The RPB2 flap loop of human RNA polymerase II is dispensable for transcription initiation and elongation

Regucalcin Is a Potential Regulator in Human Cancer: Aiming to Expand into Cancer Therapy

Regucalcin, a calcium-binding protein lacking the EF-hand motif, was initially discovered in 1978. Its name is indicative of its function in calcium signaling regulation. The rgn gene encodes for regucalcin and is situated on the X chromosome in both humans and vertebrates. Regucalcin regulates pivotal enzymes involved in signal transduction and has an inhibitory function, which includes protein kinases, protein phosphatases, cysteinyl protease, nitric oxide dynthetase, aminoacyl-transfer ribonucleic acid (tRNA) synthetase, and protein synthesis. This cytoplasmic protein is transported to the nucleus where it regulates deoxyribonucleic acid and RNA synthesis as well as gene expression. Overexpression of regucalcin inhibits proliferation in both normal and cancer cells in vitro, independent of apoptosis. During liver regeneration in vivo, endogenous regucalcin suppresses cell growth when overexpressed. Regucalcin mRNA and protein expressions are significantly downregulated in tumor tissues of patients with various types of cancers. Patients exhibiting upregulated regucalcin in tumor tissue have shown prolonged survival. The decrease of regucalcin expression is linked to the advancement of cancer. Overexpression of regucalcin carries the potential for preventing and treating carcinogenesis. Additionally, extracellular regucalcin has displayed control over various types of human cancer cells. Regucalcin may hold a prominent role as a regulatory factor in cancer development. Supplying the regucalcin gene could prove to be a valuable asset in cancer treatment. The therapeutic value of regucalcin suggests its potential significance in treating cancer patients. This review delves into the most recent research on the regulatory role of regucalcin in human cancer development, providing a novel approach for treatment.

The overexpressed regucalcin represses the growth via regulating diverse pathways linked to EGF signaling in human ovarian cancer SK-OV-3 cells: Involvement of extracellular regucalcin

AIMS

Regucalcin, which plays a multifunctional role in cell regulation, contributes as a suppressor in carcinogenesis. Survival of cancer patients is prolonged with high expression of regucalcin in tumor tissues. Ovarian cancer is the most lethal in gynecologic malignancies. This study elucidates the repressive role of regucalcin on the growth of human ovarian cancer SK-OV-3 cells that are resistant to cytotoxic cancer drugs.

MATERIALS AND METHODS

SK-OV-3 wild type-cells and regucalcin-overexpressing cells (transfectants) were cultured in Dulbecco's Modification of Eagle's Medium containing 10 % fetal bovine serum.

KEY FINDINGS

Colony formation and proliferation of SK-OV-3 cells were repressed by regucalcin overexpression. The suppressive effects of regucalcin on proliferation were independent of cell death. The proliferation of SK-OV-3 wild-type cells was repressed by various inhibitors, including cell cycle, signaling processes, and transcriptional activity. The effects of all inhibitors were not revealed in transfectants, suggesting the involvement of multiple signaling pathways in regucalcin effects. Of note, the overexpressed regucalcin declined the levels of Ras, Akt, mitogen-activating protein kinase, NF-κB p65, β-catenin, and STAT3, while it raised the levels of tumor suppressors p53 and Rb, and cell cycle inhibitor p21. Interestingly, the stimulatory effects of epidermal growth factor (EGF) on cell proliferation were blocked in regucalcin-overexpressing cells. Extracellular regucalcin repressed the proliferation independent of the death of SK-OV-3 cells and blocked EGF-enhanced cell proliferation.

SIGNIFICANCES

The overexpressed regucalcin may repress cell proliferation by targeting diverse signal pathways, including EGF signaling. This study offers a novel approach to the treatment of ovarian cancer with regucalcin.

