We study dynamic and reversible RNA and DNA methylation in gene expression regulation with chemical and biological tools.

Research Interests:

Our research program spans a broad range of chemical biology, nucleic acid chemistry and biology, RNA biology, and epigenetics. We discovered the first RNA demethylase and characterized functions of different RNA methylation binding proteins. We uncovered transcriptional and post-transcriptional gene expression regulation pathways mediated by dynamic RNA modifications such as N ⁶ -methyladenosine (m ⁶ A). We developed enabling methods to map RNA and DNA modifications, and we are exploring functional importance of different RNA modifications in diverse biological systems. We also invent new genomic methods to accurately monitor transcription and chromatin state.

RNA Methylation

Cellular RNAs contain more than a hundred fifty structurally distinct post-transcriptional modifications at thousands of sites. Some RNA modifications are dynamic and may have critical regulatory roles analogous to those of protein and DNA modifications. Understanding the scope and mechanisms of dynamic RNA modifications thus represents an emerging research frontier in biology and medicine. The internal N ⁶ -methyladenosine (m ⁶ A) modification in messenger RNA is one of the most abundant RNA modifications in eukaryotes. This base modification is present on average in ~3 sites of every mRNA in mammals. This modification has been shown to be critical to cell differentiation, animal development, and a range of biological signaling and stress response. We propose that RNA modifications are used by cells to group hundreds to thousands of transcripts for coordinated translation regulation and transcriptome turnover.

Erasers : In 2011, we reported that m ⁶ A in mammalian mRNA can be oxidatively demethylated in vitro and inside cells by FTO (a fat mass and obesity-associated protein), a major obesity factor, as the first known RNA demethylase. We subsequently identified ALKBH5 as the second RNA demethylase that controls mammalian spermatogenesis. These and other results from our laboratory indicate the presence of a new mode of regulation through reversible RNA methylation in mammalian cells.

Readers : Our recent work has characterized the YTH family proteins as the reader proteins that affect stability and translation of methylated transcripts in mammalian cells. Functional characterizations revealed that YTHDF2 affects cytoplasmic localization and mediates the decay of methylated mRNA, YTHDF1 promotes translation of methylated mRNA by facilitating translation initiation, and other readers affect mRNA storage, transport, and cellular localization. Some of these proteins play essential roles in animal development and critical to human diseases. We continue to uncover the physiological significance of the mRNA methylation in various cell differentiation and development events and their underlying mechanisms.

Writers : We have identified a core complex comprised of two subunits: METTL3 and METTL14, and an accessory factor WTAP, which mediates cellular m ⁶ A RNA methylation. Cellular RNA methylation level can have profound impacts on normal cell differentiation and cancer cell proliferation. Our current work focuses on how the methylation selectivity is achieved.

Transcriptional regulation : Our most recent work discovered the presence of m ⁶ A in chromatin-associated regulatory RNAs (carRNAs) that include promoter-associated RNAs, enhancer RNAs and repeat RNAs. The m ⁶ A methylation regulates levels of these carRNAs and controls transcription and chromatin state. The carRNA m ⁶ A could be recognized by different m ⁶ A-binding proteins, which recruit different chromatin factors to shape local chromatin state. We further showed that the RNA demethylase FTO mediates m ⁶ A demethylation on retrotransposon RNAs to notably regulate local and global chromatin state and affect mammalian and plant development. This new layer transcriptional regulation could have profound impacts on gene expression regulation in a wide range of biological processes.

We are also developing sequencing methods to precisely map the m ⁶ A mark and other RNA modifications transcriptome-wide. We are also exploring other RNA methylation and demethylation events.

DNA Methylation, Hydroxymethylation, and Oxidative Demethylation

DNA is not merely a combination of four genetic nucleobases, namely, A, T, C, and G.  It also contains modifications that play crucial roles throughout biology. For example, 5-methylcytosine (5mC), the fifth DNA base which is a crucial epigenetic mark, constitutes ~2-8% of the total cytosines in human genomic DNA and impacts a broad range of biological functions. Recently, the presence of oxidized 5mC, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), have been discovered in mammalian cells and tissues as the sixth, seventh, and eighth DNA bases. A group of iron(II)/αKG-dependent dioxygenases, the TET proteins, have been shown to utilize dioxygen to oxidize 5mC to these new base modifications in the mammalian genome. We have developed effective sequencing technologies to map their precise locations and dissect the exact functional roles of these newly discovered DNA base modifications. We have recently invented new methods to perform highly effective sequencing of DNA 5mC and its derivatives. We are exploring these DNA marks as disease diagnosis and prognosis markers.

