Eukaryotic chromatin consisting of nucleosomes connected by linker DNA is organized into higher order structures, which is facilitated by linker histone H1. Formation of chromatin compacts and protects the genome, but also hinders DNA transactions. Cells have evolved mechanisms to modify/remodel chromatin resulting in chromatin states suitable for genome functions. The high mobility group box (HMGB) proteins are non-histone chromatin architectural factors characterized by one or more HMGB motifs that bind DNA in a sequence nonspecific fashion. They play a major role in chromatin dynamics. The Saccharomyces cerevisiae (yeast hereafter) HMGB protein Hmo1 contains two HMGB motifs. However, unlike a canonical HMGB protein that has an acidic C-terminus, Hmo1 ends with a lysine rich, basic, C-terminus, resembling linker histone H1. Hmo1 exhibits characteristics of both HMGB proteins and linker histones in its multiple functions. For instance, Hmo1 promotes transcription by RNA polymerases I and II like canonical HMGB proteins but makes chromatin more compact/stable like linker histones. Recent studies have demonstrated that Hmo1 destabilizes/disrupts nucleosome similarly as other HMGB proteins in vitro and acts to maintain a common topological architecture of genes in yeast genome. This minireview reviews the functions of Hmo1 and the underlying mechanisms, highlighting recent discoveries.

Diamond-Blackfan anemia (DBA) is a rare genetic disorder affecting the bone marrow\'s ability to produce red blood cells, leading to severe anemia and various physical abnormalities. Approximately 75% of DBA cases involve heterozygous mutations in ribosomal protein (RP) genes, classifying it as a ribosomopathy, with RPS19 being the most frequently mutated gene. Non-RP mutations, such as in GATA1, have also been identified. Current treatments include glucocorticosteroids, blood transfusions, and hematopoietic stem cell transplantation (HSCT), with HSCT being the only curative option, albeit with challenges like donor availability and immunological complications. Gene therapy, particularly using lentiviral vectors and CRISPR/Cas9 technology, emerges as a promising alternative. This review explores the potential of gene therapy, focusing on lentiviral vectors and CRISPR/Cas9 technology in combination with non-integrating lentiviral vectors, as a curative solution for DBA. It highlights the transformative advancements in the treatment landscape of DBA, offering hope for individuals affected by this condition.

Although alternative splicing (AS) is a major mechanism that adds diversity to gene expression patterns, its precise role in generating variability in ribosomal proteins, known as ribosomal heterogeneity, remains unclear. The ribosomal protein S24 (RPS24) gene, encoding a ribosomal component, undergoes AS; however, in-depth studies have been challenging because of three microexons between exons 4 and 6. We conducted a detailed analysis of RPS24 AS isoforms using a direct approach to investigate the splicing junctions related to these microexons, focusing on four AS isoforms. Each of these isoforms showed tissue specificity and relative differences in expression among cancer types. Significant differences in the proportions of these RPS24 AS isoforms between cancerous and normal tissues across diverse cancer types were also observed. Our study highlighted a significant correlation between the expression levels of a specific RPS24 AS isoform and the epithelial-mesenchymal transition process in lung and breast cancers. Our research contributes to a better understanding of the intricate regulatory mechanisms governing AS of ribosomal protein genes and highlights the biological implications of RPS24 AS isoforms in tissue development and tumorigenesis.

Transcriptional noise is proposed to participate in cell fate changes, but contributions to mammalian cell differentiation systems, including cancer, remain associative. Cancer evolution is driven by genetic variability, with modulatory or contributory participation of epigenetic variants. Accumulation of epigenetic variants enhances transcriptional noise, which can facilitate cancer cell fate transitions. Acute myeloid leukaemia (AML) is an aggressive cancer with strong epigenetic dependencies, characterized by blocked differentiation. It constitutes an attractive model to probe links between transcriptional noise and malignant cell fate regulation. Gcn5/KAT2A is a classical epigenetic transcriptional noise regulator. Its loss increases transcriptional noise and modifies cell fates in stem and AML cells. By reviewing the analysis of KAT2A-depleted pre-leukaemia and leukaemia models, I discuss that the net result of transcriptional noise is diversification of cell fates secondary to alternative transcriptional programmes. Cellular diversification can enable or hinder AML progression, respectively, by differentiation of cell types responsive to mutations, or by maladaptation of leukaemia stem cells. KAT2A-dependent noise-responsive genes participate in ribosome biogenesis and KAT2A loss destabilizes translational activity. I discuss putative contributions of perturbed translation to AML biology, and propose KAT2A loss as a model for mechanistic integration of transcriptional and translational control of noise and fate decisions. This article is part of a discussion meeting issue \'Causes and consequences of stochastic processes in development and disease\'.

