Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Diversity and evolution of chromatin regulatory states across eukaryotes

ABSTRACT: Histone post-translational modifications (hPTMs) are key regulators of chromatin states, influencing gene expression, epigenetic memory, and transposable element repression across eukaryotic genomes. While many hPTMs are evolutionarily conserved, the extent to which the chromatin states they define are similarly preserved remains unclear. Here, we developed a combinatorial indexing ChIP-seq method to simultaneously profile specific hPTMs across diverse eukaryotic lineages, including amoebozoans, rhizarians, discobans, and cryptomonads. Our analyses revealed highly conserved euchromatin states at active gene promoters and gene bodies. In contrast, we observed diverse configurations of repressive heterochromatin states associated with silenced genes and transposable elements, characterized by various combinations of hPTMs such as H3K9me3, H3K27me3 and/or different H3K79 methylations. These findings suggest that while core hPTMs are ancient and broadly conserved, their functional readout has diversified throughout eukaryotic evolution, shaping lineage-specific chromatin landscapes.

INSTRUMENT(S):

ORGANISM(S): Acanthamoeba Castellanii Bigelowiella Natans Nematostella Vectensis Physcomitrella Patens Subsp. Patens (moss) Guillardia Theta Saccharomyces Cerevisiae (baker's Yeast) Arabidopsis Thaliana (mouse-ear Cress) Naegleria Gruberi Tetrahymena Thermophila Creolimax Fragrantissima Dictyostelium Discoideum (slime Mold) Spizellomyces Punctatus

SUBMITTER: Cristina Chiva

LAB HEAD: Arnau Sebé-Pedrós

PROVIDER: PXD069944 | Pride | 2026-04-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	2025MH000_CRNA_001b_01_45pto_DDA.raw	Raw
	2025MH000_CRNA_002b_01_45pto_DDA.raw	Raw
	2025MH000_CRNA_003b_01_45pto_DDA.raw	Raw
	2025MH000_CRNA_Nvec-second.pdResult	Other
	2025MZ000_CRNA_001B_01_45pto_DDA.raw	Raw

Items per page:

1 - 5 of 49

Similar Datasets

A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution

Project description:Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites

2022-08-12 | PXD031991 | Pride

Improved Mass Spectrometry-based methods to study histone propionylation

Project description:Histone post-translational modifications (PTMs) have crucial roles in a multitude of cellular processes, their aberrant levels have been linked with numerous diseases, including cancer. Although histone PTM investigations have focused so far on methylations and acetylations, alternative long-chain acylations emerged as new dimension, as they are linked to cellular metabolic states and affect gene expression through mechanisms distinct from those regulated by acetylation. Mass spectrometry (MS) is the most powerful, comprehensive and unbiased method to study histone PTMs. Typical protocols for histone PTM analysis do not allow identification of naturally occurring propionylation and butyrylation. Here, we present improved state-of-the-art sample preparation and analysis protocols to quantitate these classes of modifications. After testing different derivatization methods coupled to protease digestion, we profiled common histone PTMs and histone acylations in seven mouse tissues and human normal and tumor breast clinical samples, obtaining a map of propionylations and butyrylations found in different tissue contexts. A quantitative histone PTM analysis also revealed a contribution of histone acylations in discriminating different tissues and breast cancer samples from the normal counterpart.

2024-07-11 | PXD050362 | Pride

NSD2 is upregulated by high-risk HPV E6/E7 and modulates epithelial differentiation in HPV-associated Head and Neck Cancer

Project description:Epigenetic alterations are a key hallmark of cancer and are increasingly recognized as promising clinical biomarkers and therapeutic targets. Head and Neck Squamous Cell Carcinomas (HNSCC) are classified into two subtypes: HPV-positive (HPV+), driven by human papillomavirus (HPV) infections, and the HPV-negative (HPV-), associated with environmental risk factors. Although exhibiting distinct molecular and clinicopathological features, both subtypes lack effective, tailored therapies. Profiling their epigenetic landscape could thus have important clinical implications. In this study, we employed a quantitative mass spectrometry approach to profile histone post-translational modification (hPTMs) in HPV+ and HPV- HNSCC.

2026-02-20 | PXD064152 | Pride

Activation of endogenous retroviruses and induction of viral mimicry by MEK1/2 inhibition in pancreatic cancer

Project description:While pancreatic ductal adenocarcinomas (PDAC) are addicted to KRAS-activating mutations, inhibitors of downstream effectors in the KRAS pathway, such as the clinically approved MEK1/2 kinases inhibitor Trametinib, are devoid of significant therapeutic effects. Nevertheless, the extensive rewiring of regulatory circuits driven by the attenuation of the KRAS pathway can induce novel functional states and vulnerabilities of potential therapeutic relevance. Here, we performed a quantitative histone post-translatinal modification analysis of PDAC cells in the initial hours after MEK1/2 inhibition by Trametinib.