Although 5mC and 6mA were discovered as DNA methylations at almost the same time decades ago, most research has been dedicated to 5mC for its abundant presence in mammals and higher plants. We have recently found that 6mA displays a unique distribution pattern in several unicellular eukaryotic organisms. 6mA marks transcription start sites (TSS) and exhibits a periodicity that marks the linker regions between adjacent nucleosomes. This new DNA mark has also been found to exist in high eukaryotes and we are exploring its potential physiological roles.

Selected References

He, P. C.; Wei, J.; Dou, X.; Harada, B. T.; Zhang, Z.; Ge, R.; Liu, C.; Zhang, L.-S.; Yu, X.; Wang, S.; Lyu, R.; Zou, Z.; Chen, M.; He, C.* Exon architecture controls mRNA m6A suppression and gene expression. Science 2023, 379, 677-682.

Wei, J.; Yu, X.; Yang, L.; Liu, X.; Gao, B.; Huang, B.; Dou, X.; Liu, J.; Zou, Z.; Cui, X. L.; Zhang, L. S.; Zhao, X.; Liu, Q.; He, P. C.; Sepich-Poore, C.; Zhong, N.; Liu, W.; Li, Y.; Kou, X.; Zhao, Y.; Wu, Y.; Cheng, X.; Chen, C.; An, Y.; Dong, X.; Wang, H.; Shu, Q.; Hao, Z.; Duan, T.; He, Y. Y.; Li, X.; Gao, S.*; Gao, Y.*; He, C.* FTO mediates LINE1 m6A demethylation and chromatin regulation in mESCs and mouse development. Science 2022, 376, 968-973.

Yu, Q.; Liu, S.; Yu, L.; Xiao, Y.; Zhang, S.; Wang, X.; Xu, Y.; Yu, H.; Li, Y.; Yang, J.; Tang, J.; Duan, H. C.; Wei, L. H.; Zhang, H.; Wei, J.; Tang, Q.; Wang, C.; Zhang, W.; Wang, Y.; Song, P.; Lu, Q.; Zhang, W.; Dong, S.; Song, B.*; He, C.*; Jia, G.* RNA demethylation increases the yield and biomass of rice and potato plants in field trials. Nat. Biotechnol. 2021, 39, 1581-1588.

Liu, J.; Dou, X.; Chen, C.; Chen, C.; Liu, C.; Xu, M. M.; Zhao, S.; Shen, B.; Gao, Y.*; Han, D.*; He, C.* N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription. Science 2020, 367, 580-586.

Han, D*.; Liu, J.; Chen, C.; Dong, L.; Liu, Y.; Chang, R.; Huang, X.; Liu, Y.; Wang, J.; Dougherty, U.; Bissonnette, M. B.; Shen, B.; Weichselbaum, R. R.; Xu, M. M.*; He C.*. Anti-tumour immunity controlled through mRNA m6A methylation and YTHDF1 in dendritic cells. Nature 2019, 566, 270-274.

Shi, H.; Zhang, X.; Weng, Y. L.; Lu, Z.; Liu, Y.; Lu, Z.; Li, J.; Hao, P.; Zhang, Y.; Zhang, F.; Wu, Y.; Delgado, J. Y.; Su, Y.; Patel, M. J.; Cao, X.; Shen, B.; Huang, X.; Ming, G. L.; Zhuang, X.; Song, H.*; He, C.*; Zhou, T.* m6A facilitates hippocampus-dependent learning and memory through YTHDF1. Nature 2018, 563, 249-253.

Zhao, B. S.; Wang, X.; Beadell, A. V.; Lu, Z.; Shi, H.; Kuuspalu, A.; Ho, R. K.; He, C. m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition. Nature 2017, 542, 475-478.

Wang, X.; Zhao, B. S.; Roundtree, I. A.; Lu, Z.; Han, D.; Ma, H.; Weng, X.; Chen, K.; Shi, H.; He, C.* N6-methyladenosine modulates messenger RNA translation efficiency. Cell 2015, 161, 1388-1399.

Wang, X.; Lu, Z.; Gomez, A.; Hon, G. C.; Yue, Y.; Han, D.; Fu, Y.; Parisien, M.; Dai, Q.; Jia, G.; Ren,B.; Pan, T.; He, C.* N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 2014, 505, 117-120.

Jia, G.; Fu, Y.; Zhao, X.; Dai, Q.; Zheng, G.; Yang, Y.; Yi, C.; Lindahl, T.; Yang, Y.-G.; He, C.* “N6-methyladesosine in nuclear RNA is a major substrate of the obesity-associated FTO” Nat. Chem. Biol. 2011, 7, 885-887.