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ChlamytinaTool: An Integrative Epigenomic Platform for Investigating Stress Adaption in Chlamydomonas reinhardtii

Álvarez González, Ana; Fernández Roces, Víctor; Krela, Rafał; Mozgova, Iva; Fraga, Mario; Meijón, Mónica; Valledor, Luis

Publisher
Zenodo
DOI
10.5281/zenodo.17073919
Repository
zenodo.org
Language
en

Abstract

Algal species are frequently exposed to suboptimal environmental conditions that impede their growth and development. Epigenetic mechanisms, such as histone modifications, DNA methylation, and chromatin remodelling, has been identified as key regulators in coordinating stress responses and adaptative process. However, the interplay between epigenomic, transcriptomic, and proteomic layers remains poorly understood. To overcome this limitation, we developed ChlamytinaTool, an integrative platform that compiles epigenomic data from the algal model species Chlamydomonas reinhardtii, including chromatin immunoprecipitation coupled to next generation sequencing (ChIP-seq), whole genome bisulfite (WGBS), methylated DNA precipitation (MeDIP-seq), and micrococcal nuclease digestion (MNase-seq). Using ChromHMM software, we generated a new universal chromatin states model based on eleven epigenetic marks: histone modifications (H3K4me3, H3K4me2, H3K9me3, H3K36me3, H3K27me3 and H3K27ac), DNA methylation (5mC and 6mA), nucleosome positioning, RNA polymerase II and PSR1 transcription factor. ChlamytinaTool enabled the integration of epigenetic marks and chromatin states with transcriptomic and proteomic data, offering new insights into regulatory mechanisms underlying stress adaptation. By combining a previously generated proteomic dataset characterizing C. reinhardtii response to combined heat and drought stress, we identified key molecular genes activated under simultaneous stress conditions, uncovering adaptive responses and potential trade-offs. To validate these in silico findings, we applied a ChIP protocol coupled with MNase digestion and qPCR. Results revealed dynamic changes in the H3K4me3 mark under combined heat and drought stress conditions, highlighting its role in activating stress-responsive genes. This study emphasizes the relevance of integrating epigenomic data into stress biology, providing novel insights into the molecular mechanisms of environmental adaptation.

Full text

Expression 0.00 0.01 0.02 0.03 0.0 0.2 0.4 0.6 0.8 1.0 N-TERMINAL ACETYLTRANSFERASE (NAT1) MITOCHONDRIAL F1F0 ATP SYNTHASE (ATP12) DEAD BOX ATP-DEPENDENT RNA HELICASE (HEL12) CHAPERONIN 60C (CPN60C) H3K4me3 Promoter First exons 2-ΔCt Enrichment **** Expression 0.00 0.01 0.02 0.03 0.04 0.0 0.2 0.4 0.6 0.8 1.0 H3K4me3 Promoter First exons 2-ΔCt Enrichment *** *** Expression 0.00 0.02 0.04 0.06 0.0 0.2 0.4 0.6 0.8 1.0 H3K4me3 Promoter First exons 2-ΔCt Enrichment ** *** *** Expression 0.00 0.005 0.010 0.015 0.0 0.2 0.4 0.6 H3K4me3 Promoter First exons 2-ΔCt Enrichment **** *** controlRT-qPCR: stress controlMNase-ChIP-qPCR: stress *0.05 ≥ p > 0.01 ** 0.01 ≥ p > 0.001 *** 0.001 ≥ p 5 h 24 h 72 h 120 h 2 5 36 154 20 21 10 24 1 1 15 33 1 A Universe background EPIGENETIC MARKS Differential background PSR1 0 h 5 h 24 h 120 h H3K27me3 H3K36me3 RNApol II H3K27ac H3K4me3 6mA H3K9me3 72 h 0 h 5 h 24 h 120 h72 h H3K4me2 nucleosome 5mC active repressive nucleosome enrichment no enrichment enrichment no enrichment C Universe background CHROMATIN STATES Differential background 0 h CS 1 CS 2 CS 3 CS 4 CS 5 CS 6 CS 7 CS 8 CS 9 CS 10 CS 11 CS 12 CS 13 CS 14 CS 15 CS 16 CS 17 CS 18 CS 19 CS 20 CS 21 CS 22 CS 23 5 h 24 h 120 h72 h 0 h 5 h 24 h 120 h72 h active repressive bivalent low signal quiescent D B Amino acid metabolism Carbohydrate metabolism Cell division Cellular respiration Chromatin organisation Coenzyme metabolism Cytoskeleton organisation DNA damage response External stimuli response Lipid metabolism Multi−process regulation Nucleotide metabolism Nutrient uptake Photosynthesis Polyamine metabolism Protein biosynthesis Protein homeostasis Protein modification Protein translocation Redox homeostasis Secondary metabolism Vesicle trafficking Regulation Upregulated Downregulated Protein count 10 20 30 40 E