Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

Production of mRNA depends critically on the rate of RNA polymerase II (Pol II) elongation. To dissect Pol II dynamics in mouse ES cells, we inhibited Pol II transcription at either initiation or promoter-proximal pause escape with Triptolide or Flavopiridol, and tracked Pol II kinetically using GRO-seq. Both inhibitors block transcription of more than 95% of genes, showing that pause escape, like initiation, is a ubiquitous and crucial step within the transcription cycle. Moreover, paused Pol II is relatively stable, as evidenced from half-life measurements at ∼3200 genes. Finally, tracking the progression of Pol II after drug treatment establishes Pol II elongation rates at over 1000 genes. Notably, Pol II accelerates dramatically while transcribing through genes, but slows at exons. Furthermore, intergenic variance in elongation rates is substantial, and is influenced by a positive effect of H3K79me2 and negative effects of exon density and CG content within genes.DOI: http://dx.doi.org/10.7554/eLife.02407.001

Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast

BACKGROUND: The generation of mature mRNAs involves interconnected processes, including transcription by RNA polymerase II (Pol II), modification of histones, and processing of pre-mRNAs through capping, intron splicing, and polyadenylation. These processes are thought to be integrated, both spatially and temporally, but it is unclear how these connections manifest at a global level with respect to chromatin patterns and transcription kinetics. We sought to clarify the relationships between chromatin, transcription and splicing using multiple genome-wide approaches in fission yeast. RESULTS: To investigate these functional interdependencies, we determined Pol II occupancy across all genes using high-density tiling arrays. We also performed ChIP-chip on the same array platform to globally map histone H3 and its H3K36me3 modification, complemented by formaldehyde-assisted isolation of regulatory elements (FAIRE). Surprisingly, Pol II occupancy was higher in introns than in exons, and this difference was inversely correlated with gene expression levels at a global level. Moreover, introns showed distinct distributions of histone H3, H3K36me3 and FAIRE signals, similar to those at promoters and terminators. These distinct transcription and chromatin patterns of intronic regions were most pronounced in poorly expressed genes. CONCLUSIONS: Our findings suggest that Pol II accumulates at the 3 ends of introns, leading to substantial transcriptional delays in weakly transcribed genes. We propose that the global relationship between transcription, chromatin remodeling, and splicing may reflect differences in local nuclear environments, with highly expressed genes being associated with abundant processing factors that promote effective intron splicing and transcriptional elongation

Detection of Supernova Neutrinos

Matter effects on neutrino oscillations in both, a supernova and the Earth, change the observed supernova neutrino spectra. We calculate the expected number of supernova neutrino interactions for ICARUS, SK and SNO detectors as a function of the distance which they traveled in the Earth. Calculations are performed for supernova type II at 10kpc from the Earth, using standard supernova neutrino fluxes described by thermal Fermi--Dirac distributions and the PREM I Earth matter density profile.Comment: Postscript file: 7 pages, 2 figures; tar-compressed file: tex source code, eps figures. To appear in Acta. Phys. Pol. B. Talk given at the XXVIII Mazurian Lakes School of Physics, Krzyze, Poland, August 31 - September 7, 200

Mouse nuclear myosin I knock-out shows interchangeability and redundancy of myosin isoforms in the cell nucleus.

Nuclear myosin I (NM1) is a nuclear isoform of the well-known "cytoplasmic" Myosin 1c protein (Myo1c). Located on the 11(th) chromosome in mice, NM1 results from an alternative start of transcription of the Myo1c gene adding an extra 16 amino acids at the N-terminus. Previous studies revealed its roles in RNA Polymerase I and RNA Polymerase II transcription, chromatin remodeling, and chromosomal movements. Its nuclear localization signal is localized in the middle of the molecule and therefore directs both Myosin 1c isoforms to the nucleus. In order to trace specific functions of the NM1 isoform, we generated mice lacking the NM1 start codon without affecting the cytoplasmic Myo1c protein. Mutant mice were analyzed in a comprehensive phenotypic screen in cooperation with the German Mouse Clinic. Strikingly, no obvious phenotype related to previously described functions has been observed. However, we found minor changes in bone mineral density and the number and size of red blood cells in knock-out mice, which are most probably not related to previously described functions of NM1 in the nucleus. In Myo1c/NM1 depleted U2OS cells, the level of Pol I transcription was restored by overexpression of shRNA-resistant mouse Myo1c. Moreover, we found Myo1c interacting with Pol II. The ratio between Myo1c and NM1 proteins were similar in the nucleus and deletion of NM1 did not cause any compensatory overexpression of Myo1c protein. We observed that Myo1c can replace NM1 in its nuclear functions. Amount of both proteins is nearly equal and NM1 knock-out does not cause any compensatory overexpression of Myo1c. We therefore suggest that both isoforms can substitute each other in nuclear processes

Nonlinear instability dynamics in a high-density, high-beta plasma

Entrainment and periodic pulling of an ion acoustic instability have been observed in the power spectra of a low-pressure high-beta plasma. The observed nonlinear phenomena can be modeled by using the van der Pol equation with a forcing term. Experimental results of the nonlinear processes are presented. Ion density fluctuations are detected on a negatively biased Langmuir probe for magnetic fields and input powers above 30 G and 900 W at 7.2 MHz respectively, and gas pressure below 1.5 mTorr. This low-frequency instability is observed in the central plasma blue core (argon II emission) and can be controlled by amplitude modulation of the radio frequency input power at frequencies close to the instability frequency

Structural visualization of key steps in human transcription initiation.

