Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis

Abstract

Background: Drought is one of the main consequences of global climate change and this problem is expected to intensify in the future. Resurrection plants evolved the ability to withstand the negative impact of long periods of almost complete desiccation and to recover at rewatering. In this respect, many physiological, transcriptomic, proteomic and genomic investigations have been performed in recent years, however, few epigenetic control studies have been performed on these valuable desiccation-tolerant plants so far.

Results: In the present study, for the first time for resurrection plants we provide evidences about the differential chromatin accessibility of Haberlea rhodopensis during desiccation stress by ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing). Based on gene similarity between species, we used the available genome of the closely related resurrection plant Dorcoceras hygrometricum to identify approximately nine hundred transposase hypersensitive sites (THSs) in H. rhodopensis. The majority of them corresponds to proximal and distal regulatory elements of different genes involved in photosynthesis, carbon metabolism, synthesis of secondary metabolites, cell signalling and transcriptional regulation, cell growth, cell wall, stomata conditioning, chaperons, oxidative stress, autophagy and others. Various types of binding motifs recognized by several families of transcription factors have been enriched from the THSs found in different stages of drought. Further, we used the previously published RNA-seq data from H. rhodopensis to evaluate the expression of transcription factors putatively interacting with the enriched motifs, and the potential correlation between the identified THS and the expression of their corresponding genes.

Conclusions: These results provide a blueprint for investigating the epigenetic regulation of desiccation tolerance in resurrection plant H. rhodopensis and comparative genomics between resurrection and non-resurrection species with available genome information.

Keywords: ATAC-seq; Desiccation tolerance; Epigenetic regulation; Gene expression; Resurrection plants; Transcription factors.

Fig. 1

Extraction of nuclei and amplification of transposase mediated tagged nucleosome DNA from various stages of desiccation in H. rhodopensis. A Stages of desiccation in H. rhodopensis based on photosynthetic performance. Control (C), moderate (D1); severe (D2), and full desiccation (D3). The averaged OJIP curves of fast fluorescence yields from samples for each stage are depicted in different colours. B Horizontal gel electrophoresis for visualization of amplified tagged nucleosome DNA library prior to sequencing. A 2% agarose gel was used for the separation of libraries; along with a 100 bp marker (M) for reference

Fig. 2

ATAC-seq datasets from various stages of desiccation of H. rhodopensis. A Representative TSS plots and heat maps for each desiccation stage, showing number of mapped sequences from the corresponding genes in D. hygrometricum genome. B Histograms of length distribution for mapped sequences in each stage of desiccation. C HCA-heatmap showing the log2 transformed Pearson correlation coefficients of ATAC‐seq replicates from all treatments. Replicates in unstressed state (C, control plants, fresh, watered) are differentially clustered from the samples of stressed plants, which are further grouped based on the level of desiccation stress; samples under severe desiccation (D2, partially dehydrated) and complete desiccation (D3, fully dehydrated) are distinctly separated from those under moderate stress (D1, moderate dehydrated)

Fig. 3

Annotation of peaks from ATAC-seq datasets and motif enrichment in promoters of THSs in different states of desiccation. A The number of peak counts of annotated THSs for each stress stage in H. rhodopensis. Colour bar represents annotation of elements according to their position of the corresponding gene. B Venn diagram illustrating distribution of annotated THSs among stress treatments. C Motif analysis in promoters of THSs found only in control, D1, D2 and D3 state. The names of the interacting transcription factors in database are given on the right panel

Fig. 4

Functional annotation of genes corresponding to identified THSs. A Functionally organized network of the enriched biological processes. Node size represents significance and colour bar shows the connectivity of groups. B Protein classes found in various stages of stress, presented by percentage. C) KEGG pathway enriched in various stress stages, presented by percentage

Fig. 5

Expression of transcription factors related with the enriched motifs during desiccation stress in H. rhodopensis. Heatmap shows the fold change (FC) of peak counts from RNA-seq data under each stress stage compared to control state. The sequences of the motifs enriched from ATAC-seq data under different desiccation conditions are presented on right side of the heatmap

Fig. 6

Correlation analysis between ATAC-seq and RNA-seq data. A Correlation network between peak counts of genes identified by ATAC-seq (blue rectangles) and RNA-seq data (green ovals). Each gene is represented twice, corresponding to peak counts from both analyses. Selected genes from different processes and pathways are presented. B Heat map of FC of peak counts of selected genes under each stress state compared to the control state for both analyses

Fig. 7

THSs and accumulation of transcripts of their corresponding genes. THSs are represented with different symbols in the top left. The log2 fold change (FC) of gene expression in D1, D2 and D3 states, compared to control (fresh state), is presented in a counter clockwise manner for each THS-corresponding gene. The outermost circle denotes the constitutively accessible genes, while the subsequent circles, as indicated in the innermost schematic diagram, represent particular stages of stress