Dynamic Transcriptome, DNA Methylome, and DNA Hydroxymethylome Networks During T-Cell Lineage Commitment |
Yoon, Byoung-Ha
(Department of Functional Genomics, University of Science and Technology (UST))
Kim, Mirang (Department of Functional Genomics, University of Science and Technology (UST)) Kim, Min-Hyeok (Department of Biological Sciences, Korea Advanced Institute of Science and Technology) Kim, Hee-Jin (Genome Editing Research Center, Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) Kim, Jeong-Hwan (Genome Editing Research Center, Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) Kim, Jong Hwan (Department of Functional Genomics, University of Science and Technology (UST)) Kim, Jina (Department of Functional Genomics, University of Science and Technology (UST)) Kim, Yong Sung (Department of Functional Genomics, University of Science and Technology (UST)) Lee, Daeyoup (Department of Biological Sciences, Korea Advanced Institute of Science and Technology) Kang, Suk-Jo (Department of Biological Sciences, Korea Advanced Institute of Science and Technology) Kim, Seon-Young (Department of Functional Genomics, University of Science and Technology (UST)) |
1 | Huang, Y., Chavez, L., Chang, X., Wang, X., Pastor, W.A., Kang, J., Zepeda-Martinez, J.A., Pape, U.J., Jacobsen, S.E., Peters, B., et al. (2014). Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells. P. Nat. Acad. Sci. USA 111, 1361-1366. DOI |
2 | Ichiyama, K., Chen, T., Wang, X., Yan, X., Kim, B.S., Tanaka, S., Ndiaye-Lobry, D., Deng, Y., Zou, Y., Zheng, P., et al. (2015). The methylcytosine dioxygenase Tet2 promotes DNA demethylation and activation of cytokine gene expression in T cells. Immunity 42, 613-626. DOI |
3 | Ip, J.Y., Tong, A., Pan, Q., Topp, J.D., Blencowe, B.J., and Lynch, K.W. (2007). Global analysis of alternative splicing during T-cell activation. RNA 13, 563-572. DOI |
4 | Kakaradov, B., Arsenio, J., Widjaja, C.E., He, Z., Aigner, S., Metz, P.J., Yu, B., Wehrens, E.J., Lopez, J., Kim, S.H., et al. (2017). Early transcriptional and epigenetic regulation of CD8(+) T cell differentiation revealed by single-cell RNA sequencing. Nat. Immunol. 18, 422-432. DOI |
5 | Katz, Y., Wang, E.T., Airoldi, E.M., and Burge, C.B. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods 7, 1009-1015. DOI |
6 | Kim, M., and Costello, J. (2017). DNA methylation: an epigenetic mark of cellular memory. Exp. Mol. Med. 49, e322. DOI |
7 | Kim, M., Park, Y.K., Kang, T.W., Lee, S.H., Rhee, Y.H., Park, J.L., Kim, H.J., Lee, D., Lee, D., Kim, S.Y., et al. (2014). Dynamic changes in DNA methylation and hydroxymethylation when hES cells undergo differentiation toward a neuronal lineage. Hum. Mol. Genet. 23, 657-667. DOI |
8 | Ko, M., An, J., and Rao, A. (2015). DNA methylation and hydroxymethylation in hematologic differentiation and transformation. Curr. Opin. Cell Biol. 37, 91-101. DOI |
9 | Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25. DOI |
10 | Komori, H.K., Hart, T., LaMere, S.A., Chew, P.V., and Salomon, D.R. (2015). Defining CD4 T cell memory by the epigenetic landscape of CpG DNA methylation. J. Immunol. 194, 1565-1579. DOI |
11 | Lee, P.P., Fitzpatrick, D.R., Beard, C., Jessup, H.K., Lehar, S., Makar, K.W., Perez-Melgosa, M., Sweetser, M.T., Schlissel, M.S., Nguyen, S., et al. (2001). A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. Immunity 15, 763-774. DOI |
