Li Lab - Research

Research Focus

Epigenetic regulation in stem cells and human diseases.

    Our research is focused on genomic imprinting. We are analyzing the acquisition and maintenance of genomic DNA methylation imprints in mouse as well as in ES and iPS cells. We are also applying our Zfp57 knockout mouse to modeling of imprinting related complex human diseases such as obesity, diabetes and cardiovascular diseases.

Genomic imprinting in stem cells

    Genomic imprinting is essential for mammalian development. Consistent with this, a majority of cloned embryos die in utero, mainly from the failure to re-establish proper genomic imprints. Cell-based therapies offer great hopes for various degenerative diseases, including Alzheimer’s disease and diabetes. Embryonic stem (ES) cells derived from nuclear transfer experiments and induced pluripotent stem (iPS) cells reprogrammed from adult cells are candidates for this therapeutic approach. However, they all have genomic imprinting defects which can inhibit differentiation and may even cause cancer. Recently, it was reported that dysregulation of the Dlk1-Dio3 imprinted domain is the only notable difference between ES cells and iPS cells (Stadtfeld, M. et al. Nature, 2010). Indeed, hypermethylation and aberrant expression of the imprinted genes were observed at the Dlk1-Dio3 imprinted region in iPS cells Therefore, it is important to know how to manipulate the genomic imprinting machinery in pluripotent stem cells including iPS and ntES cells so that proper development of different lineages of cells can be achieved for therapeutic applications. 

    The current major focus of our lab is to analyze acquisition and maintenance of genomic imprinting in stem cells as well as in mouse embryos. Recently, we discovered that Zfp57 is highly enriched in ES cells and is a key regulator in genomic imprinting at multiple imprinted regions including the Dlk1-Dio3 domain. Loss of Zfp57 results in loss of DNA methylation genomic imprints at these imprinted regions. Consistent with our finding, mutations in human Zfp57 result in hypomethylation at multiple imprinted regions. Currently we are actively investigating the underlying mechanisms of ZFP57-associated complexes in the acquisition and maintenance of DNA methylation imprints in both mouse embryos and ES cells.

Mechanisms in genomic imprinting

    Despite that genomic imprinting was identified in mammals almost three decades ago, many unanswered questions persist about the nature of genomic imprinting memory and about how genomic imprints are established and maintained. Zfp57 has both maternal and zygotic functions and it exhibits maternal-zygotic embryonic lethality, the first one identified in mammals. ZFP57 maintains both paternal and maternal genomic imprints and may target DNA methyltransferases to the imprinting control regions (ICR). Interestingly, these germline-derived differential DNA methylation imprints at the ICRs can be lost in embryos in the absence of both maternal and zygotic Zfp57 and they can be acquired in mouse embryos in the presence of zygotic Zfp57 even though they are not established in the germline. Moreover, acquisition of DNA methylation in mouse embryos occurs in an allele-specific fashion, suggesting the presence of DNA methylation-independent heritable imprinting memory such as heritable histone modifications. Therefore, further functional analysis of ZFP57 in genomic imprinting will help us to achieve a better understanding of the molecular nature of imprinting memory as well as the temporal and developmental control of DNA methylation imprints.

Modeling complex human diseases

    Dysregulation of imprinting genes can lead to cancer, neurological diseases, diabetes and other kinds of human diseases. Indeed, mutations in human ZFP57 are associated with transient neonatal diabetes, congenital heart defects and abnormal development of the nervous system. We have independently discovered that Zfp57 mutant mouse is obese and display similar defects in the cardiovascular system. Thus, our Zfp57 mutant mouse could serve as useful animal models for complex human diseases such as obesity, diabetes and cardiovascular diseases.

Figure 1.  RNA in-situ hybridization reveals that Zfp57 is expressed specifically in the oocytes (purple stain) within the follicles.


Figure 2.  ZFP57 is involved in the acquisition, maintenance and re-acquisition of DNA methylation genomic imprints. Paternal chromosomes are indicated by blue lines. IG, IG-DMR. SN, Snrpn DMR. Black circles, methylated CpGs. White circles, unmethylated CpGs. Shaded circles, partially methylated CpGs. -/-, a homozygous Zfp57 embryo. -/+, a heterozygous Zfp57 embryo derived from a null female. Differential DNA methylation at the CpG sites of imprinting control regions (ICR) is reset during gametogenesis. In sperm, the CpG sites at the IG-DMR (IG) of the Dlk1-Dio3 imprinted domain are methylated while those at the Snrpn DMR (SN) are unmethylated. By contrast, methylation occurs at the Snrpn DMR but not at the IG-DMR in the ooytes derived from wild-type females. Upon fertilization, differential methylation is reconstituted at the ICRs in the wild-type zygote (Zygote (1)). These germline-derived differential DNA methylation imprints are resistant to genome-wide pronuclear demethylation in the zygote and stably maintained in wild-type embryos. Without zygotic ZFP57, differential DNA methylation is partially lost in the zygotic mutant embryos around mid-gestation (Midgestation Embryo (A)). When both maternal and zygotic ZFP57 are absent, differential DNA methylation is completely missing in the mid-gestation maternal-zygotic mutant embryos (Midgestation Embryo (B)). Without maternal ZFP57, DNA methylation is not established at the CpG sites of the Snrpn DMR in the oocytes derived from Zfp57 homozygous female mice. In pre-implantation embryos lacking maternal ZFP57 (Zygote (2)), differential DNA methylation at the Snrpn DMR remains absent. Intriguingly, differential DNA methylation is re-acquired allele-specifically at the maternal chromosome of the Snrpn DMR in the presence of the zygotic ZFP57 in about 50% of the heterozygous embryos derived from null female mice (Li et al., 2008).

lab info

Xiajun (John) Li

212-241-4160 (office)
212-241-3532 (res. coordinator)
212-241-3397 (lab)
212-860-9279 (fax)

lab members:
Liu, Lizhi
Ng, Sheau-Fang

see photos and more here.
key publications

Shamis Y., Cullen D., Liu L., Yang G., Ng S-F, Xiao L., Bell, F., Ray C., Takikawa S., Moskowitz I., Cai C., Yang X. and Li X.,
Maternal and zygotic Zfp57 modulate NOTCH signaling in cardiac development. 
Proc Natl Acad Sci USA 112(16): E2020-9. doi: 10.1073/pnas.1415541112.

Li, X.,
Genomic imprinting is a parental effect established in mammalian germ cells. 
Current Topics in Developmental Biology. 102:35-59.

Zuo, X., Sheng, J., Lau, H., McDonald, CM, Andrade, M., Cullen, DE, Bell, FT, Iacovino M., Kyba, M., Xu, G. and Li, X.,
The zinc finger protein ZFP57 requires its cofactor to recruit DNA methyltransferases and maintains the DNA methylation imprint in 
embryonic stem cells via its transcriptional repression domain.
J. Biol. Chem., DOI: 10.1093/molehr/gaq028.

Li, X., (Invited paper)
Extending the maternal-zygotic effect with genomic imprinting.  
Molecular Human Reproduction, 16 (9): 695-703.

Li, X.*, Ito, M., Zhou, F., Youngson, N., Zuo, X., Leder, P. & Ferguson-Smith, A.C.,
A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. 
Developmental Cell, 15: 547-557 (*, corresponding author) (Previewed in Developmental Cell 15: 487-8, 2008).

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