Mammalian genomic imprinting

Bartolomei, M. S.; Ferguson-Smith, A. C.

doi:10.1101/cshperspect.a002592

PreprintCited by 518Genetic Syndromes and ImprintingEpigenetics and DNA MethylationGenomics and Chromatin Dynamics

Mammalian genomic imprinting

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Bartolomei, M. S., Ferguson-Smith, A. C.·2011·Cold Spring Harbor Perspectives in Biology

DOI 10.1101/cshperspect.a002592PMC PMC3119911

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Abstract

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.
“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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McGrath, J. M., & Solter, D. (1983) · Journal of Experimental Zoology · doi:10.1002/jez.1402280218 · Cited by 113 · see citing works
Genome imprinting phenomena on mouse chromosome 7
Searle, A. G., & BEECHEY, C. V. (1990) · Genetics Research · doi:10.1017/s0016672300035333 · Cited by 112 · see citing works
Gene Dosage Effects of the Imprinted Delta-Like Homologue 1 (Dlk1/Pref1) in Development: Implications for the Evolution of Imprinting
da Rocha, S. T., Charalambous, M., Lin, S., Gutteridge, I., Ito, Y., Gray, D., Dean, W., & Ferguson‐Smith, A. C. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000392 · Cited by 106 · see citing works
Deficiency of Rbbp1/Arid4a and Rbbp1l1/Arid4b alters epigenetic modifications and suppresses an imprinting defect in the PWS/AS domainPreprint
Wu, M., Tsai, T., & Beaudet, A. L. (2006) · Genes & Development · doi:10.1101/gad.1452206 · Cited by 100 · see citing works
Dlk1 Influences Differentiation and Function of β Lymphocytes
Raghunandan, R., Ruiz‐Hidalgo, M. J., Jia, Y., Ettinger, R., Rudikoff, E. K., Riggins, P. S., Farnsworth, R., Tesfaye, A., Laborda, J., & Bauer, S. R. (2008) · Stem Cells and Development · doi:10.1089/scd.2007.0102 · Cited by 92 · see citing works
Conserved interaction between distinct Kruppel-associated box domains and the transcriptional intermediary factor 1 beta
Åbrink, M. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.041616998 · Cited by 90 · see citing works
Maintenance of Paternal Methylation and Repression of the Imprinted H19 Gene Requires MBD3
Reese, K. J., Lin, S., Verona, R. I., Schultz, R. M., & Bartolomei, M. S. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030137 · Cited by 89 · see citing works
The Notch Signaling Pathway Controls the Size of the Ocular Lens by Directly Suppressing p57Kip2 Expression
Jia, J., Lin, M., Zhang, L., York, J. P., & Zhang, P. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.00780-07 · Cited by 82 · see citing works
Imprinting of the human L3MBTL gene, a polycomb family member located in a region of chromosome 20 deleted in human myeloid malignancies
Li, J., Bench, A. J., Vassiliou, G. S., Fourouclas, N., Ferguson‐Smith, A. C., & Green, A. R. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0308195101 · Cited by 76 · see citing works
DNA methyltransferase 1o functions during preimplantation development to preclude a profound level of epigenetic variation
Cirio, M. C., Martel, J., Mann, M. R. W., Toppings, M., Bartolomei, M. S., Trasler, J. M., & Chaillet, J. R. (2008) · Developmental Biology · doi:10.1016/j.ydbio.2008.09.015 · Cited by 67 · see citing works
Three-dimensional conformation at the H19/Igf2 locus supports a model of enhancer tracking
Engel, N., Raval, A., Thorvaldsen, J. L., & Bartolommei, S. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn200 · Cited by 64 · see citing works
Molecular mechanisms regulating phenotypic outcome in paternal and maternal uniparental disomy for chromosome 14
Ogata, T., Kagami, M., & Ferguson‐Smith, A. C. (2008) · Epigenetics · doi:10.4161/epi.3.4.6550 · Cited by 58 · see citing works
Perceptive enzymes
Ferguson‐Smith, A. C., & Greally, J. M. (2007) · Nature · doi:10.1038/449148a · Cited by 44 · see citing works