12 | Mallory, M.J., Allon, S.J., Qiu, J., Gazzara, M.R., Tapescu, I., Martinez, N.M., Fu, X.D., and Lynch, K.W. (2015). Induced transcription and stability of CELF2 mRNA drives widespread alternative splicing during T-cell signaling. P. Nat. Acad. Sci. USA 112, E2139-2148. DOI |
13 | Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. and Genome Project Data Processing, S. (2009). The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079. DOI |
14 | Lienhard, M., Grimm, C., Morkel, M., Herwig, R., and Chavez, L. (2014). MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics 30, 284-286. DOI |
15 | Lister, R., Pelizzola, M., Dowen, R.H., Hawkins, R.D., Hon, G., Tonti-Filippini, J., Nery, J.R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009). Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315-322. DOI |
16 | Samstein, R.M., Arvey, A., Josefowicz, S.Z., Peng, X., Reynolds, A., Sandstrom, R., Neph, S., Sabo, P., Kim, J.M., Liao, W., et al. (2012). Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification. Cell 151, 153-166. DOI |
17 | Martinez, N.M., Agosto, L., Qiu, J., Mallory, M.J., Gazzara, M.R., Barash, Y., Fu, X.D., and Lynch, K.W. (2015). Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation. Genes Dev. 29, 2054-2066. DOI |
18 | Mingueneau, M., Kreslavsky, T., Gray, D., Heng, T., Cruse, R., Ericson, J., Bendall, S., Spitzer, M.H., Nolan, G.P., Kobayashi, K., et al. (2013). The transcriptional landscape of T cell differentiation. Nat. Immunol. 14, 619-632. DOI |
19 | Naito, T., Tanaka, H., Naoe, Y., and Taniuchi, I. (2011). Transcriptional control of T-cell development. Int. Immunol. 23, 661-668. DOI |
20 | Sellars, M., Huh, J.R., Day, K., Issuree, P.D., Galan, C., Gobeil, S., Absher, D., Green, M.R., and Littman, D.R. (2015). Regulation of DNA methylation dictates Cd4 expression during the development of helper and cytotoxic T cell lineages. Nat. Immunol. 16, 746-754. DOI |
21 | Serandour, A.A., Avner, S., Oger, F., Bizot, M., Percevault, F., Lucchetti-Miganeh, C., Palierne, G., Gheeraert, C., Barloy-Hubler, F., Peron, C.L., et al. (2012). Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers. Nucleic Acids Res. 40, 8255-8265. DOI |
22 | Smith, Z.D., and Meissner, A. (2013). DNA methylation: roles in mammalian development. Nature reviews. Genetics 14, 204-220. DOI |
23 | Stadler, M.B., Murr, R., Burger, L., Ivanek, R., Lienert, F., Scholer, A., van Nimwegen, E., Wirbelauer, C., Oakeley, E.J., Gaidatzis, D., et al. (2011). DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490-495. |
24 | Swamy, M., Pathak, S., Grzes, K.M., Damerow, S., Sinclair, L.V., van Aalten, D.M., and Cantrell, D.A. (2016). Glucose and glutamine fuel protein O-GlcNAcylation to control T cell self-renewal and malignancy. Nat. Immunol. 17, 712-720. DOI |
25 | Team, R.C. (2013). R: A language and environment for statistical computing. |
26 | Trapnell, C., Pachter, L., and Salzberg, S.L. (2009). TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111. DOI |
27 | Wang, E.T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S.F., Schroth, G.P., and Burge, C.B. (2008). Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476. DOI |
28 | Tsagaratou, A., Aijo, T., Lio, C.W., Yue, X., Huang, Y., Jacobsen, S.E., Lahdesmaki, H., and Rao, A. (2014). Dissecting the dynamic changes of 5-hydroxymethylcytosine in T-cell development and differentiation. P. Nat. Acad. Sci. USA 111, E3306-3315. DOI |
29 | Villani, A.C., Satija, R., Reynolds, G., Sarkizova, S., Shekhar, K., Fletcher, J., Griesbeck, M., Butler, A., Zheng, S., Lazo, S., et al. (2017). Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. Science 356. |
