@article{pmid38167730,

title = {Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions},

author = {Phoebe Lut Fei Tam and Ming Fung Cheung and Lu Yan Chan and Danny Leung},

doi = {10.1038/s41467-023-44578-0},

issn = {2041-1723},

year  = {2024},

date = {2024-01-01},

journal = {Nat Commun},

volume = {15},

number = {1},

pages = {15},

abstract = {SETDB1 is an essential histone methyltransferase that deposits histone H3 lysine 9 trimethylation (H3K9me3) to transcriptionally repress genes and repetitive elements. The function of differential H3K9me3 enrichment between cell-types remains unclear. Here, we demonstrate mutual exclusivity of H3K9me3 and CTCF across mouse tissues from different developmental timepoints. We analyze SETDB1 depleted cells and discover that H3K9me3 prevents aberrant CTCF binding independently of DNA methylation and H3K9me2. Such sites are enriched with SINE B2 retrotransposons. Moreover, analysis of higher-order genome architecture reveals that large chromatin structures including topologically associated domains and subnuclear compartments, remain intact in SETDB1 depleted cells. However, chromatin loops and local 3D interactions are disrupted, leading to transcriptional changes by modifying pre-existing chromatin landscapes. Specific genes with altered expression show differential interactions with dysregulated cis-regulatory elements. Collectively, we find that cell-type specific targets of SETDB1 maintain cellular identities by modulating CTCF binding, which shape nuclear architecture and transcriptomic networks.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38003607,

title = {The Molecular Impacts of Retrotransposons in Development and Diseases},

author = {Phoebe Lut Fei Tam and Danny Leung},

doi = {10.3390/ijms242216418},

issn = {1422-0067},

year  = {2023},

date = {2023-11-01},

journal = {Int J Mol Sci},

volume = {24},

number = {22},

abstract = {Retrotransposons are invasive genetic elements that constitute substantial portions of mammalian genomes. They have the potential to influence nearby gene expression through their -regulatory sequences, reverse transcription machinery, and the ability to mold higher-order chromatin structures. Due to their multifaceted functions, it is crucial for host fitness to maintain strict regulation of these parasitic sequences to ensure proper growth and development. This review explores how subsets of retrotransposons have undergone evolutionary exaptation to enhance the complexity of mammalian genomes. It also highlights the significance of regulating these elements, drawing on recent studies conducted in human and murine systems.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37639608,

title = {Differential second messenger signaling via dopamine neurons bidirectionally regulates memory retention},

author = {Mai Takakura and Yu Hong Lam and Reiko Nakagawa and Man Yung Ng and Xinyue Hu and Priyanshu Bhargava and Abdalla G Alia and Yuzhe Gu and Zigao Wang and Takeshi Ota and Yoko Kimura and Nao Morimoto and Fumitaka Osakada and Ah Young Lee and Danny Leung and Tomoyuki Miyashita and Juan Du and Hiroyuki Okuno and Yukinori Hirano},

doi = {10.1073/pnas.2304851120},

issn = {1091-6490},

year  = {2023},

date = {2023-09-01},

journal = {Proc Natl Acad Sci U S A},

volume = {120},

number = {36},

pages = {e2304851120},

abstract = {Memory formation and forgetting unnecessary memory must be balanced for adaptive animal behavior. While cyclic AMP (cAMP) signaling via dopamine neurons induces memory formation, here we report that cyclic guanine monophosphate (cGMP) signaling via dopamine neurons launches forgetting of unconsolidated memory in . Genetic screening and proteomic analyses showed that neural activation induces the complex formation of a histone H3K9 demethylase, Kdm4B, and a GMP synthetase, Bur, which is necessary and sufficient for forgetting unconsolidated memory. Kdm4B/Bur is activated by phosphorylation through NO-dependent cGMP signaling via dopamine neurons, inducing gene expression, including  encoding a presynaptic protein. Accordingly, Kdm4B/Bur activation induced presynaptic changes. Our data demonstrate a link between cGMP signaling and synapses via gene expression in forgetting, suggesting that the opposing functions of memory are orchestrated by distinct signaling via dopamine neurons, which affects synaptic integrity and thus balances animal behavior.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gao2023,

title = {Single-cell analysis reveals transcriptomic and epigenomic impacts on the maternal–fetal interface following SARS-CoV-2 infection},

author = {Lin Gao and Vrinda Mathur and Sabrina Ka Man Tam and Xuemeng Zhou and Ming Fung Cheung and Lu Yan Chan and Guadalupe Estrada-Gutiérrez and Bo Wah Leung and Sakita Moungmaithong and Chi Chiu Wang and Liona C. Poon and Danny Leung},

