RNA-Seq Analysis of the Arabidopsis Transcriptome in Pluripotent Calli

Histone modification-dependent production of peptide hormones facilitates acquisition of pluripotency during leaf-to-callus transition in Arabidopsis

Chromatin configuration is critical for establishing tissue identity and changes substantially during tissue identity transitions. The crucial scientific and agricultural technology of in vitro tissue culture exploits callus formation from diverse tissue explants and tissue regeneration via de novo organogenesis. We investigated the dynamic changes in H3ac and H3K4me3 histone modifications during leaf-to-callus transition in Arabidopsis thaliana. We analyzed changes in the global distribution of H3ac and H3K4me3 during the leaf-to-callus transition, focusing on transcriptionally active regions in calli relative to leaf explants, defined by increased accumulation of both H3ac and H3K4me3. Peptide signaling was particularly activated during callus formation; the peptide hormones RGF3, RGF8, PIP1 and PIPL3 were upregulated, promoting callus proliferation and conferring competence for de novo shoot organogenesis. The corresponding peptide receptors were also implicated in peptide-regulated callus proliferation and regeneration capacity. The effect of peptide hormones in plant regeneration is likely at least partly conserved in crop plants. Our results indicate that chromatin-dependent regulation of peptide hormone production not only stimulates callus proliferation but also establishes pluripotency, improving the overall efficiency of two-step regeneration in plant systems.

Insights into plant regeneration: cellular pathways and DNA methylation dynamics

Plants, known for their immobility, employ various mechanisms against stress and damage. A prominent feature is the formation of callus tissue-a cellular growth phenomenon that remains insufficiently explored, despite its distinctive cellular plasticity compared to vertebrates. Callus formation involves dedifferentiated cells, with a subset attaining pluripotency. Calluses exhibit an extraordinary capacity to reinitiate cellular division and undergo structural transformations, generating de novo shoots and roots, thereby developing into regenerated plants-a testament to the heightened developmental plasticity inherent in plants. In this way, plant regeneration through clonal propagation is a widely employed technique for vegetative reproduction. Thus, exploration of the biological components involved in regaining pluripotency contributes to the foundation upon which methods of somatic plant propagation can be advanced. This review provides an overview of the cellular pathway involved in callus and subsequent de novo shoot formation from already differentiated plant tissue, highlighting key genes critical to this process. In addition, it explores the intricate realm of epigenetic regulatory processes, emphasizing the nuanced dynamics of DNA methylation that contribute to plant regeneration. Finally, we briefly discuss somaclonal variation, examining its relation to DNA methylation, and investigating the heritability of epigenomic changes in crops.

Differential expression and co-localization of transcriptional factors during callus transition to differentiation for shoot organogenesis in the water fern Ceratopteris richardii

BACKGROUND AND AIMS

In flowering plants, regeneration can be achieved by a variety of approaches, and different sets of transcriptional factors are involved in these processes. However, regeneration in taxa other than flowering plants remains a mystery. Ceratopteris richardii is a representative fern capable of both direct and indirect organogenesis, and we aimed to investigate the genetics underlying the transition from callus proliferation to differentiation.

METHODS

Morphological and histological analyses were used to determine the type of regeneration involved. RNA sequencing and differential gene expression were used to investigate how the callus switches from proliferation to differentiation. Phylogenetic analysis and RNA in situ hybridization were used to understand whether transcriptional factors are involved in this transition.

KEY RESULTS

The callus formed on nascent leaves and subsequently developed the shoot pro-meristem and shoot meristem, thus completing indirect de novo shoot organogenesis in C. richardii. Genes were differentially expressed during the callus transition from proliferation to differentiation, indicating a role for photosynthesis, stimulus response and transmembrane signalling in this transition and the involvement of almost all cell layers that make up the callus. Transcriptional factors were either downregulated or upregulated, which were generally in many-to-many orthology with genes known to be involved in callus development in flowering plants, suggesting that the genetics of fern callus development are both conserved and divergent. Among them, an STM-like, a PLT-like and an ethylene- and salt-inducible ERF gene3-like gene were expressed simultaneously in the vasculature but not in the other parts of the callus, indicating that the vasculature played a role in the callus transition from proliferation to differentiation.

CONCLUSIONS

Indirect de novo shoot organogenesis could occur in ferns, and the callus transition from proliferation to differentiation required physiological changes, differential expression of transcriptional factors and involvement of the vasculature.