30 | von Boehmer, H., Teh, H.S., and Kisielow, P. (1989). The thymus selects the useful, neglects the useless and destroys the harmful. Immunol. Today 10, 57-61. DOI |
31 | Wilson, C.B., Makar, K.W., Shnyreva, M., and Fitzpatrick, D.R. (2005). DNA methylation and the expanding epigenetics of T cell lineage commitment. Semin. Immunol. 17, 105-119. DOI |
32 | Yu, M., Hon, G.C., Szulwach, K.E., Song, C.X., Zhang, L., Kim, A., Li, X., Dai, Q., Shen, Y., Park, B., et al. (2012). Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149, 1368-1380. DOI |
33 | Yui, M.A., and Rothenberg, E.V. (2014). Developmental gene networks: a triathlon on the course to T cell identity. Nat. Rev. Immunol. 14, 529-545. DOI |
34 | Bernstein, B.E., Meissner, A., and Lander, E.S. (2007). The mammalian epigenome. Cell 128, 669-681. DOI |
35 | Zhang, J.A., Mortazavi, A., Williams, B.A., Wold, B.J., and Rothenberg, E.V. (2012). Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell 149, 467-482. DOI |
36 | Zhao, M., Wang, J., Liao, W., Li, D., Li, M., Wu, H., Zhang, Y., Gershwin, M.E., and Lu, Q. (2016). Increased 5- hydroxymethylcytosine in CD4(+) T cells in systemic lupus erythematosus. J. Autoimmun. 69, 64-73. DOI |
37 | Anders, S., and Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biol 11, R106. DOI |
38 | Atamas, S.P., Choi, J., Yurovsky, V.V., and White, B. (1996). An alternative splice variant of human IL-4, IL-4 delta 2, inhibits IL-4-stimulated T cell proliferation. J. Immunol. 156, 435-441. |
39 | Baek, S.J., Kim, M., Bae, D.H., Kim, J.H., Kim, H.J., Han, M.E., Oh, S.O., Kim, Y.S., and Kim, S.Y. (2016). Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer. Oncotarget 7, 25620-25631. |
40 | David-Fung, E.S., Butler, R., Buzi, G., Yui, M.A., Diamond, R.A., Anderson, M.K., Rowen, L., and Rothenberg, E.V. (2009). Transcription factor expression dynamics of early T-lymphocyte specification and commitment. Dev. Biol. 325, 444-467. DOI |
41 | Feng, Y., and Rudensky, A.Y. (2015). DNA methylation secures CD4(+) and CD8(+) T cell lineage borders. Nature Immunol. 16, 681-683. DOI |
42 | Guo, J.U., Su, Y., Zhong, C., Ming, G.L., and Song, H. (2011). Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145, 423-434. DOI |
43 | Germain, R.N. (2002). T-cell development and the CD4-CD8 lineage decision. Nature Reviews. Immunol. 2, 309-322. DOI |
44 | Godfrey, D.I., Kennedy, J., Suda, T., and Zlotnik, A. (1993). A developmental pathway involving four phenotypically and functionally distinct subsets of CD3-CD4-CD8- triple-negative adult mouse thymocytes defined by CD44 and CD25 expression. J. Immunol. 150, 4244-4252. |
45 | A Andrews, S. (2010). FastQC: a quality control tool for high throughput sequence data. |
46 | Huang, G., Zhang, P., Hirai, H., Elf, S., Yan, X., Chen, Z., Koschmieder, S., Okuno, Y., Dayaram, T., Growney, J.D., et al. (2008). PU.1 is a major downstream target of AML1 (RUNX1) in adult mouse hematopoiesis. Nat. Genet. 40, 51-60. DOI |
47 | Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H., and Glass, C.K. (2010). Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589. DOI |
48 | Hon, G.C., Rajagopal, N., Shen, Y., McCleary, D.F., Yue, F., Dang, M.D., and Ren, B. (2013). Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat. Genet. 45, 1198-1206. DOI |
49 | Hon, G.C., Song, C.X., Du, T., Jin, F., Selvaraj, S., Lee, A.Y., Yen, C.A., Ye, Z., Mao, S.Q., Wang, B.A., et al. (2014). 5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation. Mol. Cell 56, 286-297. DOI |