Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine
Year: 2019
Type: article
Abstract: The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia.Rare TCF4 coding variants are found in individuals with Pitt-Hopkins syndrome -an intellectual disability and autism spectrum disorder.TCF4 contains a C-terminal basic-helix-loop-helix (bHLH) DNA binding domain which recognizes the enhancer-box (E-box) element 5'-CANNTG-3' (where N = any nucleotide).A subset of the TCF4-occupancy sites have the expanded consensus binding specificity 5'-C(A/G)-CANNTG-3', with an added outer Cp(A/G) dinucleotide such as that found in the promoter for CNIH3, a gene involved in opioid dependence.In mammalian genomes, particularly brain, the CpG and CpA dinucleotides can be methylated at the 5-position of cytosine (5mC), and then may undergo successive oxidations to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC) forms.We find that, in the context of 5'-0 CG-1 CA-2 CG-3 TG-3'(where the numbers indicate successive dinucleotides), modification of the central E-box 2 CG has very little effect on TCF4 binding and E-box 1 CA modification has a negative influence on binding, while modification of the flanking 0 CG, particularly carboxylation, has a strong positive impact on TCF4 binding to DNA.Crystallization of TCF4 in complex with unmodified or 5caC-modified oligonucleotides revealed that the basic region of bHLH domain adopts multiple conformations, including an extended loop going through the DNA minor groove, or the N-terminal portion of a long helix binding in the DNA major groove.The different protein conformations enable arginine 576 (R576) to interact, respectively, with a thymine in the minor groove, a phosphate group of DNA backbone, or 5caC in the major groove.The Pitt-Hopkins syndrome mutations affect five arginine residues in the basic region, two of them (R569 and R576) involved in 5caC recognition.Our analyses indicate, and suggest a structural basis for, the preferential recognition of 5caC by this transcription factor which is centrally important in brain development.
Authors: Jie Yang, John R. Horton, Xing Zhang, Xiaodong Cheng
Institution: The University of Texas MD Anderson Cancer Center
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: bronze
OpenAlex ID: W2997682948