Chromatin; DNA Damage; Genetics; Histones; Neural Crest; Stem Cells; Cellular Reprogramming
Stem Cell Center, Yale: Stem Cell Genetics
The ultimate goal of this laboratory is the understanding of how genetic information is processed and extracted from mammalian genomes. We mainly focused on a mechanism known as “Epigenetics”, i.e. regulating expression of genes without changing their DNA sequences. Epigenetics is closely linked to development and embryonic stem cells (ES cells) as distinct groups of genes are dynamically expressed or silenced during embryonic development and ES cells, while the DNA sequences of genes are essentially the same as adult tissues and cells.Therefore, embryonic stem cells serve as our major experimental system.While we have been discovering several unexpected, stem cell-specific mechanisms recently, such as N6-mA, we are also witnessing the emerging theme that the novel mechanisms can be “hijacked” by human diseases. As they are rarely utilized by normal adult tissues and cells, these mechanisms serve as perfect therapeutic targets.
Specialized Terms: Chromatin biology; Histone variants; Modifications and chromatin remodeling complexes; Cellular reprogramming (iPS) and stem cell biology; Mammalian neural crest cell; Mammalian DNA damage response
Extensive Research Description
The essential components of epigenetics- The basic unit of our genome is nucleosomes, a complex in which ~146 bases of the DNA molecule wrap around a group of proteins called histones.Histones are among the most conserved proteins during evolution; only a few differences in their composition (amino acid residues) are found among yeast and human histones.
Intriguingly, higher eukaryotic genomes, especially the mammalian, contain specialized histones, known as the histone variants, which are often only presented in a very small portion of the genome (1-5%) and yet play critical roles in various biological process, ranging from differentiation/development to DNA repair/replication. A major research interest in my lab is to understand how the deposition and functions of histone variants are regulated.A recent work from my lab discovered unexpected roles of a histone variant in determination of the quality of cell induced pluripotent stem (iPS) cells (Wu et al. 2014).
Chemical modifications on histones is a very important aspect of epigenetic regulation; more than a hundred such modifications have been discovered to date. On the other hand, the dogma stated that 5-methyl-Cytidine (5mC) and its derivatives is the only form of chemical modification on mammalian DNA.Other modifications, such as N6-methyl-adenine (N6-mA) had been long thought to only exist in bacteria, viruses and a limited number of simple eukaryotes. Our most recent discovery of N6-mA “puts paid to” this dogma (Nature news and view). This paradigm-shifting discovery opens up a brand new research direction in mammalian epigenetics, which we are excited to explore (Wu et al. 2016).
Last but not least, we are interested in endogenous retrotransposons in mammalian genomes.These remnants of the ancient viruses once invaded our genome and later became domesticated. Although long considered as “junk” DNA, they have received lots of attention recently as they play surprising roles in ES cells and early embryogenesis.First, they are considered as a driving force in genome evolution; as Barbara McClintock pointed out several decades ago, they are the key factor for an organism to develop new traits under environmental stress. Second, recent studies have implicated them in early development, especially at morula stage embryos (2-cell to 16-cell). Third, their frequent (50%) remobilization (de novo jumping) in human carcinomas (breast, prostate, colon etc) has been implicated in tumor progression. Therefore, we are striving to understand the epigenetic mechanisms for regulating retrotransposon functions.
Our interests in stem cells and cellular reprogramming- Embryonic stem cells, which can self-renew endlessly and differentiate into every cell type in the human body, contain the blueprints of our existence. They hold the promise of curing any disease or condition caused by tissue loss or aging, including Alzheimer’s, Huntington’s and blood cell loss from chemotherapy.Due to ethical concerns, however, the availability of embryonic stem cells is highly limited. In addition, given the diversity of human populations, transplanting cells derived from a few common lines of embryonic stem cells may lead to immune rejection and other complications in a patient population.The recent advent of cellular reprogramming technology, a breakthrough that was recognized with the Noble Prize in 2012, provides an attractive solution to these issues.With the addition of a few genes, differentiated cells (such as skin or hair follicle cells) can be “reprogrammed” to become like embryonic stem cells and then further induced into cells of interest. This means that if cellular reprogramming becomes medically viable, a patient with Alzheimer’s disease can be cured by cells derived from her own skin or hair, which would be free from the risk of immune rejection. Although promising, current cellular reprogramming technology needs significant improvements for future clinical applications to become feasible. A major gateway issue is the uneven quality among reprogrammed cell lines: over 95% of reprogrammed cells do not behave like embryonic stem cells.Therefore, understanding the mechanisms controlling the quality of reprogrammed cells and ultimately developing novel methods to improve their quality is not only a fundamental question for those of us engaged in basic scientific research, but of great importance to regenerative medicine.Our laboratory has recently shed the first light on this intriguing “quality control” issue by demonstrating the surprising role of histone variant in determination of the cell fate stability of iPS cells.
