Transcription by RNA polymerase II (RNA Pol II) relies on the elongation factors PAF1 complex (PAF), RTF1, and SPT6. Here, we use rapid factor depletion and multi-omics analysis to investigate how ...these elongation factors influence RNA Pol II elongation activity in human cells. Whereas depletion of PAF subunits PAF1 and CTR9 has little effect on cellular RNA synthesis, depletion of RTF1 or SPT6 strongly compromises RNA Pol II activity, albeit in fundamentally different ways. RTF1 depletion decreases RNA Pol II velocity, whereas SPT6 depletion impairs RNA Pol II progression through nucleosomes. These results show that distinct elongation factors stimulate either RNA Pol II velocity or RNA Pol II progression through chromatin in vivo. Further analysis provides evidence for two distinct barriers to early elongation: the promoter-proximal pause site and the +1 nucleosome. It emerges that the first barrier enables loading of elongation factors that are required to overcome the second and subsequent barriers to transcription.
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•The PAF1 complex and SPT6 have positive roles in transcription elongation•RTF1 and SPT6 stimulate RNA polymerase II elongation in distinct ways•Depletion of RTF1 decreases RNA polymerase II velocity•Loss of SPT6 hinders RNA polymerase II progression through nucleosomes
Metazoan gene transcription requires RNA polymerase II and a large number of factors that help the polymerase to pass through genes. Žumer et al. utilize rapid depletion of endogenous proteins from human cells and sequencing approaches to show two distinct mechanisms of two such elongation factors: one controls polymerase speed, and the other controls polymerase passage through chromatin.
The stability of mRNA is one of the major determinants of gene expression. Although a wealth of sequence elements regulating mRNA stability has been described, their quantitative contributions to ...half-life are unknown. Here, we built a quantitative model for
based on functional mRNA sequence features that explains 59% of the half-life variation between genes and predicts half-life at a median relative error of 30%. The model revealed a new destabilizing 3' UTR motif, ATATTC, which we functionally validated. Codon usage proves to be the major determinant of mRNA stability. Nonetheless, single-nucleotide variations have the largest effect when occurring on 3' UTR motifs or upstream AUGs. Analyzing mRNA half-life data of 34 knockout strains showed that the effect of codon usage not only requires functional decapping and deadenylation, but also the 5'-to-3' exonuclease Xrn1, the nonsense-mediated decay genes, but not no-go decay. Altogether, this study quantitatively delineates the contributions of mRNA sequence features on stability in yeast, reveals their functional dependencies on degradation pathways, and allows accurate prediction of half-life from mRNA sequence.
At the end of protein-coding genes, RNA polymerase (Pol) II undergoes a concerted transition that involves 3′-processing of the pre-mRNA and transcription termination. Here, we present a genome-wide ...analysis of the 3′-transition in budding yeast. We find that the 3′-transition globally requires the Pol II elongation factor Spt5 and factors involved in the recognition of the polyadenylation (pA) site and in endonucleolytic RNA cleavage. Pol II release from DNA occurs in a narrow termination window downstream of the pA site and requires the “torpedo” exonuclease Rat1 (XRN2 in human). The Rat1-interacting factor Rai1 contributes to RNA degradation downstream of the pA site. Defects in the 3′-transition can result in increased transcription at downstream genes.
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•Pcf11 and Ysh1 are globally required for the 3′-transition at protein-coding genes•Spt5 binds pre-mRNA near the pA site and contributes to the 3′-transition•Rat1 is globally required for Pol II release from DNA in a narrow termination window
RNA polymerase II undergoes a concerted transition at the 3′ end of protein coding genes. Baejen et al. present a genome-wide analysis of this 3′-transition in budding yeast. They show that this transition requires the Spt5 elongation factor and demonstrate that polymerase II release from DNA requires the Rat1 exonuclease.
This article studies the strength, forms, and areas of intermunicipal cooperation, and their advantages, disadvantages, and spatial characteristics based on the example of the Ljubljana urban region. ...Surveys, interviews, data analysis of joint administration and joint companies, and analysis of joint development projects show that cooperation in joint municipal administration is limited to parking authorities and the intermunicipal inspectorate, joint companies dealing with communal infrastructure and traffic, and joint projects mainly focusing on economic infrastructure, tourism, mobility, spatial and development planning, and applying for EU projects. The areas of former municipalities, the municipalities in Ljubljana Marsh Nature Park, and the municipalities that are part of the Development Partnership of the Center of Slovenia connect more often than other areas. The advantages of cooperation include better opportunities for EU funding, economizing, and joint representation of municipal interests, whereas disadvantages include problems with coordinating funding and a lengthy coordination period, which is additionally hindered by unsuitable legislation and a lack of financial incentives, human resources, time, and ideas.
