Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair

Cheng, Yan; Dodd, Thomas; Yu, Jina; Leung, Bernice; Xu, Jun; Oh, Juntaek; Wang, Dong; Ivanov, Ivaylo

doi:10.1038/s41467-021-27295-4

Cited by 15 publications

(10 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We propose that the steric exclusion of Spt4/5 by the lesion-induced strong interaction between Rad26 and Rpb4/7 is a major step in committing a lesion-stalled Pol II to TC-NER. Furthermore, a previous computational study suggested that tethering Rad26-NTD with Pol II Rpb4/7 is important for Pol II-Rad26 complex assembly and plays a key role in anchoring Rad26 to Pol II and establishing a productive orientation with respect to the transcription bubble (30).…”

Section: Discussionmentioning

confidence: 99%

Elf1 promotes Rad26’s interaction with lesion-arrested Pol II for transcription-coupled repair

Sarsam,

Xu,

Lahiri

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Transcription-coupled nucleotide excision repair (TC-NER) is a highly conserved DNA repair pathway that removes bulky lesions in the transcribed genome. Cockayne syndrome B protein (CSB), or its yeast ortholog Rad26, has been known for decades to play important roles in the lesion-recognition steps of TC-NER. Another conserved protein ELOF1, or its yeast ortholog Elf1, was recently identified as a core transcription-coupled repair factor. How Rad26 distinguishes between RNA polymerase II (Pol II) stalled at a DNA lesion or other obstacles and what role Elf1 plays in this process remains unknown. Here, we present cryo-EM structures of Pol II-Rad26 complexes stalled at different obstacles that show that Rad26 uses a universal mechanism to recognize a stalled Pol II but interacts more strongly with a lesion-arrested Pol II. A cryo-EM structure of lesion-arrested Pol II-Rad26 bound to Elf1 revealed that Elf1 induces new interactions between Rad26 and Pol II when the complex is stalled at a lesion. Biochemical and genetic data support the importance of the interplay between Elf1 and Rad26 in TC-NER initiation.

show abstract

Section: Discussionmentioning

confidence: 99%

Elf1 promotes Rad26’s interaction with lesion-arrested Pol II for transcription-coupled repair

Sarsam,

Xu,

Lahiri

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…69 Even though these statistical techniques have not been applied to other RNA-based machines involved in RNA metabolism, remarkable applications were done in related systems. [111][112][113][114][115] These methods therefore appear to be a powerful instrument in helping to elucidate the working principles of RNP-machineries.…”

Section: Unraveling the Molecular Principles Of Rnp-machinery Functionmentioning

confidence: 99%

Establishing the catalytic and regulatory mechanism of RNA‐based machineries

Borišek

Aupič

Magistrato

2022

WIREs Comput Mol Sci

View full text Add to dashboard Cite

Ribonucleoprotein (RNP)-machineries are comprised of intricate networks of long noncoding RNAs and proteins that allow them to actively participate in transcription, RNA processing, and translation. RNP-machineries thus play vital roles in gene expression and regulation. Recent advances in cryo-EM techniques provided a wealth of near-atomic-level resolution structures setting the basis for understanding how these fascinating multiscale complexes exert their diverse roles. However, these structures represent only isolated snapshots of the plastic and highly dynamic RNPmachineries and are thus insufficient to comprehensively assess their multifaceted mechanisms. In this review, we discuss the role and merit of allatom simulations in disentangling the mechanism of eukaryotic RNA-based machineries responsible for RNA processing. We showcase how all-atom simulations can capture their large-scale functional movements, trace the signaling pathways that are at the root of their massive conformational remodeling, explain recognition mechanisms of specific RNA sequences, and, lastly, unravel the chemical mechanisms underlying the formation of functional RNA strands. Finally, we review the methodological pitfalls and outline future challenges in modeling key functional aspects of these large molecular engines with all-atom simulations. In addition to providing insights into the most basic processes that govern all forms of life, in-depth mechanistic comprehension of RNP-machineries offers a foundation for developing innovative therapeutic strategies against the variety of human diseases linked to deregulated RNA metabolism. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics K E Y W O R D S cryo-EM, molecular dynamics, ribonucleoproteins, RNA catalysis, RNA processing Jure Borišek and Jana Aupič contributed equally to the study.

show abstract

“…Adding to the complexity, NER features two sub-pathways, global genome NER (GG-NER) and transcription-coupled NER (TC-NER), that differ only in the damage recognition step. TC-NER 4 – 6 is essential for lesion removal from the template strand during transcription and is activated by the recruitment of Cockayne Syndrome B protein (CSB) to lesion-arrested RNA polymerase II (Pol II) 7 – 12 . By contrast, in GG-NER a heterotrimeric complex of XPC, HR23B and Centrin 2 (CETN2) 13 detects the lesion and, in a twist-to-open mechanism, melts the DNA duplex at the damaged site 14 – 19 .…”

Section: Introductionmentioning

confidence: 99%

Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases

Cheng

Dodd

et al. 2023

Nat Commun

Self Cite

View full text Add to dashboard Cite

Transcription factor IIH (TFIIH) is a protein assembly essential for transcription initiation and nucleotide excision repair (NER). Yet, understanding of the conformational switching underpinning these diverse TFIIH functions remains fragmentary. TFIIH mechanisms critically depend on two translocase subunits, XPB and XPD. To unravel their functions and regulation, we build cryo-EM based TFIIH models in transcription- and NER-competent states. Using simulations and graph-theoretical analysis methods, we reveal TFIIH’s global motions, define TFIIH partitioning into dynamic communities and show how TFIIH reshapes itself and self-regulates depending on functional context. Our study uncovers an internal regulatory mechanism that switches XPB and XPD activities making them mutually exclusive between NER and transcription initiation. By sequentially coordinating the XPB and XPD DNA-unwinding activities, the switch ensures precise DNA incision in NER. Mapping TFIIH disease mutations onto network models reveals clustering into distinct mechanistic classes, affecting translocase functions, protein interactions and interface dynamics.

show abstract

Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair

Cited by 15 publications

References 67 publications

Elf1 promotes Rad26’s interaction with lesion-arrested Pol II for transcription-coupled repair

Elf1 promotes Rad26’s interaction with lesion-arrested Pol II for transcription-coupled repair

Establishing the catalytic and regulatory mechanism of RNA‐based machineries

Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases

Contact Info

Product

Resources

About