Genomic imprinting: A balance between antagonistic roles of parental chromosomes
Kinoshita, T., Ikeda, Y., & Ishikawa, R. (2008) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2008.07.018 · Cited by 43 · see citing works
Imprinting in Human Disease with Special Reference to Transient Neonatal Diabetes and Beckwith-Wiedemann Syndrome
Temple, I. K. (2007) · KARGER eBooks · doi:10.1159/000109638 · Cited by 31 · see citing works
Complementation hypothesis: the necessity of a monoallelic gene expression mechanism in mammalian development
Kaneko‐Ishino, T., Kohda, T., Ono, R., & Ishino, F. (2006) · Cytogenetic and Genome Research · doi:10.1159/000090811 · Cited by 28 · see citing works
Conserved interaction between distinct Krüppel-associated box domains and the transcriptional intermediary factor 1 β
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L3mbtl, the mouse orthologue of the imprinted L3MBTL, displays a complex pattern of alternative splicing and escapes genomic imprinting
Li, J., Bench, A. J., Piltz, S., Vassiliou, G. S., Baxter, E. J., Ferguson‐Smith, A. C., & Green, A. R. (2005) · Genomics · doi:10.1016/j.ygeno.2005.06.012 · Cited by 22 · see citing works
Maintenance of paternal methylation and repression of the imprinted H19 gene requires MBD3
Reese, K. J., Lin, S., Verona, R. I., Schultz, R. M., & Bartolomei, M. S. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0030137.eor · Cited by 5 · see citing works

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Sorted by citations

Genomic Imprinting in MammalsPreprint
Barlow, D. P., & Bartolomei, M. S. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a018382 · Cited by 706 · see citing works
“To date, many more maternally than paternally methylated gametic DMRs have been identified (Bartolomei and Ferguson-Smith 2011).”
Background
X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease
Lee, J. T., & Bartolomei, M. S. (2013) · Cell · doi:10.1016/j.cell.2013.02.016 · Cited by 674 · see citing works
“Most ICRs are methylated in the female germline during oocyte growth (Bartolomei and Ferguson-Smith, 2011).”
Background
Phenotypic impact of genomic structural variation: insights from and for human disease
Weischenfeldt, J., Symmons, O., Spitz, F., & Korbel, J. O. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3373 · Cited by 648 · see citing works
Pubertal development and regulation
Abreu, A. P., & Kaiser, U. B. (2016) · The Lancet Diabetes & Endocrinology · doi:10.1016/s2213-8587(15)00418-0 · Cited by 611 · see citing works
Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression
Engreitz, J., Ollikainen, N., & Guttman, M. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.126 · Cited by 580 · see citing works
Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA
Calarco, J. P., Borges, F., Donoghue, M. T. A., Ex, F. V., Jullien, P. E., Lopes, T., Gardner, R., Berger, F., Feijó, J. A., Becker, J. D., et al. (2012) · Cell · doi:10.1016/j.cell.2012.09.001 · Cited by 556 · see citing works
“For example, imprinted genes in the mouse are expressed predominantly from either the paternal allele or from thematernal allele in the diploid embryo and so must be reprogrammed in the germline depending on its sex (Bartolomei and Ferguson-Smith, 2011).”
Genomic Imprinting and Physiological Processes in Mammals
Tucci, V., Isles, A. R., Kelsey, G., Ferguson‐Smith, A. C., Tucci, V., Bartolomei, M. S., Benvenisty, N., Bourc’his, D., Charalambous, M., Dulac, C. G., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.043 · Cited by 549 · see citing works
“There are only three known paternally derived germline methylation imprints and these are all intergenic; i n contrast, over twenty ICRs are generated in the maternal germline and these are all at CpG-rich promoters (Bartolomei and Ferguson-Smith, 2011).”
Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome
Xie, W., Barr, C. L., Kim, A., Yue, F., Lee, A. Y., Eubanks, J., Dempster, E. L., & Ren, B. (2012) · Cell · doi:10.1016/j.cell.2011.12.035 · Cited by 543 · see citing works
Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing
Latos, P. A., Pauler, F. M., Koerner, M. V., Senergin, B. H., Hudson, Q. J., Stocsits, R. R., Allhoff, W., Stricker, S. H., Klement, R. M., Warczok, K. E., et al. (2012) · Science · doi:10.1126/science.1228110 · Cited by 542 · see citing works
Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes
Beliveau, B. J., Boettiger, A. N., Avendaño, M. S., Jungmann, R., McCole, R. B., Joyce, E. F., Kim-Kiselak, C., Bantignies, F., Fonseka, C. Y., Erceg, J., et al. (2015) · Nature Communications · doi:10.1038/ncomms8147 · Cited by 384 · see citing works
“…and chromosomal regions would greatly advance our capacity to investigate phenomena such as X-inactivation 40 , imprinted gene expression 41 , and random mono-allelic expression 42 ; the few methods that are available either rely on relatively inefficient enzymatic signal amplification…”
Transgenerational inheritance: Models and mechanisms of non–DNA sequence–based inheritance
Miska, E. A., & Ferguson-Smith, A. C. (2016) · Science · doi:10.1126/science.aaf4945 · Cited by 367 · see citing works
Self-citation
Daddy Issues: Paternal Effects on Phenotype
Rando, O. J. (2012) · Cell · doi:10.1016/j.cell.2012.10.020 · Cited by 292 · see citing works
Bisphenol A Exposure Disrupts Genomic Imprinting in the Mouse
Susiarjo, M., Sasson, I. E., Mesaros, C., & Bartolomei, M. S. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003401 · Cited by 292 · see citing works
“As imprinted genes play a critical role in placental development [35], we determined whether aberrant imprinting induced by BPA exposure was associated with abnormal placental phenotypes.”
Background
Mechanisms of epigenetic memory
D’Urso, A., & Brickner, J. H. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.04.004 · Cited by 281 · see citing works
“For example, in many organisms including humans, genomic imprinting, the exclusive expression of a single parental allele (maternal or paternal), can lead to phenotypic differences between genetically identical individuals [73].”
Background
SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development
Xu, Q., Xiang, Y., Wang, Q., Wang, L., Brind’Amour, J., Bogutz, A., Zhang, Y., Zhang, B., Yu, G., Xia, W., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0398-7 · Cited by 272 · see citing works
I’m Eating for Two: Parental Dietary Effects on Offspring Metabolism
Rando, O. J., & Simmons, R. A. (2015) · Cell · doi:10.1016/j.cell.2015.02.021 · Cited by 271 · see citing works
“Of course, a small subset of cytosine methylation on the paternal genome escapes erasure, with paternally contributed methylation at a subset of imprinted loci providing the canonical examples (Bartolomei and Ferguson-Smith, 2011).”
Bipartite structure of the inactive mouse X chromosome
Deng, X., Ma, W., Ramani, V., Hill, A. J., Yang, F., Ay, F., Berletch, J. B., Blau, C. A., Shendure, J., Duan, Z., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0728-8 · Cited by 255 · see citing works
“In contrast, X-linked genes are subject to silencing by X chromosome inactivation (XCI) on one of the two homologs in female somatic cells [2], and a subset of autosomal genes are subject to imprinting and expressed from either the paternal or maternal allele [3].”
BackgroundResultInfluential
Role of Tet1 in erasure of genomic imprinting
Yamaguchi, S., Shen, L., Liu, Y., Sendler, D. J., & Zhang, Y. (2013) · Nature · doi:10.1038/nature12805 · Cited by 246 · see citing works
Genomic imprinting in development, growth, behavior and stem cells
Plasschaert, R. N., & Bartolomei, M. S. (2014) · Development · doi:10.1242/dev.101428 · Cited by 235 · see citing works
The Role of KRAB-ZFPs in Transposable Element Repression and Mammalian Evolution
Yang, P., Wang, Y., & Macfarlan, T. S. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.08.006 · Cited by 225 · see citing works
“In mice, the differential establishment of heterochromatin and DNA methylation at imprint control regions (ICRs) in the germline and their maintenance during embryonic development is crucial for imprinted gene regulation [74,75].”
