Saturation of front propagation in a reaction-diffusion process describing plasma damage in porous low-k materials

We propose a three-component reaction-diffusion system yielding an asymptotic logarithmic time-dependence for a moving interface. This is naturally related to a Stefan-problem for which both one-sided Dirichlet-type and von Neumann-type boundary conditions are considered. We integrate the dependence of the interface motion on diffusion and reaction parameters and we observe a change from transport behavior and interface motion \sim t^1/2 to logarithmic behavior \sim ln t as a function of time. We apply our theoretical findings to the propagation of carbon depletion in porous dielectrics exposed to a low temperature plasma. This diffusion saturation is reached after about 1 minute in typical experimental situations of plasma damage in microelectronic fabrication. We predict the general dependencies on porosity and reaction rates.Comment: Accepted for publication in Phys. Rev.

Detection of V617F mutation of gene jak2 at patients with chronic myeloproliferative neoplasms

The aim of the work was to create a protocol for detecting the V617F mutation of the gene jak2 in samples of patients with chronic myeloproliferative neoplasm which is necessary to unify the procedures of the analysis of blood samples according to WHO criteria for this group of diseases. Methods. Mutation was revealed using reverse transcriptase PCR and direct sequencing of PCR products. Results. Six samples of blood of patients with polycythemia vera were analyzed and the mutation V617F was detected in all six cases. This mutation was not detected in any of RNA samples of healthy donors. A case of simultaneous detection of mutations V617F and fused bcr/abl gene in CML patient was described. Conclusions. The proposed method for detecting the V617F mutation allows molecular genetic differential diagnosis of myeloproliferative neoplasm as well.Мета. Створити протокол, який дозволяє виявляти мутацію V617F гена jak2 у зразках РНК хворих на хронічні мієлопроліферативні неоплазми, що неохідно для уніфікації процедур аналізу зразків крові згідно з чинними критеріями ВОЗ для даної групи захворювань. Методи. Мутацію визначали за допомогою зворотно-транскриптазної полімеразної ланцюгової реакції та прямого секвенування продуктів полімеразної ланцюгової реакції. Результати. Проаналізовано шість зразків крові хворих на справжню поліцитемію і у всіх випадках виявлено мутацію V617F. Дану мутацію не знайдено в жодному з контрольних зразків РНК здорових донорів. Описано випадок одночасного виявлення мутації V617F та злитого гена bcr/abl у хворої на хронічну мієлоїдну лейкемію. Висновки. Запропонований метод дозволяє визначати мутацію V617F, що дає змогу використовувати його для молекулярно-генетичної диференційної діагностики мієлопроліферативних неоплазм.Цель. Создание протокола для виявления мутации V617F гена jak2 в образцах РНК больных с хроническими миелопролиферативными неоплазмами, что необходимо для унификации процедур анализа образцов крови согласно настоящим критериям ВОЗ для данной группы заболеваний. Методы. Мутацию определяли с помощью обратно-транскриптазной полимеразной цепной реакции и прямого секвенирования продуктов ПЦР. Результаты. Проанализированы шесть образцов крови больных истинной полицитемией и во всех случаях обнаружена мутация V617F. Эта мутация не найдена ни в одном из контрольных образцов РНК здоровых доноров. Описан случай одновременного выявления мутации V617F и слитого гена bcr/abl у больной с хронической миелоидной лейкемией. Выводы. Предложенный метод позволяет определять мутацию V617F, его также можно использовать для молекулярно-генетической дифференциальной диагностики миелопролиферативных неоплазм

Improved identification of enriched peptide–RNA cross-links from ribonucleoprotein particles (RNPs) by mass spectrometry

Direct UV cross-linking combined with mass spectrometry (MS) is a powerful tool to identify hitherto non-characterized protein–RNA contact sites in native ribonucleoprotein particles (RNPs) such as the spliceosome. Identification of contact sites after cross-linking is restricted by: (i) the relatively low cross-linking yield and (ii) the amount of starting material available for cross-linking studies. Therefore, the most critical step in such analyses is the extensive purification of the cross-linked peptide–RNA heteroconjugates from the excess of non-crosslinked material before MS analysis. Here, we describe a strategy that combines small-scale reversed-phase liquid chromatography (RP-HPLC) of UV-irradiated and hydrolyzed RNPs, immobilized metal-ion affinity chromatography (IMAC) to enrich cross-linked species and their analysis by matrix-assisted laser desorption/ionisation (MALDI) MS(/MS). In cases where no MS/MS analysis can be performed, treatment of the enriched fractions with alkaline phosphatase leads to unambiguous identification of the cross-linked species

