4Y52

Crystal structure of 5-Carboxycytosine Recognition by RNA Polymerase II during Transcription Elongation.

Summary for 4Y52

• Entry DOI: 10.2210/pdb4y52/pdb
• Related: 4Y7N
• Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerases I, II, and III subunit RPABC4, DNA (29-MER), ... (15 entities in total)
• Functional Keywords: rna polymerase ii, 5-carboxycytosine, transcription elongation, dna demethylation, transcription-dna-rna complex, transcription/dna/rna
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 13
• Total formula weight: 486287.90

Authors

Wang, L.,Chong, J.,Wang, D. (deposition date: 2015-02-11, release date: 2015-07-15, Last modification date: 2023-09-27)

Primary citation

Wang, L.,Zhou, Y.,Xu, L.,Xiao, R.,Lu, X.,Chen, L.,Chong, J.,Li, H.,He, C.,Fu, X.D.,Wang, D.
Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex.
Nature, 523:621-625, 2015

PubMed Abstract: DNA methylation at selective cytosine residues (5-methylcytosine (5mC)) and their removal by TET-mediated DNA demethylation are critical for setting up pluripotent states in early embryonic development. TET enzymes successively convert 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), with 5fC and 5caC subject to removal by thymine DNA glycosylase (TDG) in conjunction with base excision repair. Early reports indicate that 5fC and 5caC could be stably detected on enhancers, promoters and gene bodies, with distinct effects on gene expression, but the mechanisms have remained elusive. Here we determined the X-ray crystal structure of yeast elongating RNA polymerase II (Pol II) in complex with a DNA template containing oxidized 5mCs, revealing specific hydrogen bonds between the 5-carboxyl group of 5caC and the conserved epi-DNA recognition loop in the polymerase. This causes a positional shift for incoming nucleoside 5'-triphosphate (NTP), thus compromising nucleotide addition. To test the implication of this structural insight in vivo, we determined the global effect of increased 5fC/5caC levels on transcription, finding that such DNA modifications indeed retarded Pol II elongation on gene bodies. These results demonstrate the functional impact of oxidized 5mCs on gene expression and suggest a novel role for Pol II as a specific and direct epigenetic sensor during transcription elongation.

PubMed: 26123024
DOI: 10.1038/nature14482

Experimental method

X-RAY DIFFRACTION (3.5 Å)