2024-06-16 | PXD043559 | Pride

Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide

Project description:Histone modifying enzymes depend on the availability of cofactors, with acetyl-CoA being required for lysine acetyltransferase (KAT) activity. The discovery that mitochondrial acyl-CoA producing enzymes are also delivered to the nucleus, suggests that high concentrations of metabolites generated locally may impact acetylation of histones and other nuclear substrates and eventually control gene regulation. Here we show that 2-ketoacid dehydrogenase complexes were stably associated with the Mediator complex in macrophages, thus providing a local supply of acetyl-CoA and increasing the generation of hyper-acetylated histone tails. Nitric oxide (NO), which is produced in large amounts in LPS-stimulated macrophages, inhibited both the activity of 2-ketoacid dehydrogenases and their association with Mediator. Consequently, NO reduced de novo histone acetylation at genomic regions with high acetyl-CoA deposition rates. Our findings indicate that a local supply of acetyl-CoA generated by Mediator-bound 2-ketoacid dehydrogenases is required to maximize acetylation of histone tails at sites of elevated HAT activity.

2024-02-14 | PXD040937 | Pride

Mammalian H4K16ac regulates the spatiotemporal order of genome replication rather than gene expression

Project description:Histone acetylation is widely assumed to directly instruct gene activation. Among acetylated residues, H4K16ac is one of the most abundant modifications, conserved across all eukaryotes. Here we analyzed histone PTM profiles in MSL KO and HDAC inhibitor-treated cells.

2025-09-29 | PXD066155 | Pride

Unperturbed dormancy recording reveals stochastic awakening strategies in endocrine treated breast cancer cells

Project description:Hormone dependent breast cancer (HDBC) is the most commonly diagnosed tumor type in women. Adjuvant endocrine therapies (ET) have been the cornerstone in the clinical management of HDBC patients for over forty years. A vast proportion of HDBC patients incur long periods of clinical dormancy following ET, with tumour awakening appearing at a steady pace for up to 25 years (Pan et al., 2017). Extensive genomic studies have demonstrated that 15-30% of clinical relapses develop recurrent genomic changes which contribute to drug resistance (i.e. ESR1 activating mutations) (Bertucci et al., 2019; Magnani et al., 2017; Razavi et al., 2018). However, even in these cases, there is no conclusive evidence around the pre-existence vs. de novo nature of these events. Here, we analyzed histone PTMs in dormant and awakened breast cancer cells treated with endocrine therapy.

2024-05-23 | PXD038030 | Pride

Multi-acetylated histones are a source of carbon for lipid synthesis

Project description:Histone modifications commonly integrate environmental stimuli to cellular metabolic outputs by affecting gene expression. Many modifications, including some histone acetylation marks, do not always correlate to transcription, thus pointing towards an alternative role of histone modifications as potential metabolic reservoirs. Using an approach that integrates mass spectrometry- based epi-proteomics and metabolomics with stable isotope tracer studies, we demonstrate that elevated lipids in histone acetyltransferase (HAT)-depleted hepatocytes result from carbon atoms flowing from the deacetylation of multi-acetylated histone H4 to fatty acids. Consistent with this, the enhanced lipid synthesis in HAT-depleted hepatocytes is dependent on the activity of histone deacetylases (HDACs) and acetyl-CoA synthetase ACSS2. Furthermore, we show that during diet-induced lipid synthesis there is a reduction of multi-acetylated histone H4 in hepatocytes and in mouse liver. In addition, overexpression of histone acetyltransferases can reverse diet-induced lipogenesis by blocking lipid droplet accumulation and maintaining the levels of multi-acetylated histone H4. This study unveils an additional link between epigenetics and metabolism whereby histone acetylation reservoirs may serve as a carbon source for lipid synthesis.

2024-02-14 | PXD042624 | Pride

Metabolic and age-associated epigenetic barriers during direct reprogramming of mouse fibroblasts into induced cardiomyocytes

Project description:Heart disease is the leading cause of mortality in developed countries. Although conventional treatments exist, novel regenerative procedures are warranted for improving patients well fare. The use of direct cardiac conversion (DCC) of fibroblasts by the expression of the cardiogenic factors Mef2c, Gata4, and Tbx5 (MGT) can create induced cardiomyocytes (iCMs). Besides holding great promise, DCC lacks clinical effectiveness especially in adult cells, and the impact of metabolic and age-associated epigenetic barriers remains elusive. Here we demonstrate by histone PTMs analysis that DCC triggers major alterations in the epigenetic landscape, which differ with age. Moreover, we show that metabolic modulation in vitro and dietary manipulations in vivo that improves DCC efficiency are accompanied by significant alterations in the histone acetylation and methylation landscape

2025-01-15 | PXD046542 | Pride

Histone post-translational modifications of Leishmania braziliensis

Project description:Eukaryotic cells have natural resources to maintain their biological activities for the organism. Epigenetics is one of these mechanisms, which plays a fundamental role in the regulation of gene expression, cell cycle progression, DNA repair, etc. Epigenetic control of gene expression occurs when chemical groups are added to some histone amino acids, resulting in dynamic changes in the structure and organization of chromatin, besides being recruiters of protein complexes. Recently, our group described the global map of post-translational modifications of histone (hPTMs) of Trypanosoma cruzi, showing that, despite being unicellular eukaryotes with a characteristic post-transcriptional gene expression, their chromatin is complex with an abundant and variable number of hPTMs. In this work, we describe, the first comprehensive and high-confidence global map, of the hPTMs of Leishmania braziliensis, the etiologic agent of leishmaniasis, distributed in all canonical and some variants.

2025-09-26 | PXD064463 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data