CTCF shapes chromatin structure and gene expression in health and disease.

CCCTC-binding factor (CTCF) is an eleven zinc finger (ZF), multivalent transcriptional regulator, that recognizes numerous motifs thanks to the deployment of distinct combinations of its ZFs. The great majority of the ~50,000 genomic locations bound by the CTCF protein in a given cell type is intergenic, and a fraction of these sites overlaps with transcriptional enhancers. Furthermore, a proportion of the regions bound by CTCF intersect genes and promoters. This suggests multiple ways in which CTCF may impact gene expression. At promoters, CTCF can directly affect transcription. At more distal sites, CTCF may orchestrate interactions between regulatory elements and help separate eu- and heterochromatic areas in the genome, exerting a chromatin barrier function. In this review, we outline how CTCF contributes to the regulation of the three-dimensional structure of chromatin and the formation of chromatin domains. We discuss how CTCF binding and architectural functions are regulated. We examine the literature implicating CTCF in controlling gene expression in development and disease both by acting as an insulator and a factor facilitating regulatory elements to efficiently interact with each other in the nuclear space.

Shine-Dalgarno Sequences Play an Essential Role in the Translation of Plastid mRNAs in Tobacco.

In prokaryotic systems, the translation initiation of many, though not all, mRNAs depends on interaction between a sequence element upstream of the start codon (the Shine-Dalgarno sequence [SD]) and a complementary sequence in the 3' end of the 16S rRNA (anti-Shine-Dalgarno sequence [aSD]). Although many chloroplast mRNAs harbor putative SDs in their 5' untranslated regions and the aSD displays strong conservation, the functional relevance of SD-aSD interactions in plastid translation is unclear. Here, by generating transplastomic tobacco (Nicotiana tabacum) mutants with point mutations in the aSD coupled with genome-wide analysis of translation by ribosome profiling, we provide a global picture of SD-dependent translation in plastids. We observed a pronounced correlation between weakened predicted SD-aSD interactions and reduced translation efficiency. However, multiple lines of evidence suggest that the strength of the SD-aSD interaction is not the only determinant of the translational output of many plastid mRNAs. Finally, the translation efficiency of mRNAs with strong secondary structures around the start codon is more dependent on the SD-aSD interaction than weakly structured mRNAs. Thus, our data reveal the importance of the aSD in plastid translation initiation, uncover chloroplast genes whose translation is influenced by SD-aSD interactions, and provide insights into determinants of translation efficiency in plastids.

AtRsgA from Arabidopsis thaliana is important for maturation of the small subunit of the chloroplast ribosome.

Plastid ribosomes are very similar in structure and function to the ribosomes of their bacterial ancestors. Since ribosome biogenesis is not thermodynamically favorable under biological conditions it requires the activity of many assembly factors. Here we have characterized a homolog of bacterial RsgA in Arabidopsis thaliana and show that it can complement the bacterial homolog. Functional characterization of a strong mutant in Arabidopsis revealed that the protein is essential for plant viability, while a weak mutant produced dwarf, chlorotic plants that incorporated immature pre-16S ribosomal RNA into translating ribosomes. Physiological analysis of the mutant plants revealed smaller, but more numerous, chloroplasts in the mesophyll cells, reduction of chlorophyll a and b, depletion of proplastids from the rib meristem and decreased photosynthetic electron transport rate and efficiency. Comparative RNA sequencing and proteomic analysis of the weak mutant and wild-type plants revealed that various biotic stress-related, transcriptional regulation and post-transcriptional modification pathways were repressed in the mutant. Intriguingly, while nuclear- and chloroplast-encoded photosynthesis-related proteins were less abundant in the mutant, the corresponding transcripts were increased, suggesting an elaborate compensatory mechanism, potentially via differentially active retrograde signaling pathways. To conclude, this study reveals a chloroplast ribosome assembly factor and outlines the transcriptomic and proteomic responses of the compensatory mechanism activated during decreased chloroplast function.

Subcutaneous implantable cardioverter-defibrillator therapy in Poland: Results of the Polish S-ICD Registry.

BACKGROUND: The use of subcutaneous implantable cardioverter-defibrillators (S-ICD) has been growing in Poland since 2014. The Polish Registry of S-ICD Implantations was run by the Heart Rhythm Section of the Polish Cardiac Society between May 2020 and September 2022 to monitor the implementation of that therapy in Poland. AIMS: To investigate and present the state-of-the-art of S-ICD implantation in Poland. METHODS: Implanting centers reported clinical data of patients undergoing S-ICD implantations and replacements, including age, sex, height, weight, underlying disease, history of pacemaker and defibrillator implantations, indications for S-ICD, electrocardiographical parameters, procedural techniques, and complications. RESULTS: Four hundred and forty patients undergoing S-ICD implantation (411) or replacement (29) were reported by 16 centers. Most patients were in New York Heart Association class II (218 patients, 53%) or I (150 patients, 36.5%). Left ventricular ejection fraction was 10%-80%, median (IQR) was 33% (25%-55%). Primary prevention indications were present in 273 patients (66.4%). Non-ischemic cardiomyopathy was reported in 194 patients (47.2%). The main reason for the choice of S-ICD were: young age (309, 75.2%), risk of infectious complications (46, 11.2%), prior infective endocarditis (36, 8.8%), hemodialysis (23, 5.6%), and immunosuppressive therapy (7, 1.7%). Electrocardiographic screening was performed in 90% of patients. The rate of adverse events was low (1.7%). No surgical complications were observed.

Chromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue.

Neurological disorders (NDs) comprise a heterogeneous group of conditions that affect the function of the nervous system. Often incurable, NDs have profound and detrimental consequences on the affected individuals' lives. NDs have complex etiologies but commonly feature altered gene expression and dysfunctions of the essential chromatin-modifying factors. Hence, compounds that target DNA and histone modification pathways, the so-called epidrugs, constitute promising tools to treat NDs. Yet, targeting the entire epigenome might reveal insufficient to modify a chosen gene expression or even unnecessary and detrimental to the patients' health. New technologies hold a promise to expand the clinical toolkit in the fight against NDs. (Epi)genome engineering using designer nucleases, including CRISPR-Cas9 and TALENs, can potentially help restore the correct gene expression patterns by targeting a defined gene or pathway, both genetically and epigenetically, with minimal off-target activity. Here, we review the implication of epigenetic machinery in NDs. We outline syndromes caused by mutations in chromatin-modifying enzymes and discuss the functional consequences of mutations in regulatory DNA in NDs. We review the approaches that allow modifying the (epi)genome, including tools based on TALENs and CRISPR-Cas9 technologies, and we highlight how these new strategies could potentially change clinical practices in the treatment of NDs.

Utilization of Subcutaneous Cardioverter-Defibrillator in Poland and Europe-Comparison of the Results of Multi-Center Registries.

The implantation of a subcutaneous cardioverter-defibrillator (S-ICD) may be used instead of a traditional transvenous system to prevent sudden cardiac death. Our aim was to compare the characteristics of S-ICD patients from the multi-center registry of S-ICD implantations in Poland with the published results of the European Snapshot Survey on S-ICD Implantation (ESSS-SICDI). We compared data of 137 Polish S-ICD patients with 68 patients from the ESSS-SICDI registry. The groups did not differ significantly in terms of sex, prevalence of ischemic cardiomyopathy, concomitant diseases, and the rate of primary prevention indication. Polish patients had more advanced heart failure (New York Heart Association (NYHA) class III: 11.7% vs. 2.9%, NYHA II: 48.9% vs. 29.4%, NYHA I: 39.4% vs. 67.7%, p < 0.05 each). Young age (75.9% vs. 50%, p < 0.05) and no vascular access (7.3% vs. 0%, p < 0.05) were more often indications for S-ICD. The percentage of patients after transvenous system removal due to infections was significantly higher in the Polish group (11% vs. 1.5%, p < 0.05). In the European population, S-ICD was more frequently chosen because of patients' active lifestyle and patients' preference (both 10.3% vs. 0%, p < 0.05). Our analysis shows that in Poland, compared to other European countries, subcutaneous cardioverters-defibrillators are being implanted in patients at a more advanced stage of chronic heart failure. The most frequent reason for choosing a subcutaneous system instead of a transvenous ICD is the young age of a patient.

Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida.

Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.

Elucidating gene function and function evolution through comparison of co-expression networks of plants.

The analysis of gene expression data has shown that transcriptionally coordinated (co-expressed) genes are often functionally related, enabling scientists to use expression data in gene function prediction. This Focused Review discusses our original paper (Large-scale co-expression approach to dissect secondary cell wall formation across plant species, Frontiers in Plant Science 2:23). In this paper we applied cross-species analysis to co-expression networks of genes involved in cellulose biosynthesis. We showed that the co-expression networks from different species are highly similar, indicating that whole biological pathways are conserved across species. This finding has two important implications. First, the analysis can transfer gene function annotation from well-studied plants, such as Arabidopsis, to other, uncharacterized plant species. As the analysis finds genes that have similar sequence and similar expression pattern across different organisms, functionally equivalent genes can be identified. Second, since co-expression analyses are often noisy, a comparative analysis should have higher performance, as parts of co-expression networks that are conserved are more likely to be functionally relevant. In this Focused Review, we outline the comparative analysis done in the original paper and comment on the recent advances and approaches that allow comparative analyses of co-function networks. We hypothesize that in comparison to simple co-expression analysis, comparative analysis would yield more accurate gene function predictions. Finally, by combining comparative analysis with genomic information of green plants, we propose a possible composition of cellulose biosynthesis machinery during earlier stages of plant evolution.