[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleA systematic search for RNA structural switches across the human transcriptome.
Journal, issue, pagesNat Methods, Vol. 21, Issue 9, Page 1634-1645, Year 2024
Publish dateJul 16, 2024
AuthorsMatvei Khoroshkin / Daniel Asarnow / Shaopu Zhou / Albertas Navickas / Aidan Winters / Jackson Goudreau / Simon K Zhou / Johnny Yu / Christina Palka / Lisa Fish / Ashir Borah / Kian Yousefi / Christopher Carpenter / K Mark Ansel / Yifan Cheng / Luke A Gilbert / Hani Goodarzi /
PubMed AbstractRNA structural switches are key regulators of gene expression in bacteria, but their characterization in Metazoa remains limited. Here, we present SwitchSeeker, a comprehensive computational and ...RNA structural switches are key regulators of gene expression in bacteria, but their characterization in Metazoa remains limited. Here, we present SwitchSeeker, a comprehensive computational and experimental approach for systematic identification of functional RNA structural switches. We applied SwitchSeeker to the human transcriptome and identified 245 putative RNA switches. To validate our approach, we characterized a previously unknown RNA switch in the 3' untranslated region of the RORC (RAR-related orphan receptor C) transcript. In vivo dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), coupled with cryogenic electron microscopy, confirmed its existence as two alternative structural conformations. Furthermore, we used genome-scale CRISPR screens to identify trans factors that regulate gene expression through this RNA structural switch. We found that nonsense-mediated messenger RNA decay acts on this element in a conformation-specific manner. SwitchSeeker provides an unbiased, experimentally driven method for discovering RNA structural switches that shape the eukaryotic gene expression landscape.
External linksNat Methods / PubMed:39014073 / PubMed Central
MethodsEM (single particle)
Resolution9.9 - 10.2 Å
Structure data

EMDB-42275: RORC mRNA 3'UTR riboswitch class A
Method: EM (single particle) / Resolution: 10.0 Å

EMDB-42276: RORC mRNA 3'UTR riboswitch class B
Method: EM (single particle) / Resolution: 10.0 Å

EMDB-42277: RORC mRNA 3'UTR riboswitch class C
Method: EM (single particle) / Resolution: 10.0 Å

EMDB-42400: RORC mRNA 3'UTR riboswitch A97G/G98A mutant class C
Method: EM (single particle) / Resolution: 9.9 Å

EMDB-42401: RORC mRNA 3'UTR riboswitch 77-GA mutant class A
Method: EM (single particle) / Resolution: 10.1 Å

EMDB-42403: RORC mRNA 3'UTR riboswitch 117-AC mutant class C
Method: EM (single particle) / Resolution: 9.9 Å

EMDB-42404: RORC mRNA 3'UTR riboswitch 117-AC mutant class B
Method: EM (single particle) / Resolution: 10.2 Å

Source
  • Homo sapiens (human)

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more