Extracellular Regucalcin Suppresses the Growth, Migration, Invasion and Adhesion of Metastatic Human Prostate Cancer Cells

Regucalcin plays a multifunctional role in the regulation of cellular function including metabolism, signaling process and transcriptional activity in maintaining cell homeostasis. Downregulated expression or activity of regucalcin contributes to the development of malignancies in various types of human cancer. Survival of cancer patients, including metastatic prostate cancer, is prolonged with high expression of regucalcin in the tumor tissues. Furthermore, we elucidate whether extracellular regucalcin conquers the growth, migration, invasion and adhesion of metastatic human prostate cancer PC-3 and DU-145 cells. Extracellular regucalcin (0.1, 1, and 10 nM) of physiologic levels inhibited colony formation and growth of PC-3 and DU-145 cells, while it did not have an effect on cell death. Repressive effects of extracellular regucalcin on the proliferation were not exhibited by the presence of inhibitors of cell cycle, intracellular signaling process and transcriptional activity, suggesting that the signals of extracellular regucalcin are transmitted to block cell growth. Furthermore, extracellular regucalcin (0.1, 1, or 10 nM) inhibited migration, invasion and adhesion of PC-3 and DU-145 cells. Mechanistically, extracellular regucalcin (10 nM) decreased the levels of various signaling proteins including Ras, hosphatidylinositol-3 kinase, mitogen-activated protein kinase, mTOR, RSK-2, caveolin-1 and integrin β1 in PC-3 cells. Thus, extracellular regucalcin may play a suppressive role in growth, migration, invasion and adhesion, which are involved in metastatic activity of human prostate cancer cells, via affecting diverse signaling processes. This study may provide a new strategy in preventing metastatic prostate cancer with exogenous regucalcin.

Extracellular regucalcin suppresses colony formation and growth independent of tumor suppressor p53 in human mammary epithelial cells

Regucalcin plays a multifunctional role in cell regulation as a suppressor in the processes of intracellular signaling and transcription, leading to inhibition of cell growth. The downregulated expression or activity of regucalcin has been shown to contribute to the development of carcinogenesis in various types of human cancer. The wild-type tumor suppressor TP53 gene encodes for a transcriptional factor p53. This protein may play a role in cell proliferation. Loss of p53 function may induce cell transformation during carcinogenesis and tumor progression of human cancer. We investigate whether or not extracellular regucalcin suppresses the proliferation of non-tumorigenic human mammary epithelial MCF 10A cells with loss of p53 in vitro. Loss of p53 did not impact colony formation and proliferation of the cells. Interestingly, p53 loss caused decrease in the cell cycle suppressor p21, but not retinoblastoma and regucalcin, as compared with those of wild-type MCF 10A cells. Notably, extracellular regucalcin suppressed colony formation and proliferation of wild-type MCF 10A cells and p53 (-/-) cells, while it did not have an effect on cell death. Mechanistically, extracellular regucalcin decreased levels of various signaling factors including Ras, phosphatidylinositol-3 kinase, mitogen-activated protein kinase (MAPK), phospho-MAPK, and signal transducer and activator of transcription 3 in wild-type MCF 10A cells and p53 (-/-) cells. Thus, extracellular regucalcin was found to suppress the growth of MCF 10A cells with loss of p53. Extracellular regucalcin may play a role as a suppressor in the growth of human mammary epithelial cells with p53 loss, providing a novel strategy for cancer.

Screening for potential nuclear substrates for the plant cell death suppressor kinase Adi3 using peptide microarrays