doi = {10.1038/s41556-023-01169-x},

issn = {14764679},

year  = {2023},

date = {2023-01-01},

journal = {Nature Cell Biology},

volume = {25},

issue = {7},

abstract = {During pregnancy the maternal–fetal interface plays vital roles in fetal development. Its disruption is frequently found in pregnancy complications. Recent studies show increased incidences of adverse pregnancy outcomes in patients with COVID-19; however, the mechanism remains unclear. Here we analysed the molecular impacts of SARS-CoV-2 infection on the maternal–fetal interface. Generating bulk and single-nucleus transcriptomic and epigenomic profiles from patients with COVID-19 and control samples, we discovered aberrant immune activation and angiogenesis patterns in distinct cells from patients. Surprisingly, retrotransposons were also dysregulated in specific cell types. Notably, reduced enhancer activities of LTR8B elements were functionally linked to the downregulation of pregnancy-specific glycoprotein genes in syncytiotrophoblasts. Our findings revealed that SARS-CoV-2 infection induced substantial changes to the epigenome and transcriptome at the maternal–fetal interface, which may be associated with pregnancy complications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lee2021,

title = {Humanizing the yeast origin recognition complex},

author = {Clare S. K. Lee and Ming Fung Cheung and Jinsen Li and Yongqian Zhao and Wai Hei Lam and Vincy Ho and Remo Rohs and Yuanliang Zhai and Danny Leung and Bik Kwoon Tye},

doi = {10.1038/s41467-020-20277-y},

issn = {20411723},

year  = {2021},

date = {2021-01-01},

journal = {Nature Communications},

volume = {12},

issue = {1},

abstract = {The Origin Recognition Complex (ORC) is an evolutionarily conserved six-subunit protein complex that binds specific sites at many locations to coordinately replicate the entire eukaryote genome. Though highly conserved in structure, ORC’s selectivity for replication origins has diverged tremendously between yeasts and humans to adapt to vastly different life cycles. In this work, we demonstrate that the selectivity determinant of ORC for DNA binding lies in a 19-amino acid insertion helix in the Orc4 subunit, which is present in yeast but absent in human. Removal of this motif from Orc4 transforms the yeast ORC, which selects origins based on base-specific binding at defined locations, into one whose selectivity is dictated by chromatin landscape and afforded with plasticity, as reported for human. Notably, the altered yeast ORC has acquired an affinity for regions near transcriptional start sites (TSSs), which the human ORC also favors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Klein2021,

title = {Replication timing maintains the global epigenetic state in human cells},

author = {Kyle N. Klein and Peiyao A. Zhao and Xiaowen Lyu and Takayo Sasaki and Daniel A. Bartlett and Amar M. Singh and Ipek Tasan and Meng Zhang and Lotte P. Watts and Shin Ichiro Hiraga and Toyoaki Natsume and Xuemeng Zhou and Timour Baslan and Danny Leung and Masato T. Kanemaki and Anne D. Donaldson and Huimin Zhao and Stephen Dalton and Victor G. Corces and David M. Gilbert},

doi = {10.1126/science.aba5545},

issn = {10959203},

year  = {2021},

date = {2021-01-01},

journal = {Science},

volume = {372},

issue = {6540},

abstract = {The temporal order of DNA replication [replication timing (RT)] is correlated with chromatin modifications and three-dimensional genome architecture; however, causal links have not been established, largely because of an inability to manipulate the global RT program. We show that loss of RIF1 causes near-complete elimination of the RT program by increasing heterogeneity between individual cells. RT changes are coupled with widespread alterations in chromatin modifications and genome compartmentalization. Conditional depletion of RIF1 causes replication-dependent disruption of histone modifications and alterations in genome architecture. These effects were magnified with successive cycles of altered RT. These results support models in which the timing of chromatin replication and thus assembly plays a key role in maintaining the global epigenetic state.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Song2021,

title = {DNA repair inhibition leads to active export of repetitive sequences to the cytoplasm triggering an inflammatory response},

author = {Xuan Song and Jacqueline T. M. Aw and Fulin Ma and Ming Fung Cheung and Danny Leung and Karl Herrup},

doi = {10.1523/JNEUROSCI.0845-21.2021},

issn = {15292401},

year  = {2021},

date = {2021-01-01},

journal = {Journal of Neuroscience},

volume = {41},

issue = {45},

abstract = {Adult-onset neurodegenerative diseases are often accompanied by evidence of a chronic inflammation that includes activation of microglial cells and altered levels of brain cytokines. Aspects of this response are likely secondary reactions to neurodegeneration, but for many illnesses the inflammation may itself be an early and even causative disease event. In such cases, the inflammation is referred to as “sterile” as it occurs in the absence of an actual bacterial or viral pathogen. A potent trigger of sterile inflammation in CNS microglia has been shown to be the presence of DNA in the cytoplasm (cytoDNA) induced either by direct DNA damage or by inhibited DNA repair. We have shown that cytoDNA comes from the cell nucleus as a result of insufficient DNA damage repair. Using wild-type and Atm-/- mouse microglia, we extend these observations here by showing that its genomic origins are not random, but rather are heavily biased toward transcriptionally inactive, intergenic regions, in particular repetitive elements and AT-rich sequences. Once released from the genome, in both males and females, we show that cytoDNA is actively exported to the cytoplasm by a CRM1-dependent mechanism. In the cytoplasm, it is degraded either by a cytosolic exonuclease, Trex1, or an autophagy pathway that ends with degradation in the lysosome. Blocking the accumulation of cytoDNA prevents the emergence of the sterile inflammation reaction. These findings offer new insights into the emergence of sterile inflammation and offer novel approaches that may be of use in combatting a wide range of neurodegenerative conditions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhou2021,

