Structural insights into human TFIIIC promoter recognition DOI Creative Commons
Wolfram Seifert-Dávila, Mathias Girbig, Luis Hauptmann

et al.

Science Advances, Journal Year: 2023, Volume and Issue: 9(27)

Published: July 7, 2023

Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to most of its target genes. Recognition intragenic A- and B-box motifs in transfer (tRNA) genes by TFIIIC modules τA τB is the first critical step for tRNA synthesis but mechanistically poorly understood. Here, we report cryo–electron microscopy structures six-subunit human complex unbound bound a gene. The module recognizes via DNA shape sequence readout through assembly multiple winged-helix domains. TFIIIC220 forms an integral part both connecting two subcomplexes ~550–amino acid residue flexible linker. Our data provide structural mechanism which high-affinity recognition anchors promoter permits scanning low-affinity A-boxes TFIIIB Pol activation.

Language: Английский

Ribosome biogenesis factors—from names to functions DOI Creative Commons
Kerstin Dörner, Chiara Ruggeri, Ivo Zemp

et al.

The EMBO Journal, Journal Year: 2023, Volume and Issue: 42(7)

Published: Feb. 10, 2023

Abstract The assembly of ribosomal subunits is a highly orchestrated process that involves huge cohort accessory factors. Most eukaryotic ribosome biogenesis factors were first identified by genetic screens and proteomic approaches pre‐ribosomal particles in Saccharomyces cerevisiae . Later, research on human synthesis not only demonstrated the requirement for many these conserved evolution, but also revealed involvement additional players, reflecting more complex pathway mammalian cells. Yet, it remained challenge field to assign function reveal their molecular mode action. Over past decade, structural, biochemical, cellular studies have largely filled this gap knowledge led detailed understanding role players during stepwise maturation. Such will be key further understand better treat diseases linked disturbed assembly, including ribosomopathies, as well different types cancer.

Language: Английский

Citations

100
Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes DOI Open Access
Yutaro Hori, Christoph Engel, Takehiko Kobayashi

et al.

Nature Reviews Molecular Cell Biology, Journal Year: 2023, Volume and Issue: 24(6), P. 414 - 429

Published: Feb. 2, 2023

Language: Английский

Citations

76
Structural basis of exoribonuclease-mediated mRNA transcription termination DOI
Yuan Zeng, Hongwei Zhang, Xiaoxian Wu

et al.

Nature, Journal Year: 2024, Volume and Issue: 628(8009), P. 887 - 893

Published: March 27, 2024

Language: Английский

Citations

22
Understanding the cell: Future views of structural biology DOI Creative Commons
Martin Beck, Roberto Covino, Inga Hänelt

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(3), P. 545 - 562

Published: Feb. 1, 2024

Determining the structure and mechanisms of all individual functional modules cells at high molecular detail has often been seen as equal to understanding how work. Recent technical advances have led a flush high-resolution structures various macromolecular machines, but despite this wealth detailed information, our cellular function remains incomplete. Here, we discuss present-day limitations structural biology highlight novel technologies that may enable us analyze functions directly inside cells. We predict progression toward cell will involve shift conceptualizing 4D virtual reality using digital twins. These capture segments in highly enriched detail, include dynamic changes, facilitate simulations processes, leading experimentally testable predictions. Transferring biological questions into algorithms learn from existing data explore solutions ultimately unveil

Language: Английский

Citations

21
DNA-directed termination of RNA polymerase II transcription DOI Creative Commons
Zhong Han,

George A. Moore,

Richard Mitter

et al.

Molecular Cell, Journal Year: 2023, Volume and Issue: 83(18), P. 3253 - 3267.e7

Published: Sept. 1, 2023

RNA polymerase II (RNAPII) transcription involves initiation from a promoter, transcriptional elongation through the gene, and termination in terminator region. In bacteria, terminators often contain specific DNA elements provoking dissociation, but RNAPII is thought to be driven entirely by protein co-factors. We used biochemical reconstitution, single-molecule studies, genome-wide analysis yeast study termination. Transcription into natural pure results spontaneous at sequences containing T-tracts. Single-molecule indicates that pausing without backtracking. The "torpedo" Rat1-Rai1 exonuclease (XRN2 humans) greatly stimulates ineffectual on other paused RNAPIIs. By contrast, factor Spt4-Spt5 (DSIF) suppresses Genome-wide further occurs transcript cleavage poly(A) site exposing new 5′ RNA-end allows loading, which then catches up with destabilized sites end transcription.