Diamond-Blackfan anemia (DBA) was the first ribosomopathy described in humans. DBA is a congenital hypoplastic anemia, characterized by macrocytic aregenerative anemia, manifesting by differentiation blockage between the BFU-e/CFU-e developmental erythroid progenitor stages. In 50 % of the DBA cases, various malformations are noted. Strikingly, for a hematological disease with a relative erythroid tropism, DBA is due to ribosomal haploinsufficiency in 24 different ribosomal protein (RP) genes. A few other genes have been described in DBA-like disorders, but they do not fit into the classical DBA phenotype (Sankaran et al., 2012; van Dooijeweert et al., 2022; Toki et al., 2018; Kim et al., 2017 [1-4]). Haploinsufficiency in a RP gene leads to defective ribosomal RNA (rRNA) maturation, which is a hallmark of DBA. However, the mechanistic understandings of the erythroid tropism defect in DBA are still to be fully defined. Erythroid defect in DBA has been recently been linked in a non-exclusive manner to a number of mechanisms that include: 1) a defect in translation, in particular for the GATA1 erythroid gene; 2) a deficit of HSP70, the GATA1 chaperone, and 3) free heme toxicity. In addition, p53 activation in response to ribosomal stress is involved in DBA pathophysiology. The DBA phenotype may thus result from the combined contributions of various actors, which may explain the heterogenous phenotypes observed in DBA patients, even within the same family.

The unicellular yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe are widely used eukaryotic model organisms. Research exploiting the tractability of these model systems has contributed significantly to our understanding of a wide range of fundamental processes. In this article, we outline the features of yeast that have similarly been exploited for undergraduate research training. We selected examples from published literature that demonstrate the utility of the yeast system for research-based learning embedded in the curriculum. We further describe a project which we designed for the team-based final-year dissertation projects module on our transnational joint programme, which investigates whether the expression and functions of the budding yeast RPL36 ribosomal protein paralogs are influenced by the overlapping long non-coding RNA genes. Students carry out the experimental procedures in a 2-week timetabled teaching block and exercise widely applicable biochemical techniques, including aseptic yeast cell culture and sample collection, RNA isolation, qRT-PCR quantitation, protein extraction and Western blot analysis, and cell cycle progression patterns using light microscopy and flow cytometry. It is challenging to design training programmes for undergraduates that are meaningful as well as practical and economical, but it is possible to transform active research projects into authentic research experiences. We consider yeast to be an ideal model organism for such projects. These can be adapted to the constraints of course schedules and explore fundamental biochemical topics which are evolutionarily conserved from yeast to mammals.

Eggs laid by mature female schistosomes are primarily responsible for the pathogenesis of schistosomiasis and critical for transmission. Consequently, elucidating the mechanism of sexual maturation as well as egg production may lead to new strategies for the control of schistosomiasis. MicroRNAs (miRNAs) are involved in multiple biological processes including reproduction in many organisms, yet their roles have not been well characterized in schistosomes. Here, we investigated microRNA-1 (miR-1), which was downregulated gradually in both male and female Schistosoma japonicum after they reached sexually maturity. The expression of miR-1, as shown with quantitative reverse transcription PCR (qRT-PCR), was lower in the reproductive organs of adult females compared with the somatic tissues. Overexpression of miR-1 in adult worms destroyed the morphological architecture of reproductive organs and reduced the subsequent oviposition, which may be due to the activation of apoptosis pathways. Through in silico analysis, 34 potential target genes of miR-1 were identified, including five ribosomal protein genes, called rp-s13, rp-l7ae, rp-l14, rp-l11 and rp-s24e. In vitro dual-luciferase reporter gene assays and miRNA overexpression experiments further validated that these ribosomal protein genes were directly regulated by miR-1. In contrast to the gene expression of miR-1, qRT-PCR and in situ hybridization experiments demonstrated these ribosomal protein genes were enriched in the sexual organs of adult females. Using RNA interference to silence the ribosomal protein genes in different developmental stages in a mouse model system, we demonstrated that these miR-1 target genes not only participated in the reproductive development of S. japonicum, but also were required for the growth and survival of the parasite in the early developmental stages. Taken together, our data suggested that miR-1 may affect the growth, reproduction and oviposition of S. japonicum by targeting the ribosomal protein genes, which provides insights for exploration of new anti-schistosome strategies.