The tomato AGC protein kinase Adi3 is a Ser/Thr kinase that functions as a negative regulator of programmed cell death through cell death suppression (CDS) activity in the nucleus. In this study, to understand the mechanism of Adi3 CDS, peptide microarrays containing random Ser- and Thr-peptide phosphorylation substrates were used to screen for downstream phosphorylation substrates. In the microarray phosphorylation assay, Adi3 showed promiscuous kinase activity more toward Ser-peptides compared to Thr-peptides, and a preference for aromatic and cyclic amino acids on both Ser- and Thr-peptides was seen. The 63 highest phosphorylated peptide sequences from the Ser-peptide microarray were selected as queries for a BLAST search against the tomato proteome. As a result, 294 candidate nuclear Adi3 substrates were selected and categorized based on their functions. Many of these proteins were classified as DNA/RNA polymerases or regulators involved in transcription and translation events. The list of potential Adi3 substrates was narrowed to eleven and four candidates were tested for phosphorylation by Adi3. Two of these candidates, RNA polymerase II 2nd largest subunit (RPB2) and the pathogen defense related transcription factor Pti5, were confirmed as Adi3 phosphorylation substrates by in vitro kinase assays. Using a mutational approach two residues, Thr675 and Thr676, were identified as Adi3 phosphorylation sites on RPB2. This study provides the foundation for understanding Adi3 CDS mechanisms in the nucleus as well as other cellular functions.

Overexpression of Regucalcin Suppresses the Growth of Human Osteosarcoma Cells in Vitro: Repressive Effect of Extracellular Regucalcin

Regucalcin plays a pivotal role as a suppressor of human carcinogenesis, and downregulation of regucalcin expression may contribute to the promotion of human osteosarcoma. Overexpression of regucalcin suppressed the proliferation of Saos-2 human osteosarcoma cells in vitro and decreased the protein levels of multiple signaling components, transcription factors, and tumor suppressors. Interestingly, extracellular regucalcin repressed colony formation and proliferation of Saos-2 cells, and reduced the protein levels of multiple signaling components, cell cycle inhibitor, and various transcription factors. Thus, regucalcin suppressed the growth of human osteosarcoma cells, providing a novel strategy with the gene therapy for treatment of osteosarcoma.

Prolonged survival of renal cancer patients is concomitant with a higher regucalcin gene expression in tumor tissues: Overexpression of regucalcin suppresses the growth of human renal cell carcinoma cells in vitro

Renal cell carcinoma (RCC), which is a type of cancer found in the kidney tubule, is among the 10 most frequently occurring human cancers. Regucalcin plays a potential role as a regulator of transcriptional activity, and its downregulated expression or activity may contribute to the promotion of human cancers. In this study, we investigated the involvement of regucalcin in human RCC. Regucalcin expression was compared in 23 normal and 29 tumor samples of kidney cortex tissues of patients with clear cell RCC obtained through the Gene Expression Omnibus (GEO) database (GSE36895). Regucalcin expression was downregulated in the tumor tissues. The prolonged survival of patients with clear cell RCC was demonstrated to be associated with a higher regucalcin gene expression in the TCGA dataset. The overexpression of regucalcin suppressed the colony formation, proliferation and the death of human clear cell RCC A498 cells in vitro. Mechanistically, the overexpression of regucalcin induced the G1 and G2/M phase cell cycle arrest of A498 cells through the suppression of multiple signaling components, including Ras, PI3 kinase, Akt and mitogen‑activated protein (MAP) kinase. Importantly, the overexpression of regucalcin led to an elevation in the levels of the tumor suppressors, p53, Rb and the cell cycle inhibitor, p21. The levels of the transcription factors, c‑fos, c‑jun, nuclear factor‑κB p65, β‑catenin and signal transducer and activator of transcription 3, were suppressed by regucalcin overexpression. On the whole, the findings of this study suggest that regucalcin plays a suppressive role in the promotion of human RCC. The overexpression of regucalcin by gene delivery systems may thus prove to be a novel therapeutic strategy for RCC.