Background
Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment
Xu, Q., & Xie, W. (2017) · Trends in Cell Biology · doi:10.1016/j.tcb.2017.10.008 · Cited by 214 · see citing works
The landscape of genomic imprinting across diverse adult human tissuesPreprint
Baran, Y., Subramaniam, M., Biton, A., Tukiainen, T., Tsang, E. K., Rivas, M. A., Pirinen, M., Gutiérrez‐Arcelus, M., Smith, K. S., Kukurba, K., et al. (2015) · Genome Research · doi:10.1101/gr.192278.115 · Cited by 219 · see citing works
Dosage Compensation of the Sex Chromosomes
Distèche, C. M. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155454 · Cited by 210 · see citing works
“Imprinted genes are normally expressed either from the maternal or paternal allele, and severe phenotypes result from aberrant expression (9).”
Background
The role of DNA methylation in ageing and cancer
Morgan, A. E., Davies, T. J., & Auley, M. T. M. (2018) · Proceedings of The Nutrition Society · doi:10.1017/s0029665118000150 · Cited by 211 · see citing works
“Inappropriate methylation during development can result in imprinting failures and diseases including Beckwith–Wiedemann, Prader– Willi, Silver–Russell and Angelmans’ syndromes((19)).”
Background
Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation
Reinius, B., & Sandberg, R. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3888 · Cited by 187 · see citing works
Paternally expressed genes predominate in the placenta
Wang, X., Miller, D. C., Harman, R. M., Antczak, D. F., & Clark, A. G. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1308998110 · Cited by 191 · see citing works
“G imprinting is a form of epigenetic modification in which gene expression differs in an allele-specific manner depending on parent of origin (1).”
BackgroundInfluential
How does epigenetics influence the course of evolution?
Ashe, A., Colot, V., & Oldroyd, B. P. (2021) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2020.0111 · Cited by 189 · see citing works
The origin and evolution of genomic imprinting and viviparity in mammals
Renfree, M. B., Suzuki, S., & Kaneko‐Ishino, T. (2012) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0151 · Cited by 179 · see citing works
Metabolic Inputs into the Epigenome
Sharma, U., & Rando, O. J. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.02.003 · Cited by 167 · see citing works
Pathogenetics of alveolar capillary dysplasia with misalignment of pulmonary veins
Szafrański, P., Gambin, T., Dharmadhikari, A. V., Akdemir, K. C., Jhangiani, S. N., Schuette, J. J., Godiwala, N., Yatsenko, S. A., Sebastian, J., Madan‐Khetarpal, S., et al. (2016) · Human Genetics · doi:10.1007/s00439-016-1655-9 · Cited by 164 · see citing works
“3 in transient neonatal diabetes mellitus 1 (OMIM 601410) (Bartolomei and Ferguson-Smith 2011 ).”
CBP/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos
Wang, M., Chen, Z., & Zhang, Y. (2022) · The EMBO Journal · doi:10.15252/embj.2022112012 · Cited by 164 · see citing works
Paternal Contributions to Offspring Health: Role of Sperm Small RNAs in Intergenerational Transmission of Epigenetic Information
Sharma, U. (2019) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2019.00215 · Cited by 165 · see citing works
Mendelian Disorders of the Epigenetic Machinery: Tipping the Balance of Chromatin States
Fahrner, J. A., & Bjornsson, H. T. (2014) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090613-094245 · Cited by 161 · see citing works
“The classical imprinting disorders have traditionally been thought to result exclusively from individual locus-specific effects occurring in cis (9).”
Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maizePreprint
Zhang, M., Xie, S., Dong, X., Zhao, X., Zeng, B., Chen, J., Li, H., Yang, W., Zhao, H., Wang, G., et al. (2013) · Genome Research · doi:10.1101/gr.155879.113 · Cited by 157 · see citing works
Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression
Strogantsev, R., Krueger, F., Yamazawa, K., Shi, H., Gould, P., Goldman-Roberts, M., McEwen, K., Sun, B., Pedersen, R., & Ferguson-Smith, A. C. (2015) · Genome Biology · doi:10.1186/s13059-015-0672-7 · Cited by 152 · see citing works
“Genomic imprinting is a mechanism of gene regulation occurring in eutherian mammals and to a lesser extent marsupials [1–3].”
BackgroundSelf-citation
Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys
Li, Y., Zheng, H., Wang, Q., Zhou, C., Wei, L., Liu, X., Zhang, W., Zhang, Y., Du, Z., Wang, X., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1390-8 · Cited by 144 · see citing works
“DNA methylation is a major epigenetic mark regulating gene repression, genomic imprinting, and X chromosome inactivation [4, 5].”
