Humans, Male, Mammals, Models, Genetic, Genomic Imprinting, Gene Expression Regulation, Developmental, DNA Methylation, RNA, Untranslated, Genetic Diseases, Inborn, Mice
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