Structural and kinetic insights into tRNA promoter engagement by yeast general transcription factor TFIIIC DOI Creative Commons
Wolfram Seifert-Dávila, Anastasiia Chaban, Florence Baudin

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 9, 2024

Transcription of transfer RNA (tRNA) genes by polymerase (Pol) III requires the general transcription factor IIIC (TFIIIC), which recognizes intragenic A-box and B-box DNA motifs type II gene promoters. However, underlying mechanism has remained elusive, in part due to missing structural information for recognition. In this study, we use single-particle cryogenic electron microscopy (cryo-EM) single-molecule fluorescence resonance energy (smFRET) reveal real-time kinetic insights into how 520-kDa yeast TFIIIC complex engages context a tRNA promoter. Cryo-EM structures τA τB subcomplexes bound were obtained at 3.7 2.5 Å resolution, respectively, while cryo-EM mapping determined specific distance relative orientation revealing fully engaged state TFIIIC. smFRET experiments show that overall recruitment residence times on are primarily governed recognition, footprinting suggest key role TFIIIB Pol following recognition

Language: Английский

Biallelic variants in GTF3C3 encoding a subunit of the TFIIIC2 complex are associated with neurodevelopmental phenotypes in humans and zebrafish DOI Creative Commons
Mohamed S. Abdel‐Hamid,

Adeline Paimboeuf,

Maha S. Zaki

et al.

Brain Communications, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

RNA polymerase III transcribes essential non-coding RNAs, a process regulated by transcription factors TFIIIB and TFIIIC. Although germline variants in TFIIIC subunit genes have been described few patients with neurodevelopmental disorders, the associated pathogenesis clinical spectrum are not yet well defined. Herein, we describe identification of biallelic GTF3C3, which encodes key component subunit, four from three unrelated families different ethnicities collected through GeneMatcher. The exhibited microcephaly, developmental delay, intellectual disability distinctive dysmorphic facies that appear recognizable very young children. Their brain imaging showed atrophy predominant cerebellar involvement, as hypoplasia frontal lobes one patient had moderate to severe simplified gyral pattern. Seizures were observed half patients. Exome/genome sequencing revealed GTF3C3 including missense (p.Cys172Gly, p.Val427Phe p.Ala509Thr) nonsense variant (p.Arg717Ter). Missense present known genetic databases occurred highly conserved residues. Knockout ortholog zebrafish recapitulated symptoms anomalies seizure susceptibility. We also reduced target gene expression knockout model. This study describes new syndrome humans underscores need for further research into biological impacts TFIIIC-linked their contribution III-related pathologies.

Language: Английский

Citations

0
RNA polymerase III transcription machinery and tRNA processing are regulated by the ubiquitin ligase Rsp5 DOI Creative Commons

Aleksandra Łopusińska,

Michał Tys,

Magdalena Boguta

et al.

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Journal Year: 2025, Volume and Issue: unknown, P. 119993 - 119993

Published: May 1, 2025

Language: Английский

Citations

0
Functional divergence of TBP homologs through distinct DNA-binding dynamics DOI Creative Commons

Jieying Cui,

James Z.J. Kwan,

Armin Faghihi

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(9)

Published: May 10, 2025

The TATA box-binding protein (TBP) is an evolutionarily conserved basal transcription factor common in the pre-initiation complex of all three eukaryotic RNA polymerases (RNA Pols). Despite their high conservation, homologous TBPs exhibit species- and tissue-specific functions that may contribute to increasingly gene expression regulation across evolutionary time. To determine molecular mechanisms tissue-specificity for TBPs, we examined ability yeast TBP murine paralogs replace endogenous mouse embryonic stem cells (mESCs). We show that, despite conservation DNA-binding domain among homologs, they cannot fully rescue lethality depletion mESCs, which correlates with inability support Pol III transcription. Furthermore, homologs differentially stress-induced reprogramming, divergent N-terminal playing a role modulating changes transcriptional response. Lastly, have vastly different DNA binding dynamics, suggesting potential mechanism distinct functional behavior observed homologs. Taken together, these data remarkable balance between flexibility essentiality

Language: Английский

Citations

0
The choreography of chromatin in RNA polymerase III regulation DOI Creative Commons

Maria Elize van Breugel,

Alan Gerber, Fred van Leeuwen

et al.

Biochemical Society Transactions, Journal Year: 2024, Volume and Issue: 52(3), P. 1173 - 1189

Published: April 26, 2024

Regulation of eukaryotic gene expression involves a dynamic interplay between the core transcriptional machinery, transcription factors, and chromatin organization modification. While this applies to by all RNA polymerase complexes, III (RNAPIII) seems be atypical with respect its mechanisms regulation. One distinctive feature most RNAPIII transcribed genes is that they are devoid nucleosomes, which relates high levels transcription. Moreover, regulatory sequences not outside but within open regions. Yet, several lines evidence suggest factors affect dynamics activity sequence alone does explain observed regulation RNAPIII. Here we discuss role modification how interact machinery DNA elements in around genes.

Language: Английский

Citations

2
DNA-dependent RNA polymerases in plants DOI Creative Commons
Dong‐Lei Yang, Kun Huang, Deyin Deng

et al.

The Plant Cell, Journal Year: 2023, Volume and Issue: 35(10), P. 3641 - 3661

Published: July 15, 2023

DNA-dependent RNA polymerases (Pols) transfer the genetic information stored in genomic DNA to all organisms. In eukaryotes, typical products of nuclear Pol I, II, and III are ribosomal RNAs, mRNAs, respectively. Intriguingly, plants possess two additional Pols, IV V, which produce small RNAs long noncoding respectively, mainly for silencing transposable elements. The five plant Pols share some subunits, but their distinct functions stem from unique subunits that interact with specific regulatory factors transcription cycles. Here, we summarize recent advances our understanding nucleus-localized including evolution, function, structures,

Language: Английский

Citations

5
The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse DOI Open Access

Parysatis Sachs,

Philipp Bergmaier,

Katrin Treutwein

et al.