title = {Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations},

author = {Xuemeng Zhou and Tsz Wing Sam and Ah Young Lee and Danny Leung},

doi = {10.1038/s41467-021-26630-z},

issn = {20411723},

year  = {2021},

date = {2021-01-01},

journal = {Nature Communications},

volume = {12},

issue = {1},

abstract = {Polymorphic integrations of endogenous retroviruses (ERVs) have been previously detected in mouse and human genomes. While most are inert, a subset can influence the activity of the host genes. However, the molecular mechanism underlying how such elements affect the epigenome and transcriptome and their roles in driving intra-specific variation remain unclear. Here, by utilizing wildtype murine embryonic stem cells (mESCs) derived from distinct genetic backgrounds, we discover a polymorphic MMERGLN (GLN) element capable of regulating H3K27ac enrichment and transcription of neighboring loci. We demonstrate that this polymorphic element can enhance the neighboring Klhdc4 gene expression in cis, which alters the activity of downstream stress response genes. These results suggest that the polymorphic ERV-derived cis-regulatory element contributes to differential phenotypes from stimuli between mouse strains. Moreover, we identify thousands of potential polymorphic ERVs in mESCs, a subset of which show an association between proviral activity and nearby chromatin states and transcription. Overall, our findings elucidate the mechanism of how polymorphic ERVs can shape the epigenome and transcriptional networks that give rise to phenotypic divergence between individuals.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Cao2020,

title = {A unified framework for integrative study of heterogeneous gene regulatory mechanisms},

author = {Qin Cao and Zhenghao Zhang and Alexander Xi Fu and Qiong Wu and Tin Lap Lee and Eric Lo and Alfred S. L. Cheng and Chao Cheng and Danny Leung and Kevin Y. Yip},

doi = {10.1038/s42256-020-0205-2},

issn = {25225839},

year  = {2020},

date = {2020-01-01},

journal = {Nature Machine Intelligence},

volume = {2},

issue = {8},

abstract = {Gene expression is regulated by a large variety of mechanisms. Previous studies attempting to model the quantitative relationships between gene expression levels and regulatory mechanisms have considered only one or a few mechanisms at a time, which cannot provide a full picture of the complex interactions among different mechanisms. This was partially due to the heterogeneity of the mechanisms, which involve different types of biological objects and data representations, making it hard to study them in a unified way. Here, we describe a flexible framework that can integrate very different types of data for studying their joint effects on gene expression. In this framework, domain knowledge is represented by metapaths, while the manifestations of their effects in actual data are summarized by an embedding of the biological objects in a latent space. We demonstrate the use of our framework in integrating several diverse types of data that are related to gene expression in different ways, including DNA contacts in three-dimensional genome architecture, protein–protein interactions, genomic neighbourhoods and broad chromatin accessibility domains. The modelling results reveal that these several types of data are able to model gene expression fairly well individually, but even better when integrated.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jiang2020,

title = {G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing, and Chromatin Looping},

author = {Qinghong Jiang and Julie Y. J. Ang and Ah Young Lee and Qin Cao and Kelly Y. Li and Kevin Y. Yip and Danny C. Y. Leung},

doi = {10.1016/j.celrep.2020.108315},

issn = {22111247},

year  = {2020},

date = {2020-01-01},

journal = {Cell Reports},

volume = {33},

issue = {4},

abstract = {G9a is an epigenetic modifier with essential roles in development. Jiang et al. show the regulation of epigenetic modifications, transcription, and chromatin structures by G9a. This protein functions through both catalytic-dependent and -independent mechanisms to repress regulatory elements and retrotransposons. Moreover, G9a affects chromatin looping by preventing aberrant CTCF/cohesin binding.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chee2018,

title = {Targeting Epigenetic Modifiers for Cancer Treatments},

author = {Chin Soon Chee and Danny Leung},

doi = {10.1007/s40495-018-0130-9},

issn = {2198641X},

year  = {2018},

date = {2018-01-01},

journal = {Current Pharmacology Reports},

volume = {4},

issue = {3},

abstract = {DNA methylation and covalent histone modifications are precisely and dynamically controlled by various epigenetic modifiers and are critical aspects of transcriptional regulation. Dysregulation of these enzymes results in a wide range of diseases including cancers. In recent years, epigenetic modifiers have become the focus of many cancer treatment studies and clinical trials. Currently, several drugs such as DNA methyltransferase inhibitors and histone deacetylase inhibitors have been approved for clinical use in cancer treatments. However, many more are on the horizon. In this review, we will discuss the roles of DNA methyltransferases, histone acetyltransferases/deacetylases, histone methyltransferases/demethylases, and acetylated histone lysine-binding proteins in oncogenesis and some of the current inhibitors targeting these epigenetic modifiers for therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhang2016,

