Basic mechanism of transcription by RNA polymerase II

Svetlov, Vladimir

doi:10.1016/j.bbagrm.2012.08.009

Cited by 55 publications

(47 citation statements)

References 107 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These results suggested that CTDP1 silencing reduced the tumor formation ability of GC cells. The primary function of FCP1, the protein encoded by CTDP1, is dephosphorylation of the CTD of RNA polymerase II, which has a critical role in the initial synthesis of mRNA and the post-transcriptional modification of mRNA (8,9). The phosphorylation of CTD in the largest subunit of RNA polymerase II mediates the assemblage of regulatory factors during the initial stages of mRNA synthesis (10,11).…”

Section: Discussionmentioning

confidence: 99%

Carboxy-terminal domain phosphatase 1 silencing results in the inhibition of tumor formation ability in gastric cancer cells

Yang

Wang

et al. 2015

Oncology Letters

View full text Add to dashboard Cite

Abstract. Gastric cancer (GC), one of the most malignant types of cancer, is the second greatest cause of cancer-associated mortality worldwide. Novel therapeutic targets for GC treatment are therefore urgently required. Carboxy-terminal domain phosphatase 1 (CTDP1) has a crucial role in the regulation of gene expression. However, to the best of our knowledge, the role of CTDP1 in GC has not previously been explored. In the present study, reverse transcription-quantitative polymerase chain reaction analysis was used to detect CTDP1 messenger RNA expression in various GC cell lines. CTDP1 was subsequently silenced in GC cells by lentivirus-mediated small interfering RNA (siRNA) infection, and the effects of CTDP1 inhibition on cell proliferation were evaluated by cell number counting, cell cycle analysis with propidium iodide staining and fluorescence-activated cell sorting (FACS) analysis, apoptotic rate with Annexin V staining and FACS analysis, as well as colony formation assay in GC cells. The results revealed that CTDP1 was highly expressed in certain GC cell lines and lentivirus-mediated siRNA infection was able to effectively silence CTDP1 expression in GC cells. CTDP1 inhibition decreased cell proliferation, arrested the cell cycle at G0/G1 phase and increased cell apoptosis in GC cells. Furthermore, the colony formation ability of GC cells was also suppressed by silencing CTDP1. Taken together these results indicated that CTDP1 has a significant role in the tumor formation ability of GC cells and is a novel and promising therapeutic target for the treatment of GC.

show abstract

Section: Discussionmentioning

confidence: 99%

Carboxy-terminal domain phosphatase 1 silencing results in the inhibition of tumor formation ability in gastric cancer cells

Yang

Wang

et al. 2015

Oncology Letters

View full text Add to dashboard Cite

show abstract

“…Finally, our findings also revealed the key contribution of the 3′-5′ phosphodiester linkage backbone on pol II transcriptional efficiency and fidelity. Previous studies on molecular recognition of RNA pol II have focused on the contributions of functional groups in nucleic acids, such as nucleotide bases, 2′-and 3′-OH of ribose (28)(29)(30)(47)(48)(49)(50). Recently, we used synthetic nucleic acid analogs to reveal the importance of chemical interactions and the intrinsic structural features of nucleic acids in controlling pol II transcriptional fidelity.…”

Section: Key Structural Features Governing Pol II Transcriptional Effmentioning

confidence: 99%

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.

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

“…In this model, the system can rapidly interconvert between the pretranslocation and posttranslocation states without the requirement of NTP hydrolysis. The motion is facilitated by thermal oscillation of the bridge helix (BH) between the straight and bent conformations; the binding of the incoming NTP will then stabilize forward translocation (14,(17)(18)(19). However, the dynamics at the atomic level and the details of the mechanism of Pol II translocation remain obscure and direct experimental approaches are limited.…”

mentioning

confidence: 99%

“…On one hand, for single subunit T7 RNAP, PPi release is suggested to be mechanically coupled to the opening motion of the O-helix (counterpart of TL) and subsequent translocation, referred to as the "power-stroke" model (15, 16). On the other hand, the Brownian ratchet model is proposed for translocation in multisubunit RNA polymerases (14,(17)(18)(19). In this model, the system can rapidly interconvert between the pretranslocation and posttranslocation states without the requirement of NTP hydrolysis.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Millisecond dynamics of RNA polymerase II translocation at atomic resolution

Silva

Weiss

Avila

et al. 2014

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

144

199

View full text Add to dashboard Cite

Transcription is a central step in gene expression, in which the DNA template is processively read by RNA polymerase II (Pol II), synthesizing a complementary messenger RNA transcript. At each cycle, Pol II moves exactly one register along the DNA, a process known as translocation. Although X-ray crystal structures have greatly enhanced our understanding of the transcription process, the underlying molecular mechanisms of translocation remain unclear. Here we use sophisticated simulation techniques to observe Pol II translocation on a millisecond timescale and at atomistic resolution. We observe multiple cycles of forward and backward translocation and identify two previously unidentified intermediate states. We show that the bridge helix (BH) plays a key role accelerating the translocation of both the RNA:DNA hybrid and transition nucleotide by directly interacting with them. The conserved BH residues, Thr831 and Tyr836, mediate these interactions. To date, this study delivers the most detailed picture of the mechanism of Pol II translocation at atomic level.Markov state model | molecular dynamics | trigger loop T he RNA polymerase is the central component of gene expression in all living organisms, transferring genetic information from DNA to RNA. In eukaryotes, the RNA polymerase II (Pol II) enzyme is responsible for transcribing DNA into messenger RNA. In the past decade, a number of X-ray crystallographic structures of Pol II have been obtained at different stages of the transcription process, providing a static picture of how this complex machine performs its function (1, 2). Transcription is a multistep process consisting of initiation, elongation, and termination, where elongation is composed of consecutive nucleotide addition cycles (NACs). In each NAC, the NTP substrate first diffuses into Pol II active site through the secondary channel (3-5) or alternatively the main channel (6). Upon correct NTP binding to the Pol II active site, the trigger loop (TL) conformation switches from an inactive open state to an active closed state (7). The closure of the active site subsequently facilitates the catalysis of the nucleotide addition reaction (7), followed by release of the pyrophosphate ion (PPi). To proceed to the next NAC, Pol II must translocate from a pretranslocation state, in which the active site is still occupied by the newly added nucleotide at 3′-RNA, to a posttranslocation state. During translocation, the template DNA and RNA must move by exactly one register, once again creating a free insertion site (i site) (1,2,5,(8)(9)(10)(11)(12)(13).Although static snapshots of X-ray structures of Pol II pretranslocation and posttranslocation states are valuable, the dynamics underlying the fundamental RNA polymerase translocation mechanism remain poorly understood (14). Two models of translocation have been proposed based on structural, biochemical, and genetic approaches. On one hand, for single subunit T7 RNAP, PPi release is suggested to be mechanically coupled to the opening motion of the O-helix (co...

show abstract

Basic mechanism of transcription by RNA polymerase II

Cited by 55 publications

References 107 publications

Carboxy-terminal domain phosphatase 1 silencing results in the inhibition of tumor formation ability in gastric cancer cells

Carboxy-terminal domain phosphatase 1 silencing results in the inhibition of tumor formation ability in gastric cancer cells

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

Millisecond dynamics of RNA polymerase II translocation at atomic resolution

Contact Info

Product

Resources

About