The Good and Bad of RNA:DNA Hybrids in Double-Strand Break Repair.

Transcription and genome stability have somewhat of a love-hate relationship. In a recent issue of Cell, Ohle et al. (2016) demonstrate a previously unappreciated mechanism by which transcription and RNA contribute to genome stability.

CRISPR-Mediated Base Editing without DNA Double-Strand Breaks.

Targeting point mutations using CRISPR/Cas9 so far has required efficient homologous recombination (HR) and donor oligonucleotides. In a recent Nature paper, Komor and colleagues (2016) describe a way to make specific base changes that does not depend on HR or donor DNA and does not involve making double-strand breaks.

Replication Origin Specification Gets a Push.

During the gap between G1 and S phases when replication origins are licensed and fired, it is possible that DNA translocases could disrupt pre-replicative complexes (pre-RCs). In this issue of Molecular Cell, Gros et al. (2015) find that pre-RCs can be pushed along DNA and retain the ability to support replication.

Regulating transcription traffic around DSBs.

If a double-strand break (DSB) occurs and either a DNA polymerase or RNA polymerase is coming along, how do we save the train? In this issue of Molecular Cell, Ui et al. (2015) describe a connection between an elongation factor and a repressive complex to prevent transcription in proximity to a DSB.

More division of labor at the eukaryotic replication fork.

Our understanding of the dynamics of replication fork-associated protein strand specificity is based largely on genetic or in vitro approaches. Yu et al. (2014) present eSPAN, a ChIP approach that reveals differences between protein abundance on nascent leading and lagging strands.

eRNAs lure NELF from paused polymerases.

RNAs transcribed from enhancers (eRNAs) have been linked to enhancer function. In this issue of Molecular Cell, Schaukowitch et al. (2014) show that upon activation, eRNAs can bind NELF and are necessary for its transient removal from promoters to release paused RNA polymerase II and drive expression of immediate-early genes in neurons.

An ultraconserved lnc to miRNA processing.

Very few specific functions have been assigned to ultraconserved regions. In this issue of Molecular Cell, Liz et al. (2014) describe how a lncRNA transcribed from an ultraconserved region can negatively regulate miRNA maturation.

When breaking is bad but repair is worse.

DNA double-strand breaks (DSBs) are a major source of genome instability; however, recent studies from Lee et al. (2014) and Orthwein et al. (2014) show why, at least during mitosis, suppression of DSB repair is important.

Ubiquitin mediates the physical and functional interaction between human DNA polymerases η and ι.

Human DNA polymerases η and ι are best characterized for their ability to facilitate translesion DNA synthesis (TLS). Both polymerases (pols) co-localize in 'replication factories' in vivo after cells are exposed to ultraviolet light and this co-localization is mediated through a physical interaction between the two TLS pols. We have mapped the polη-ι interacting region to their respective ubiquitin-binding domains (UBZ in polη and UBM1 and UBM2 in polι), and demonstrate that ubiquitination of either TLS polymerase is a prerequisite for their physical and functional interaction.

Eukaryotic Y-family polymerases bypass a 3-methyl-2'-deoxyadenosine analog in vitro and methyl methanesulfonate-induced DNA damage in vivo.

N3-methyl-adenine (3MeA) is the major cytotoxic lesion formed in DNA by S(N)2 methylating agents. The lesion presumably blocks progression of cellular replicases because the N3-methyl group hinders interactions between the polymerase and the minor groove of DNA. However, this hypothesis has yet to be rigorously proven, as 3MeA is intrinsically unstable and is converted to an abasic site, which itself is a blocking lesion.

Controlling the subcellular localization of DNA polymerases iota and eta via interactions with ubiquitin.

Y-family DNA polymerases have spacious active sites that can accommodate a wide variety of geometric distortions. As a consequence, they are considerably more error-prone than high-fidelity replicases. It is hardly surprising, therefore, that the in vivo activity of these polymerases is tightly regulated, so as to minimize their inadvertent access to primer-termini.

Switching from high-fidelity replicases to low-fidelity lesion-bypass polymerases.

Replication of damaged DNA often requires a DNA polymerase in addition to the cell's normal replicase. Recent research has begun to shed light on the switch from a high-fidelity replicative polymerase to a low-fidelity translesion polymerase that occurs at a stalled replication fork. A picture is emerging in which eukaryotic replicative clamps are posttranslationally modified by ubiquitination, SUMOylation or phosphorylation.

Investigating the role of the little finger domain of Y-family DNA polymerases in low fidelity synthesis and translesion replication.

Dpo4 and Dbh are Y-family polymerases that originate from two closely related strains of Sulfolobaceae. Quite surprisingly, however, the two polymerases exhibit different enzymatic properties in vitro. For example, Dpo4 can replicate past a variety of DNA lesions, yet Dbh does so with a much lower efficiency.

Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase.

The first occupation-associated cancers to be recognized were the sooty warts (cancers of the scrotum) suffered by chimney sweeps in 18th century England. In the 19th century, high incidences of skin cancers were noted among fuel industry workers. By the early 20th century, malignant skin tumors were produced in laboratory animals by repeatedly painting them with coal tar.

129-derived strains of mice are deficient in DNA polymerase iota and have normal immunoglobulin hypermutation.

Recent studies suggest that DNA polymerase eta (poleta) and DNA polymerase iota (poliota) are involved in somatic hypermutation of immunoglobulin variable genes. To test the role of poliota in generating mutations in an animal model, we first characterized the biochemical properties of murine poliota. Like its human counterpart, murine poliota is extremely error-prone when catalyzing synthesis on a variety of DNA templates in vitro.

Replication of a cis-syn thymine dimer at atomic resolution.

Ultraviolet light damages DNA by catalysing covalent bond formation between adjacent pyrimidines, generating cis-syn cyclobutane pyrimidine dimers (CPDs) as the most common lesion. CPDs block DNA replication by high-fidelity DNA polymerases, but they can be efficiently bypassed by the Y-family DNA polymerase pol eta. Mutations in POLH encoding pol eta are implicated in nearly 20% of xeroderma pigmentosum, a human disease characterized by extreme sensitivity to sunlight and predisposition to skin cancer.