Language: Английский

Citations

28
Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase DOI Creative Commons
Rishi K. Vishwakarma, M. Zuhaib Qayyum, Paul Babitzke

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(7)

Published: Feb. 6, 2023

NusG is a transcription elongation factor that stimulates pausing in Gram+ bacteria including B. subtilis by sequence-specific interaction with conserved pause-inducing − 11 TTNTTT −6 motif found the non-template DNA (ntDNA) strand within bubble. To reveal structural basis of NusG-dependent pausing, we determined cryo-EM structure paused complex (PTC) containing RNA polymerase (RNAP), NusG, and ntDNA strand. The rearranges bubble positioning three consecutive T residues cleft between β-lobe domain RNAP. We revealed RNAP swivel module rotation (swiveling), which widens (swiveled state) narrows (non-swiveled β-lobe, an intrinsic motion directly linked to trigger loop (TL) folding, essential conformational change all cellular RNAPs for synthesis reaction. also structures escaping from state. These mechanism NusG-ntDNA inhibits transition swiveled non-swiveled states, thereby preventing TL folding allosterically. This reduced formation hairpin exit channel. Thus, pause half-life can be modulated strength and/or stability hairpin. interact are widely bacteria, suggesting widespread.

Language: Английский

Citations

25
Cryo-EM structures of the plant plastid-encoded RNA polymerase DOI Creative Commons
Xiaoxian Wu,

Wenhui Mu,

Li Fan

et al.

Cell, Journal Year: 2024, Volume and Issue: 187(5), P. 1127 - 1144.e21

Published: Feb. 1, 2024

Language: Английский

Citations

17
KLF7 regulates super-enhancer-driven IGF2BP2 overexpression to promote the progression of head and neck squamous cell carcinoma DOI Creative Commons
Hongshi Cai, Jianfeng Liang,

Yaoqi Jiang

et al.

Journal of Experimental & Clinical Cancer Research, Journal Year: 2024, Volume and Issue: 43(1)

Published: March 5, 2024

Abstract Background Head and neck squamous carcinoma (HNSCC) is known for its high aggressiveness susceptibility to cervical lymph node metastasis, which greatly contributes poor prognosis. During tumorigenesis, many types of cancer cells acquire oncogenic super-enhancers (SEs) that drive the overexpression oncogenes, thereby maintaining malignant progression. This study aimed identify validate role SE-associated genes in progression HNSCC. Methods We identified HNSCC cell-specific through H3K27Ac ChIP-seq overlapped them with HNSCC-associated obtained from The Cancer Genome Atlas (TCGA) dataset Gene Expression Omnibus (GEO) datasets using weighted gene coexpression network analysis (WGCNA) hub genes. expression IGF2BP2 KLF7 was detected clinical samples. To determine biological IGF2BP2, we performed CCK-8, colony formation assay, Transwell migration invasion orthotopic xenograft model experiments. Furthermore, utilized a CRISPR/Cas9 gene-editing system, small-molecule inhibitors, ChIP-qPCR, dual-luciferase reporter assays investigate molecular mechanisms upstream transcription factors. Results Our as exhibited aberrant tissues. Increased observed be linked unfavorable prognosis patients. Both vitro vivo experiments confirmed promotes tumorigenicity metastasis by promoting cell proliferation, migration, invasion. Mechanistically, IGF2BP2-SE region displayed enrichment H3K27Ac, BRD4, MED1, led inhibition deactivation transcriptional program. Additionally, found induce directly bind promoter SE regions. Moreover, abundance positive correlation Patients both showed poorer Lastly, demonstrated small molecule inhibitor JQ1, targeting attenuated proliferation metastatic abilities cells. Conclusions reveals critical mediated Targeting programs may represent potential therapeutic strategy managing

Language: Английский

Citations

13
Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis DOI
Leonard Schärfen, Isaac W. Vock, Matthew D. Simon

et al.

Molecular Cell, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

Citations

1
Structure and mechanism of the plant RNA polymerase V DOI Creative Commons
Guohui Xie, Xuan Du, Hongmiao Hu

et al.

Science, Journal Year: 2023, Volume and Issue: 379(6638), P. 1209 - 1213

Published: March 9, 2023

In addition to the conserved RNA polymerases I III (Pols III) in eukaryotes, two atypical polymerases, Pols IV and V, specifically produce noncoding RNA-directed DNA methylation pathway plants. Here, we report on structures of cauliflower Pol V free elongation conformations. A tyrosine residue NRPE2 stacks with a double-stranded branch transcription bubble potentially attenuate by inducing stalling. The nontemplate strand is captured enhance backtracking, thereby increasing 3'-5' cleavage, which likely underpins V's high fidelity. also illuminate mechanism stalling enhanced may be important for retention chromatin serve its function tethering downstream factors methylation.

Language: Английский

Citations

20