title = {Isoform Switch of TET1 Regulates DNA Demethylation and Mouse Development},

author = {Wenhao Zhang and Weikun Xia and Qiujun Wang and Aaron J. Towers and Jiayu Chen and Rui Gao and Yu Zhang and Chia Yen and Ah Young Lee and Yuanyuan Li and Chen Zhou and Kaili Liu and Jing Zhang and Tian Peng Gu and Xiuqi Chen and Zai Chang and Danny Leung and Shaorong Gao and Yong Jiang and Wei Xie},

doi = {10.1016/j.molcel.2016.10.030},

issn = {10974164},

year  = {2016},

date = {2016-01-01},

journal = {Molecular Cell},

volume = {64},

issue = {6},

abstract = {The methylcytosine oxidase TET proteins play important roles in DNA demethylation and development. However, it remains elusive how exactly they target substrates and execute oxidation. Interestingly, we found that, in mice, the full-length TET1 isoform (TET1e) is restricted to early embryos, embryonic stem cells (ESCs), and primordial germ cells (PGCs). By contrast, a short isoform (TET1s) is preferentially expressed in somatic cells, which lacks the N terminus including the CXXC domain, a DNA-binding module that often recognizes CpG islands (CGIs) where TET1 predominantly occupies. Unexpectedly, TET1s can still bind CGIs despite the fact that its global chromatin binding is significantly reduced. Interestingly, global chromatin binding, but not targeted binding at CGIs, is correlated with TET1-mediated demethylation. Finally, mice with exclusive expression of Tet1s failed to erase imprints in PGCs and displayed developmental defects in progeny. These data show that isoform switch of TET1 regulates epigenetic memory erasure and mouse development.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Leung2015,

title = {Integrative analysis of haplotype-resolved epigenomes across human tissues},

author = {Danny Leung and Inkyung Jung and Nisha Rajagopal and Anthony Schmitt and Siddarth Selvaraj and Ah Young Lee and Chia An Yen and Shin Lin and Yiing Lin and Yunjiang Qiu and Wei Xie and Feng Yue and Manoj Hariharan and Pradipta Ray and Samantha Kuan and Lee Edsall and Hongbo Yang and Neil C. Chi and Michael Q. Zhang and Joseph R. Ecker and Bing Ren},

doi = {10.1038/nature14217},

issn = {14764687},

year  = {2015},

date = {2015-01-01},

journal = {Nature},

volume = {518},

issue = {7539},

abstract = {Allelic differences between the two homologous chromosomes can affect the propensity of inheritance in humans; however, the extent of such differences in the human genome has yet to be fully explored. Here we delineate allelic chromatin modifications and transcriptomes among a broad set of human tissues, enabled by a chromosome-spanning haplotype reconstruction strategy. The resulting large collection of haplotype-resolved epigenomic maps reveals extensive allelic biases in both chromatin state and transcription, which show considerable variation across tissues and between individuals, and allow us to investigate cis-regulatory relationships between genes and their control sequences. Analyses of histone modification maps also uncover intriguing characteristics of cis-regulatory elements and tissue-restricted activities of repetitive elements. The rich data sets described here will enhance our understanding of the mechanisms by which cis-regulatory elements control gene expression programs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Integrative analysis of 111 reference human epigenomes},

