Loop extrusion as a mechanism for formation of DNA damage repair foci.

The repair of DNA double-strand breaks (DSBs) is essential for safeguarding genome integrity. When a DSB forms, the PI3K-related ATM kinase rapidly triggers the establishment of megabase-sized, chromatin domains decorated with phosphorylated histone H2AX (γH2AX), which act as seeds for the formation of DNA-damage response foci1. It is unclear how these foci are rapidly assembled to establish a 'repair-prone' environment within the nucleus. Topologically associating domains are a key feature of 3D genome organization that compartmentalize transcription and replication, but little is known about their contribution to DNA repair processes2,3. Here we show that topologically associating domains are functional units of the DNA damage response, and are instrumental for the correct establishment of γH2AX-53BP1 chromatin domains in a manner that involves one-sided cohesin-mediated loop extrusion on both sides of the DSB. We propose a model in which H2AX-containing nucleosomes are rapidly phosphorylated as they actively pass by DSB-anchored cohesin. Our work highlights the importance of chromosome conformation in the maintenance of genome integrity and demonstrates the establishment of a chromatin modification by loop extrusion.

A cohesin/HUSH- and LINC-dependent pathway controls ribosomal DNA double-strand break repair.

The ribosomal DNA (rDNA) represents a particularly unstable locus undergoing frequent breakage. DNA double-strand breaks (DSBs) within rDNA induce both rDNA transcriptional repression and nucleolar segregation, but the link between the two events remains unclear. Here we found that DSBs induced on rDNA trigger transcriptional repression in a cohesin- and HUSH (human silencing hub) complex-dependent manner throughout the cell cycle. In S/G2 cells, transcriptional repression is further followed by extended resection within the interior of the nucleolus, DSB mobilization at the nucleolar periphery within nucleolar caps, and repair by homologous recombination. We showed that nuclear envelope invaginations frequently connect the nucleolus and that rDNA DSB mobilization, but not transcriptional repression, involves the nuclear envelope-associated LINC complex and the actin pathway. Altogether, our data indicate that rDNA break localization at the nucleolar periphery is not a direct consequence of transcriptional repression but rather is an active process that shares features with the mobilization of persistent DSB in active genes and heterochromatin.

One-step generation of multiple gene knock-outs in the diatom Phaeodactylum tricornutum by DNA-free genome editing.

Recently developed transgenic techniques to explore and exploit the metabolic potential of microalgae present several drawbacks associated with the delivery of exogenous DNA into the cells and its subsequent integration at random sites within the genome. Here, we report a highly efficient multiplex genome-editing method in the diatom Phaeodactylum tricornutum, relying on the biolistic delivery of CRISPR-Cas9 ribonucleoproteins coupled with the identification of two endogenous counter-selectable markers, PtUMPS and PtAPT. First, we demonstrate the functionality of RNP delivery by positively selecting the disruption of each of these genes. Then, we illustrate the potential of the approach for multiplexing by generating double-gene knock-out strains, with 65% to 100% efficiency, using RNPs targeting one of these markers and PtAureo1a, a photoreceptor-encoding gene. Finally, we created triple knock-out strains in one step by delivering six RNP complexes into Phaeodactylum cells. This approach could readily be applied to other hard-to-transfect organisms of biotechnological interest.

The stability of an mRNA is influenced by its concentration: a potential physical mechanism to regulate gene expression.

Changing mRNA stability is a major post-transcriptional way of controlling gene expression, particularly in newly encountered conditions. As the concentration of mRNA is the result of an equilibrium between transcription and degradation, it is generally assumed that at constant transcription, any change in mRNA concentration is the consequence of mRNA stabilization or destabilization. However, the literature reports many cases of opposite variations in mRNA concentration and stability in bacteria. Here, we analyzed the causal link between the concentration and stability of mRNA in two phylogenetically distant bacteria Escherichia coli and Lactococcus lactis. Using reporter mRNAs, we showed that modifying the stability of an mRNA had unpredictable effects, either higher or lower, on its concentration, whereas increasing its concentration systematically reduced stability. This inverse relationship between the concentration and stability of mRNA was generalized to native genes at the genome scale in both bacteria. Higher mRNA turnover in the case of higher concentrations appears to be a simple physical mechanism to regulate gene expression in the bacterial kingdom. The consequences for bacterial adaptation of this control of the stability of an mRNA by its concentration are discussed.

[Oncogenic and tumour suppressor microRNAs]. / Micro-ARN: oncogènes et suppresseurs de tumeurs.

microRNAs constitute one of the most important discovery in the past few years in the field of gene expression regulation. They can precisely regulate the expression of a specific protein by inhibiting its translation and/or promoting the degradation of its mRNA. In several cancers, the expression of some microRNAs is misregulated, pointing toward the existence of microRNAs with oncogenic or tumour suppressor properties. The miR-17-92 miRNA cluster has been reported to have a pro-oncogenic role in a mouse model system of Myc-induced B cell lymphoma. Some of its targets mRNAs code for proteins with pro-apoptotic or anti-proliferative functions, which shed some light on the mechanism of action of this cluster. On the other hand, a tumour suppressor miRNA like let-7 targets mRNAs coding for oncogenes and is frequently down-regulated in cancers. The finding that c-Myc controls the expression of several of these microRNAs reveals new information on how misregulation of this proto-oncogene can promote tumorigenesis.

In vivo targeting of the yeast Pop2 deadenylase subunit to reporter transcripts induces their rapid degradation and generates new decay intermediates.

Deadenylation is the rate-limiting step of mRNA decay, yet little is known about the mechanism regulating this process. In yeast, deadenylation is mainly mediated by the Pop2-Ccr4 complex. We tested whether the selective recruitment of this deadenylase to target mRNAs was sufficient to stimulate their decay in vivo. For this purpose, the Pop2 factor was fused to a U1A RNA binding domain while U1A binding sites were inserted in untranslated regions of a reporter transcript. Analysis of the reporter fate in strains expressing the Pop2-U1A-RBD fusion demonstrated a specific activation of target mRNA decay. Increased mRNA degradation involved accumulation of deadenylated mRNAs that was not detected when the control factors Dcp2 or Pub1 were tethered to the same transcript. The rapid target mRNA degradation was also accompanied by the appearance of new decay intermediates generated by the 3' -5' trimming of the corresponding 3' -untranslated region. Interestingly, this process was not mediated by the exosome but may result from the activity of the Pop2-Ccr4 deadenylase itself. These results indicate that selective recruitment of the Pop2-Ccr4 deadenylase is sufficient to activate mRNA decay, even though this process can also be stimulated by additional mechanisms. Furthermore, deadenylase recruitment affects the downstream path of mRNA decay.