Transcriptional Changes in Damask Rose Suspension Cell Culture Revealed by RNA Sequencing

Damask roses (Rosa x damascena) are widely used in cosmetics and pharmaceutics. Here, we established an in vitro suspension cell culture for calli derived from damask rose petals. We analyzed rose suspension cell transcriptomes obtained at two different time points by RNA sequencing to reveal transcriptional changes during rose suspension cell culture. Of the 580 coding RNAs (1.3%) highly expressed in the suspension rose cells, 68 encoded cell wall-associated proteins. However, most RNAs encoded by the chloroplasts and mitochondria are not expressed. Many highly expressed coding RNAs are involved in translation, catalyzing peptide synthesis in ribosomes. Moreover, the amide metabolic process producing naturally occurring alkaloids was the most abundant metabolic process during the propagation of rose suspension cells. During rose cell propagation, coding RNAs involved in the stress response were upregulated at an early stage, while coding RNAs associated with detoxification and transmembrane transport were upregulated at the late stage. We used transcriptome analyses to reveal important biological processes and molecular mechanisms during rose suspension cell culture. Most non-coding (nc) RNAs were not expressed in the rose suspension cells, but a few ncRNAs with unknown functions were highly expressed. The expression of ncRNAs and their target coding RNAs was highly correlated. Taken together, we revealed significant biological processes and molecular mechanisms occurring during rose suspension cell culture using transcriptome analyses.

Unraveling Epigenetic Changes in A. thaliana Calli: Impact of HDAC Inhibitors

The ability for plant regeneration from dedifferentiated cells opens up the possibility for molecular bioengineering to produce crops with desirable traits. Developmental and environmental signals that control cell totipotency are regulated by gene expression via dynamic chromatin remodeling. Using a mass spectrometry-based approach, we investigated epigenetic changes to the histone proteins during callus formation from roots and shoots of Arabidopsis thaliana seedlings. Increased levels of the histone H3.3 variant were found to be the major and most prominent feature of 20-day calli, associated with chromatin relaxation. The methylation status in root- and shoot-derived calli reached the same level during long-term propagation, whereas differences in acetylation levels provided a long-lasting imprint of root and shoot origin. On the other hand, epigenetic signs of origin completely disappeared during 20 days of calli propagation in the presence of histone deacetylase inhibitors (HDACi), sodium butyrate, and trichostatin A. Each HDACi affected the state of post-translational histone modifications in a specific manner; NaB-treated calli were epigenetically more similar to root-derived calli, and TSA-treated calli resembled shoot-derived calli.

Evaluating Tartary Buckwheat Genotypes with High Callus Induction Rates and the Transcriptomic Profiling during Callus Formation

Due to their complex genotypes, low in vitro regeneration rates, and difficulty in obtaining transgenic plants, studies concerning basic biological research and molecular breeding in Tartary buckwheat (TB) are greatly limited. In this study, the hypocotyls of 60 genotypes of TB (TBC1~60) were used as explants. Of these, TBC14 was selected due to a high callus induction rate of 97.78% under dark and a proliferation coefficient (PC) of 28.2 when cultured on MS medium supplemented with 2.0 mg/L of 2,4-D and 1.5 mg/L of 6-BA. Subsequently, the samples of the calli obtained from TBC14 were collected at 0, 10, 20, and 30 d, and their transcriptomes were sequenced where identified. GO enrichment led to the detection of the most significant active gene set, which was the DNA binding transcription factor activity. The DEGs related to the pathways concerning metabolism, the biosynthesis of secondary metabolites, and hormone signal transduction were the most enriched in the KEGG database. The sets of MYB, AP2/ERF, and bHLH TFs exhibited the highest number of DEGs. Using this enrichment analysis, 421 genes encoding TFs, 47 auxin- and cytokinin-related genes, and 6 signal transduction-associated genes were screened that may play significant roles in callus formation (CF) in TB. Furthermore, FtPinG0008123200.01 (bZIP), a key gene promoting CF, was screened in terms of the weighted gene co-expression network associated with the various stages of CF. Our study not only provides valuable information about the molecular mechanism of CF but also reveals new genes involved in this process.

