Dynamic RNA Modifications in Gene Expression Regulation

A decade has passed since SUMO (small ubiquitin-related modifier) was discovered to be a reversible post-translational protein modifier. During this time many enzymes that participate in regulated SUMO-conjugation and -deconjugation pathways have been identified and characterized. In parallel, the search for SUMO substrates has produced a long list of targets, which appear to be involved in most cellular functions. Sumoylation is a highly dynamic process and its outcomes are extremely diverse, ranging from changes in localization to altered activity and, in some cases, stability of the modified protein. At first glance, these effects have nothing in common; however, it seems that they all result from changes in the molecular interactions of the sumoylated proteins.

Concepts in sumoylation: a decade on

Since the beginning of the century, the mammalian sirtuin protein family (comprising SIRT1-SIRT7) has received much attention for its regulatory role, mainly in metabolism and ageing. Sirtuins act in different cellular compartments: they deacetylate histones and several transcriptional regulators in the nucleus, but also specific proteins in other cellular compartments, such as in the cytoplasm and in mitochondria. As a consequence, sirtuins regulate fat and glucose metabolism in response to physiological changes in energy levels, thereby acting as crucial regulators of the network that controls energy homeostasis and as such determines healthspan.

/pdf/sirtuins-as-regulators-of-metabolism-and-healthspan-jvf88hfgf7.pdf

Sirtuins as regulators of metabolism and healthspan

The nucleolus is a distinct subnuclear compartment that was first observed more than 200 years ago. Nucleoli assemble around the tandemly repeated ribosomal DNA gene clusters and 28S, 18S and 5.8S ribosomal RNAs (rRNAs) are transcribed as a single precursor, which is processed and assembled with the 5S rRNA into ribosome subunits. Although the nucleolus is primarily associated with ribosome biogenesis, several lines of evidence now show that it has additional functions. Some of these functions, such as regulation of mitosis, cell-cycle progression and proliferation, many forms of stress response and biogenesis of multiple ribonucleoprotein particles, will be discussed, as will the relation of the nucleolus to human diseases.

The multifunctional nucleolus

Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl functional groups from the lysine residues of both histone and nonhistone proteins. In humans, there are 18 HDAC enzymes that use either zinc- or NAD(+)-dependent mechanisms to deacetylate acetyl lysine substrates. Although removal of histone acetyl epigenetic modification by HDACs regulates chromatin structure and transcription, deacetylation of nonhistones controls diverse cellular processes. HDAC inhibitors are already known potential anticancer agents and show promise for the treatment of many diseases.

https://cshperspectives.cshlp.org/content/6/4/a018713.full.pdf?cited-by=yes;6/4/a018713

Erasers of Histone Acetylation: The Histone Deacetylase Enzymes

Direct binding of CoREST1 to SUMO-2/3 contributes to gene-specific repression by the LSD1/CoREST1/HDAC complex.

Post-translational modification of many transcription factors and cofactors by the small ubiquitin-related modifier SUMO has been correlated with transcriptional repression.  Recent investigations of the molecular mechanisms underlying SUMO-dependent repression have identified diverse chromatin modifying enzymes and chromatin associated proteins as effectors of SUMO-dependent changes in chromatin structure and gene expression. A surprising diversity of proteins has been identified to be recruited to promoters in a SUMO-dependent manner, including the histone deacetylase HDAC2, the histone demethylase LSD1, the histone methyltransferase SETDB1, the nucleosome remodeling ATPase Mi-2, and chromatin-associated proteins HP1 and L3MBTL1 and -2. These findings suggest that SUMOylation plays a central role in coordinating histone modifications and chromatin structure important for regulation of gene expression.

SUMO engages multiple corepressors to regulate chromatin structure and transcription.

ATR Protects the Genome against R Loops through a MUS81-Triggered Feedback Loop.

Recruitment of DNA repair proteins to DNA damage sites is a critical step for DNA repair. Post-translational modifications of proteins at DNA damage sites serve as DNA damage codes to recruit specific DNA repair factors. Here, we show that mRNA is locally modified by m5C at sites of DNA damage. The RNA methyltransferase TRDMT1 is recruited to DNA damage sites to promote m5C induction. Loss of TRDMT1 compromises homologous recombination (HR) and increases cellular sensitivity to DNA double-strand breaks (DSBs). In the absence of TRDMT1, RAD51 and RAD52 fail to localize to sites of reactive oxygen species (ROS)-induced DNA damage. In vitro, RAD52 displays an increased affinity for DNA:RNA hybrids containing m5C-modified RNA. Loss of TRDMT1 in cancer cells confers sensitivity to PARP inhibitors in vitro and in vivo. These results reveal an unexpected TRDMT1-m5C axis that promotes HR, suggesting that post-transcriptional modifications of RNA can also serve as DNA damage codes to regulate DNA repair.

m5C modification of mRNA serves a DNA damage code to promote homologous recombination.

https://www.cell.com/molecular-cell/pdf/S1097-2765(14)00910-1.pdf

Jian Ouyang

Papers

Direct binding of CoREST1 to SUMO-2/3 contributes to gene-specific repression by the LSD1/CoREST1/HDAC complex.

SUMO engages multiple corepressors to regulate chromatin structure and transcription.

ATR Protects the Genome against R Loops through a MUS81-Triggered Feedback Loop.

m5C modification of mRNA serves a DNA damage code to promote homologous recombination.

Noncovalent interactions with SUMO and ubiquitin orchestrate distinct functions of the SLX4 complex in genome maintenance