The pause-initiation limit restricts transcription activation in human cells.

Eukaryotic gene transcription is often controlled at the level of RNA polymerase II (Pol II) pausing in the promoter-proximal region. Pausing Pol II limits the frequency of transcription initiation ('pause-initiation limit'), predicting that the pause duration must be decreased for transcriptional activation. To test this prediction, we conduct a genome-wide kinetic analysis of the heat shock response in human cells. We show that the pause-initiation limit restricts transcriptional activation at most genes. Gene activation generally requires the activity of the P-TEFb kinase CDK9, which decreases the duration of Pol II pausing and thereby enables an increase in the productive initiation frequency. The transcription of enhancer elements is generally not pause limited and can be activated without CDK9 activity. Our results define the kinetics of Pol II transcriptional regulation in human cells at all gene classes during a natural transcription response

Anisotropic valence-->core x-ray fluorescence from a [Rh(en)3][Mn(N)(CN)5]·H2O single crystal: Experimental results and density functional calculations

High resolution x-ray fluorescence spectra have been recorded for emission in different directions from a single crystal of the compound [Rh(en)3][Mn(N)(CN)5]·H2O. The spectra are interpreted by comparison with density functional theory (DFT) electronic structure calculations. The Kbeta[double-prime] line, which is strongly polarized along the Mn–N axis, can be viewed as an N(2s)-->Mn(1s) transition, and the angular dependence is understood within the dipole approximation. The so-called Kbeta2,5 region has numerous contributions but is dominated by Mn(4p) and C(2s)-->Mn(1s) transitions. Transition energy splittings are found in agreement with those of calculated occupied molecular orbitals to within 1 eV. Computed relative transition probabilities reproduce experimentally observed trends

Structures of mammalian RNA polymerase II pre-initiation complexes

The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast1,2,3,4,5,6,7,8,9 and human10,11 PIC and a topological model for DNA opening by the general transcription factor TFIIH12,13,14. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5–2.8 Å resolution, and resolve the structure of TFIIH at 2.9–4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation

The evolution of hearing and balance.

New genetic tools have allowed researchers to compare how the brainstem auditory and vestibular nuclei develop in embryonic chicks and mice

Structural basis of transcription initiation by RNA polymerase II.

Transcription of eukaryotic protein-coding genes commences with the assembly of a conserved initiation complex, which consists of RNA polymerase II (Pol II) and the general transcription factors, at promoter DNA. After two decades of research, the structural basis of transcription initiation is emerging. Crystal structures of many components of the initiation complex have been resolved, and structural information on Pol II complexes with general transcription factors has recently been obtained. Although mechanistic details await elucidation, available data outline how Pol II cooperates with the general transcription factors to bind to and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the promoter

Structure of an inactive RNA polymerase II dimer

Eukaryotic gene transcription is carried out by three RNA polymerases: Pol I, Pol II and Pol III. Although it has long been known that Pol I can form homodimers, it is unclear whether and how the two other RNA polymerases dimerize. Here we present the cryo-electron microscopy (cryo-EM) structure of a mammalian Pol II dimer at 3.5 Å resolution. The structure differs from the Pol I dimer and reveals that one Pol II copy uses its RPB4-RPB7 stalk to penetrate the active centre cleft of the other copy, and vice versa, giving rise to a molecular handshake. The polymerase clamp domain is displaced and mobile, and the RPB7 oligonucleotide-binding fold mimics the DNA–RNA hybrid that occupies the cleft during active transcription. The Pol II dimer is incompatible with nucleic acid binding as required for transcription and may represent an inactive storage form of the polymerase

Structure and function of the initially transcribing RNA polymerase II–TFIIB complex

The general transcription factor (TF) IIB is required for RNA polymerase (Pol) II initiation and extends with its B-reader element into the Pol II active centre cleft. Low-resolution structures of the Pol II– TFIIB complex1,2 indicated how TFIIB functions in DNA recruitment, but they lacked nucleic acids and half of the B-reader, leaving other TFIIB functions3,4 enigmatic. Here we report crystal structures of the Pol II–TFIIB complex from the yeast Saccharomyces cerevisiae at 3.4A˚ resolution and of an initially transcribing complex that additionally contains theDNAtemplate and a 6-nucleotide RNAproduct.The structures reveal the entire B-reader and protein– nucleic acid interactions, and together with functional data lead to a more complete understanding of transcription initiation. TFIIB partially closes the polymerase cleft to position DNA and assist in its opening. The B-reader does not reach the active site but binds the DNA template strand upstream to assist in the recognition of the initiator sequence and in positioning the transcription start site. TFIIB rearranges active-site residues, induces binding of the catalytic metal ion B, and stimulates initial RNA synthesis allosterically. TFIIB then prevents the emergingDNA–RNAhybrid duplex from tilting, which would impair RNA synthesis. When the RNA grows beyond 6 nucleotides, it is separated from DNA and is directed to its exit tunnel by the B-reader loop. Once the RNA grows to 12–13 nucleotides, it clashes with TFIIB, triggering TFIIB displacement and elongation complex formation. Similar mechanisms may underlie all cellular transcription because all eukaryotic and archaeal RNA polymerases use TFIIB-like factors5, and the bacterial initiation factor sigma has TFIIB-like topology1,2 and contains the loop region 3.2 that resembles the B-reader loop in location, charge and function6–8. TFIIB and its counterparts may thus account for the two fundamental properties that distinguish RNA from DNA polymerases: primer-independent chain initiation and product separation from the template

Parametric instabilities in magnetized multicomponent plasmas

This paper investigates the excitation of various natural modes in a magnetized bi-ion or dusty plasma. The excitation is provided by parametrically pumping the magnetic field. Here two ion-like species are allowed to be fully mobile. This generalizes our previous work where the second heavy species was taken to be stationary. Their collection of charge from the background neutral plasma modifies the dispersion properties of the pump and excited waves. The introduction of an extra mobile species adds extra modes to both these types of waves. We firstly investigate the pump wave in detail, in the case where the background magnetic field is perpendicular to the direction of propagation of the pump wave. Then we derive the dispersion equation relating the pump to the excited wave for modes propagating parallel to the background magnetic field. It is found that there are a total of twelve resonant interactions allowed, whose various growth rates are calculated and discussed.Comment: Published in May 2004; this is a late submission to the archive. 14 pages, 8 figure