5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription

Kellinger, Matthew W.; Song, Chun-Xiao; Chong, Jenny; Lu, Xingyu; He, Chuanchuan; Wang, Dong

doi:10.1038/nsmb.2346

Cited by 208 publications

(242 citation statements)

References 33 publications

Supporting

Mentioning

228

Contrasting

Unclassified

Order By: Relevance

“…Unlike the midway conformer, the insert conformer does not form a hydrogen bond between the 5-carboxyl moiety and Q531, thus confers no negative effect on GTP addition. Consistent with these findings, in vitro nucleotide incorporation assay showed significantly decreased RNA extension at the position opposite to the 5caC in the template, as reported earlier by the same team [6]. To further validate the interaction between 5caC and Q531, the team tested two mutants (Rbp2 Q531H and Q531A) of yeast Pol II and found that the Q531H mutant behaves similarly to the wild-type Pol II because of the hydrogen bond formation between the His residue (as appears in mammalian Rbp2) and 5caC.…”

supporting

confidence: 90%

See 1 more Smart Citation

RNA Pol II as a sensor of 5caC

Xue

2015

Cell Res

View full text Add to dashboard Cite

supporting

confidence: 90%

“…by Kellinger et al demonstrated that 5fC/5caC induce a transient pause of RNA polymerase II elongation complex (Pol II EC) in vitro [6], implying that these modifications may alter gene expression, but the biochemical mechanisms and biological relevance behind this observation remain elusive.…”

mentioning

confidence: 99%

RNA Pol II as a sensor of 5caC

Xue

2015

Cell Res

View full text Add to dashboard Cite

“…The assay was carried out as previously described (51,55). Briefly, nucleotide incorporation assays were conducted by preincubating 50 nM scaffold with 200 nM pol II for 10 min in elongation buffer at 22°C.…”

Section: Methodsmentioning

confidence: 99%

“…The pol II elongation complexes for transcription assays were assembled using established methods (51,55). Briefly, an aliquot of 5′-32 P-labeled RNA was annealed with a 1.5-fold amount of template DNA and twofold amount of nontemplate DNA to form RNA/DNA scaffold in elongation buffer [20 mM Tris·HCl (pH = 7.5), 40 mM KCl, 5 mM MgCl 2 ].…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Strand-specific (asymmetric) contribution of phosphodiester linkages on RNA polymerase II transcriptional efficiency and fidelity

Zhang

Chong

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

Nonenzymatic RNA polymerization in early life is likely to introduce backbone heterogeneity with a mixture of 2′-5′ and 3′-5′ linkages. On the other hand, modern nucleic acids are dominantly composed of 3′-5′ linkages. RNA polymerase II (pol II) is a key modern enzyme responsible for synthesizing 3′-5′-linked RNA with high fidelity. It is not clear how modern enzymes, such as pol II, selectively recognize 3′-5′ linkages over 2′-5′ linkages of nucleic acids. In this work, we systematically investigated how phosphodiester linkages of nucleic acids govern pol II transcriptional efficiency and fidelity. Through dissecting the impacts of 2′-5′ linkage mutants in the pol II catalytic site, we revealed that the presence of 2′-5′ linkage in RNA primer only modestly reduces pol II transcriptional efficiency without affecting pol II transcriptional fidelity. In sharp contrast, the presence of 2′-5′ linkage in DNA template leads to dramatic decreases in both transcriptional efficiency and fidelity. These distinct effects reveal that pol II has an asymmetric (strand-specific) recognition of phosphodiester linkage. Our results provided important insights into pol II transcriptional fidelity, suggesting essential contributions of phosphodiester linkage to pol II transcription. Finally, our results also provided important understanding on the molecular basis of nucleic acid recognition and genetic information transfer during molecular evolution. We suggest that the asymmetric recognition of phosphodiester linkage by modern nucleic acid enzymes likely stems from the distinct evolutionary pressures of template and primer strand in genetic information transfer during molecular evolution.2′-5′ phosphodiester linkage | trigger loop | synthetic nucleic acid analogues T he remarkable capacity of RNA as the functional catalyst as well as the genetic information carrier provides a strong support for the RNA world hypothesis, in which RNA is proposed to play a key role in the early evolution of primitive life before DNA and protein (enzyme) evolved (1, 2). One critical issue for RNA replication in early life is backbone heterogeneity because RNA contains both 2′-OH and 3′-OH, in which both can form phosphodiester bond during RNA polymerization. Indeed, previous studies revealed that nonenzymatic RNA replication would lead to a mixture of 2′-5′ and 3′-5′ linkages (Fig. 1A) (3-9). The 2′-5′-linked nucleic acids can form duplex structures by themselves or by pairing with natural nucleic acids (10-15). The 2′-5′ linkage substitutions in some functional RNAs retain molecular recognition and catalytic properties (16)(17)(18)(19). These discoveries suggested that the 2′-5′ linkage in nucleic acids could be an important alternative linkage during early evolution.This backbone heterogeneity problem is largely eliminated during evolution. Modern nucleic acids are dominated by 3′-5′ linkages. The 2′-5′ RNA linkages are only present in a few specific processes. One example is the formation of lariat RNA intron during splicing, where the 2′-OH of an...

show abstract

Chemoselective labeling and site‐specific mapping of 5‐formylcytosine as a cellular nucleic acid modification

2018

View full text Add to dashboard Cite

DNA methylation has a profound impact on the regulation of gene expression in normal cell development, and aberrant methylation has been recognized as a key factor in the pathogenesis of human diseases such as cancer. The discovery of modified nucleobases arising from 5-methylcytosine (5mC) through consecutive oxidation to give 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) has stimulated intense research efforts regarding the biological functions of these epigenetic marks. This Review focuses on the sensitive detection and quantitation of 5fC in DNA and RNA by chemoselective labeling, which aims at discriminating between 5fC and its thymine counterpart 5-formyluracil (5fU), and summarizes single-base resolution sequencing methods for locus-specific mapping of 5mC and its oxidized derivatives.

show abstract

5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription

Cited by 208 publications

References 33 publications

RNA Pol II as a sensor of 5caC

RNA Pol II as a sensor of 5caC

Strand-specific (asymmetric) contribution of phosphodiester linkages on RNA polymerase II transcriptional efficiency and fidelity

Chemoselective labeling and site‐specific mapping of 5‐formylcytosine as a cellular nucleic acid modification

Contact Info

Product

Resources

About