The Human TET2 Gene Contains Three Distinct Promoter Regions With Differing Tissue and Developmental Specificities.

Hong Lou,Tyler R Shank,Kevin J Ho,Luke L Cai,Michael R Verneris,Andy S Huang,Stephen K Anderson,Hongchuan Li,Michael Dean,Michael L Nickerson

doi:10.3389/fcell.2019.00099

Abstract

Tet methylcytosine dioxygenase 2 (TET2) is a tumor suppressor gene that is inactivated in a wide range of hematological cancers. TET2 enzymatic activity converts 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC), an essential step in DNA demethylation. Human TET2 is highly expressed in pluripotent cells and down-regulated in differentiated cells: however, transcriptional regulation of the human TET2 gene has not been investigated in detail. Here we define three promoters within a 2.5 kb region located ∼ 87 kb upstream of the first TET2 coding exon. The three promoters, designated as Pro1, Pro2, and Pro3, generate three alternative first exons, and their presence in TET2 mRNAs varies with cell type and developmental stage. In general, all three TET2 transcripts are more highly expressed in human tissues rich in hematopoietic stem cells, such as spleen and bone marrow, compared to other tissues, such as brain and kidney. Transcripts from Pro2 are expressed by a broad range of tissues and at a significantly higher level than Pro1 or Pro3 transcripts. Pro3 transcripts were highly expressed by embryoid bodies generated from the H9 ES cell line, and the major Pro3 transcript is an alternatively spliced mRNA isoform that produces a truncated TET2 protein lacking the catalytic domain. Our study demonstrates distinct tissue-specific mechanisms of TET2 transcriptional regulation during early pluripotent states and in differentiated cell types.

Highlights

DNA methylation plays a critical role in regulating gene expression during development
Transcript isolated from human fetal kidney has been reported (GenBank# BX640738) that terminates at a polyA site in the fourth intron, resulting in a truncated 1165 aa open reading frame that lacks the C-terminal TET2 catalytic domain (TET2-1a)
The weak expression of the truncated TET2 protein relative to the full-length protein suggests that the majority of TET2 transcripts in these cell lines contain the full coding sequence

Summary

Introduction

DNA methylation plays a critical role in regulating gene expression during development. The TET2 protein plays an important role in the epigenetic regulation of gene expression during embryogenesis (Dawlaty et al, 2013), differentiation of hematopoietic cells (Ko et al, 2011), cancer development (Ito et al, 2010; Ko et al, 2010; Zhang et al, 2010; Meisel et al, 2018), and it is involved in somatic cell reprogramming (Doege et al, 2012; Costa et al, 2013). Despite numerous studies on TET family members via loss- and gain-of-function approaches, the transcriptional mechanisms underlying tissuespecific expression of the human gene have not been fully explored (Ito et al, 2010; Wu et al, 2011; Pan et al, 2017; Yang et al, 2018). The expression of a given gene can be exquisitely complex, due to the presence of multiple transcription start sites that drive the expression of alternative mRNA isoforms (Djebali et al, 2012)

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