This is the first comprehensive study to detail changes in chromatin, histone acetylation, and transcription during nitrogen starvation, highlighting the importance of Esa1 and H4Ac in this process.
Abstract
Macroautophagy/autophagy is a process that degrades intracellular components and is strongly triggered by nitrogen starvation (-N). Some ATG (autophagy related) genes are activated at the transcriptional level in nitrogen starvation; however, a full understanding of transcriptional induction and the role of chromatin during this process remains unclear. To address this, we measured the occupancy of RNA polymerase II (Pol II), histone H3, and acetylated H4 (H4Ac) under nutrient-rich and -N conditions by ChIP-seq. We found that most genes are rapidly downregulated within 15-30 min, including ribosomal protein (RP) and biogenesis (RiBi) genes. Meanwhile, genes involved in amino acid (AA) biosynthesis are upregulated, along with many ATG genes. Unexpectedly, RP and RiBi genes were reinduced by 3 hours. Furthermore, many upregulated genes remained active during prolonged starvation. Histones are typically removed from promoters during transcription activation. Consistent with this, we found that most induced genes exhibited histone eviction and increased H4 acetylation at their promoters, suggesting a possible role for histone acetylation in their activation. In line with this, depleting Esa1, an essential H4 histone acetyltransferase, nearly abolished the induction of ribosomal biosynthetic genes and many AA biosynthetic genes. Sustained activation of many genes during prolonged starvation highlights the vital role of transcription in supporting autophagy and cell survival. This is the first comprehensive study to detail changes in chromatin, histone acetylation, and transcription during nitrogen starvation, highlighting the importance of Esa1 and H4Ac in this process.
Together, the findings establish hY3 as a ribosome-bound regulator of translation and stress responses, positioning it as a determinant of cell fate under metabolic stress.
GLORI sequencing is applied to generate single-base resolution transcriptome-wide m6A maps in seven bacterial species to provide a quantitative atlas of bacterial m6A and establish a foundation for understanding its regulatory and evolutionary roles.
Youyue Li, Letong Xu, Na Liu et al.· Cell Reports· 0 citations
Background: Histone 3 lysine 27 tri-methylation (H3K27me3) is a chromatin mark typically associated with transcriptional repression. Histone demethylation, and particularly the removal of H3K27me3, has been linked to abiotic stress tolerance in plants. However, less is known about its role in biotic stress responses. Methods: We exploited immunity-related transcriptomics data combined with chromatin-state data to identify an association between chromatin modifications and plant immunity in Arabidopsis thaliana. We also measured the expression and H3K27me3 levels at immune-responsive loci, at Col-0 and at histone deacetylase mutants. Results: We identified H3K27me3 as a mark correlated with the silencing of defence gene loci. Moreover, we showed that the expression of a subset of flg22-induced genes is repressed by H3K27me3 prior to elicitation, and that expression negatively correlates with the mark upon activation of immunity. Notably, our studies also revealed a role for the H3K27 demethylase REF6 in plant defence. Loss of REF6 allows ectopic H3K27me3 deposition at target genes, revealing that these loci are actively regulated by the demethylase. Conclusions: Our data provide insight into the regulation of plant immune responses through chromatin dynamics.
Evangelia-Niki Pentari, Rory Osborne, A. J. Pardal et al.· Genes· 0 citations
It is shown that Bacteroides instead rely on a different family of RNA-binding proteins, more typical of eukaryotes than bacteria, to survive cold stress, and that these proteins promote survival under the conditions encountered during transmission.
Hyelan Lee, Anubhav Basu, Carin K. Vanderpool· bioRxiv· 0 citations
GCN2 is established as a major sensor mediating the early hepatic response to SAA deprivation, and a transcriptional program essential for maintaining amino acid homeostasis is defined, highlighting a coordinated adaptive response to acute SAA deprivation.
Valérie Carraro, M. Cherpaz, L. Longechamp et al.· Journal of Molecular Biology· 0 citations
Chromatin remodeling plays a central role in regulating plant development and physiology by shaping the gene expression patterns that drive biological processes. Among epigenetic modifications, histone acetylation is particularly relevant as it alters chromatin structure and influences transcriptional activity. MYST-type histone acetyltransferases (HAT) are evolutionarily conserved components of the Nucleosome Acetyltransferase of histone H4 (NuA4) complex, a key regulator that acetylates histones H4, H2A, and the histone variant H2A.Z. Growing evidence supports the presence of a canonical NuA4-C in plants, similar to that described in yeast. In this review, we summarize recent studies that have begun to uncover its broad role in plant biology, highlighting its involvement in diverse processes such as the skoto- to photomorphogenesis switch, chloroplast development, shade avoidance responses, thermomorphogenesis, the vegetative-to-reproductive transition, plant growth, reproduction and hormonal signalling. In addition, we discuss recent advances in understanding the crosstalk of NuA4-C-mediated H4ac and H2A.Z deposition with other chromatin remodeling complexes in plants. Although significant progress has been made, a full understanding of the complex functions remains unavailable. Current evidence indicates that NuA4-C in yeast and TIP60 in humans are central regulators of transcription, acting not only through histone acetylation but also by influencing transcription elongation and RNA splicing, although direct evidence for similar functions in plant NuA4-C still remains limited. This regulatory role might be critical for integrating developmental programs with environmental signalling pathways. While initial insights into the recruitment of NuA4-C to target genes have emerged, further research is needed to clarify how its activity is controlled and modulated in different biological contexts.
María Guillem-Bernal, J. Barrero-Gil, J. A. Jarillo et al.· Journal of Experimental Bota...· 0 citations