Prolonged survival of patients with colorectal cancer is associated with a higher regucalcin gene expression: Overexpression of regucalcin suppresses the growth of human colorectal carcinoma cells in vitro

Regucalcin plays a crucial role as a regulator of transcriptional signaling activity, and its decreased expression or activity may contribute to the promotion of human carcinogenesis. A higher regucalcin expression in the tumor tissues has been demonstrated to prolong the survival of patients with various types of cancer, including pancreatic cancer, breast cancer, liver cancer and lung adenocarcinoma. The involvement of regucalcin in human colorectal cancer was investigated in the current study. Regucalcin gene expression and the survival data of 62 patients with colorectal cancer were obtained though the Gene Expression Omnibus (GEO) database (GSE12945) for outcome analysis. The data of gene expression revealed that the prolonged survival of patients with colorectal cancer was associated with a higher regucalcin gene expression in tumor tissues. The overexpression of regucalcin suppressed colony formation and proliferation, and induced the death of human colorectal carcinoma RKO cells cultured in a medium containing fetal bovine serum in vitro. Mechanistically, the overexpression of regucalcin induced the G1 and G2/M phase cell cycle arrest of the RKO cells through the suppression of multiple signaling pathways, including Ras, Akt, mitogen-activated protein (MAP) kinase and SAPK/JNK. Of note, the overexpression of regucalcin induced an increase in the levels of the tumor suppressors, p53 and Rb, and the cell cycle inhibitor, p21. Moreover, the levels of the transcription factors, c‑fos, c‑jun, nuclear factor (NF)‑κB p65, β-catenin and signal transducer and activator of transcription 3 (Stat3), were suppressed by the overexpression of regucalcin. On the whole, the findings of this study suggest that regucalcin plays a crucial role as a suppressor in human colorectal cancer, and that the suppressed expression of the regucalcin gene may predispose patients to the promotion of colorectal cancer. The overexpression of regucalcin by gene delivery may thus prove to be a novel therapeutic strategy for colorectal cancer.

Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators

NusG/RfaH/Spt5 transcription elongation factors are the only transcription regulators conserved across all life. Bacterial NusG regulates RNA polymerase (RNAP) elongation complexes (ECs) across most genes, enhancing elongation by suppressing RNAP backtracking and coordinating ρ-dependent termination and translation. The NusG paralog RfaH engages the EC only at operon polarity suppressor (ops) sites and suppresses both backtrack and hairpin-stabilized pausing. We used single-particle cryoelectron microscopy (cryo-EM) to determine structures of ECs at ops with NusG or RfaH. Both factors chaperone base-pairing of the upstream duplex DNA to suppress backtracking, explaining stimulation of elongation genome-wide. The RfaH-opsEC structure reveals how RfaH confers operon specificity through specific recognition of an ops hairpin in the single-stranded nontemplate DNA and tighter binding to the EC to exclude NusG. Tight EC binding by RfaH sterically blocks the swiveled RNAP conformation necessary for hairpin-stabilized pausing. The universal conservation of NusG/RfaH/Spt5 suggests that the molecular mechanisms uncovered here are widespread.

Survival of lung cancer patients is prolonged with higher regucalcin gene expression: suppressed proliferation of lung adenocarcinoma A549 cells in vitro

Regucalcin plays a crucial role as a suppressor of transcription signaling, and its diminished expression or activity may play a key role in human carcinogenesis. Higher regucalcin expression has been demonstrated to prolong survival of the patients of pancreatic cancer, breast cancer, and hepatocellular carcinoma. Moreover, we investigated an involvement of regucalcin in human lung cancer. Human non-small cell lung cancer (NSCLC) accounts for over 80% in human lung cancer and is one of the leading causes of malignancy-related mortality with fewer than 16% patients surviving beyond 5 years. In this study, gene expression and survival data of 204 lung adenocarcinoma patients were obtained through the gene expression omnibus database (GSE31210) for outcome analysis. Gene expression data demonstrated that prolonged survival in lung cancer patients is associated with higher regucalcin gene expression. Overexpression of regucalcin suppressed the proliferation, cell death, and migration of human lung adenocarcinoma NSCLC A549 cells in vitro. Mechanistically, regucalcin induced G1 and G2/M phase cell cycle arrest of A549 cells through suppression of multiple signaling pathways including Ras, Akt, MAP kinase, and SAPK/JNK. Moreover, overexpression of regucalcin caused decreases in the oncogenes c-fos and c-myc and elevation of the tumor suppressers p53 and Rb. These findings suggest that regucalcin may play a potential role as a suppressor of human lung cancer, and that downregulation of regucalcin expression may predispose patients to development of lung cancer. Overexpression of regucalcin using gene delivery may constitute a novel therapeutic approach to treating lung cancer.