Advanced paternal age effects in neurodevelopmental disorders—review of potential underlying mechanisms
Janecka, M., Mill, J., Basson, M. A., Goriely, A., Spiers, H., Reichenberg, A., Schalkwyk, L., & Fernandes, C. (2017) · Translational Psychiatry · doi:10.1038/tp.2016.294 · Cited by 140 · see citing works
The role of methylation of DNA in environmental adaptation
Flores, K. B., Wolschin, F., & Amdam, G. V. (2013) · Integrative and Comparative Biology · doi:10.1093/icb/ict019 · Cited by 143 · see citing works
Evolution and function of genomic imprinting in plantsPreprint
Rodrigues, J. A., & Zilberman, D. (2015) · Genes & Development · doi:10.1101/gad.269902.115 · Cited by 143 · see citing works
“Manymammalian imprintedgenesaffect resourceacquisition fromthematernal parent either by direct regulation of nutrient transfer from the placenta and embryo growth or through influence on maternal–offspring interactions (Bartolomei and Ferguson-Smith 2011).”
Background
Characterization of global loss of imprinting in fetal overgrowth syndrome induced by assisted reproduction
Chen, Z., Hagen, D. E., Elsik, C. G., Ji, T., Morris, C. J., Moon, L. E., & Rivera, R. M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1422088112 · Cited by 141 · see citing works
“Am J Med Genet C Semin Med Genet 137C(1):12–23.”
BackgroundInfluential
Transgenerational Epigenetic Effects on Brain Functions
Bohacek, J., Gapp, K., Saab, B. J., & Mansuy, I. M. (2012) · Biological Psychiatry · doi:10.1016/j.biopsych.2012.08.019 · Cited by 137 · see citing works
Allele-Specific Methylome and Transcriptome Analysis Reveals Widespread Imprinting in the Human Placenta
Hamada, H., Okae, H., Toh, H., Chiba, H., Hiura, H., Shirane, K., Sato, T., Suyama, M., Yaegashi, N., Sasaki, H., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.08.021 · Cited by 134 · see citing works
Epigenetic Research in Neuropsychiatric Disorders: the “Tissue Issue”
Bakulski, K. M., Halladay, A., Hu, V. W., Mill, J., & Fallin, M. D. (2016) · Current Behavioral Neuroscience Reports · doi:10.1007/s40473-016-0083-4 · Cited by 127 · see citing works
Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species
Waters, A. J., Bilinski, P., Eichten, S. R., Vaughn, M. W., Ross‐Ibarra, J., Gehring, M. A., & Springer, N. M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1309182110 · Cited by 130 · see citing works
“Imprinting is observed in both flowering plants and mammals (1–3) but there are differences in the mechanisms and organization of imprinted genes in these organisms (1, 4).”
Background
A Novel View of the Adult Stem Cell Compartment From the Perspective of a Quiescent Population of Very Small Embryonic-Like Stem Cells
Ratajczak, M. Z., Ratajczak, J., Suszyńska, M., Miller, D. M., Kucia, M., & Shin, D. (2017) · Circulation Research · doi:10.1161/circresaha.116.309362 · Cited by 127 · see citing works
“Based on the ability of uncultured VSELs to (1) differentiate in vivo into multiple mesenchymal lineages and (2) generate osseous tissues at low density, Taichman et al58 proposed that VSELs fulfill many of the required characteristics of precursors for MSCs. Recently, a similar bone-forming potential of human VSELs h…”
BackgroundInfluential
Epigenetic regulation in development: is the mouse a good model for the human?
Hanna, C. W., Demond, H., & Kelsey, G. (2018) · Human Reproduction Update · doi:10.1093/humupd/dmy021 · Cited by 126 · see citing works
Long noncoding RNA: an emerging player in diabetes and diabetic kidney disease
Guo, J., Liu, Z., & Gong, R. (2019) · Clinical Science · doi:10.1042/cs20190372 · Cited by 126 · see citing works
Intergenerational Transfer of Epigenetic Information in SpermPreprint
Rando, O. J. (2016) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a022988 · Cited by 126 · see citing works
Dosage compensation of the sex chromosomes and autosomes
Distèche, C. M. (2016) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2016.04.013 · Cited by 125 · see citing works
“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].”