author = {Roadmap Epigenomics Consortium and Anshul Kundaje and Wouter Meuleman and Jason Ernst and Misha Bilenky and Angela Yen and Alireza Heravi-Moussavi and Pouya Kheradpour and Zhizhuo Zhang and Jianrong Wang and Michael J. Ziller and Viren Amin and John W. Whitaker and Matthew D. Schultz and Lucas D. Ward and Abhishek Sarkar and Gerald Quon and Richard S. Sandstrom and Matthew L. Eaton and Yi Chieh Wu and Andreas R. Pfenning and Xinchen Wang and Melina Claussnitzer and Yaping Liu and Cristian Coarfa and R. Alan Harris and Noam Shoresh and Charles B. Epstein and Elizabeta Gjoneska and Danny Leung and Wei Xie and R. David Hawkins and Ryan Lister and Chibo Hong and Philippe Gascard and Andrew J. Mungall and Richard Moore and Eric Chuah and Angela Tam and Theresa K. Canfield and R. Scott Hansen and Rajinder Kaul and Peter J. Sabo and Mukul S. Bansal and Annaick Carles and Jesse R. Dixon and Kai How Farh and Soheil Feizi and Rosa Karlic and Ah Ram Kim and Ashwinikumar Kulkarni and Daofeng Li and Rebecca Lowdon and Ginell Elliott and Tim R. Mercer and Shane J. Neph and Vitor Onuchic and Paz Polak and Nisha Rajagopal and Pradipta Ray and Richard C. Sallari and Kyle T. Siebenthall and Nicholas A. Sinnott-Armstrong and Michael Stevens and Robert E. Thurman and Jie Wu and Bo Zhang and Xin Zhou and Arthur E. Beaudet and Laurie A. Boyer and Philip L. De Jager and Peggy J. Farnham and Susan J. Fisher and David Haussler and Steven J. M. Jones and Wei Li and Marco A. Marra and Michael T. McManus and Shamil Sunyaev and James A. Thomson and Thea D. Tlsty and Li Huei Tsai and Wei Wang and Robert A. Waterland and Michael Q. Zhang and Lisa H. Chadwick and Bradley E. Bernstein and Joseph F. Costello and Joseph R. Ecker and Martin Hirst and Alexander Meissner and Aleksandar Milosavljevic and Bing Ren and John A. Stamatoyannopoulos and Ting Wang and Manolis Kellis},

doi = {10.1038/nature14248},

issn = {14764687},

year  = {2015},

date = {2015-01-01},

journal = {Nature},

volume = {518},

issue = {7539},

abstract = {The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease-and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schultz2015,

title = {Human body epigenome maps reveal noncanonical DNA methylation variation},

author = {Matthew D. Schultz and Yupeng He and John W. Whitaker and Manoj Hariharan and Eran A. Mukamel and Danny Leung and Nisha Rajagopal and Joseph R. Nery and Mark A. Urich and Huaming Chen and Shin Lin and Yiing Lin and Inkyung Jung and Anthony D. Schmitt and Siddarth Selvaraj and Bing Ren and Terrence J. Sejnowski and Wei Wang and Joseph R. Ecker},

doi = {10.1038/nature14465},

issn = {14764687},

year  = {2015},

date = {2015-01-01},

journal = {Nature},

volume = {523},

issue = {7559},

abstract = {Understanding the diversity of human tissues is fundamental to disease and requires linking genetic information, which is identical in most of an individualâ €™ s cells, with epigenetic mechanisms that could have tissue-specific roles. Surveys of DNA methylation in human tissues have established a complex landscape including both tissue-specific and invariant methylation patterns. Here we report high coverage methylomes that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence. By combining these diverse data types with each individualsâ €™ phased genome, we identified widespread tissue-specific differential CG methylation (mCG), partially methylated domains, allele-specific methylation and transcription, and the unexpected presence of non-CG methylation (mCH) in almost all human tissues. mCH correlated with tissue-specific functions, and using this mark, we made novel predictions of genes that escape X-chromosome inactivation in specific tissues. Overall, DNA methylation in several genomic contexts varies substantially among human tissues.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kelsey2015,

title = {Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST},

author = {Angela D. Kelsey and Christine Yang and Danny Leung and Jakub Minks and Thomas Dixon-McDougall and Sarah E. L. Baldry and Aaron B. Bogutz and Louis Lefebvre and Carolyn J. Brown},

doi = {10.1186/s13059-015-0774-2},

issn = {1474760X},

year  = {2015},

date = {2015-01-01},

journal = {Genome Biology},

volume = {16},

issue = {1},

abstract = {Background: X-chromosome inactivation is a striking example of epigenetic silencing in which expression of the long non-coding RNA XIST initiates the heterochromatinization and silencing of one of the pair of X chromosomes in mammalian females. To understand how the RNA can establish silencing across millions of basepairs of DNA we have modelled the process by inducing expression of XIST from nine different locations in human HT1080 cells. Results: Localization of XIST, depletion of Cot-1 RNA, perinuclear localization, and ubiquitination of H2A occurs at all sites examined, while recruitment of H3K9me3 was not observed. Recruitment of the heterochromatic features SMCHD1, macroH2A, H3K27me3, and H4K20me1 occurs independently of each other in an integration site-dependent manner. Silencing of flanking reporter genes occurs at all sites, but the spread of silencing to flanking endogenous human genes is variable in extent of silencing as well as extent of spread, with silencing able to skip regions. The spread of H3K27me3 and loss of H3K27ac correlates with the pre-existing levels of the modifications, and overall the extent of silencing correlates with the ability to recruit additional heterochromatic features. Conclusions: The non-coding RNA XIST functions as a cis-acting silencer when expressed from nine different locations throughout the genome. A hierarchy among the features of heterochromatin reveals the importance of interaction with the local chromatin neighborhood for optimal spread of silencing, as well as the independent yet cooperative nature of the establishment of heterochromatin by the non-coding XIST RNA.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Leung2014,