Prolonged survival in hepatocarcinoma patients with increased regucalcin gene expression: HepG2 cell proliferation is suppressed by overexpression of regucalcin in vitro

Hepatocellular carcinoma (HCC) is one of the most common malignant cancers worldwide and ranks third in overall global cancer-related mortality rates. Importantly, in this study gene expression data demonstrate that prolonged survival in HCC patients is associated with increased regucalcin gene expression. Regucalcin has been shown to play a pivotal role as a transcription repressor and diminished expression or activity of regucalcin may play a key role in the development of human carcinogenesis. Indeed, overexpression of regucalcin suppressed the proliferation, cell death, and migration of human HCC HepG2 cells in vitro. Mechanistically, regucalcin induced G1 and G2/M phase cell cycle arrest of HepG2 cells through suppression of multiple signaling pathways including Ras, Akt, MAP kinase and SAPK/JNK and by increasing the tumor suppressors p53 and Rb. Furthermore, the oncogenes c-fos and c-myc were suppressed by overexpression of regucalcin, and overexpression of regucalcin caused an increase in p21 and a decrease in NF-κB p65 and β-catenin. These findings suggest that regucalcin may play a potential role as a suppressor of human HCC, and that diminished expression of regucalcin may predispose patients to development of HCC. Overexpression of regucalcin may constitute a novel therapeutic approach to treating HCC.

Potential suppressive effects of gentian violet on human breast cancer MDA-MB-231 cells in vitro: Comparison with gemcitabine

Gentian violet (GV), a cationic triphenylmethane dye, is used as an antifungal and antibacterial agent. Recently, attention has been focused on GV as a potential chemotherapeutic and antiangiogenic agent. The present study was undertaken to determine the suppressive effects of GV on human breast cancer MDA-MB-231 cells in vitro. The proliferation of MDA-MB-231 cells was suppressed by culture with GV (1-200 nM). The suppressive effects of GV on cell proliferation were not potentiated in the presence of various inhibitors that induce cell cycle arrest in vitro. This finding suggested that GV inhibits G1 and G2/M phase cell cycle arrest in MDA-MB-231 cells. The suppressive effects of GV on proliferation are mediated through the inhibition of various signaling pathways or nuclear transcription in vitro. Moreover, the suppressive effects of GV on cell proliferation were compared with that of gemcitabine, a strong antitumor agent that induces nuclear DNA damage. Notably, the culture with gemcitabine >50 nM suppressed cell proliferation, while the effects of GV were observed at >1 nM. The suppressive effects of gemcitabine on cell proliferation were not potentiated by GV. Overall, the present study demonstrated that GV exhibits a potential suppressive effect on the proliferation of human breast cancer MDA-MB-231 cells in vitro.

Increased regucalcin gene expression extends survival in breast cancer patients: Overexpression of regucalcin suppresses the proliferation and metastatic bone activity in MDA-MB-231 human breast cancer cells in vitro