A Common Molecular Signature Indicates the Pre-Meristematic State of Plant Calli

In response to different degrees of mechanical injury, certain plant cells re-enter the division cycle to provide cells for tissue replenishment, tissue rejoining, de novo organ formation, and/or wound healing. The intermediate tissue formed by the dividing cells is called a callus. Callus formation can also be induced artificially in vitro by wounding and/or hormone (auxin and cytokinin) treatments. The callus tissue can be maintained in culture, providing starting material for de novo organ or embryo regeneration and thus serving as the basis for many plant biotechnology applications. Due to the biotechnological importance of callus cultures and the scientific interest in the developmental flexibility of somatic plant cells, the initial molecular steps of callus formation have been studied in detail. It was revealed that callus initiation can follow various ways, depending on the organ from which it develops and the inducer, but they converge on a seemingly identical tissue. It is not known, however, if callus is indeed a special tissue with a defined gene expression signature, whether it is a malformed meristem, or a mass of so-called "undifferentiated" cells, as is mostly believed. In this paper, I review the various mechanisms of plant regeneration that may converge on callus initiation. I discuss the role of plant hormones in the detour of callus formation from normal development. Finally, I compare various Arabidopsis gene expression datasets obtained a few days, two weeks, or several years after callus induction and identify 21 genes, including genes of key transcription factors controlling cell division and differentiation in meristematic regions, which were upregulated in all investigated callus samples. I summarize the information available on all 21 genes that point to the pre-meristematic nature of callus tissues underlying their wide regeneration potential.

Dynamic changes in DNA methylation occur in TE regions and affect cell proliferation during leaf-to-callus transition in Arabidopsis

Plant somatic cells can be reprogrammed into pluripotent cell mass, called callus, through a two-step in vitro tissue culture method. Incubation on callus-inducing medium triggers active cell proliferation to form a pluripotent callus. Notably, DNA methylation is implicated during callus formation, but a detailed molecular process regulated by DNA methylation remains to be fully elucidated. Here, we compared genome-wide DNA methylation profiles between leaf and callus tissues in Arabidopsis using whole-genome bisulphite-sequencing. Global distribution of DNA methylation showed that CHG methylation was increased, whereas CHH methylation was reduced especially around transposable element (TE) regions during the leaf-to-callus transition. We further analysed differentially expressed genes around differentially methylated TEs (DMTEs) during the leaf-to-callus transition and found that genes involved in cell cycle regulation were enriched and also constituted a coexpression gene network along with pluripotency regulators. In addition, a conserved DNA sequence analysis for upstream cis-elements led us to find a putative transcription factor associated with cell fate transition. CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) was newly identified as a regulator of plant regeneration, and consistently, the cca1lhy mutant displayed altered phenotypes in callus proliferation. Overall, these results suggest that DNA methylation coordinates cell cycle regulation during callus formation, and CCA1 may act as a key upstream coordinator at least in part in the processes.

Transcriptomic Changes in Internode Explants of Stinging Nettle during Callogenesis

Callogenesis, the process during which explants derived from differentiated plant tissues are subjected to a trans-differentiation step characterized by the proliferation of a mass of cells, is fundamental to indirect organogenesis and the establishment of cell suspension cultures. Therefore, understanding how callogenesis takes place is helpful to plant tissue culture, as well as to plant biotechnology and bioprocess engineering. The common herbaceous plant stinging nettle (Urtica dioica L.) is a species producing cellulosic fibres (the bast fibres) and a whole array of phytochemicals for pharmacological, nutraceutical and cosmeceutical use. Thus, it is of interest as a potential multi-purpose plant. In this study, callogenesis in internode explants of a nettle fibre clone (clone 13) was studied using RNA-Seq to understand which gene ontologies predominate at different time points. Callogenesis was induced with the plant growth regulators α-napthaleneacetic acid (NAA) and 6-benzyl aminopurine (BAP) after having determined their optimal concentrations. The process was studied over a period of 34 days, a time point at which a well-visible callus mass developed on the explants. The bioinformatic analysis of the transcriptomic dataset revealed specific gene ontologies characterizing each of the four time points investigated (0, 1, 10 and 34 days). The results show that, while the advanced stage of callogenesis is characterized by the iron deficiency response triggered by the high levels of reactive oxygen species accumulated by the proliferating cell mass, the intermediate and early phases are dominated by ontologies related to the immune response and cell wall loosening, respectively.

