High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes DOI Creative Commons
Emma L. Peterman, Deon Ploessl, Kasey S. Love

et al.

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

Published: Nov. 26, 2024

Abstract Concentrations of RNAs and proteins provide important determinants cell fate. Robust gene circuit design requires an understanding how the combined actions individual genetic components influence both mRNA protein levels. Here, we simultaneously measure levels in single cells using HCR Flow-FISH for a set commonly used synthetic promoters. We find that promoters generate differences abundance effective translation rate these transcripts. Stronger not only transcribe more RNA but also show higher rates. While strength promoter is largely preserved upon genome integration with identical elements, choice polyadenylation signal coding sequence can large profiles mRNAs proteins. long-read direct sequencing to characterize full-length isoforms observe remarkable uniformity from transgenic units. Together, our high-resolution profiling offers insight into impact common on transcriptional translational mechanisms. By developing novel framework quantifying expression transgenes, have established system comparing native regulation building robust systems.

Language: Английский

The GC-content at the 5′ ends of human protein-coding genes is undergoing mutational decay DOI Creative Commons
Yi Qiu,

Yoon Mo Kang,

Christopher Korfmann

et al.

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: Aug. 13, 2024

Abstract Background In vertebrates, most protein-coding genes have a peak of GC-content near their 5′ transcriptional start site (TSS). This feature promotes both the efficient nuclear export and translation mRNAs. Despite importance for RNA metabolism, its general features, origin, maintenance remain mysterious. We investigate evolutionary forces shaping at (TSS) through comparative genomic analysis nucleotide substitution rates between different species by examining human de novo mutations. Results Our data suggests that GC-peaks TSSs were present in last common ancestor amniotes, likely vertebrates. observe apes rodents, where recombination is directed away from PRDM9, end gene currently undergoing mutational decay. canids, which lack PRDM9 perform TSSs, increasing. show these patterns extend into open reading frame, thus impacting synonymous codon position choices. Conclusions results indicate dynamics this GC-peak amniotes largely shaped historic recombination. Since decay towards mutation rate equilibrium default state non-functional DNA, observed decrease rodents indicates not being maintained selection on those species.

Language: Английский

Citations

5
Structural and Functional Insights into Targeting GCCG Sites in the EGFR Promoter by Two DNA Intercalators to Inhibit Breast Cancer Metastasis DOI Creative Commons

Chih-Chun Chang,

Hsin‐Ju Li, Roshan Satange

et al.

Journal of Medicinal Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: March 3, 2025

Chemotherapeutic drugs are commonly used to treat cancers lacking targeted therapy options. However, their low specificity limits treatment effectiveness. We report here that the cooperative binding of doxorubicin (Dox) with actinomycin D (ActD) enhances for consecutive GCCG sites in DNA. Using X-ray crystallography, we determined crystal structure ActD and Dox bound d(AGCCGT)2 intercalation at GpC site induces a novel mode adjacent CpG step. This ensures snug fit, avoids steric clashes, specificity. Transcriptome analysis revealed combining synergistically down-regulates EGFR TNBC cells. Additionally, it reduces promoter activity. In vivo, combination significantly suppresses tumor growth outperforms standard cyclophosphamide regimen inhibiting metastasis. study highlights targeting activated pathway sequence-specific DNA-targeting drug combinations as potential treatment.

Language: Английский

Citations

0
Coupling mechanisms coordinating mRNA translation with stages of the mRNA lifecycle DOI Creative Commons
Valeria Famà, Lucia Coscujuela Tarrero,

Roberto Albanese

et al.

RNA Biology, Journal Year: 2025, Volume and Issue: unknown

Published: March 21, 2025

Gene expression involves a series of consequential processes, beginning with mRNA synthesis and culminating in translation. Traditionally studied as linear sequence events, recent findings challenge this perspective, revealing coupling mechanisms that coordinate key steps gene expression, even when spatially temporally distant. In review, we focus on translation, the final stage examine its stages metabolism: synthesis, processing, export, decay. For each these provide an overview known instances Furthermore, discuss role high-throughput technologies uncovering intricate interactions genome-wide scale. Finally, highlight challenges propose future directions to advance our understanding how orchestrate robust adaptable programs.

Language: Английский

Citations

0
Genome biology of long non-coding RNAs in humans: a virtual karyotype DOI Creative Commons
A. Palma, Giulia Buonaiuto, Monica Ballarino

et al.

Computational and Structural Biotechnology Journal, Journal Year: 2025, Volume and Issue: 27, P. 575 - 584

Published: Jan. 1, 2025

Language: Английский

Citations

0
High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes DOI Creative Commons
Emma L. Peterman, Deon Ploessl, Kasey S. Love

et al.

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

Published: Nov. 26, 2024

Abstract Concentrations of RNAs and proteins provide important determinants cell fate. Robust gene circuit design requires an understanding how the combined actions individual genetic components influence both mRNA protein levels. Here, we simultaneously measure levels in single cells using HCR Flow-FISH for a set commonly used synthetic promoters. We find that promoters generate differences abundance effective translation rate these transcripts. Stronger not only transcribe more RNA but also show higher rates. While strength promoter is largely preserved upon genome integration with identical elements, choice polyadenylation signal coding sequence can large profiles mRNAs proteins. long-read direct sequencing to characterize full-length isoforms observe remarkable uniformity from transgenic units. Together, our high-resolution profiling offers insight into impact common on transcriptional translational mechanisms. By developing novel framework quantifying expression transgenes, have established system comparing native regulation building robust systems.

Language: Английский

Citations

2