Shi Laboratory Recent Publications

Principal Contributions to Science


Greer, EL.+, *, Blanco, MA+., Gu, L., Sendinc, E., Liu, JZ, Aristizábal-Corrales, D., Hsu, C-H., Aravind, L., He, C., and Shi, Y*. (2015). DNA methylation on N6-adenine in C. elegansCell, Vol 161 (4): 868-878. (Cover) (Mini-review, Cell 2015 Vol 161:710-13). +equal contribution *co-corresponding.


Guo, R+., Zheng, LJ+ ., Park, J.W., Xu, WQ., Chen, H., Qiu, JS., Lv RT., Wang, ZT., Yang, PY., Wu, FZ., Shi, XB., Fu, XD., Shi, G.YJ, Xing, Y*., Lan, F*., and Shi, Y* (2014). BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation decorated chromatin to regulated pre-mRNA processing. Mol Cell, Vol 56(2): 298-310. +equal contribution, *co-corresponding.

Alpatov R+, Lesch BJ+, Nakamoto-Kinoshita M, Blanco A, Chen S, Stützer A, Armache KJ, Simon MD, Xu C, Ali M, Murn J, Prisic S, Kutateladze TG, Vakoc CR, Min J, Kingston RE, Fischle W,Warren ST, Page DC and Shi Y. (2014) A Chromatin-Dependent Role of the Fragile X Mental Retardation Protein FMRP in the DNA Damage Response. Cell 157(4):869-81. +equal contribution.


Qi, HH+., Sarkissian, M+., Hu, G.Q., Zhao, Z.B., Bhattacharjee, A., Gordon, B., Lim, S., Lan, F., Yaghi, NK., Garcia B., Brizuela, L., Zhao, KJ., Roberts, TM*, and Shi, Y*. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature 446:503-07. +equal contribution, *co-corresponding.


Lan, F., Bayliss, PE., Rinn, J., Whetstine JR., Wang JK., Chen, SZ., Iwase, S., Alpatov, R., Issaeva, I., Canaani, E., Roberts, TM., Chang, HY., and Shi, Y. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449:689-94. (Mini-review Cell 2007 Vol 131: 29-32)

Lan, F+., Collins, R+., De Cegli, R., Alpatov, R., Horton, J.R., Shi, XB, Gozani, R., Cheng, XD*, and Shi, Y*. Recognition of unmethylated H3K4 links BHC80 to LSD1 mediated gene repression. Nature 448:718-23. +equal contribution, *co-corresponding.

Lan, F., Zaratiegui, M., Villen, J., Vaughn, M., Verdel, A., Gygi, S., Moazed, D., Martienssen, R. and Shi, Y. S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatin gene transcription.  Mol Cell 26: 89-101. [mini-review Mol Cell. 2007 Apr 27;26(2):160-2.]

Iwase, S, Lan, F., Bayliss, P., de la Torre-Ubieta, L., Qi, H., Huarte, M., Whetstine, JR.,Bonni, A., Roberts, T., and Shi, Y. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases.  Cell 128:1077-88.


Whetstine, JR., Nottke, A., Lan, F., Huarte, M., Smolikov, S., Chen, Z., Spooner, E., Li, E., Zhang, G., Colaiacovo, M., and Shi, Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125:467-481.  [Commented in Research Highlight, Nat. Rev. Mol. Cell. Biol. June, 2006].


Shi, Y.J., Lan, F., Matson, C., Mulligan, P., Whetstine, J.R., Cole, P.A., Casero, R.A. and Shi, Y. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell Vol 119:941-953. [Mini-review Cell 119:903-906.  Findings highlighted in Science 306:2171 (2004), Nature 433:29 (2005), Nature Reviews Mol. Cell Biol. (2005).


Shi, Y. J., Sawada, J-I., Sui, G.C., Affar, E.B., Whetstine, J., Lan, F., Ogawa, H., Luke, M., P-S., Nakatani, Y., and Shi, Y. Coordinated histone modifications mediated by a CtBP co-repressor complex. Nature 422:735-8.


Sui, G.C., Soohoo, C, Affar, E.B., Shi, Y.J., Forrester, W., and Shi, Y. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells.  Proc. Natl. Acad. Sci. USA.  99:5515-20.


Luo, G-Z., Blanco, M.A., Greer, E.L., He, C., and Shi, Y. (2015). N6 methyldeoxyadenosine: A new epigenetic mark in eukaryotes? Nat Rev Mol. Cell. Biol. In press.

Brookes, E. and Shi, Y (2014). Disparate epigenetic mechanisms of human disease, Ann Rev Genet. Vol 48:237-68.

Badeaux AI, Shi Y (2013). Chromatin as a platform and storage device for cellular signaling events. Nature Rev Mol Biol. Vol 14(4): 211-24.

Greer EL, Shi Y. (2012) Dynamic regulation of histone methylation in health, disease, and inheritance. Nat Rev Genet. Vol 13:343-357.

Iwase S, Shi Y. (2011) Histone and DNA modifications in mental retardation. Prog Drug Res. Vol 67: 147-73.

Mosammaparast N, Shi Y. (2010) Reversal of histone methylation: Biochemical and molecular mechanisms of histone demethylases. Ann Rev Biochem. Vol 79:155-79. PMC exempt

Nottke AC, Colaiacovo M, Shi Y. (2009) Developmental roles for the histone lysine demethylases. Development. Vol 136(6):879-89.

Lan F, Nottke AC, Shi Y. (2008) Mechanisms involved in the regulation of histone lysine demethylases. Curr Opin Cell Biol. Vol 20:316-325.

Shi Y. (2007) Histone demethylases: emerging roles in development, physiology and disease. Nat Rev Genet. Vol 8:829-33.

Shi Y*, Whetstine J. (2007) Dynamic regulation of histone lysine methylation by demethylases. Mol Cell. Vol 25:1-14. *Corresponding author.

Shi YJ, Shi Y. (2004) Metabolic enzymes in transcription-a direct link between metabolism and regulated gene expression? Trends in Genetics. Vol 20:445-52.

Shi Y. (2003) Mammalian RNAi for the masses. Trends in Genetics. Vol 19: 9-12 (#1 downloaded article among all of Elsevier publications in 2003).