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https://www.readbyqxmd.com/read/29775583/correlating-transcription-initiation-and-conformational-changes-by-a-single-subunit-rna-polymerase-with-near-base-pair-resolution
#1
Hye Ran Koh, Rahul Roy, Maria Sorokina, Guo-Qing Tang, Divya Nandakumar, Smita S Patel, Taekjip Ha
We provide a comprehensive analysis of transcription in real time by T7 RNA Polymerase (RNAP) using single-molecule fluorescence resonance energy transfer by monitoring the entire life history of transcription initiation, including stepwise RNA synthesis with near base-pair resolution, abortive cycling, and transition into elongation. Kinetically branching pathways were observed for abortive initiation with an RNAP either recycling on the same promoter or exchanging with another RNAP from solution. We detected fast and slow populations of RNAP in their transition into elongation, consistent with the efficient and delayed promoter release, respectively, observed in ensemble studies...
May 17, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29771928/chip-exo-interrogation-of-crp-dna-and-rnap-holoenzyme-interactions
#2
Haythem Latif, Stephen Federowicz, Ali Ebrahim, Janna Tarasova, Richard Szubin, Jose Utrilla, Karsten Zengler, Bernhard O Palsson
Numerous in vitro studies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChIP-exo) was applied to study Crp binding in vivo and at genome-scale. Surprisingly, Crp was found to provide little to no protection of the DNA motif under activating conditions. Instead, Crp demonstrated binding patterns that closely resembled those generated by σ70...
2018: PloS One
https://www.readbyqxmd.com/read/29771376/rna-dna-and-dna-dna-base-pairing-at-the-upstream-edge-of-the-transcription-bubble-regulate-translocation-of-rna-polymerase-and-transcription-rate
#3
Maria KIreeva, Cyndi Trang, Gayane Matevosyan, Joshua Turek-Herman, Vitaly Chasov, Lucyna Lubkowska, Mikhail Kashlev
Translocation of RNA polymerase (RNAP) along DNA may be rate-limiting for transcription elongation. The Brownian ratchet model posits that RNAP rapidly translocates back and forth until the post-translocated state is stabilized by NTP binding. An alternative model suggests that RNAP translocation is slow and poorly reversible. To distinguish between these two models, we take advantage of an observation that pyrophosphorolysis rates directly correlate with the abundance of the pre-translocated fraction. Pyrophosphorolysis by RNAP stabilized in the pre-translocated state by bacteriophage HK022 protein Nun was used as a reference point to determine the pre-translocated fraction in the absence of Nun...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29769289/metarrestin-a-perinucleolar-compartment-inhibitor-effectively-suppresses-metastasis
#4
Kevin J Frankowski, Chen Wang, Samarjit Patnaik, Frank J Schoenen, Noel Southall, Dandan Li, Yaroslav Teper, Wei Sun, Irawati Kandela, Deqing Hu, Christopher Dextras, Zachary Knotts, Yansong Bian, John Norton, Steve Titus, Marzena A Lewandowska, Yiping Wen, Katherine I Farley, Lesley Mathews Griner, Jamey Sultan, Zhaojing Meng, Ming Zhou, Tomas Vilimas, Astin S Powers, Serguei Kozlov, Kunio Nagashima, Humair S Quadri, Min Fang, Charles Long, Ojus Khanolkar, Warren Chen, Jinsol Kang, Helen Huang, Eric Chow, Esthermanya Goldberg, Coral Feldman, Romi Xi, Hye Rim Kim, Gary Sahagian, Susan J Baserga, Andrew Mazar, Marc Ferrer, Wei Zheng, Ali Shilatifard, Jeffrey Aubé, Udo Rudloff, Juan Jose Marugan, Sui Huang
Metastasis remains a leading cause of cancer mortality due to the lack of specific inhibitors against this complex process. To identify compounds selectively targeting the metastatic state, we used the perinuclear compartment (PNC), a complex nuclear structure associated with metastatic behaviors of cancer cells, as a phenotypic marker for a high-content screen of over 140,000 structurally diverse compounds. Metarrestin, obtained through optimization of a screening hit, disassembles PNCs in multiple cancer cell lines, inhibits invasion in vitro, suppresses metastatic development in three mouse models of human cancer, and extends survival of mice in a metastatic pancreatic cancer xenograft model with no organ toxicity or discernable adverse effects...