Moreover, since the epigenetic landscape of stem cells are drastically different from that of differentiated cells, we also use stem cells as a valuable source in search of novel epigenetic mechanism. One good example is the discovery of N6-mA. Although rare in normal adult tissues and cells, these mechanisms are often “hijacked” by human diseases, so these mechanisms serve as perfect therapeutic targets.
DNA Methylation on N6-adenine in mammalian embryonic stem cells.
Wu T, Wang T, Seetin MG, Lai Y, Lin K, Zhu, S, Liu Y, Byrum SD, Mackintosh SG, Tackette A, Wang G, Hon LS, Fang G , Swenberg JA and Xiao A * DNA Methylation on N6-adenine in mammalian embryonic stem cells. (2016) Nature in press doi:10.1038/nature17640 online: march 30, 2016
Extensive Nuclear Reprogramming Underlies Lineage Conversion into Functional Trophoblast Stem-like Cells.
Benchetrit, H, Herman, S, van Wietmarschen, N, Wu, T, Makedonski, K, Maoz, N, Yom Tov, N, Stave, D, Lasry, R, Zayat, V, Xiao, A, Lansdorp, PM, Sebban, S, Buganim, Y*. Extensive Nuclear Reprogramming Underlies Lineage Conversion into Functional Trophoblast Stem-like Cells. Cell Stem Cell. doi:10.1016/j.stem.2015.08.006
Histone Variant Histone Variant H2A.X-Mediated Epigenetic Mechanisms are Critical for Maintaining Genome Stability and Pluripotency in ES and iPS Cells.
Wu T, Stadtfeld M, Tseng Z, Liu Y, Tahmasian M, Hochedlinger K & Xiao A*. Histone Variant Histone Variant H2A.X-Mediated Epigenetic Mechanisms are Critical for Maintaining Genome Stability and Pluripotency in ES and iPS Cells. (2014) Cell stem cell 15 (3) 281-294 PMID: 25192463 Previewed by Cells stem cell, Quality control: H2A.X links to better iPSCs. (2014) Cell stem cell 15 (3) 259-260
Previewed by Cells stem cell, Quality control: H2A.X links to better iPSCs.
Buganim Y., Markoulaki S, Wietmarschen N., Hoke H., Wu T., Ganz K., Akhtar-Zaidi B., He Y., Abraha B., Porubsky D., Kulenkampff E., Faddah D., Shi L., Gao Q., Sarkar Q., Cohen M., Goldman J., Nery J., Schultz M.,. Ecker J., Xiao A., Young R., Lansdorp P. and Jaenisch R*. The developmental potential of iPSCs is greatly influenced by the selection of the reprogramming factors. (2014) Cell Stem Cell 15(3) 295-309 PMID: 25192464 Previewed by Cells stem cell, Quality control: H2A.X links to better iPSCs. (2014) Cell stem cell 15 (3) 259-2603.
Maintains Telomere Length Homeostasis of Embryonic Stem Cells by Mediating Subtelomeric Heterochromatin Silencing.
Dai J., Liu Y., Na L., Chiourea M., Okuka M., Wu T, Chunlin M., Wang L, Wang L, Yin Y., Yuan J., Zuo B., Wang F., Ye X., Li Z, Pan X., Yin Z., Chen L., Keefe D.J., Gagos S., Xiao A.* and Liu L* Rif1 Maintains Telomere Length Homeostasis of Embryonic Stem Cells by Mediating Subtelomeric Heterochromatin Silencing. (2014) Developmental Cell 29(1) 7-19 PMID: 24735877
WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity.
Xiao A., Li H., Shechter D., Ahn S.H.,. Fabrizio L.A., Erdjument-Bromage H., Ishibe-Murakami S., Wang B., Tempst P., Hoffman K., Patel D.J., Elledge, S.J., and Allis C.D. (2009) WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity. Nature (research article) 457, 57-62 See news and view, Nature V458, 581
Methylation of RUNX1 by PRMT1 abrogates SIN3A binding and potentiates its transcriptional activity.
