Mechanism of RNA polymerase I selection by transcription factor UAF

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Preribosomal RNA is selectively transcribed by RNA polymerase (Pol) I in eukaryotes. The yeast transcription factor upstream activating factor (UAF) represses Pol II transcription and mediates Pol I preinitiation complex (PIC) formation at the 35 S ribosomal RNA gene. To visualize the molecular intermediates toward PIC formation, we determined the structure of UAF in complex with native promoter DNA and transcription factor TATA-box-binding protein (TBP). We found that UAF recognizes DNA using a hexameric histone-like scaffold with markedly different interactions compared with the nucleosome and the histone-fold-rich transcription factor IID (TFIID). In parallel, UAF positions TBP for Core Factor binding, which leads to Pol I recruitment, while sequestering it from DNA and Pol II/III–specific transcription factors. Our work thus reveals the structural basis of RNA Pol selection by a transcription factor.

Abstract

UAF uses a histone-like hexamer for DNA recognition and Pol I–selective positioning of TBP at the 35 S rRNA gene promoter.

Related collections

Most cited references 60

Record: found
Abstract: found
Article: not found

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

Ali Punjani, John Rubinstein, David J. Fleet … (2017)

A software tool, cryoSPARC, addresses the speed bottleneck in cryo-EM image processing, enabling automated macromolecular structure determination in hours on a desktop computer without requiring a starting model.

0 comments Cited 2687 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

UCSF ChimeraX : Structure visualization for researchers, educators, and developers

Eric F. Pettersen, Thomas Goddard, Conrad Huang … (2021)

UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic "undo" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax.

0 comments Cited 2411 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Automated electron microscope tomography using robust prediction of specimen movements.

David Mastronarde (2005)

A new method was developed to acquire images automatically at a series of specimen tilts, as required for tomographic reconstruction. The method uses changes in specimen position at previous tilt angles to predict the position at the current tilt angle. Actual measurement of the position or focus is skipped if the statistical error of the prediction is low enough. This method allows a tilt series to be acquired rapidly when conditions are good but falls back toward the traditional approach of taking focusing and tracking images when necessary. The method has been implemented in a program, SerialEM, that provides an efficient environment for data acquisition. This program includes control of an energy filter as well as a low-dose imaging mode, in which tracking and focusing occur away from the area of interest. The program can automatically acquire a montage of overlapping frames, allowing tomography of areas larger than the field of the CCD camera. It also includes tools for navigating between specimen positions and finding regions of interest.

0 comments Cited 1477 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Florence Baudin:

ORCID: https://orcid.org/0000-0003-0816-0861

Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - review & editing

Brice Murciano:

ORCID: https://orcid.org/0000-0001-8886-2972

Role: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: VisualizationRole: Writing - review & editing

Herman K. H. Fung:

ORCID: https://orcid.org/0000-0001-9568-1782

Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing

Simon A. Fromm:

ORCID: https://orcid.org/0000-0002-2094-1911

Role: Formal analysisRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing - review & editing

Simone Mattei:

ORCID: https://orcid.org/0000-0002-2005-8977

Role: ResourcesRole: SupervisionRole: Writing - review & editing

Julia Mahamid:

ORCID: https://orcid.org/0000-0001-6968-041X

Role: Funding acquisitionRole: SupervisionRole: Writing - review & editing

Christoph W. Müller:

ORCID: https://orcid.org/0000-0003-2176-8337

Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: ValidationRole: Writing - review & editing

Journal

Journal ID (nlm-ta): Sci Adv

Journal ID (iso-abbrev): Sci Adv

Journal ID (publisher-id): sciadv

Journal ID (hwp): advances

Title: Science Advances

Publisher: American Association for the Advancement of Science

ISSN (Electronic): 2375-2548

Publication date Collection: April 2022

Publication date (Electronic, pub): 20 April 2022

Volume: 8

Issue: 16

Electronic Location Identifier: eabn5725

Affiliations

[1 ]Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

[2 ]EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany.

Author notes

[* ]Corresponding author. Email: christoph.mueller@ 123456embl.de

[†]

These authors contributed equally to this work.

Author information

Florence Baudin https://orcid.org/0000-0003-0816-0861

Brice Murciano https://orcid.org/0000-0001-8886-2972

Herman K. H. Fung https://orcid.org/0000-0001-9568-1782

Simon A. Fromm https://orcid.org/0000-0002-2094-1911

Simone Mattei https://orcid.org/0000-0002-2005-8977

Julia Mahamid https://orcid.org/0000-0001-6968-041X

Christoph W. Müller https://orcid.org/0000-0003-2176-8337

Article

Publisher ID: abn5725

DOI: 10.1126/sciadv.abn5725

PMC ID: 9020658

PubMed ID: 35442737

SO-VID: bad2bb78-dc28-4190-af7c-45c68880f99e

Copyright © Copyright © 2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date received : 06 December 2021

Date accepted : 02 March 2022

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100010661, Horizon 2020 Framework Programme;

Award ID: COFUND 664726

Funded by: FundRef http://dx.doi.org/10.13039/100013060, European Molecular Biology Laboratory;

Mechanism of RNA polymerase I selection by transcription factor UAF

Read this article at

Abstract

Abstract

Abstract

Related collections

RNA drug delivery

Most cited references 60

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

UCSF ChimeraX : Structure visualization for researchers, educators, and developers

Automated electron microscope tomography using robust prediction of specimen movements.

Author and article information

Contributors

Journal

Affiliations

Author notes

Author information

Article

History

Funding

Categories

Custom metadata

Comments

Comment on this article

Similar content 363

Cited by 5

Most referenced authors 1,118