May 16, 2018: Science Translational Medicine
https://www.readbyqxmd.com/read/29768209/influenza-virus-mounts-a-two-pronged-attack-on-host-rna-polymerase-ii-transcription
#5
David L V Bauer, Michael Tellier, Mónica Martínez-Alonso, Takayuki Nojima, Nick J Proudfoot, Shona Murphy, Ervin Fodor
Influenza virus intimately associates with host RNA polymerase II (Pol II) and mRNA processing machinery. Here, we use mammalian native elongating transcript sequencing (mNET-seq) to examine Pol II behavior during viral infection. We show that influenza virus executes a two-pronged attack on host transcription. First, viral infection causes decreased Pol II gene occupancy downstream of transcription start sites. Second, virus-induced cellular stress leads to a catastrophic failure of Pol II termination at poly(A) sites, with transcription often continuing for tens of kilobases...
May 15, 2018: Cell Reports
https://www.readbyqxmd.com/read/29766532/root-expressed-phytochromes-b1-and-b2-but-not-phya-and-cry2-regulate-shoot-growth-in-nature
#6
Youngjoo Oh, Variluska Fragoso, Francesco Guzzonato, Sang-Gyu Kim, Chung-Mo Park, Ian T Baldwin
While photoreceptors are expressed throughout all plant organs, most studies have focused on their function in aerial parts with laboratory-grown plants. Photoreceptor function in naturally dark-grown roots of plants in their native habitats are lacking. We characterized patterns of photoreceptor expression in field- and glasshouse-grown Nicotiana attenuata plants, silenced the expression of PhyB1/B2/A/Cry2 whose root transcripts levels were greater/equal to those of shoots, and by micrografting combined empty vector transformed shoots onto photoreceptor-silenced roots, creating chimeric plants with "blind" roots but "sighted" shoots...
May 15, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29764934/structure-specific-recognition-protein-1-ssrp1-is-an-elongated-homodimer-that-binds-histones
#7
Gabriele Marcianò, Stefano Da Vela, Giancarlo Tria, Dmitri I Svergun, Olwyn Byron, Danny T Huang
The histone chaperone complex facilitates chromatin transcription (FACT) plays important roles in DNA repair, replication, and transcription. In the formation of this complex, structure-specific recognition protein-1 (SSRP1) heterodimerizes with suppressor of Ty 16 (SPT16). SSRP1 also has SPT16-independent functions, but how SSRP1 functions alone remains elusive. Here, using analytical ultracentrifugation (AUC) and small-angle X-ray scattering (SAXS) techniques, we characterized human SSRP1 and that from the amoeba Dictyostelium discoideum and show that both orthologs form an elongated homodimer in solution...
May 15, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29763857/the-pillars-of-land-plants-new-insights-into-stem-development
#8
REVIEW
Antonio Serrano-Mislata, Robert Sablowski
In spite of its central importance in evolution, plant architecture and crop improvement, stem development remains poorly understood relative to other plant organs. Here, we summarise current knowledge of stem ontogenesis and its regulation, including insights from new image analysis and biophysical approaches. The stem initiates in the rib zone (RZ) of the shoot apical meristem, under transcriptional control by DELLA and BLH proteins. Links have emerged between these regulators and cell proliferation, patterning and oriented growth in the RZ...
May 12, 2018: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/29760462/distinct-mechanisms-coordinate-transcription-and-translation-under-carbon-and-nitrogen-starvation-in-escherichia-coli
#9
Sukanya Iyer, Dai Le, Bo Ryoung Park, Minsu Kim
Bacteria adapt to environmental stress by producing proteins that provide stress protection. However, stress can severely perturb the kinetics of gene expression, disrupting protein production. Here, we characterized how Escherichia coli mitigates such perturbations under nutrient stress through the kinetic coordination of transcription and translation. We observed that, when translation became limiting under nitrogen starvation, transcription elongation slowed accordingly. This slowdown was mediated by (p)ppGpp, the alarmone whose primary role is thought to be promoter regulation...
May 14, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29758107/locking-the-non-template-dna-to-control-transcription
#10
Yuri Nedialkov, Dmitri Svetlov, Georgiy A Belogurov, Irina Artsimovitch
Universally conserved NusG/Spt5 factors reduce RNA polymerase pausing and arrest. In a widely accepted model, these proteins bridge the RNA polymerase clamp and lobe domains across the DNA channel, inhibiting the clamp opening to promote pause-free RNA synthesis. However, recent structures of paused transcription elongation complexes show that the clamp does not open and suggest alternative mechanisms of antipausing. Among these mechanisms, direct contacts of NusG/Spt5 proteins with the nontemplate DNA in the transcription bubble have been proposed to prevent unproductive DNA conformations and thus inhibit arrest...