Background
Random Monoallelic Gene Expression Increases upon Embryonic Stem Cell Differentiation
Eckersley-Maslin, M. A., Thybert, D., Bergmann, J. H., Marioni, J. C., Flicek, P., & Spector, D. L. (2014) · Developmental Cell · doi:10.1016/j.devcel.2014.01.017 · Cited by 123 · see citing works
“Well characterized and extensively studied examples include X-chromosome inactivation (reviewed in Guidi et al., 2004; Schulz and Heard, 2013), and genomic imprinting (reviewed in Bartolomei and Ferguson-Smith, 2011; McAnally and Yampolsky, 2010).”
Background
The KCNQ1OT1 imprinting control region and non-coding RNA: new properties derived from the study of Beckwith–Wiedemann syndrome and Silver–Russell syndrome cases
Chiesa, N., Crescenzo, A. D., Mishra, K., Perone, L., Carella, M., Palumbo, O., Mussa, A., Sparago, A., Cerrato, F., Russo, S., et al. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr419 · Cited by 123 · see citing works
“The molecular basis for ICR recognition during imprinting establishment is still undefined (1,2).”
Background
Stem cells in the hood: the skeletal muscle niche
Pannérec, A., Marazzi, G., & Sassoon, D. A. (2012) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2012.07.004 · Cited by 122 · see citing works
Evolving insights on how cytosine methylation affects protein-DNA binding
Dantas Machado, A. C., Zhou, T., Rao, S., Goel, P., Rastogi, C., Lazarovici, A., Bussemaker, H. J., & Rohs, R. (2015) · Briefings in Functional Genomics · doi:10.1093/bfgp/elu040 · Cited by 124 · see citing works
“genomic imprinting [3] and genome reprogramming”
Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions
Skinner, M. K., Manikkam, M., Haque, M. M., Zhang, B., & Savenkova, M. I. (2012) · Genome biology · doi:10.1186/gb-2012-13-10-r91 · Cited by 122 · see citing works
“Therefore, an epigenetic DNA methylation region can regulate the expression of a number of distal genes [17,28].”
BackgroundInfluential
Epigenetics and imprinting in human disease
Kalish, J. M., Jiang, C., & Bartolomei, M. S. (2014) · The International Journal of Developmental Biology · doi:10.1387/ijdb.140077mb · Cited by 119 · see citing works
“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).”
Method
Allelic H3K27me3 to allelic DNA methylation switch maintains noncanonical imprinting in extraembryonic cells
Chen, Z., Yin, Q., Inoue, A., Zhang, C., & Zhang, Y. (2019) · Science Advances · doi:10.1126/sciadv.aay7246 · Cited by 118 · see citing works
“, germline or primary differentially methylated regions (DMRs)], maintained in preimplantation embryos when global epigenetic reprogramming takes place, and eventually erased in primordial germ cells to reset the sperm- or oocyte-specific imprints (1).”
BackgroundInfluential
Genome accessibility is widely preserved and locally modulated during mitosisPreprint
Hsiung, C., Morrissey, C. S., Udugama, M., Frank, C. L., Keller, C. A., Baek, S., Giardine, B., Crawford, G. E., Sung, M.-H., Hardison, R., et al. (2015) · Genome Research · doi:10.1101/gr.180646.114 · Cited by 114 · see citing works
“…DNA methylation patterns specifically in mitosis, given its well-established role in epigenetic memory on the time scales of organismal development (Bartolomei and Ferguson-Smith 2011), it is reasonable to assume that DNA methylation is unaltered during mitosis and thus might contribute to one…”
Parent-offspring conflict and the evolution of infant-directed song
Mehr, S. A., & Krasnow, M. M. (2017) · Evolution and Human Behavior · doi:10.1016/j.evolhumbehav.2016.12.005 · Cited by 115 · see citing works
“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).”
Background
Forging our understanding of lncRNAs in the brain
Andersen, R., & Lim, D. A. (2017) · Cell and Tissue Research · doi:10.1007/s00441-017-2711-z · Cited by 112 · see citing works
Random monoallelic expression: regulating gene expression one allele at a time
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Environmentally induced epigenetic toxicity: potential public health concerns
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Rebooting the Epigenomes during Mammalian Early Embryogenesis
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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).”