MET1-Dependent DNA Methylation Represses Light Signaling and Influences Plant Regeneration in Arabidopsis

Plant somatic cells can be reprogrammed into a pluripotent cell mass, called callus, which can be subsequently used for de novo shoot regeneration through a two-step in vitro tissue culture method. MET1-dependent CG methylation has been implicated in plant regeneration in Arabidopsis, because the met1-3 mutant exhibits increased shoot regeneration compared with the wild-type. To understand the role of MET1 in de novo shoot regeneration, we compared the genome-wide DNA methylomes and transcriptomes of wild-type and met1-3 callus and leaf. The CG methylation patterns were largely unchanged during leaf-to-callus transition, suggesting that the altered regeneration phenotype of met1-3 was caused by the constitutively hypomethylated genes, independent of the tissue type. In particular, MET1-dependent CG methylation was observed at the blue light receptor genes, CRYPTOCHROME 1 (CRY1) and CRY2, which reduced their expression. Coexpression network analysis revealed that the CRY1 gene was closely linked to cytokinin signaling genes. Consistently, functional enrichment analysis of differentially expressed genes in met1-3 showed that gene ontology terms related to light and hormone signaling were overrepresented. Overall, our findings indicate that MET1-dependent repression of light and cytokinin signaling influences plant regeneration capacity and shoot identity establishment.

Transcriptome comparison between pluripotent and non-pluripotent calli derived from mature rice seeds

In vitro plant regeneration involves a two-step practice of callus formation and de novo organogenesis. During callus formation, cellular competence for tissue regeneration is acquired, but it is elusive what molecular processes and genetic factors are involved in establishing cellular pluripotency. To explore the mechanisms underlying pluripotency acquisition during callus formation in monocot plants, we performed a transcriptomic analysis on the pluripotent and non-pluripotent rice calli using RNA-seq. We obtained a dataset of differentially expressed genes (DEGs), which accounts for molecular processes underpinning pluripotency acquisition and maintenance. Core regulators establishing root stem cell niche were implicated in pluripotency acquisition in rice callus, as observed in Arabidopsis. In addition, KEGG analysis showed that photosynthetic process and sugar and amino acid metabolism were substantially suppressed in pluripotent calli, whereas lipid and antioxidant metabolism were overrepresented in up-regulated DEGs. We also constructed a putative coexpression network related to cellular pluripotency in rice and proposed potential candidates conferring pluripotency in rice callus. Overall, our transcriptome-based analysis can be a powerful resource for the elucidation of the molecular mechanisms establishing cellular pluripotency in rice callus.

Natural Variation in Plant Pluripotency and Regeneration

Plant regeneration is essential for survival upon wounding and is, hence, considered to be a strong natural selective trait. The capacity of plant tissues to regenerate in vitro, however, varies substantially between and within species and depends on the applied incubation conditions. Insight into the genetic factors underlying this variation may help to improve numerous biotechnological applications that exploit in vitro regeneration. Here, we review the state of the art on the molecular framework of de novo shoot organogenesis from root explants in Arabidopsis, which is a complex process controlled by multiple quantitative trait loci of various effect sizes. Two types of factors are distinguished that contribute to natural regenerative variation: master regulators that are conserved in all experimental systems (e.g., WUSCHEL and related homeobox genes) and conditional regulators whose relative role depends on the explant and the incubation settings. We further elaborate on epigenetic variation and protocol variables that likely contribute to differential explant responsivity within species and conclude that in vitro shoot organogenesis occurs at the intersection between (epi) genetics, endogenous hormone levels, and environmental influences.

Systematic Analysis of Differential H3K27me3 and H3K4me3 Deposition in Callus and Seedling Reveals the Epigenetic Regulatory Mechanisms Involved in Callus Formation in Rice