Zhao X, Jankovic V, Gural A, Huang G, Pardanani A, Menendez S, Zhang J, Dunne R, Xiao A, Erdjument-Bromage H, Allis CD, Tempst P, Nimer SD. Genes Dev. 2008 Mar 1;22(5):640-53. doi: 10.1101/gad.1632608.
Astrocyte inactivation of the pRb pathway predisposes mice to malignant astrocytoma development that is accelerated by PTEN mutation.
Xiao A., Wu H., Louis D.N., Pandolfi P.P., and Van Dyke T.A. (2002) Astrocyte inactivation of the pRb pathway predisposes mice to malignant astrocytoma development that is accelerated by PTEN Mutation. Cancer Cell 1: 157-66.
Full List of PubMed Publications
- Choi J, Huebner AJ, Clement K, Walsh RM, Savol A, Lin K, Gu H, Di Stefano B, Brumbaugh J, Kim SY, Sharif J, Rose CM, Mohammad A, Odajima J, Charron J, Shioda T, Gnirke A, Gygi S, Koseki H, Sadreyev RI, Xiao A, Meissner A, Hochedlinger K: Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells. Nature. 2017 Aug 10; 2017 Jul 26. PMID: 28746311
- Wu TP, Wang T, Seetin MG, Lai Y, Zhu S, Lin K, Liu Y, Byrum SD, Mackintosh SG, Zhong M, Tackett A, Wang G, Hon LS, Fang G, Swenberg JA, Xiao AZ: DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature. 2016 Apr 21; 2016 Mar 30. PMID: 27027282
- Benchetrit H, Herman S, van Wietmarschen N, Wu T, Makedonski K, Maoz N, Yom Tov N, Stave D, Lasry R, Zayat V, Xiao A, Lansdorp PM, Sebban S, Buganim Y: Extensive Nuclear Reprogramming Underlies Lineage Conversion into Functional Trophoblast Stem-like Cells. Cell Stem Cell. 2015 Nov 5; 2015 Sep 24. PMID: 26412562
- Dan J, Yang J, Liu Y, Xiao A, Liu L: Roles for Histone Acetylation in Regulation of Telomere Elongation and Two-cell State in Mouse ES Cells. J Cell Physiol. 2015 Oct. PMID: 25752831
- Liu Y, Xiao A: Adaption by Rewiring Epigenetic Landscapes. Cell Stem Cell. 2015 Sep 3. PMID: 26340521
- Buganim Y, Markoulaki S, van Wietmarschen N, Hoke H, Wu T, Ganz K, Akhtar-Zaidi B, He Y, Abraham BJ, Porubsky D, Kulenkampff E, Faddah DA, Shi L, Gao Q, Sarkar S, Cohen M, Goldmann J, Nery JR, Schultz MD, Ecker JR, Xiao A, Young RA, Lansdorp PM, Jaenisch R: The developmental potential of iPSCs is greatly influenced by reprogramming factor selection. Cell Stem Cell. 2014 Sep 4. PMID: 25192464
- Wu T, Liu Y, Wen D, Tseng Z, Tahmasian M, Zhong M, Rafii S, Stadtfeld M, Hochedlinger K, Xiao A: Histone variant H2A.X deposition pattern serves as a functional epigenetic mark for distinguishing the developmental potentials of iPSCs. Cell Stem Cell. 2014 Sep 4. PMID: 25192463
- Dan J, Liu Y, Liu N, Chiourea M, Okuka M, Wu T, Ye X, Mou C, Wang L, Wang L, Yin Y, Yuan J, Zuo B, Wang F, Li Z, Pan X, Yin Z, Chen L, Keefe DL, Gagos S, Xiao A, Liu L: Rif1 maintains telomere length homeostasis of ESCs by mediating heterochromatin silencing. Dev Cell. 2014 Apr 14. PMID: 24735877
- Tseng Z, Wu T, Liu Y, Zhong M, Xiao A: Using native chromatin immunoprecipitation to interrogate histone variant protein deposition in embryonic stem cells. Methods Mol Biol. 2014. PMID: 25030915
- Liu Y, Xiao A: Epigenetic regulation in neural crest development. Birth Defects Res A Clin Mol Teratol. 2011 Aug; 2011 May 25. PMID: 21618405