Aberrant RNA methylation triggers recruitment of an alkylation repair complex

Tsao, Ning; Brickner, Joshua R.; Rodell, Rebecca; Ganguly, Adit; Wood, Matthew D.; Oyeniran, Clément; Ahmad, Tanveer; Sun, Hua; Bacolla, Albino; Zhang, Lisheng; Lukinović, Valentina; Soll, Jennifer M.; Townley, Brittany; Casanova, Alexandre G.; Tainer, John A.; He, Chuan; Vindigni, Alessandro; Reynoird, Nicolas; Mosammaparast, Nima

doi:10.1016/j.molcel.2021.09.024

Cited by 23 publications

(37 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We recently characterized a link between alkylation damage responses and RNF113A , a gene associated with NP-TTD (Brickner et al, 2017; Corbett et al, 2015; Mendelsohn et al, 2020; Tessarech et al, 2020; Tsao et al, 2021). We were curious about the molecular mechanism of pathology associated with TTDN1 , which is the most commonly altered gene associated with repair-proficient TTD (Faghri et al ., 2008).…”

Section: Resultsmentioning

confidence: 99%

“…However, non-photosensitive cases retain the severe neurological and developmental phenotypes seen in photosensitive patients. While TF II Eβ has roles in transcription initiation, RNF113A functions in RNA splicing and recruitment of the ASCC complex, which in turn may affect nascent transcription (Tsao et al ., 2021; Williamson et al ., 2017). Although seemingly diverse, this heterogeneity may at least partially converge on gene expression, which has led to the hypothesis that the hallmark features of TTD are a consequence of disturbed gene expression and protein instability, although these explanations do not satisfy the seemingly specific phenotypes in TTD, such as brittle, sulfur deficient hair.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

A condensate forming tether for lariat debranching enzyme is defective in non-photosensitive trichothiodystrophy

Townley¹,

Buerer

Bacolla

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

The pre-mRNA life cycle requires intron processing; yet, how intron processing defects influence splicing and gene expression is unclear. Here, we find TTDN1, which is frequently mutated in non-photosensitive trichothiodystrophy (NP-TTD), functionally links intron lariat processing to the spliceosome. The conserved TTDN1 C-terminal region directly binds lariat debranching enzyme DBR1, while its N-terminal intrinsically disordered region (IDR) binds the intron binding complex (IBC). The IDR forms condensates in vitro and is needed for IBC interaction. TTDN1 loss causes significant intron lariat accumulation, as well as splicing and gene expression defects, mirroring phenotypes observed in NP-TTD patient cells. Ttdn1-/- mice recapitulate intron processing defects and neurodevelopmental phenotypes seen in NP-TTD. A DBR1-IDR fusion recruits DBR1 to the IBC and circumvents the requirement for TTDN1, suggesting this tethering role as the major molecular function for TTDN1. Collectively, our findings unveil key functional connections between lariat processing, splicing outcomes, and NP-TTD molecular pathology.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A condensate forming tether for lariat debranching enzyme is defective in non-photosensitive trichothiodystrophy

Townley¹,

Buerer

Bacolla

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…This study did not generate any unique data sets or codes. Please refer to Tsao et al. (2021) for the experimental data generated using this protocol.…”

Section: Data and Code Availabilitymentioning

confidence: 99%

“…The approach is highly quantitative and can simultaneously detect several methylated nucleosides in a single experiment. For complete details on the use and execution of this protocol, please refer to Tsao et al. (2021) .…”

mentioning

confidence: 99%

See 1 more Smart Citation

Protocol to analyze and quantify protein-methylated RNA interactions in mammalian cells with a combination of RNA immunoprecipitation and nucleoside mass spectrometry

2022

Self Cite

View full text Add to dashboard Cite

The Molecular Basis of Human ALKBH3 Mediated RNA N¹‐methyladenosine (m¹A) Demethylation

Zhang,

Duan,

Paduch

et al. 2024

Angewandte Chemie

Self Cite

View full text Add to dashboard Cite

N1‐methyladenosine (m1A) is a prevalent post‐transcriptional RNA modification, and the distribution and dynamics of the modification play key epitranscriptomic roles in cell development. At present, the human AlkB Fe(II)/α‐ketoglutarate‐dependent dioxygenase family member ALKBH3 is the only known mRNA m1A demethylase, but its catalytic mechanism remains unclear. Here, we present the structures of ALKBH3‐oligo crosslinked complexes obtained with the assistance of a synthetic antibody crystallization chaperone. Structural and biochemical results showed that ALKBH3 utilized two β‐hairpins (β4‐loop‐β5 and β′‐loop‐β′′) and the α2 helix to facilitate single‐stranded substrate binding. Moreover, a bubble‐like region around Asp194 and a key residue inside the active pocket (Thr133) enabled specific recognition and demethylation of m1A‐ and 3‐methylcytidine (m3C)‐modified substrates. Mutation of Thr133 to the corresponding residue in the AlkB Fe(II)/α‐ketoglutarate‐dependent dioxygenase family members FTO or ALKBH5 converted ALKBH3 substrate selectivity from m1A to N6‐methyladenosine (m6A), as did Asp194 deletion. Our findings provide a molecular basis for understanding the mechanisms of substrate recognition and m1A demethylation by ALKBH3. This study is expected to aid structure‐guided design of chemical probes for further functional studies and therapeutic applications.

show abstract

Aberrant RNA methylation triggers recruitment of an alkylation repair complex

Abstract: Highlights d Alkylated RNA, but not DNA, recruits ASCC-ALKBH3 in an RNF113A-dependent manner d This alkylation repair pathway suppresses transcription and R-loop accumulation d Alkylated pre-mRNA activates RNF113A E3 ligase activity in vitro

Cited by 23 publications

References 55 publications

A condensate forming tether for lariat debranching enzyme is defective in non-photosensitive trichothiodystrophy

A condensate forming tether for lariat debranching enzyme is defective in non-photosensitive trichothiodystrophy

Protocol to analyze and quantify protein-methylated RNA interactions in mammalian cells with a combination of RNA immunoprecipitation and nucleoside mass spectrometry

The Molecular Basis of Human ALKBH3 Mediated RNA N¹‐methyladenosine (m¹A) Demethylation

Contact Info

Product

Resources

About

Aberrant RNA methylation triggers recruitment of an alkylation repair complex

Abstract: Highlights d Alkylated RNA, but not DNA, recruits ASCC-ALKBH3 in an RNF113A-dependent manner d This alkylation repair pathway suppresses transcription and R-loop accumulation d Alkylated pre-mRNA activates RNF113A E3 ligase activity in vitro

Cited by 23 publications

References 55 publications

A condensate forming tether for lariat debranching enzyme is defective in non-photosensitive trichothiodystrophy

A condensate forming tether for lariat debranching enzyme is defective in non-photosensitive trichothiodystrophy

Protocol to analyze and quantify protein-methylated RNA interactions in mammalian cells with a combination of RNA immunoprecipitation and nucleoside mass spectrometry

The Molecular Basis of Human ALKBH3 Mediated RNA N1‐methyladenosine (m1A) Demethylation

Contact Info

Product

Resources

About

The Molecular Basis of Human ALKBH3 Mediated RNA N¹‐methyladenosine (m¹A) Demethylation