Plant growth and development occurs through meristematic cell activity, and cell fate transition is accompanied by epigenetic modifications. Callus with cell pluripotency exhibits the ability to undergo continued cell division, and is ideal for studying plant meristematic differentiation. By comparing the differential epigenetic modifications between callus and seedling, the changes in chromatin state and effects of various epigenetic modifications on the growth and development of plants can be revealed, and the key genes related to plant growth and development can be identified, providing novel insights into the regulation of plant growth and development. In this study, we performed ChIP assays using various antibodies in rice seed-induced callus and seedlings grown for about 15 days to examine the differential deposition of H3K27me3 and H3K4me3. Furthermore, data for DNase I-hypersensitive sites in the corresponding tissues were downloaded from National Center for Biotechnology Information. We analyzed 4,562 callus H3K27me3-decreased genes especially those encoding transcription factors in callus, and found that most of the transcription factors, including AP2-ERREBP, NAC, and HB gene families, were related to growth and development. Genes related to meristemization, such as OsWOX9, OsWOX11, OsPLT4, OsPLT5, and OsSHR, were also included. In contrast, H3K4me3 positively regulated callus characteristics through its higher deposition in the callus than in the seedling. We further performed transcriptomic analysis on 45 sets of Affymetrix GeneChip arrays and identified 1,565 genes preferentially expressed in the callus. Callus development and root development in rice were found to share a common regulatory mechanism. We found that these genes, which are associated with meristems, require the removal of H3K27me3 and the deposition of H3K4me3, and DNase I-hypersensitive sites to maintain a relatively active state in the callus than in the seedling. The present study provides novel data about the epigenetic mechanisms involved in callus formation and additional resources for the study of cell division and differentiation in plants.

Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation

BACKGROUND

Maize is one of the primary crops of genetic manipulation, which provides an excellent means of promoting stress resistance and increasing yield. However, the differences in induction and regeneration capacity of embryonic callus (EC) among various genotypes result in genotypic dependence in genetic transformation.

RESULTS

In this study, embryonic calli of two maize inbred lines with strong redifferentiation capacity and two lines with weak redifferentiation capability were separately subjected to transcriptome sequencing analysis during the early redifferentiation stages (stage I, 1-3 d; stage II, 4-6 d; stage III, 7-9 d) along with their corresponding controls. A total of ~ 654.72 million cDNA clean reads were yielded, and 62.64%~ 69.21% clean reads were mapped to the reference genome for each library. In comparison with the control, the numbers of differentially expressed genes (DEGs) for the four inbred lines identified in the three stages ranged from 1694 to 7193. By analyzing the common and specific DEGs of the four materials, we found that there were 321 upregulated genes and 386 downregulated genes identified in the high-regeneration lines (141 and DH40), whereas 611 upregulated genes and 500 downregulated genes were specifically expressed in the low-regeneration lines (ZYDH381-1 and DH3732). Analysis of the DEG expression patterns indicated a sharp change at stage I in both the high- and low-regeneration lines, which suggested that stage I constitutes a crucial period for EC regeneration. Notably, the specific common DEGs of 141 and DH40 were mainly associated with photosynthesis, porphyrin and chlorophyll metabolism, ribosomes, and plant hormone signal transduction. In contrast, the DEGs in ZYDH381-1 and DH3732 were mainly related to taurine and hypotaurine metabolism, nitrogen metabolism, fatty acid elongation, starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant circadian rhythm. More importantly, WOX genes, which have an ancestral role in embryo development in seed plants and promote the regeneration of transformed calli, were specifically upregulated in the two high-regeneration lines.

CONCLUSIONS

Our research contributes to the elucidation of molecular regulation during early redifferentiation in the maize embryonic callus.

Callus, Dedifferentiation, Totipotency, Somatic Embryogenesis: What These Terms Mean in the Era of Molecular Plant Biology?

Recent findings call for the critical overview of some incorrectly used plant cell and tissue culture terminology such as dedifferentiation, callus, totipotency, and somatic embryogenesis. Plant cell and tissue culture methods are efficient means to preserve and propagate genotypes with superior germplasm as well as to increase genetic variability for breading. Besides, they are useful research tools and objects of plant developmental biology. The history of plant cell and tissue culture dates back to more than a century. Its basic methodology and terminology were formulated preceding modern plant biology. Recent progress in molecular and cell biology techniques allowed unprecedented insights into the underlying processes of plant cell/tissue culture and regeneration. The main aim of this review is to provide a theoretical framework supported by recent experimental findings to reconsider certain historical, even dogmatic, statements widely used by plant scientists and teachers such as "plant cells are totipotent" or "callus is a mass of dedifferentiated cells," or "somatic embryos have a single cell origin." These statements are based on a confused terminology. Clarification of it might help to avoid further misunderstanding and to overcome potential "terminology-raised" barriers in plant research.

