ERH proteins: connecting RNA processing to tumorigenesis?

Impact of Asp/Glu-ADP-ribosylation on protein-protein interaction and protein function

PARylation plays critical role in regulating multiple cellular processes such as DNA damage response and repair, transcription, RNA processing, and stress response. More than 300 human proteins have been found to be modified by PARylation on acidic residues, that is, Asp (D) and Glu (E). We used the deep-learning tool AlphaFold to predict protein-protein interactions (PPIs) and their interfaces for these proteins based on coevolution signals from joint multiple sequence alignments (MSAs). AlphaFold predicted 260 confident PPIs involving PARylated proteins, and about one quarter of these PPIs have D/E-PARylation sites in their predicted PPI interfaces. AlphaFold predictions offer novel insights into the mechanisms of PARylation regulations by providing structural details of the PPI interfaces. D/E-PARylation sites have a preference to occur in coil regions and disordered regions, and PPI interfaces containing D/E-PARylation sites tend to occur between short linear sequence motifs in disordered regions and globular domains. The hub protein PCNA is predicted to interact with more than 20 proteins via the common PIP box motif and the structurally variable flanking regions. D/E-PARylation sites were found in the interfaces of key components of the RNA transcription and export complex, the SF3a spliceosome complex, and H/ACA and C/D small nucleolar ribonucleoprotein complexes, suggesting that systematic PARylation have a profound effect in regulating multiple RNA-related processes such as RNA nuclear export, splicing, and modification. Finally, PARylation of SUMO2 could modulate its interaction with CHAF1A, thereby representing a potential mechanism for the cross-talk between PARylation and SUMOylation in regulation of chromatin remodeling.

Systematic identification of factors involved in the silencing of germline genes in mouse embryonic stem cells

In mammals, many germline genes are epigenetically repressed to prevent their illegitimate expression in somatic cells. To advance our understanding of the mechanisms restricting the expression of germline genes, we analyzed their chromatin signature and performed a CRISPR-Cas9 knock-out screen for genes involved in germline gene repression using a Dazl-GFP reporter system in mouse embryonic stem cells (mESCs). We show that the repression of germline genes mainly depends on the polycomb complex PRC1.6 and DNA methylation, which function additively in mESCs. Furthermore, we validated novel genes involved in the repression of germline genes and characterized three of them: Usp7, Shfm1 (also known as Sem1) and Erh. Inactivation of Usp7, Shfm1 or Erh led to the upregulation of germline genes, as well as retrotransposons for Shfm1, in mESCs. Mechanistically, USP7 interacts with PRC1.6 components, promotes PRC1.6 stability and presence at germline genes, and facilitates DNA methylation deposition at germline gene promoters for long term repression. Our study provides a global view of the mechanisms and novel factors required for silencing germline genes in embryonic stem cells.

ERH: a plug-and-play protein important for gene silencing and cell cycle progression

In metazoans, most proteins have pleiotropic cellular functions and have the ability to interact with several factors to accomplish these different functions. This is the case of eukaryotic ERH proteins, a family of homodimeric proteins involved in DNA replication and cell cycle control as well as in gene silencing by contributing either to the biogenesis of small interference RNAs (miRNAs, piRNAs) or to the recruitment of RNA decay machineries. Very recently, several crystal structures describing complexes formed by eukaryotic ERH proteins and several small peptides from various partners have highlighted the existence of different binding sites on the surface of ERH proteins. In this issue of The FEBS Journal, Wang et al. present the crystal structure of the complex formed between the human ERH protein and a short peptide of the CIZ1 protein, one of its partners. Altogether, this information will be particularly important for future studies aimed at dissecting the different biological functions governed by this family of highly conserved proteins. Comment on: https://doi.org/10.1111/febs.16611.

Molecular basis for the recognition of CIZ1 by ERH

Enhancer of rudimentary homologue (ERH), a small protein conserved in eukaryotes, is involved in a wide spectrum of cellular events, including cell cycle progression, piRNA biogenesis, miRNA maturation and gene expression. Human ERH is recruited to replication foci by CDKN1A-interacting zinc finger protein 1 (CIZ1), and plays an important role in cell growth control. However, the molecular basis for CIZ1 recognition by ERH remains unknown. By using GST pull-down experiment, we found that a fragment within CIZ1, upstream of its first zinc finger, is sufficient for binding to ERH. We solved the structure of CIZ1-bound ERH, in which the ERH dimer binds to two CIZ1 fragments to form a 2 : 2 heterotetramer. CIZ1 forms intermolecular antiparallel β-strands with ERH, and its binding surface on ERH is distinct from those of other known ERH-binding ligands. The ERH-CIZ1 interface was further validated by mutagenesis and binding experiments. Our structural study complemented by biochemistry experiments not only provides insights into a previously unidentified ligand-binding mode for ERH but also sheds light on the understanding of evolutionarily conserved roles for ERH orthologs.

Proteomics separates adult-type diffuse high-grade gliomas in metabolic subgroups independent of 1p/19q codeletion and across IDH mutational status

High-grade adult-type diffuse gliomas are malignant neuroepithelial tumors with poor survival rates in combined chemoradiotherapy. The current WHO classification is based on IDH1/2 mutational and 1p/19q codeletion status. Glioma proteome alterations remain undercharacterized despite their promise for a better molecular patient stratification and therapeutic target identification. Here, we use mass spectrometry to characterize 42 formalin-fixed, paraffin-embedded (FFPE) samples from IDH-wild-type (IDHwt) gliomas, IDH-mutant (IDHmut) gliomas with and without 1p/19q codeletion, and non-neoplastic controls. Based on more than 5,500 quantified proteins and 5,000 phosphosites, gliomas separate by IDH1/2 mutational status but not by 1p/19q status. Instead, IDHmut gliomas split into two proteomic subtypes with widespread perturbations, including aerobic/anaerobic energy metabolism. Validations with three independent glioma proteome datasets confirm these subgroups and link the IDHmut subtypes to the established proneural and classic/mesenchymal subtypes in IDHwt glioma. This demonstrates common phenotypic subtypes across the IDH status with potential therapeutic implications for patients with IDHmut gliomas.

Screening the Potential Biomarkers of COVID-19-Related Thrombosis Through Bioinformatics Analysis

A high proportion of critically ill patients with coronavirus disease 2019 (COVID-19) experience thrombosis, and there is a strong correlation between anticoagulant therapy and the COVID-19 survival rate, indicating that common COVID-19 and thrombosis targets have potential therapeutic value for severe COVID-19.Gene expression profiling data were downloaded from Gene Expression Omnibus (GEO), and common differentially expressed genes (co-DEGs) were identified. The potential biological functions of these co-DEGs were explored by functional enrichment analysis, and protein–protein interaction (PPI) networks were constructed to elucidate the molecular mechanisms of the co-DEGs. Finally, hub genes in the co-DEG network were identified, and correlation analysis was performed.We identified 8320 upregulated genes and 7651 downregulated genes from blood samples of COVID-19 patients and 368 upregulated genes and 240 downregulated genes from blood samples of thrombosis patients. The enriched cellular component terms were mainly related to cytosolic ribosomes and ribosomal subunits. The enriched molecular function terms were mainly related to structural constituents of ribosomes and electron transfer activity. Construction of the PPI network and identification of hub genes ultimately confirmed that RPS7, IGF1R, DICER1, ERH, MCTS1, and TNPO1 were jointly upregulated hub genes, and FLNA and PXN were jointly downregulated hub genes.The identification of novel potential biomarkers provides new options for treating COVID-19-related thrombosis and reducing the rate of severe COVID-19.