Orthogonal IMiD-Degron Pairs Induce Selective Protein Degradation in Cells DOI Creative Commons
Patrick J. Brennan,

Rebecca E. Saunders,

Mary Spanou

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 16, 2024

Abstract Immunomodulatory imide drugs (IMiDs) including thalidomide, lenalidomide, and pomalidomide, can be used to induce degradation of a protein interest that is fused short zinc finger (ZF) degron motif. These IMiDs, however, also endogenous neosubstrates, IKZF1 IKZF3. To improve selectivity, we took bump-and-hole approach design screen bumped IMiD analogs against 8380 ZF mutants. This yielded analog induces efficient mutant degron, while not affecting other cellular proteins, In proof-of-concept studies, this system was applied TRIM28, disease-relevant with no known small molecule binders. We anticipate will make valuable addition the current arsenal systems for use in target validation. One-Sentence Summary Engineered zinc-finger-based degrons enable targeted induced by selective molecular glues.

Язык: Английский

RNA polymerase II dynamics shape enhancer–promoter interactions DOI
Gilad Barshad, James J. Lewis, Alexandra G. Chivu

и другие.

Nature Genetics, Год журнала: 2023, Номер 55(8), С. 1370 - 1380

Опубликована: Июль 10, 2023

Язык: Английский

Процитировано

77
New insights into genome folding by loop extrusion from inducible degron technologies DOI
Elzo de Wit, Elphège P. Nora

Nature Reviews Genetics, Год журнала: 2022, Номер 24(2), С. 73 - 85

Опубликована: Сен. 30, 2022

Язык: Английский

Процитировано

60
Transcriptional elongation control in developmental gene expression, aging, and disease DOI Creative Commons
Yuki Aoi, Ali Shilatifard

Molecular Cell, Год журнала: 2023, Номер 83(22), С. 3972 - 3999

Опубликована: Ноя. 1, 2023

Язык: Английский

Процитировано

38
Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing DOI Creative Commons

Bonnie Su,

Seychelle M. Vos

Molecular Cell, Год журнала: 2024, Номер 84(7), С. 1243 - 1256.e5

Опубликована: Фев. 23, 2024

Metazoan gene expression regulation involves pausing of RNA polymerase (Pol II) in the promoter-proximal region genes and is stabilized by DSIF NELF. Upon depletion elongation factors, NELF appears to accompany elongating Pol II past pause sites; however, prior work indicates that prevents elongation. Here, we report cryoelectron microscopy structures II-DSIF-NELF complexes with two distinct conformations corresponding paused poised states. The state supports stalling, whereas enables transcription as it does not support a tilted RNA-DNA hybrid. Further, can accommodate TFIIS binding II, allowing for reactivation at or backtracking sites. Finally, observe NELF-A tentacle interacts RPB2 protrusion necessary pausing. Our results define how pausing, reactivation, II.

Язык: Английский

Процитировано

10
NELF focuses sites of initiation and maintains promoter architecture DOI Creative Commons
Juan F. Santana, Benjamin M. Spector, Gustavo Suárez

и другие.

Nucleic Acids Research, Год журнала: 2024, Номер 52(6), С. 2977 - 2994

Опубликована: Янв. 9, 2024

Many factors control the elongation phase of transcription by RNA polymerase II (Pol II), a process that plays an essential role in regulating gene expression. We utilized cells expressing degradation tagged subunits NELFB, PAF1 and RTF1 to probe effects depletion on nascent transcripts using PRO-Seq chromatin architecture DFF-ChIP. Although NELF is involved promoter proximal pausing, NELFB had only minimal effect level paused almost no productive elongation. Instead, increased utilization downstream start sites caused dramatic, genome-wide loss H3K4me3 marked nucleosomes. Depletion both major transcript bodies also initiation site changes like those seen with depletion. Our study confirmed first nucleosome encountered during early highly positioned respect TSS. In contrast, positions nucleosomes regions are heterogeneous influenced transcription. propose model defining function general modification blocking initiation.

Язык: Английский

Процитировано

9
The transcription factor GABPA is a master regulator of naive pluripotency DOI Creative Commons
Chengjie Zhou, Meng Wang, Chunxia Zhang

и другие.