Background
Epigenetic aberrations in human pluripotent stem cells
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“Thus, alteration in a single region can drive both biallelic expression and silencing of multiple genes (Bartolomei & Ferguson-Smith, 2011).”
Epigenetic Reprogramming in Early Animal DevelopmentPreprint
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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…”
Background
Methodological aspects of whole-genome bisulfite sequencing analysis
Adusumalli, S., Omar, M. F. M., Soong, R., & Benoukraf, T. (2014) · Briefings in Bioinformatics · doi:10.1093/bib/bbu016 · Cited by 101 · see citing works
“[87–90].”
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Toward a More Precise and Informative Nomenclature Describing Fetal and Neonatal Male Germ Cells in Rodents1
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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].”
Background
Quantitative 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 95 · see citing works
“…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).”
Background
The 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 94 · see citing works
A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiationPreprint
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Background
The molecular function and clinical phenotype of partial deletions of the IGF2/H19 imprinting control region depends on the spatial arrangement of the remaining CTCF-binding sites
Beygo, 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 · see citing works
“Histone modifications likely contribute to the establishment and/or maintenance of the differential expression of the imprinted genes on the parental alleles (4,5).”
Background
Using next-generation RNA sequencing to identify imprinted genes
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“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.,…”
Background
Targeted 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 · see citing works
“(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.”
Background
Igf2-H19, an imprinted tandem gene, is an important regulator of embryonic development, a guardian of proliferation of adult pluripotent stem cells, a regulator of longevity, and a ‘passkey’ to cancerogenesis
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BackgroundInfluential
Placental 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 · see citing works
“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…”
Background
DNA 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 · see citing works
Dynamics of DNA Methylation in Aging and Alzheimer's Disease
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“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).”
Background
Aberrant 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 · see citing works
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 84 · see citing works
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 84 · see citing works
Genomic Imprinting in the Arabidopsis Embryo Is Partly Regulated by PRC2
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BackgroundInfluential
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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 84 · see citing works
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Champagne, F. A. (2016) · Development and Psychopathology · doi:10.1017/s0954579416000808 · Cited by 80 · see citing works
“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).”
Background
Reactive oxygen species-induced alterations in H19-Igf2 methylation patterns, seminal plasma metabolites, and semen quality
Darbandi, 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 78 · see citing works
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DNA methylation in spermatozoa as a prospective marker in andrology
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“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).”
Background
Long noncoding RNA (lncRNA) H19: An essential developmental regulator with expanding roles in cancer, stem cell differentiation, and metabolic diseases
Liao, 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 · see citing works
“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…”
Background
The 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 75 · see citing works
“Genomic imprinting refers to the mechanism that drives parent-specific, monoallelic expression of a subset of genes in mammals (Bartolomei & Ferguson-Smith, 2011).”
Background
Effects of Cadmium Exposure on DNA Methylation at Imprinting Control Regions and Genome-Wide in Mothers and Newborn Children
Cowley, 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 76 · see citing works
Poly(ADP-ribosyl)ation Acts in the DNA Demethylation of Mouse Primordial Germ Cells Also with DNA Damage-Independent Roles
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“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].”
Background
DNMT1, 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 · see citing works
Conservation through the lens of (mal)adaptation: Concepts and meta‐analysis
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A multi-method approach to the molecular diagnosis of overt and borderline 11p15.5 defects underlying Silver–Russell and Beckwith–Wiedemann syndromes
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 · see citing works
“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…”
Background
Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing
Chen, Z., Hagen, D., Wang, J., Elsik, C., Ji, T.-M., Siqueira, L., Hansen, P., & Rivera, R. M. (2016) · Epigenetics · doi:10.1080/15592294.2016.1184805 · Cited by 54 · see citing works
“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.”
BackgroundInfluential
DNA 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 70 · see citing works
Effect of oocyte vitrification on deoxyribonucleic acid methylation of H19, Peg3, and Snrpn differentially methylated regions in mouse blastocysts
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 · see citing works

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)
DOI: 10.1101/cshperspect.a002592
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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