May 14, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29757477/reading-of-the-non-template-dna-by-transcription-elongation-factors
#11
Vladimir Svetlov, Evgeny Nudler
Unlike transcription initiation and termination, which have easily discernable signals such as promoters and terminators, elongation is regulated through a dynamic network involving RNA/DNA pause signals and states- rather than sequence-specific protein interactions. A report by Nedialkov et al. (in press) provides experimental evidence for sequence-specific recruitment of elongation factor RfaH to transcribing RNA polymerase (RNAP) and outlines the mechanism of gene expression regulation by restraint ("locking") of the DNA non-template strand...
May 14, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29743242/cyclin-dependent-kinase-7-cdk7-mediated-phosphorylation-of-the-cdk9-activation-loop-promotes-p-tefb-assembly-with-tat-and-proviral-hiv-reactivation
#12
Uri Mbonye, Benlian Wang, Giridharan Gokulrangan, Wuxian Shi, Sichun Yang, Jonathan Karn
The HIV trans-activator Tat recruits the host transcription elongation factor P-TEFb to stimulate proviral transcription. Phosphorylation of Thr186 on the activation loop (T-loop) of cyclin-dependent kinase 9 (CDK9) is essential for its kinase activity and assembly of CDK9 and cyclin T1 (CycT1) to form functional P-TEFb. Phosphorylation of a second highly conserved T-loop site, Ser175, alters the competitive binding of Tat and the host recruitment factor bromodomain containing 4 (BRD4) to P-TEFb. Here, we investigated the intracellular mechanisms that regulate these key phosphorylation events required for HIV transcription...
May 9, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29742401/distribution-of-initiation-times-reveals-mechanisms-of-transcriptional-regulation-in-single-cells
#13
Sandeep Choubey, Jane Kondev, Alvaro Sanchez
Transcription is the dominant point of control of gene expression. Biochemical studies have revealed key molecular components of transcription and their interactions, but the dynamics of transcription initiation in cells is still poorly understood. This state of affairs is being remedied with experiments that observe transcriptional dynamics in single cells using fluorescent reporters. Quantitative information about transcription initiation dynamics can also be extracted from experiments that use electron micrographs of RNA polymerases caught in the act of transcribing a gene (Miller spreads)...
May 8, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29741668/dynamic-chromosomal-tuning-of-a-novel-gau1-lncing-driver-at-chr12p13-32-accelerates-tumorigenesis
#14
Peiwei Chai, Ruobing Jia, Renbing Jia, Hui Pan, Shaoyun Wang, Hongyan Ni, Huixue Wang, Chuandi Zhou, Yingyun Shi, Shengfang Ge, He Zhang, Xianqun Fan
Aberrant chromatin transformation dysregulates gene expression and may be an important driver of tumorigenesis. However, the functional role of chromosomal dynamics in tumorigenesis remains to be elucidated. Here, using in vitro and in vivo experiments, we reveal a novel long noncoding (lncing) driver at chr12p13.3, in which a novel lncRNA GALNT8 Antisense Upstream 1 (GAU1) is initially activated by an open chromatin status, triggering recruitment of the transcription elongation factor TCEA1 at the oncogene GALNT8 promoter and cis-activates the expression of GALNT8...
May 8, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29741610/aff4-promotes-tumorigenesis-and-tumor-initiation-capacity-of-head-and-neck-squamous-cell-carcinoma-cells-by-regulating-sox2
#15
Peng Deng, Jiongke Wang, Xuefeng Zhang, Xingyu Wu, Ning Ji, Jing Li, Min Zhou, Lu Jiang, Xin Zeng, Qianming Chen
Super elongation complex (SEC) controls gene transcription by releasing Pol II from pausing. Previous studies have shown that dysfunction of SEC was associated with multiple human cancers, such as leukemia and breast cancer. However, the role of SEC in head and neck squamous cell carcinoma (HNSCC) development remains largely unknown. In this study, we found expression of AF4/FMR2 family member 4 (AFF4), the core component of SEC, was upregulated dramatically in HNSCC cell lines and tumor tissues. By using siRNA-mediated depletion and overexpression of AFF4, we demonstrated AFF4 promoted proliferation, migration and invasion of HNSCC cells...
