Processing of CD45 pre-mRNA is a well-established model system to study the regulatory mechanisms of alternative splicing. CD45 is a trans-membrane protein tyrosine phosphatase that initiates signaling through antigen receptors by dephosphorylating the inhibitory tyrosine on Src family kinases. Variable exclusion of exons 4-6 of CD45 transcripts is tightly correlated with stages of lymphocyte development. We previously showed that the RNA binding protein, hnRNPLL, influences exclusion of exons 4 and 6 of CD45 transcripts, but not exon 5. Considering the growing evidence for DNA-mediated regulation of spliceosome assembly, we explored the hypothesis that exon 5 inclusion is mediated by the epigenetic structure of the CD45 gene (PTPRC). Through our studies in primary lymphocytes and cell lines, we found that the methylation-sensitive DNA binding protein, CCCTC-binding factor (CTCF), promotes inclusion of weak exons in spliced mRNA by mediating pol II pausing. Binding of CTCF to exon 5 of the gene encoding CD45 is associated with pol II accumulation and inclusion of the weak exon in mature transcripts. In contrast, methylation of CD45 exon 5 DNA on 5-cytosine ablates CTCF binding, abolishes local pol II pausing and results in exclusion of exon 5 from CD45 transcripts. Combined RNA-seq and CTCF ChIP-seq analysis in CTCF depleted cells indicated that intragenic CTCF is a global regulator of alternative pre-mRNA splicing. CTCF binding specifically promotes inclusion of weak upstream exons in spliced mRNA, supporting a model in which CTCF-mediated pol II pausing provides favorable spatiotemporal conditions for spliceosome assembly at weak exons. These findings provide a framework for epigenetic regulation of splicing outcome through reciprocal heritable changes in DNA methylation and CTCF binding, and established the first mechanistic link between DNA methylation and pre-mRNA splicing. The resulting manuscript was published in Nature in November 2011. Our future goals for this project are to understand the mechanism supporting de novo methylation of exon 5 during lymphocyte development and the impact of additional associated changes at the epigenetic level on CD45 pre-mRNA processing.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
Application #
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
National Cancer Institute Division of Basic Sciences
Zip Code
Sinclair, Wilson R; Arango, Daniel; Shrimp, Jonathan H et al. (2017) Profiling Cytidine Acetylation with Specific Affinity and Reactivity. ACS Chem Biol 12:2922-2926
Nanan, Kyster K; Ocheltree, Cody; Sturgill, David et al. (2017) Independence between pre-mRNA splicing and DNA methylation in an isogenic minigene resource. Nucleic Acids Res 45:12780-12797
Marina, Ryan J; Oberdoerffer, Shalini (2016) Epigenomics meets splicing through the TETs and CTCF. Cell Cycle 15:1397-9
Marina, Ryan J; Sturgill, David; Bailly, Marc A et al. (2016) TET-catalyzed oxidation of intragenic 5-methylcytosine regulates CTCF-dependent alternative splicing. EMBO J 35:335-55
Oberdoerffer, Shalini (2012) A conserved role for intragenic DNA methylation in alternative pre-mRNA splicing. Transcription 3:106-9
Shukla, Sanjeev; Oberdoerffer, Shalini (2012) Co-transcriptional regulation of alternative pre-mRNA splicing. Biochim Biophys Acta 1819:673-83