Structural basis of Integrator-dependent RNA polymerase II termination

The Integrator complex can terminate RNA polymerase II (Pol II) in the promoter-proximal region of genes. Previous work has shed light on how Integrator binds to the paused elongation complex consisting of Pol II, the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) and how it cleaves the nascent RNA transcript, but has not explained how Integrator removes Pol II from the DNA template. Here we present three cryo-electron microscopy structures of the complete Integrator–PP2A complex in different functional states. The structure of the pre-termination complex reveals a previously unresolved, scorpion-tail-shaped INTS10–INTS13–INTS14–INTS15 module that may use its ‘sting’ to open the DSIF DNA clamp and facilitate termination. The structure of the post-termination complex shows that the previously unresolved subunit INTS3 and associated sensor of single-stranded DNA complex (SOSS) factors prevent Pol II rebinding to Integrator after termination. The structure of the free Integrator–PP2A complex in an inactive closed conformation reveals that INTS6 blocks the PP2A phosphatase active site. These results lead to a model for how Integrator terminates Pol II transcription in three steps that involve major rearrangements

Structural insights into how Prp5 proofreads the pre-mRNA branch site

During the splicing of introns from precursor messenger RNAs (pre-mRNAs), the U2 small nuclear ribonucleoprotein (snRNP) must undergo stable integration into the spliceosomal A complex-a poorly understood, multistep process that is facilitated by the DEAD-box helicase Prp5 (refs. 1-4). During this process, the U2 small nuclear RNA (snRNA) forms an RNA duplex with the pre-mRNA branch site (the U2-BS helix), which is proofread by Prp5 at this stage through an unclear mechanism5. Here, by deleting the branch-site adenosine (BS-A) or mutating the branch-site sequence of an actin pre-mRNA, we stall the assembly of spliceosomes in extracts from the yeast Saccharomyces cerevisiae directly before the A complex is formed. We then determine the three-dimensional structure of this newly identified assembly intermediate by cryo-electron microscopy. Our structure indicates that the U2-BS helix has formed in this pre-A complex, but is not yet clamped by the HEAT domain of the Hsh155 protein (Hsh155HEAT), which exhibits an open conformation. The structure further reveals a large-scale remodelling/repositioning of the U1 and U2 snRNPs during the formation of the A complex that is required to allow subsequent binding of the U4/U6.U5 tri-snRNP, but that this repositioning is blocked in the pre-A complex by the presence of Prp5. Our data suggest that binding of Hsh155HEAT to the bulged BS-A of the U2-BS helix triggers closure of Hsh155HEAT, which in turn destabilizes Prp5 binding. Thus, Prp5 proofreads the branch site indirectly, hindering spliceosome assembly if branch-site mutations prevent the remodelling of Hsh155HEAT. Our data provide structural insights into how a spliceosomal helicase enhances the fidelity of pre-mRNA splicing

Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1

Ubiquitin ligases (E3s) are pivotal specificity determinants in the ubiquitin system by selecting substrates and decorating them with distinct ubiquitin signals. However, structure determination of the underlying, specific E3-substrate complexes has proven challenging owing to their transient nature. In particular, it is incompletely understood how members of the catalytic cysteine-driven class of HECT-type ligases (HECTs) position substrate proteins for modification. Here, we report a cryogenic electron microscopy (cryo-EM) structure of the full-length human HECT HACE1, along with solution-based conformational analyses by small-angle X-ray scattering and hydrogen–deuterium exchange mass spectrometry. Structure-based functional analyses in vitro and in cells reveal that the activity of HACE1 is stringently regulated by dimerization-induced autoinhibition. The inhibition occurs at the first step of the catalytic cycle and is thus substrate-independent. We use mechanism-based chemical crosslinking to reconstitute a complex of activated, monomeric HACE1 with its major substrate, RAC1, determine its structure by cryo-EM and validate the binding mode by solution-based analyses. Our findings explain how HACE1 achieves selectivity in ubiquitinating the active, GTP-loaded state of RAC1 and establish a framework for interpreting mutational alterations of the HACE1–RAC1 interplay in disease. More broadly, this work illuminates central unexplored aspects in the architecture, conformational dynamics, regulation and specificity of full-length HECTs

Regulation of 3′ splice site selection after step 1 of splicing by spliceosomal C* proteins

Alternative precursor messenger RNA splicing is instrumental in expanding the proteome of higher eukaryotes, and changes in 3′ splice site (3'ss) usage contribute to human disease. We demonstrate by small interfering RNA–mediated knockdowns, followed by RNA sequencing, that many proteins first recruited to human C* spliceosomes, which catalyze step 2 of splicing, regulate alternative splicing, including the selection of alternatively spliced NAGNAG 3′ss. Cryo–electron microscopy and protein cross-linking reveal the molecular architecture of these proteins in C* spliceosomes, providing mechanistic and structural insights into how they influence 3'ss usage. They further elucidate the path of the 3′ region of the intron, allowing a structure-based model for how the C* spliceosome potentially scans for the proximal 3′ss. By combining biochemical and structural approaches with genome-wide functional analyses, our studies reveal widespread regulation of alternative 3′ss usage after step 1 of splicing and the likely mechanisms whereby C* proteins influence NAGNAG 3′ss choices