May 8, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/29741479/the-universally-conserved-transcription-factor-rfah-is-recruited-to-a-hairpin-structure-of-the-non-template-dna-strand
#16
Philipp Konrad Zuber, Irina Artsimovitch, Monali NandyMazumdar, Zhaokun Liu, Yuri Nedialkov, Kristian Schweimer, Paul Rösch, Stefan H Knauer
RfaH, a transcription regulator of the universally conserved NusG/Spt5 family, utilizes a unique mode of recruitment to elongating RNA polymerase to activate virulence genes. RfaH function depends critically on an ops sequence, an exemplar of a consensus pause, in the non-template DNA strand of the transcription bubble. We used structural and functional analyses to elucidate the role of ops in RfaH recruitment . Our results demonstrate that ops induces pausing to facilitate RfaH binding and establishes direct contacts with RfaH...
May 9, 2018: ELife
https://www.readbyqxmd.com/read/29740707/sucrose-affects-the-developmental-transition-of-rhizomes-in-oryza-longistaminata
#17
Kanako Bessho-Uehara, Jovano Erris Nugroho, Hirono Kondo, Rosalyn B Angeles-Shim, Motoyuki Ashikari
Oryza longistaminata, the African wild rice, can propagate vegetatively through rhizomes. Rhizomes elongate horizontally underground as sink organs, however, they undergo a developmental transition that shifts their growth to the surface of the ground to become aerial stems. This particular stage is essential for the establishment of new ramets. While several determinants such as abiotic stimuli and plant hormones have been reported as key factors effecting developmental transition in aerial stem, the cause of this phenomenon in rhizome remains elusive...
May 8, 2018: Journal of Plant Research
https://www.readbyqxmd.com/read/29740129/born-to-run-control-of-transcription-elongation-by-rna-polymerase-ii
#18
REVIEW
Fei Xavier Chen, Edwin R Smith, Ali Shilatifard
The dynamic regulation of transcription elongation by RNA polymerase II (Pol II) is an integral part of the implementation of gene expression programmes during development. In most metazoans, the majority of transcribed genes exhibit transient pausing of Pol II at promoter-proximal regions, and the release of Pol II into gene bodies is controlled by many regulatory factors that respond to environmental and developmental cues. Misregulation of the elongation stage of transcription is implicated in cancer and other human diseases, suggesting that mechanistic understanding of transcription elongation control is therapeutically relevant...
May 8, 2018: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29739305/comparative-analysis-of-protein-coding-and-long-non-coding-transcripts-based-on-rna-sequence-features
#19
Oxana A Volkova, Yury V Kondrakhin, Timur A Kashapov, Ruslan N Sharipov
RNA plays an important role in the intracellular cell life and in the organism in general. Besides the well-established protein coding RNAs (messenger RNAs, mRNAs), long non-coding RNAs (lncRNAs) have gained the attention of recent researchers. Although lncRNAs have been classified as non-coding, some authors reported the presence of corresponding sequences in ribosome profiling data (Ribo-seq). Ribo-seq technology is a powerful experimental tool utilized to characterize RNA translation in cell with focus on initiation (harringtonine, lactimidomycin) and elongation (cycloheximide)...
April 2018: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29737555/characterization-of-mirna-transcriptome-profiles-related-to-breast-muscle-development-and-intramuscular-fat-deposition-in-chickens
#20
Shouyi Fu, Yinli Zhao, Yuanfang Li, Guoxi Li, Yi Chen, Zhuanjian Li, Guirong Sun, Hong Li, Xiangtao Kang, Fengbin Yan
Studies of the miRNA expression profiles associated with the postnatal late development of skeletal muscle and IMF deposition are lacking in chicken. Here, we evaluated the patterns of muscle fiber growth and IMF deposition in breast muscle in the Chinese domestic breed called Gushi chicken, where we constructed four small RNA libraries from breast muscle tissues at 6, 14, 22, and 30 weeks. A total of 388 known miRNAs and 31 novel miRNAs were identified based on four small RNA libraries. Comparative analysis identified 92 significant differentially expressed (SDE) miRNAs based on six combinations...
May 8, 2018: Journal of Cellular Biochemistry
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