title = {Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1},

author = {Danny Leung and Tingting Du and Ulrich Wagner and Wei Xie and Ah Young Lee and Preeti Goyal and Yujing Li and Keith E. Szulwach and Peng Jin and Matthew C. Lorincz and Bing Ren},

doi = {10.1073/pnas.1322273111},

issn = {10916490},

year  = {2014},

date = {2014-01-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {111},

issue = {18},

abstract = {During mammalian development, DNA methylation patterns need to be reset in primordial germ cells (PGCs) and preimplantation embryos. However, many LTR retrotransposons and imprinted genes are impervious to such global epigenetic reprogramming via hitherto undefined mechanisms. Here, we report that a subset of such genomic regions are resistant to widespread erasure of DNA methylation in mouse embryonic stem cells (mESCs) lacking the de novo DNA methyltransferases (Dnmts) Dnmt3a and Dnmt3b. Intriguingly, these loci are enriched for H3K9me3 in mESCs, implicating this mark in DNA methylation homeostasis. Indeed, deletion of the H3K9 methyltransferase SET domain bifurcated 1 (Setdb1) results in reduced H3K9me3 and DNA methylation levels at specific loci, concomitant with increased 5-hydroxymethylation (5hmC) and ten-eleven translocation 1 binding. Taken together, these data reveal that Setdb1 promotes the persistence of DNA methylation in mESCs, likely reflecting one mechanism by which DNA methylation is maintained at LTR retrotransposons and imprinted genes during developmental stages when DNA methylation is reprogrammed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Xie2013,

title = {Epigenomic analysis of multilineage differentiation of human embryonic stem cells},

author = {Wei Xie and Matthew D. Schultz and Ryan Lister and Zhonggang Hou and Nisha Rajagopal and Pradipta Ray and John W. Whitaker and Shulan Tian and R. David Hawkins and Danny Leung and Hongbo Yang and Tao Wang and Ah Young Lee and Scott A. Swanson and Jiuchun Zhang and Yun Zhu and Audrey Kim and Joseph R. Nery and Mark A. Urich and Samantha Kuan and Chia An Yen and Sarit Klugman and Pengzhi Yu and Kran Suknuntha and Nicholas E. Propson and Huaming Chen and Lee E. Edsall and Ulrich Wagner and Yan Li and Zhen Ye and Ashwinikumar Kulkarni and Zhenyu Xuan and Wen Yu Chung and Neil C. Chi and Jessica E. Antosiewicz-Bourget and Igor Slukvin and Ron Stewart and Michael Q. Zhang and Wei Wang and James A. Thomson and Joseph R. Ecker and Bing Ren},

doi = {10.1016/j.cell.2013.04.022},

issn = {10974172},

year  = {2013},

date = {2013-01-01},

journal = {Cell},

volume = {153},

issue = {5},

abstract = {Epigenetic mechanisms have been proposed to play crucial roles in mammalian development, but their precise functions are only partially understood. To investigate epigenetic regulation of embryonic development, we differentiated human embryonic stem cells into mesendoderm, neural progenitor cells, trophoblast-like cells, and mesenchymal stem cells and systematically characterized DNA methylation, chromatin modifications, and the transcriptome in each lineage. We found that promoters that are active in early developmental stages tend to be CG rich and mainly engage H3K27me3 upon silencing in nonexpressing lineages. By contrast, promoters for genes expressed preferentially at later stages are often CG poor and primarily employ DNA methylation upon repression. Interestingly, the early developmental regulatory genes are often located in large genomic domains that are generally devoid of DNA methylation in most lineages, which we termed DNA methylation valleys (DMVs). Our results suggest that distinct epigenetic mechanisms regulate early and late stages of ES cell differentiation. © 2013 Elsevier Inc.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Leung2012,

title = {Silencing of endogenous retroviruses: When and why do histone marks predominate?},

author = {Danny C. Leung and Matthew C. Lorincz},

doi = {10.1016/j.tibs.2011.11.006},

issn = {09680004},

year  = {2012},

date = {2012-01-01},

journal = {Trends in Biochemical Sciences},

volume = {37},

issue = {4},

abstract = {Retrotransposons, such as endogenous retroviruses (ERVs), have colonized the genomes of all metazoans. As retrotransposition can be deleterious, numerous pathways have evolved to repress the expression of these parasitic elements. For example, methylation of the fifth carbon of the cytosine base in DNA (5-methylcytosine, 5mC) is required for transcriptional silencing of ERVs in differentiated cells. However, this epigenetic mark is generally dispensable for ERV silencing during early stages of mouse embryogenesis and in mouse embryonic stem cells (mESCs). In this Opinion, we evaluate recent findings on the exceptional role of covalent modifications of histones in ERV silencing in these cell types. In addition, we discuss the potential role of TET proteins, which catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), in perturbing transcriptional silencing, and propose that histone modification-based pathways may be used to silence ERVs during those developmental stages when DNA methylation-mediated silencing is compromised. © 2011.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Penetrance of biallelic SMARCAL1 mutations is associated with environmental and genetic disturbances of gene expression},

