RNase H1 and H2 Are Differentially Regulated to Process RNA-DNA Hybrids

Lockhart, Arianna; Pires, Vanessa Borges; Bento, Fábio; Kellner, Vanessa; Luke-Glaser, Sarah; Yakoub, George; Ulrich, Helle D.; Luke, Brian

doi:10.1016/j.celrep.2019.10.108

Cited by 108 publications

(129 citation statements)

References 39 publications

(76 reference statements)

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“…Consistently, upon fractionation of cell lysates, RNase H2 is more prominently chromatin-associated in G2/M than in S phase, but to a lesser extent in G1 (Lockhart et al, 2019), suggesting that postreplicative chromatin association of RNase H2 may be a more general feature and not just restricted to telomeres. The same work further demonstrated that G2 phase-restricted RNase H2 expression is sufficient to allow its functions both in R-loop removal and RER; while restricting expression to S phase in fact causes defects in Rloop processing as well as RER-related toxicity (Lockhart et al, 2019). It may thus be crucial to limit the peak of RNase H2 activity to a postreplicative period, possibly to minimize generation of DNA double-strand breaks arising from encounters of an oncoming replication fork with RNase H2-induced nicks during S phase.…”

Section: Rer Regulationmentioning

confidence: 68%

“…While RNase H2 did not localize to particular genomic regions in chromatin immunoprecipitations from asynchronously growing yeast cells (Zimmer & Koshland, 2016), it could be crosslinked to telomeres in cells synchronized late in S phase, at times when the bulk of genomic DNA has been replicated (Graf et al, 2017). Consistently, upon fractionation of cell lysates, RNase H2 is more prominently chromatin-associated in G2/M than in S phase, but to a lesser extent in G1 (Lockhart et al, 2019), suggesting that postreplicative chromatin association of RNase H2 may be a more general feature and not just restricted to telomeres. The same work further demonstrated that G2 phase-restricted RNase H2 expression is sufficient to allow its functions both in R-loop removal and RER; while restricting expression to S phase in fact causes defects in Rloop processing as well as RER-related toxicity (Lockhart et al, 2019).…”

Section: Rer Regulationmentioning

confidence: 84%

“…In any case, the significance of the PIP-box within the RNase H2 complex requires clarification. While RNH201 mRNA expression peaks twice during the yeast cell cycle, during S phase and again during G2/M phase (Arudchandran et al, 2000), the protein accumulates progressively from G1 (where expression is very low) through to M phase (Lockhart et al, 2019). All other, non-catalytic RNase H2 subunit proteins are constitutively expressed throughout the cell cycle, and the complex resides exclusively within the nuclear compartment (Reijns et al, 2012;Lockhart et al, 2019).…”

Section: Rer Regulationmentioning

confidence: 99%

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Molecular and physiological consequences of faulty eukaryotic ribonucleotide excision repair

Kellner

Luke

2019

The EMBO Journal

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The duplication of the eukaryotic genome is an intricate process that has to be tightly safe-guarded. One of the most frequently occurring errors during DNA synthesis is the mis-insertion of a ribonucleotide instead of a deoxyribonucleotide. Ribonucleotide excision repair (RER) is initiated by RNase H2 and results in errorfree removal of such mis-incorporated ribonucleotides. If left unrepaired, DNA-embedded ribonucleotides result in a variety of alterations within chromosomal DNA, which ultimately lead to genome instability. Here, we review how genomic ribonucleotides lead to chromosomal aberrations and discuss how the tight regulation of RER timing may be important for preventing unwanted DNA damage. We describe the structural impact of unrepaired ribonucleotides on DNA and chromatin and comment on the potential consequences for cellular fitness. In the context of the molecular mechanisms associated with faulty RER, we have placed an emphasis on how and why increased levels of genomic ribonucleotides are associated with severe autoimmune syndromes, neuropathology, and cancer. In addition, we discuss therapeutic directions that could be followed for pathologies associated with defective removal of ribonucleotides from doublestranded DNA.