Genes, Journal Year: 2023, Volume and Issue: 14(9), P. 1793 - 1793

Published: Sept. 13, 2023

In vertebrates, SMARCAD1 participates in transcriptional regulation, heterochromatin maintenance, DNA repair, and replication. The molecular basis underlying its involvement these processes is not well understood. We identified the RNA polymerase III general transcription factor TFIIIC as an interaction partner of native mouse human models using endogenous co-immunoprecipitations. has dual functionality, acting a genome organizer separating chromatin domains. found that partnership with conserved across different mammalian cell types, from somatic to pluripotent cells. Using purified proteins, we confirmed their direct. A gene expression analysis suggested dispensable for function ESCs. distribution ESC distinct, unlike yeast, enriched at active tRNA genes. Further SMARCAD1-binding partners differentiated cells reveals associates several factors have key regulatory roles organization, such cohesin, laminB, DDX5. Together, our work suggests first time enzyme organization nuclei through interactions architectural proteins.

Language: Английский

Citations

5
Biallelic variants in GTF3C3 result in an autosomal recessive disorder with intellectual disability DOI Creative Commons
Lachlan De Hayr, Laura E.R. Blok, Kerith‐Rae Dias

et al.

Genetics in Medicine, Journal Year: 2024, Volume and Issue: unknown, P. 101253 - 101253

Published: Dec. 1, 2024

Language: Английский

Citations

1
Mechanism of Interaction Between the Transactivation Domain of N-MYC and the DNA-Binding Surface of TFIIIC5 DOI Creative Commons
Eoin Leen, Sharon Yeoh,

Eka Sahak

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 20, 2024

ABSTRACT N-myc is a member of the myc family transcription factors, which are powerful drivers cellular growth and consequently, important oncoproteins. interacts with many factors complexes to affect transcription. One such complex RNA Polymerase III assembly factor, TFIIIC, six-member that essential for small, structured RNA. TFIIIC mutually restrict each other’s chromatin association, their contributes quality control in mRNA We previously demonstrated largely intrinsically disordered transactivation domain directly sub-complex τA. Structural studies by others show DNA binding τA mediated TFIIIC3, suggests TFIIIC5 at most secondary site DNA. Here we identified as key N-myc. used an integrated approach combining NMR, HDX mass spectrometry, pull-downs biophysical assays elucidate molecular basis interaction. Two sequences bind interface TFIIIC5. AlphaFold modelling predicts high-confidence mode higher affinity motif overlaps predicted intramolecular C-terminal acidic plug TFIIIC5, removal enhances The same two motifs also interact Aurora-A kinase, competes during S-phase. This model elucidates how N-myc:TFIIIC5 interaction other interactions, providing mutual censoring function regulation. GRAPHICAL

Language: Английский

Citations

0
A dynamic histone-based chromatin regulatory toolkit underpins genome and developmental evolution in an invertebrate clade DOI Creative Commons
Francisco M. Martín-Zamora, Joby Cole, Rory D. Donnellan

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 23, 2024

Abstract Eukaryotic histones protect and package nuclear DNA into nucleosomes. The dynamic addition removal of posttranslational modifications on these proteins define regulatory regions that play a central role in genome chromatin biology. However, our understanding mechanisms animals is primarily based few model systems, preventing general how histone-based regulation unfolds promotes phenotypic variation during animal embryogenesis. Here, we apply comprehensive multi-omics approach to dissect the complement Annelida, one largest invertebrate phyla. Annelids exhibit conserved histone repertoire organised clusters dynamically regulated, hyperaccessible chromatin. unlike other with reduced genomes, worm Dimorphilus gyrociliatus shows dramatically streamlined repertoire, revealing compaction has lineage-specific effects regulation. Notably, annelid Owenia fusiformis two H2A.X variants co-occur animals, sometimes associate fast cell divisions, represent unique case widespread parallel evolution variant Eukarya. Histone-modifying enzyme complements are largely amongst annelids. Yet, temporal differences expression set modifiers correlate distinct ontogenetic traits adult landscapes modifications, as revealed by quantitative mass spectrometry O. Capitella teleta. Collectively, unparalleled analysis epigenetics within non-model phylum informs regulation, presenting framework explore this fundamental layer contributes developmental morphological diversification annelids generally.

Language: Английский

Citations

0
Functional divergence of TBP homologs through distinct DNA binding dynamics DOI Creative Commons

Jieying Cui,

James Z.J. Kwan,

Armin Faghihi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 7, 2024

Abstract The TATA box-binding protein (TBP) is an evolutionarily conserved basal transcription factor common in the pre-initiation complex of all three eukaryotic RNA polymerases (RNA Pols). Despite their high conservation, homologous TBPs exhibit species- and tissue-specific functions that may contribute to increasingly gene expression regulation across evolutionary time. To determine molecular mechanisms tissue-specificity for TBPs, we examined ability yeast TBP murine paralogs replace endogenous mouse embryonic stem cells. We show that, despite conservation DNA binding domain among homologs, they cannot fully rescue lethality depletion mESCs, largely due inability support Pol III transcription. Furthermore, homologs differentially stress-induced reprogramming, with divergent N-terminal playing a role modulating changes transcriptional response. Lastly, have vastly different dynamics, suggesting potential mechanism distinct functional behavior observed homologs. Taken together, these data remarkable balance between flexibility essentiality

Language: Английский

Citations

0