RNA polymerase II (RNA Pol II) has been recognized as a passively regulated multi-subunit holoenzyme. However, the extent to which RNA Pol II subunits might be important beyond the RNA Pol II complex remains unclear. Here, fractions containing disassociated RPB3 (dRPB3) were identified by size exclusion chromatography in various cells. Through a unique strategy, i.e., \"specific degradation of disassociated subunits (SDDS),\" we demonstrated that dRPB3 functions as a regulatory component of RNA Pol II to enable the preferential control of 3\' end processing of ribosomal protein genes directly through its N-terminal domain. Machine learning analysis of large-scale genomic features revealed that the little elongation complex (LEC) helps to specialize the functions of dRPB3. Mechanistically, dRPB3 facilitates CBC-PCF11 axis activity to increase the efficiency of 3\' end processing. Furthermore, RPB3 is dynamically regulated during development and diseases. These findings suggest that RNA Pol II gains specific regulatory functions by trapping disassociated subunits in mammalian cells.

BACKGROUND: Thrombosis directly affects the quality of life with increased mortality. The RPL5 (L5) gene on intron 6 on chromosome 1p22, rs6604026 is associated with multiple sclerosis risk, whereas RPL9 (L9) on 8 exons on chromosome 4p14 has been documented so far as being an essential involvement in the proliferation of protein synthesized cells mostly by gene products.
OBJECTIVE: The aim of this work was to assess genetic variants of RPL5 and RPL9 and thrombosis to characterize their role in the diagnosis of thrombosis among the Saudi population.
METHODS: The cross-sectional study involved 100 Saudi patients diagnosed with thrombosis (arterial or venous) in 50 healthy individuals as controls in the same age and sex groups. Primers were designed RPL5 and RPL9 for molecular analysis. The Sanger System ABI-3730xL (Hong Kong) automatic sequencing was used for DNA sequencing. Statistical analysis was performed using the Prism 5 and SPSS version-21 programs.
RESULTS: The male / female age ratio was 66.7 / 57.4, and the mean age was 61.2 years. Most of the patients were self-identifiable and without a previous history of thrombosis (61.0%). Most of the patients had just been diagnosed, that is, in the last five years (74.0%), about 43% of the patients underwent treatment using combination therapy (Aspirin and oral anticoagulants). New gene variants of RPL5 (5 SNPs) and RPL9 (9 SNPs) were detected in Saudi thrombotic patients.
CONCLUSIONS: Mutations in RPL5 and RPL9 were reported in all thrombotic patients, represented by a new variant of the ribosomal protein gene and correlated with thrombosis in the Saudi population. These results may reflect an association between the ribosomal protein SNP gene and the incidence and progression of thrombosis in the Saudi population.

BACKGROUND: Our previous studies have revealed the roles of ribosomal protein (RP) genes in the abiotic stress responses of rice.
METHODS: In the current investigation, we examine the possible involvement of these genes in insect stress responses. We have characterized the RP genes that included both Ribosomal Protein Large (RPL) and Ribosomal Protein Small (RPS) subunit genes in response to infestation by two economically important insect pests, the brown planthopper (BPH) and the Asian rice gall midge (GM) in rice. Differential transcript patterns of seventy selected RP genes were studied in a susceptible and a resistant genotype of indica rice: BPT5204 and RPNF05, respectively. An in silico analyses of the upstream regions of these genes also revealed the presence of cis-elements that are associated with wound signaling.
RESULTS: We identified the genes that were up or downregulated in either one of the genotypes, or both of them after pest infestation. The transcript patterns of a majority of the genes were found to be temporally-regulated by both the pests. In the resistant RPNF05, BPH infestation activated RPL15, L51 and RPS5a genes while GM infestation induced RPL15, L18a, L22, L36.2, L38, RPS5, S9.2 and S25a at a certain point of time. These genes that were particularly upregulated in the resistant genotype, RPNF05, but not in BPT5204 suggest their potential involvement in plant resistance against either of the two pests studied.
CONCLUSIONS: Taken together, RPL15, L51, L18a, RPS5, S5a, S9.2, and S25a appear to be the genes with possible roles in insect resistance in rice.