author = {Alireza Baradaran-Heravi and Kyoung Sang Cho and Bas Tolhuis and Mrinmoy Sanyal and Olena Morozova and Marie Morimoto and Leah I. Elizondo and Darren Bridgewater and Joanna Lubieniecka and Kimberly Beirnes and Clara Myung and Danny Leung and Hok Khim Fam and Kunho Choi and Yan Huang and Kira Y. Dionis and Jonathan Zonana and Kory Keller and Peter Stenzel and Christy Mayfield and Thomas Lücke and Arend Bokenkamp and Marco A. Marra and Maarten Van Lohuizen and David B. Lewis and Chad Shaw and Cornelius F. Boerkoel},

doi = {10.1093/hmg/dds083},

issn = {09646906},

year  = {2012},

date = {2012-01-01},

journal = {Human Molecular Genetics},

volume = {21},

issue = {11},

abstract = {Biallelic mutations of the DNA annealing helicase SMARCAL1 (SWI/SNF-related, matrix-associated, actindependent regulator of chromatin, subfamily a-like 1) cause Schimke immuno-osseous dysplasia (SIOD, MIM 242900), an incompletely penetrant autosomal recessive disorder. Using human, Drosophila and mouse models, we show that the proteins encoded by SMARCAL1 orthologs localize to transcriptionally active chromatin and modulate gene expression. We also show that, as found in SIOD patients, deficiency of the SMARCAL1 orthologs alone is insufficient to cause disease in fruit flies and mice, although such deficiency causes modest diffuse alterations in gene expression. Rather, disease manifests when SMARCAL1 deficiency interacts with genetic and environmental factors that further alter gene expression. We conclude that the SMARCAL1 annealing helicase buffers fluctuations in gene expression and that alterations in gene expression contribute to the penetrance of SIOD.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Leung2011,

title = {Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment, but not the maintenance, of proviral silencing},

author = {Danny C. Leung and Kevin B. Dong and Irina A. Maksakova and Preeti Goyal and Ruth Appanah and Sandra Lee and Makoto Tachibana and Yoichi Shinkai and Bernhard Lehnertz and Dixie L. Mager and Fabio Rossi and Matthew C. Lorincz},

doi = {10.1073/pnas.1014660108},

issn = {10916490},

year  = {2011},

date = {2011-01-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

volume = {108},

issue = {14},

abstract = {Methylation on lysine 9 of histone H3 (H3K9me) and DNA methylation play important roles in the transcriptional silencing of specific genes and repetitive elements. Both marks are detected on class I and II endogenous retroviruses (ERVs) in murine embryonic stem cells (mESCs). Recently, we reported that the H3K9-specific lysine methyltransferase (KMTase) Eset/Setdb1/KMT1E is required for H3K9me3 and the maintenance of silencing of ERVs in mESCs. In contrast, G9a/Ehmt2/KMT1C is dispensable, despite the fact that this KMTase is required for H3K9 dimethylation (H3K9me2) and efficient DNA methylation of these retroelements. Transcription of the exogenous retrovirus (XRV) Moloney murine leukemia virus is rapidly extinguished after integration in mESCs, concomitant with de novo DNA methylation. However, the role that H3K9 KMTases play in this process has not been addressed. Here, we demonstrate that G9a, but not Suv39h1 or Suv39h2, is required for silencing of newly integrated Moloney murine leukemia virus-based vectors in mESCs. The silencing defect in G9a-/- cells is accompanied by a reduction of H3K9me2 at the proviral LTR, indicating that XRVs are direct targets of G9a. Furthermore, de novo DNA methylation of newly integrated proviruses is impaired in the G9a-/- line, phenocopying proviral DNA methylation and silencing defects observed in Dnmt3a-deficient mESCs. Once established, however, maintenance of silencing of XRVs, like ERVs, is dependent exclusively on the KMTase Eset. Taken together, these observations reveal that in mESCs, the H3K9 KMTase G9a is required for the establishment, but not for the maintenance, of silencing of newly integrated proviruses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Karimi2011,

title = {DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mescs},

author = {Mohammad M. Karimi and Preeti Goyal and Irina A. Maksakova and Misha Bilenky and Danny Leung and Jie Xin Tang and Yoichi Shinkai and Dixie L. Mager and Steven Jones and Martin Hirst and Matthew C. Lorincz},