Central settlements in Slovenia in 2016 Nared, Janez; Bole, David; Breg Valjavec, Mateja ...
Acta geographica Slovenica : Geografski zbornik,
01/2017, Letnik:
57, Številka:
2
Journal Article
Recenzirano
Odprti dostop
This article presents central settlements in Slovenia and their main characteristics in 2016. We defined central settlements based on services of general interest and the population of an individual ...settlement, and developed the analysis further by using competitiveness indicators. We defined 360 central settlements at six levels of centrality, among which the significance of Ljubljana as a national center of international importance and the significance of intermunicipal, local, and rural centers are increasing. The significance of certain regional centers at the second and third levels of centrality is decreasing. The level of services of general interest supplied to Slovenian territory is relatively appropriate, but it should be improved by promoting competitiveness, especially in centers of national and regional importance.
Facilitates chromatin transcription (FACT) is a histone chaperone that supports transcription through chromatin in vitro, but its functional roles in vivo remain unclear. Here, we analyze the in vivo ...functions of FACT with the use of multi-omics analysis after rapid FACT depletion from human cells. We show that FACT depletion destabilizes chromatin and leads to transcriptional defects, including defective promoter-proximal pausing and elongation, and increased premature termination of RNA polymerase II. Unexpectedly, our analysis revealed that promoter-proximal pausing depends not only on the negative elongation factor (NELF) but also on the +1 nucleosome, which is maintained by FACT.
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•The histone chaperone FACT maintains chromatin structure in transcribed regions•FACT has a positive role in transcription elongation in vivo•Loss of FACT reduces RNA polymerase II elongation velocity and processivity•FACT maintains +1 nucleosome integrity, which stabilizes promoter-proximal pausing
Žumer et al. investigate the mechanism by which the histone chaperone FACT regulates chromatin and transcription. They reveal multifaceted roles for FACT in maintaining chromatin architecture and controlling transcription at multiple stages of the transcription cycle. The authors also show that the +1 nucleosome, which depends on FACT, regulates transcription.
Članek prikazuje rezultate raziskave, s katero smo želeli ugotoviti, katere so tiste turistične prakse, ki jih turisti kot trajnostne dojemajo na slovenskih turističnih destinacijah s trajnostnim ...certifikatom Slovenia Green. Izbrali smo osem destinacij. Poglavitna metoda dela je bilo anketiranje, kateremu je sledila analiza rezultatov. Analizirali smo 1444 anket. Ugotovili smo, da trajnostni certifikat za turistične destinacije pozna le slabih 50 % anketirancev, da je najbolj prepoznavna trajnostna praksa na destinacijah možnost uporabe vode za pitje iz pipe ter da je največja pomanjkljivost na destinacijah neustrezen javni potniški promet. Ugotavljamo, da bi destinacije morale investirati v učinkovitejšo propagando trajnostnega certifikata in posebej na področju javnega potniškega prometa storiti vidnejši napredek.
With the research we wanted to find out what are the tourism practices that tourists perceive as sustainable at tourist destinations in Slovenia that have the Slovenia Green sustainability ...certificate. We have selected eight destinations. The main method of work was surveying, followed by the analysis of the results. We analyzed 1444 surveys. We found that only 50% of respondents know about the sustainability certificate for tourist destinations, that the most recognizable sustainable practice in destinations is the possibility of using water for drinking from the tap, and that the biggest drawback in destinations is inadequate public passenger transport. We conclude that destinations should invest in more effective propaganda of the sustainability certificate and make more visible progress, especially in the field of public passenger transport.
This volume discusses various aspects of planning public transport in the Ljubljana Urban Region, in which it highlights the cooperation between Ljubljana as a metropolis and its functionally ...connected countryside. After studying the basic social processes that guide development in this region, such as centralization and suburbanization, it focuses on traffic and public transport in this region. It analyzes the traffic flows, road use, and commuting, and dedicates special attention to commuting times. Suitable measures and best-practice examples are presented for the cases of unsustainable mobility that were indentified, especially with regard to improving spatial and temporal accessibility and transfer points in the public transport network. Proposals for integrating spatial and transport planning were developed, and ideas about drafting the development of public passenger transport in the selected corridor in the Ljubljana Urban Region were presented.
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