Molecular double clips within RepID WD40 domain control chromatin binding and CRL4-substrate assembly

RepID depletion enhances TWS119-induced erythropoiesis through chromatin reprogramming and transcription factor recruitment

BACKGROUND

Erythrocytes, derived from hematopoietic stem cells, are essential for oxygen transport, ensuring survival in all vertebrate animals. The process of erythropoiesis is associated with gene expression changes, but many key regulatory factors that govern erythroid differentiation remain to be fully understood.

OBJECTIVE

This study investigates the role of TWS119, a known GSK3β inhibitor, in inducing erythropoiesis in K562 erythroleukemia cells and explores the impact of Replication initiation determinant protein (RepID) depletion on the process.

METHODS

K562 cells were treated with TWS119 and erythropoiesis markers including various erythrocytic phenotypes were assessed. Chromatin-immunoprecipitation analysis was employed to examine the changes in chromatin structure and gene expression regulation. The impact of RepID depletion on TWS119-induced erythropoiesis was also evaluated by analyzing globin promoter euchromatinization and NRF2 binding.

RESULTS

TWS119 treatment led to erythrocytic phenotypes in K562 cells, such as red pellet formation, enucleation, and nucleus condensation, along with the upregulation of erythropoiesis markers. Furthermore, RepID depletion accelerated TWS119-mediated erythropoiesis. Chromatin-immunoprecipitation analysis revealed euchromatinization of the globin promoter and enhanced NRF2 binding in RepID-depleted cells, suggesting a mechanism of gene expression regulation during erythropoiesis.

CONCLUSION

This study demonstrates that TWS119 can induce erythropoiesis in K562 cells, and that RepID depletion enhances this process by modulating chromatin structure and facilitating transcription factor binding. These findings highlight a RepID-dependent mechanism in the regulation of gene expression during erythropoiesis.

GWAS identifies novel loci linked to seedling growth traits in highly diverse barley population under drought stress

Climate changes refer to long-term shifts in temperature and weather patterns that may cause drought, one of the major stresses hindering seed germination, plant growth, and crop productivity. Barley (Hordeum vulgare L) is considered one of the most drought-stress-tolerant cereals and may be used for elucidating genes for drought tolerance at seed germination and seedling stages that would pave the way toward improving the performance of all cereals. The current study was performed at IPK-Gatersleben (Germany) in 2023. Our aim was to explore the genetic basis of germination and seedling traits under drought stress (20% PEG6000 treatment) in a 198 global spring barley collection genotyped with 38,632 SNPs via Genotyping by Sequencing (GBS). The drought treatment significantly reduced the seed germination parameters and seedling traits in the genotypes of a global barley collection. Drought tolerance indices (DTI) for the measured germination and seedling traits indicate delayed and lower germination speed under drought stress than the control. The shoot fresh weight was the most affected trait, with a DTI of 37.4, followed by the seedling fresh weight SDLFW (DTI = 46.3) and root fresh weight (DTI = 47). In contrast, the root length DTI was the least affected trait by drought (78.2), followed by RDW DTI (72.8). GWAS was conducted using single-locus (CMLM) and multi-locus models (MLMM, Farm-CPU, BLINK), with significant marker-trait associations determined at -log10 (1.29E-06) ≥ 5.88. In our present study, we identified 79 highly significant SNPs distributed across the seven barley chromosomes related to the germination and seedling growth parameters under both control and drought conditions. Gene annotation of these highly significant SNPs revealed that 35 SNPs were in the exonic regions of genes that play roles in important plant biological and physiological processes. Further analysis exhibited 35 high-confidence candidate genes influencing barley germination and seedling growth under control and drought conditions. These genes represent promising targets for breeding and genetic enhancement efforts to improve drought tolerance in barley, potentially extending these benefits to other cereal crops.

Genome-wide identification and analysis of WD40 proteins reveal that NtTTG1 enhances drought tolerance in tobacco (Nicotiana tabacum)

BACKGROUND

WD40 proteins, which are highly prevalent in eukaryotes, play important roles in plant development and stress responses. However, systematic identification and exploration of WD40 proteins in tobacco have not yet been conducted.

RESULTS

In this study, a total of 399 WD40 regulatory genes were identified in common tobacco (Nicotiana tabacum). Gene structure and motif analysis revealed structural and functional diversity among different clades of tobacco WD40 regulatory genes. The expansion of tobacco WD40 regulatory genes was mainly driven by segmental duplication and purifying selection. A potential regulatory network of NtWD40s suggested that NtWD40s might be regulated by miRNAs and transcription factors in various biological processes. Expression pattern analysis via transcriptome analysis and qRT-PCR revealed that many NtWD40s exhibited tissue-specific expression patterns and might be involved in various biotic and abiotic stresses. Furthermore, we have validated the critical role of NtTTG1, which was located in the nuclei of trichome cells, in enhancing the drought tolerance of tobacco plants.

CONCLUSIONS

Our study provides comprehensive information to better understand the evolution of WD40 regulatory genes and their roles in different stress responses in tobacco.