doi = {10.1016/j.stem.2011.04.004},

issn = {19345909},

year  = {2011},

date = {2011-01-01},

journal = {Cell Stem Cell},

volume = {8},

issue = {6},

abstract = {DNA methylation and histone H3 lysine 9 trimethylation (H3K9me3) play important roles in silencing of genes and retroelements. However, a comprehensive comparison of genes and repetitive elements repressed by these pathways has not been reported. Here we show that in mouse embryonic stem cells (mESCs), the genes upregulated after deletion of the H3K9 methyltransferase Setdb1 are distinct from those derepressed in mESC deficient in the DNA methyltransferases Dnmt1, Dnmt3a, and Dnmt3b, with the exception of a small number of primarily germline-specific genes. Numerous endogenous retroviruses (ERVs) lose H3K9me3 and are concomitantly derepressed exclusively in SETDB1 knockout mESCs. Strikingly, ∼15% of upregulated genes are induced in association with derepression of promoter-proximal ERVs, half in the context of "chimeric" transcripts that initiate within these retroelements and splice to genic exons. Thus, SETDB1 plays a previously unappreciated yet critical role in inhibiting aberrant gene transcription by suppressing the expression of proximal ERVs. © 2011 Elsevier Inc.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Matsui2010,

title = {Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET},

author = {Toshiyuki Matsui and Danny Leung and Hiroki Miyashita and Irina A. Maksakova and Hitoshi Miyachi and Hiroshi Kimura and Makoto Tachibana and Matthew C. Lorincz and Yoichi Shinkai},

doi = {10.1038/nature08858},

issn = {00280836},

year  = {2010},

date = {2010-01-01},

journal = {Nature},

volume = {464},

issue = {7290},

abstract = {Endogenous retroviruses (ERVs), retrovirus-like elements with long terminal repeats, are widely dispersed in the euchromatic compartment in mammalian cells, comprising ∼10% of the mouse genome1. These parasitic elements are responsible for >10% of spontaneous mutations2. Whereas DNA methylation has an important role in proviral silencing in somatic and germ-lineage cells3-5, an additional DNA-methylation-independent pathway also functions in embryonal carcinoma and embryonic stem (ES) cells to inhibit transcription of the exogenous gammaretrovirus murine leukaemia virus (MLV)6-8. Notably, a recent genome-wide study revealed that ERVs are also marked by histone H3 lysine 9 trimethylation (H3K9me3) and H4K20me3 in ES cells but not in mouse embryonic fibroblasts9. However, the role that these marks have in proviral silencing remains unexplored. Here we show that the H3K9 methyltransferase ESET (also called SETDB1 or KMT1E) and the Krüppel-associated box (KRAB)-associated protein 1 (KAP1, also called TRIM28)10,11 are required for H3K9me3 and silencing of endogenous and introduced retroviruses specifically in mouse ES cells. Furthermore, whereas ESET enzymatic activity is crucial for HP1 binding and efficient proviral silencing, the H4K20 methyltransferases Suv420h1 and Suv420h2 are dispensable for silencing. Notably, in DNA methyltransferase triple knockout (Dnmt1 -/- Dnmt3a-/- Dnmt3b-/-) mouse ES cells, ESET and KAP1 binding and ESET-mediated H3K9me3 are maintained and ERVs are minimally derepressed. We propose that a DNA-methylation-independent pathway involving KAP1 and ESET/ESET-mediated H3K9me3 is required for proviral silencing during the period early in embryogenesis when DNA methylation is dynamically reprogrammed. © 2010 Macmillan Publishers Limited. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dong2008,

title = {DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity},

author = {Kevin B. Dong and Irina A. Maksakova and Fabio Mohn and Danny Leung and Ruth Appanah and Sandra Lee and Hao W. Yang and Lucia L. Lam and Dixie L. Mager and Dirk Schübeler and Makoto Tachibana and Yoichi Shinkai and Matthew C. Lorincz},

doi = {10.1038/emboj.2008.193},

issn = {02614189},

year  = {2008},

date = {2008-01-01},

journal = {EMBO Journal},

volume = {27},

issue = {20},

abstract = {Histone H3K9 methylation is required for DNA methylation and silencing of repetitive elements in plants and filamentous fungi. In mammalian cells however, deletion of the H3K9 histone methyltransferases (HMTases) Suv39h1 and Suv39h2 does not affect DNA methylation of the endogenous retrovirus murine leukaemia virus, indicating that H3K9 methylation is dispensable for DNA methylation of retrotransposons, or that a different HMTase is involved. We demonstrate that embryonic stem (ES) cells lacking the H3K9 HMTase G9a show a significant reduction in DNA methylation of retrotransposons, major satellite repeats and densely methylated CpG-rich promoters. Surprisingly, demethylated retrotransposons remain transcriptionally silent in G9a-/- cells, and show only a modest decrease in H3K9me2 and no decrease in H3K9me3 or HP1α binding, indicating that H3K9 methylation per se is not the relevant trigger for DNA methylation. Indeed, introduction of catalytically inactive G9a transgenes partially 'rescues' the DNA methylation defect observed in G9a -/- cells. Taken together, these observations reveal that H3K9me3 and HP1α recruitment to retrotransposons occurs independent of DNA methylation in ES cells and that G9a promotes DNA methylation independent of its HMTase activity. © 2008 European Molecular Biology Organization | All Rights Reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}