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Section: Rer Regulationmentioning

confidence: 68%

Section: Rer Regulationmentioning

confidence: 84%

Section: Rer Regulationmentioning

confidence: 99%

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Molecular and physiological consequences of faulty eukaryotic ribonucleotide excision repair

Kellner

Luke

2019

The EMBO Journal

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“…Another possibility could be that DOT1B modulates RH2 activity. Interestingly, yeast RH2 was shown to perform all its functions in the G2-phase of the cell cycle (112). It would be interesting to figure out if this is also true for trypanosomal RH2, and if DOT1B contributes via a cell cycle-dependent interaction.…”

Section: Discussionmentioning

confidence: 98%

A DOT1B/Ribonuclease H2 protein complex is involved in R-loop processing, genomic integrity and antigenic variation inTrypanosoma brucei

Eisenhuth

Vellmer

Butter

et al. 2020

Preprint

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The parasite Trypanosoma brucei periodically changes the expression of protective variant surface glycoproteins (VSGs) to evade its host's immune system in a process known as antigenic variation.One route to change VSG expression is the transcriptional activation of a previously silent VSG expression site (ES), a subtelomeric region containing the VSG genes. Homologous recombination of a different VSG from a large reservoir into the active ES represents another route. The conserved histone methyltransferase DOT1B is involved in transcriptional silencing of inactive ES and influences ES switching kinetics. The molecular machinery that enables DOT1B to execute these regulatory functions remains elusive, however. To better understand DOT1B-mediated regulatory processes, we purified DOT1B-associated proteins using complementary biochemical approaches. We identified several novel DOT1B-interactors. One of these was the Ribonuclease H2 complex, previously shown to resolve RNA-DNA hybrids, maintain genome integrity, and play a role in antigenic variation. Our study revealed that DOT1B depletion results in an increase in RNA-DNA hybrids, accumulation of DNA damage and recombination-based ES switching events. Surprisingly, a similar pattern of VSG deregulation was observed in Ribonuclease H2 mutants. We propose that both proteins act together in resolving R-loops to ensure genome integrity and contribute to the tightly-regulated process of antigenic variation.

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“…Eukaryotic RNase H enzymes are classified into two main types, RNase H1 and RNase H2, that are differentially regulated during the cell cycle and differ in the range of substrates they act on. [ 61 ] Both types can resolve DNA:RNA hybrids in R‐loops and, in addition, RNase H2 plays a specialized function in the cleavage of single ribonucleotides embedded in the genome. [ 62 ] RNase H enzymes have been directly linked to the degradation of DNA:RNA hybrids formed at DSBs and several observations support their functional contribution to DNA repair.…”

Section: Resolution Of Dna:rna Hybrids At Dsbsmentioning

confidence: 99%

RNA at DNA Double‐Strand Breaks: The Challenge of Dealing with DNA:RNA Hybrids

2020

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RNA polymerase II is recruited to DNA double-strand breaks (DSBs), transcribes the sequences that flank the break and produces a novel RNA type that has been termed damage-induced long non-coding RNA (dilncRNA). DilncRNAs can be processed into short, miRNA-like molecules or degraded by different ribonucleases. They can also form double-stranded RNAs or DNA:RNA hybrids. The DNA:RNA hybrids formed at DSBs contribute to the recruitment of repair factors during the early steps of homologous recombination (HR) and, in this way, contribute to the accuracy of the DNA repair. However, if not resolved, the DNA:RNA hybrids are highly mutagenic and prevent the recruitment of later HR factors. Here recent discoveries about the synthesis, processing, and degradation of dilncRNAs are revised. The focus is on RNA clearance, a necessary step for the successful repair of DSBs and the aim is to reconcile contradictory findings on the effects of dilncRNAs and DNA:RNA hybrids in HR.

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RNase H1 and H2 Are Differentially Regulated to Process RNA-DNA Hybrids

Abstract: Highlights d RNase H2 efficiently processes R-loops and rNMPs postreplicatively d rNMPs processed by RNase H2 in S phase require Rad52mediated repair d RNase H1 functions independently of the cell cycle d RNase H1 responds to R-loop-induced stress

Cited by 108 publications

References 39 publications

Molecular and physiological consequences of faulty eukaryotic ribonucleotide excision repair

Molecular and physiological consequences of faulty eukaryotic ribonucleotide excision repair

A DOT1B/Ribonuclease H2 protein complex is involved in R-loop processing, genomic integrity and antigenic variation inTrypanosoma brucei

RNA at DNA Double‐Strand Breaks: The Challenge of Dealing with DNA:RNA Hybrids

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