Human breast cancer is highly metastatic to bone and drives bone turnover. Breast cancer metastases cause osteolytic lesions and skeletal damage that leads to bone fractures. Regucalcin, which plays a pivotal role as an inhibitor of signal transduction and transcription activity, has been suggested to act as a suppressor of human cancer. In the present study, we compared the clinical outcome between 44 breast cancer patients with higher regucalcin expression and 43 patients with lower regucalcin expression. Prolonged relapse-free survival was identified in the patients with increased regucalcin gene expression. We further demonstrated that overexpression of full length, but not alternatively spliced variants of regucalcin, induces G1 and G2/M phase cell cycle arrest, suppressing the proliferation of MDA-MB-231 cells, a commonly used in vitro model of human breast cancer that metastasize to bone causing osteolytic lesions. Overexpression of regucalcin was found to suppress multiple signaling pathways including Akt, MAP kinase and SAPK/JNK, and NF-κB p65 and β-catenin along with increased p53, a tumor suppressor, and decreased K-ras, c-fos and c-jun. Moreover, we found that co-culture of regucalcin-overexpressing MDA-MB-231 cells with mouse bone marrow cells prevented enhanced osteoclastogenesis and suppressed mineralization in mouse bone marrow cells in vitro. Taken together, the present study suggests that regucalcin may have important anticancer properties in human breast cancer patients. Mechanistically, these effects are likely mediated through suppression of multiple signaling pathways, upregulation of p53 and downregulation of oncogenes leading to anti-proliferative effects and reduced metastases to bone, a phenotype associated with poor clinical outcome.

Prolonged survival in pancreatic cancer patients with increased regucalcin gene expression: Overexpression of regucalcin suppresses the proliferation in human pancreatic cancer MIA PaCa-2 cells in vitro

Approximately 90% of all pancreatic cancers are pancreatic ductal adenocarcinomas (PDAC). PDAC is a highly aggressive malignancy and is one of the deadliest. This poor clinical outcome is due to the prominent resistance of pancreatic cancer to drug and radiation therapies. Regucalcin plays a pivotal role as a suppressor protein in signal transduction in various types of cells including tumor tissues. We demonstrated that the prolonged survival is induced in PDAC patients with increased regucalcin gene expression using a dataset of PDAC obtained from GEO database (GSE17891) together with the clinical annotation data file. Moreover, overexpression of regucalcin with full length was demonstrated to suppress the proliferation, cell death and migration in human pancreatic cancer MIA PaCa-2 (K-ras mutated) cells that possess resistance to drug and radiation therapies. Suppressive effects of regucalcin on cell proliferation and death were not seen in the cells overexpressed with regucalcin cDNA alternatively spliced variants (deleted exon 4 or deleted exon 4 and 5). Regucalcin was suggested to induce G1 and G2/M phase cell cycle arrest in MIA PaCa-2 cells. Suppressive effects of regucalcin on cell proliferation were independent of cell death. Overexpression of regucalcin was found to suppress signaling pathways including Akt, MAP kinase and SAPK/JNK, to increase the protein levels of p53, a tumor suppresser, and to decrease K-ras, c-fos and c-jun, a oncogene, by suppressing signaling pathways that are related to signaling of K-ras. Regucalcin may play a potential role as a suppressor protein in human pancreatic cancer.

The flavonoid p-hydroxycinnamic acid exhibits anticancer effects in human pancreatic cancer MIA PaCa-2 cells in vitro: Comparison with gemcitabine

Pancreatic cancer is a highly aggressive malignancy with a notoriously dismal prognosis. A major contributor to this poor clinical outcome is pancreatic cancer's prominent chemoresistance. The present study was undertaken to determine whether the flavonoid p‑hydroxycinnamic acid (HCA), which is a botanical factor, possesses anticancer effects on cloned human pancreatic cancer MIA PaCa‑2 cells that possess resistance to radiation therapy in vitro. Proliferation of MIA PaCa‑2 cells was suppressed after culture with HCA (10‑1,000 nM). Such an effect was also noted in human pancreatic cancer Pt45P1 cells. In the MIA PaCa‑2 cells, HCA induced G1 and G2/M phase cell cycle arrest in the cells. The suppressive effects of HCA on proliferation were suggested to be mediated through the inhibition of various signaling pathways related to nuclear factor‑κB (NF‑κB), extracellular signal‑regulated kinase (ERK), protein kinase C, phosphatidylinositol 3‑kinase (PI3K) or nuclear transcription activity. Moreover, HCA was found to stimulate cell death in the MIA PaCa‑2 and Pt45P1 cells in vitro. The anticancer effects of HCA on MIA PaCa‑2 cells were exhibited at a lower concentration than gemcitabine, a potent cancer drug. The flavonoid HCA may be a useful tool in the therapy of human pancreatic cancer in vivo.

Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes

The RNA polymerase II (Pol II) is a eukaryotic enzyme that catalyzes the synthesis of the messenger RNA using a DNA template. Despite numerous biochemical and biophysical studies, it remains elusive whether the “secondary channel” is the only route for NTP to reach the active site of the enzyme or if the “main channel” could be an alternative. On this regard, crystallographic structures of Pol II have been extremely useful to understand the structural basis of transcription, however, the conformation of the unpaired non-template DNA part of the full transcription bubble (TB) is still unknown. Since diffusion routes of the nucleoside triphosphate (NTP) substrate through the main channel might overlap with the TB region, gaining structural information of the full TB is critical for a complete understanding of Pol II transcription process. In this study, we have built a structural model of Pol II with a complete transcription bubble based on multiple sources of existing structural data and used Molecular Dynamics (MD) simulations together with structural analysis to shed light on NTP entry pathways. Interestingly, we found that although both channels have enough space to allow NTP loading, the percentage of MD conformations containing enough space for NTP loading through the secondary channel is twice higher than that of the main channel. Further energetic study based on MD simulations with NTP loaded in the channels has revealed that the diffusion of the NTP through the main channel is greatly disfavored by electrostatic repulsion between the NTP and the highly negatively charged backbones of nucleotides in the non-template DNA strand. Taken together, our results suggest that the secondary channel is the major route for NTP entry during Pol II transcription.

In eukaryotic cells, the RNA polymerase II (Pol II) is a central enzyme that reads the genetic information encoded in the DNA template to synthetize a messenger RNA. To perform its function, Pol II needs to have the substrate nucleoside triphosphate (NTP) diffuse into its deeply buried active site. Despite numerous efforts, the NTP entry routes remain elusive: NTP could diffuse only through the secondary channel, or also via the main channel. The structural information of the transcription bubble is essential to study this process, however, the unpaired non-template DNA of the transcription bubble is absent in the available X-ray crystal structures. In this regard, we have built a structural model of the Pol II elongation complex with reconstructed transcription bubble using existing experimental data. We then performed Molecular Dynamics (MD) simulations and applied structural analysis to study the routes of NTP diffusion. We found that sterically the probability of NTP loading through the secondary channel is more than twice that of the main channel. Further analysis of the non-bonded energetic contributions to NTP diffusion suggests that NTP diffusion through the main channel is greatly disfavored by the electrostatic repulsion between the substrate and negatively charged backbones of nucleotides in the non-template strand of the transcription bubble. Altogether, our findings suggest that the secondary channel is the more favorable NTP diffusion route for Pol II transcription elongation.

The evolutionarily conserved Pol II flap loop contributes to proper transcription termination on short yeast genes

Current models of transcription termination factor recruitment to the RNA polymerase II (Pol II) transcription complex rely exclusively on the direct interaction between the termination factor and phosphorylated isoforms of the Pol II C-terminal domain (CTD). Here, we report that the Pol II flap loop is needed for physical interaction of Pol II with the Pcf11/Clp1 subcomplex of cleavage factor IA (CF IA), which functions in both 3? end processing and Pol II termination, and for proper termination of short RNAs in vitro and in vivo. Deletion of the flap loop reduces the in vivo interaction of Pol II with CF IA but increases the association of Nrd1 during stages of the transcription cycle when the CTD is predominantly Ser5 phosphorylated. We propose a model in which the flap loop coordinates a binding equilibrium between the competing termination factors Pcf11 and Nrd1 to Pol II during termination of short RNA synthesis.