RepID represses megakaryocytic differentiation by recruiting CRL4A-JARID1A at DAB2 promoter

BACKGROUND

Megakaryocytes (MKs) are platelet precursors, which arise from hematopoietic stem cells (HSCs). While MK lineage commitment and differentiation are accompanied by changes in gene expression, many factors that modulate megakaryopoiesis remain to be uncovered. Replication initiation determinant protein (RepID) which has multiple histone-code reader including bromodomain, cryptic Tudor domain and WD40 domains and Cullin 4-RING E3 ubiquitin ligase complex (CRL4) recruited to chromatin mediated by RepID have potential roles in gene expression changes via epigenetic regulations. We aimed to investigate whether RepID-CRL4 participates in transcriptional changes required for MK differentiation.

METHODS

The PCR array was performed using cDNAs derived from RepID-proficient or RepID-deficient K562 erythroleukemia cell lines. Correlation between RepID and DAB2 expression was examined in the Cancer Cell Line Encyclopedia (CCLE) through the CellMinerCDB portal. The acceleration of MK differentiation in RepID-deficient K562 cells was determined by estimating cell sizes as well as counting multinucleated cells known as MK phenotypes, and by qRT-PCR analysis to validate transcripts of MK markers using phorbol 12-myristate 13-acetate (PMA)-mediated MK differentiation condition. Interaction between CRL4 and histone methylation modifying enzymes were investigated using BioGRID database, immunoprecipitation and proximity ligation assay. Alterations of expression and chromatin binding affinities of RepID, CRL4 and histone methylation modifying enzymes were investigated using subcellular fractionation followed by immunoblotting. RepID-CRL4-JARID1A-based epigenetic changes on DAB2 promoter were analyzed by chromatin-immunoprecipitation and qPCR analysis.

RESULTS

RepID-deficient K562 cells highly expressing MK markers showed accelerated MKs differentiation exhibiting increases in cell size, lobulated nuclei together with reaching maximum levels of MK marker expression earlier than RepID-proficient K562 cells. Recovery of WD40 domain-containing RepID constructs in RepID-deficient background repressed DAB2 expression. CRL4A formed complex with histone H3K4 demethylase JARID1A in soluble nucleus and loaded to the DAB2 promoter in a RepID-dependent manner during proliferation condition. RepID, CRL4A, and JARID1A were dissociated from the chromatin during MK differentiation, leading to euchromatinization of the DAB2 promoter.

CONCLUSION

This study uncovered a role for the RepID-CRL4A-JARID1A pathway in the regulation of gene expression for MK differentiation, which can form the basis for the new therapeutic approaches to induce platelet production. Video Abstract.

RepID represses megakaryocytic differentiation by recruiting CRL4A-JARID1A at DAB2 promoter

Background Megakaryocytes (MKs) are platelet precursors, which arise from hematopoietic stem cells (HSCs). While MK lineage commitment and differentiation are accompanied by changes in gene expression, many factors that modulate megakaryopoiesis remain to be uncovered. Replication origin binding protein (RepID) which has multiple histone-code reader including bromodomain, cryptic Tudor domain and WD40 domains and Cullin 4-RING ubiquitin ligase complex (CRL4) recruited to chromatin mediated by RepID have potential roles in gene expression changes via epigenetic regulations. We aimed to investigate whether RepID-CRL4 participates in transcriptional changes required for MK differentiation. Methods The PCR array was performed using cDNAs derived from RepID-proficient or RepID-deficient K562 erythroleukemia cell lines. Correlation between RepID and DAB2 expression was examined in the Cancer Cell Line Encyclopedia (CCLE) through the CellMinerCDB portal. The acceleration of MK differentiation in RepID-deficient K562 cells was determined by estimating cell sizes as well as counting multinucleated cells known as MK phenotypes, and by qRT-PCR analysis to validate transcripts of MK markers using phorbol 12-myristate 13-acetate (PMA)-mediated MK differentiation condition. Interaction between CRL4 and histone methylation modifying enzymes were investigated using BioGRID database, immunoprecipitation and proximity ligation assay. Alterations of expression and chromatin binding affinities of RepID, CRL4 and histone methylation modifying enzymes were investigated using subcellular fractionation followed by immunoblotting. RepID-CRL4-JARID1A-based epigenetic changes on DAB2 promoter were analyzed by chromatin-immunoprecipitation and qPCR analysis. Results RepID-deficient K562 cells highly expressing MK markers showed accelerated MKs differentiation exhibiting increases in cell size, lobulated nuclei together with reaching maximum levels of MK marker expression earlier than RepID-proficient K562 cells. Recovery of WD40 domain-containing RepID constructs in RepID-deficient background repressed DAB2 expression. CRL4A formed complex with histone H3K4 demethylase JARID1A in soluble nucleus and loaded to the DAB2 promoter in a RepID-dependent manner during proliferation condition. RepID, CRL4A, and JARID1A were dissociated from the chromatin during MK differentiation, leading to euchromatinization of the DAB2 promoter. Conclusion This study uncovered a role for the RepID-CRL4A-JARID1A pathway in the regulation of gene expression for MK differentiation, which can form the basis for the new therapeutic approaches to induce platelet production.