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TET ‐catalyzed oxidation of intragenic 5‐methylcytosine regulates CTCF ‐dependent alternative splicing
Author(s) -
Marina Ryan J,
Sturgill David,
Bailly Marc A,
Thenoz Morgan,
Varma Garima,
Prigge Maria F,
Nanan Kyster K,
Shukla Sanjeev,
Haque Nazmul,
Oberdoerffer Shalini
Publication year - 2015
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.15252/embj.201593235
Subject(s) - ctcf , biology , 5 methylcytosine , rna splicing , exon , alternative splicing , dna methylation , microbiology and biotechnology , genetics , gene , rna , gene expression , enhancer
Intragenic 5‐methylcytosine and CTCF mediate opposing effects on pre‐ mRNA splicing: CTCF promotes inclusion of weak upstream exons through RNA polymerase II pausing, whereas 5‐methylcytosine evicts CTCF , leading to exon exclusion. However, the mechanisms governing dynamic DNA methylation at CTCF ‐binding sites were unclear. Here, we reveal the methylcytosine dioxygenases TET 1 and TET 2 as active regulators of CTCF ‐mediated alternative splicing through conversion of 5‐methylcytosine to its oxidation derivatives. 5‐hydroxymethylcytosine and 5‐carboxylcytosine are enriched at an intragenic CTCF‐binding sites in the CD 45 model gene and are associated with alternative exon inclusion. Reduced TET levels culminate in increased 5‐methylcytosine, resulting in CTCF eviction and exon exclusion. In vitro analyses establish the oxidation derivatives are not sufficient to stimulate splicing, but efficiently promote CTCF association. We further show genomewide that reciprocal exchange of 5‐hydroxymethylcytosine and 5‐methylcytosine at downstream CTCF‐binding sites is a general feature of alternative splicing in naïve and activated CD 4 + T cells. These findings significantly expand our current concept of the pre‐ mRNA “splicing code” to include dynamic intragenic DNA methylation catalyzed by the TET proteins.