Nature Cell Biology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 2, 2025

Abstract The establishment of naive pluripotency is a continuous process starting with the generation inner cell mass (ICM) that then differentiates into epiblast (EPI). Recent studies have revealed key transcription factors (TFs) for ICM formation, but which TFs initiate EPI specification remains unknown. Here, using targeted rapid protein degradation system, we show GABPA not only regulator major ZGA, also master specifier required by regulating 47% genes during E3.5 to E4.5 transition. Chromatin binding dynamics analysis suggests controls formation at least partly gene promoters occupied regulators TFAP2C and SOX2 establish E4.5. Our study uncovers as regulator, supports notion mammalian requires dynamic stepwise multi-TF regulatory network.

Язык: Английский

Процитировано

1
Reshaping transcription and translation dynamics during the awakening of the zygotic genome DOI Creative Commons
Louise Maillard, Pierre Bensidoun, Mounia Lagha

и другие.

Current Opinion in Genetics & Development, Год журнала: 2025, Номер 92, С. 102344 - 102344

Опубликована: Апрель 7, 2025

During the oocyte-to-embryo transition, transcriptome and proteome are dramatically reshaped. This transition entails a shift from maternally inherited mRNAs to newly synthesized transcripts, produced during zygotic genome activation (ZGA). Furthermore, crucial transcription translation selectivity is required for early embryonic development. Studies across various model organisms have revealed conserved cis- trans-regulatory mechanisms dictating regimes by which mRNA proteins this critical phase. In article, we highlight recent technological conceptual advances that deepen our understanding of how tuning both evolves ZGA.

Язык: Английский

Процитировано

1
Rapid and specific degradation of endogenous proteins in mouse models using auxin-inducible degrons DOI Creative Commons
Lewis Macdonald,

Gillian C.A. Taylor,

Jennifer Margaret Brisbane

и другие.

eLife, Год журнала: 2022, Номер 11

Опубликована: Июнь 23, 2022

Auxin-inducible degrons are a chemical genetic tool for targeted protein degradation and widely used to study function in cultured mammalian cells. Here, we develop CRISPR-engineered mouse lines that enable rapid highly specific of tagged endogenous proteins vivo. Most but not all cell types competent degradation. By combining ligand titrations with crosses generate animals different allelic combinations, show kinetics depend upon the dose protein, ligand, E3 ligase substrate receptor TIR1. Rapid condensin I II - two essential regulators mitotic chromosome structure revealed both complexes individually required division precursor lymphocytes, their differentiated peripheral lymphocyte derivatives. This generalisable approach provides unprecedented temporal control over models, implications studying biological pathways modelling drug activity tissues.

Язык: Английский

Процитировано

32
The NELF pausing checkpoint mediates the functional divergence of Cdk9 DOI Creative Commons
Michael DeBerardine, Gregory T. Booth, Philip Versluis

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Май 13, 2023

Abstract Promoter-proximal pausing by RNA Pol II is a rate-determining step in gene transcription that hypothesized to be prominent point at which regulatory factors act. The factor NELF known induce and stabilize pausing, but not all kinds of are NELF-mediated. Here, we find NELF-depleted Drosophila melanogaster cells functionally recapitulate the NELF-independent previously observed fission yeast (which lack NELF). Critically, only NELF-mediated establishes strict requirement for Cdk9 kinase activity release paused into productive elongation. Upon inhibition Cdk9, with efficiently shutdown transcription, while cells, defective, non-productive continues unabated. By introducing checkpoint evolution was likely critical enable increased regulation higher eukaryotes, as availability can restricted limit without inducing wasteful, transcription.

Язык: Английский

Процитировано

21
Auxin-Inducible Degron System: An Efficient Protein Degradation Tool to Study Protein Function DOI Creative Commons

Kundurthi Phanindhar,

Rakesh K. Mishra

BioTechniques, Год журнала: 2023, Номер 74(4), С. 186 - 198

Опубликована: Апрель 1, 2023

Targeted protein degradation, with its rapid depletion kinetics, allows the measurement of acute changes in cell. The auxin-inducible degron (AID) system, rapidly degrades AID-tagged proteins only presence auxin. AID system being inducible makes study essential genes and dynamic processes like cell differentiation, cycle genome organization feasible. degradation has been adapted to yeast, protozoans, C. elegans, Drosophila, zebrafish, mouse mammalian lines. Using researchers have unveiled novel functions for at developmental stages that were previously difficult investigate due early lethality. This comprehensive review discusses development, advancements, applications drawbacks compares it other available systems.

Язык: Английский

Процитировано

15