Eukaryotic transcription initiation requires the assembly of general transcription factors into a pre-initiation complex that ensures the accurate loading of RNA polymerase II (Pol II) at the transcription start site. The molecular mechanism and function of this assembly have remained elusive due to lack of structural information. Here we have used an in vitro reconstituted system to study the stepwise assembly of human TBP, TFIIA, TFIIB, Pol II, TFIIF, TFIIE and TFIIH onto promoter DNA using cryo-electron microscopy. Our structural analyses provide pseudo-atomic models at various stages of transcription initiation that illuminate critical molecular interactions, including how TFIIF engages Pol II and promoter DNA to stabilize both the closed pre-initiation complex and the open-promoter complex, and to regulate start--initiation complexes, combined with the localization of the TFIIH helicases XPD and XPB, support a DNA translocation model of XPB and explain its essential role in promoter opening

Spin polarized liquid 3He

We have employed the constrained variational method to study the influence of spin polarization on the ground state properties of liquid $^3{\rm He}$. The spin polarized phase, we have found, has stronger correlation with respect to the unpolarized phase. It is shown that the internal energy of liquid $^3{\rm He}$ increases by increasing polarization with no crossing point between polarized and unpolarized energy curves over the liquid density range. The obtained internal energy curves show a bound state, even in the case of fully spin polarized matter. We have also investigated the validity of using a parabolic formula for calculating the energy of spin polarized liquid $^3{\rm He}$. Finally, we have compared our results with other calculations.Comment: 16 pages, 6 figure

Coherency Matrix Decomposition-Based Polarimetric Persistent Scatterer Interferometry

© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes,creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.The rationale of polarimetric optimization techniques is to enhance the phase quality of the interferograms by combining adequately the different polarization channels available to produce an improved one. Different approaches have been proposed for polarimetric persistent scatterer interferometry (PolPSI). They range from the simple and computationally efficient BEST, where, for each pixel, the polarimetric channel with the best response in terms of phase quality is selected, to those with high-computational burden like the equal scattering mechanism (ESM) and the suboptimum scattering mechanism (SOM). BEST is fast and simple, but it does not fully exploit the potentials of polarimetry. On the other side, ESM explores all the space of solutions and finds the optimal one but with a very high-computational burden. A new PolPSI algorithm, named coherency matrix decomposition-based PolPSI (CMD-PolPSI), is proposed to achieve a compromise between phase optimization and computational cost. Its core idea is utilizing the polarimetric synthetic aperture radar (PolSAR) coherency matrix decomposition to determine the optimal polarization channel for each pixel. Three different PolSAR image sets of both full- (Barcelona) and dual-polarization (Murcia and Mexico City) are used to evaluate the performance of CMD-PolPSI. The results show that CMD-PolPSI presents better optimization results than the BEST method by using either $D_{\mathrm{ A}}$ or temporal mean coherence as phase quality metrics. Compared with the ESM algorithm, CMD-PolPSI is 255 times faster but its performance is not optimal. The influence of the number of available polarization channels and pixel's resolutions on the CMD-PolPSI performance is also discussed.Peer ReviewedPostprint (author's final draft

Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation.

RNA Polymerase II (Pol II) and transcription factors form concentrated hubs in cells via multivalent protein-protein interactions, often mediated by proteins with intrinsically disordered regions. During Herpes Simplex Virus infection, viral replication compartments (RCs) efficiently enrich host Pol II into membraneless domains, reminiscent of liquid-liquid phase separation. Despite sharing several properties with phase-separated condensates, we show that RCs operate via a distinct mechanism wherein unrestricted nonspecific protein-DNA interactions efficiently outcompete host chromatin, profoundly influencing the way DNA-binding proteins explore RCs. We find that the viral genome remains largely nucleosome-free, and this increase in accessibility allows Pol II and other DNA-binding proteins to repeatedly visit nearby DNA binding sites. This anisotropic behavior creates local accumulations of protein factors despite their unrestricted diffusion across RC boundaries. Our results reveal underappreciated consequences of nonspecific DNA binding in shaping gene activity, and suggest additional roles for chromatin in modulating nuclear function and organization