JMJ30-mediated demethylation of H3K9me3 drives tissue identity changes to promote callus formation in Arabidopsis

Plant somatic cells can be reprogrammed by in vitro tissue culture methods, and massive genome-wide chromatin remodeling occurs, particularly during callus formation. Since callus tissue resembles root primordium, conversion of tissue identity is essentially required when leaf explants are used. Consistent with the fact that the differentiation state is defined by chromatin structure, which permits limited gene profiles, epigenetic changes underlie cellular reprogramming for changes to tissue identity. Although a histone methylation process suppressing leaf identity during leaf-to-callus transition has been demonstrated, the epigenetic factor involved in activation of root identity remains elusive. Here, we report that JUMONJI C DOMAIN-CONTAINING PROTEIN 30 (JMJ30) stimulates callus formation by promoting expression of a subset of LATERAL ORGAN BOUNDARIES-DOMAIN (LBD) genes that establish root primordia. The JMJ30 protein binds to promoters of the LBD16 and LBD29 genes along with AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 and activates LBD expression. Consistently, the JMJ30-deficient mutant displays reduced callus formation with low LBD transcript levels. The ARF-JMJ30 complex catalyzes the removal of methyl groups from H3K9me3, especially at the LBD16 and LBD29 loci to activate their expression during leaf-to-callus transition. Moreover, the ARF-JMJ30 complex further recruits ARABIDOPSIS TRITHORAX-RELATED 2 (ATXR2), which promotes deposition of H3K36me3 at the LBD16 and LBD29 promoters, and the tripartite complex ensures stable LBD activation during callus formation. These results indicate that the coordinated epigenetic modifications promote callus formation by establishing root primordium identity.

Telomere elongation upon transfer to callus culture reflects the reprogramming of telomere stability control in Arabidopsis

KEY MESSAGE

Standard pathways involved in the regulation of telomere stability do not contribute to gradual telomere elongation observed in the course of A. thaliana calli propagation. Genetic and epigenetic changes accompanying the culturing of plant cells have frequently been reported. Here we aimed to characterize the telomere homeostasis during long term callus propagation. While in Arabidopsis thaliana calli gradual telomere elongation was observed, telomeres were stable in Nicotiana tabacum and N. sylvestris cultures. Telomere elongation during callus propagation is thus not a general feature of plant cells. The long telomere phenotype in Arabidopsis calli was correlated neither with changes in telomerase activity nor with activation of alternative mechanisms of telomere elongation. The dynamics of telomere length changes was maintained in mutant calli with loss of function of important epigenetic modifiers but compromised in the presence of epigenetically active drug zebularine. To examine whether the cell culture-induced disruption of telomere homeostasis is associated with the modulated structure of chromosome ends, epigenetic properties of telomere chromatin were analysed. Albeit distinct changes in epigenetic modifications of telomere histones were observed, these were broadly stochastic. Our results show that contrary to animal cells, the structure and function of plant telomeres is not determined significantly by the epigenetic character of telomere chromatin. Set of differentially transcribed genes was identified in calli, but considering the known telomere- or telomerase-related functions of respective proteins, none of these changes per se was apparently related to the elongated telomere phenotype. Based on our data, we propose that the disruption in telomere homeostasis in Arabidopsis calli arises from the interplay of multiple factors, as a part of reprogramming of plant cells to long-term culture conditions.

Transcriptional profiling of the CAM plant Agave salmiana reveals conservation of a genetic program for regeneration

In plants, the best characterized plant regeneration process is de novo organogenesis. This type of regeneration is characterized by the formation of a multicellular structure called callus. Calli are induced via phytohormone treatment of plant sections. The callus formation in plants like Agave species with Crassulacean Acid Metabolism (CAM) is poorly studied. In this study, we induced callus formation from Agave salmiana leaves and describe cell arrangement in this tissue. Moreover, we determined and analyzed the transcriptional program of calli, as well as those of differentiated root and leaf tissues, by using RNA-seq. We were able to reconstruct 170,844 transcripts of which 40,644 have a full Open Reading Frame (ORF). The global profile obtained by Next Generation Sequencing (NGS) reveals that several callus-enriched protein coding transcripts are orthologs of previously reported factors highly expressed in Arabidopsis calli. At least 62 genes were differentially expressed in Agave calli, 50 of which were up-regulated. Several of these are actively involved in the perception of, and response to, auxin and cytokinin. Not only are these the first results for the A. salmiana callus, but they provide novel data from roots and leaves of this Agave species, one of the largest non-tree plants in nature.

Dynamic Epigenetic Changes during Plant Regeneration

Plants have the remarkable ability to drive cellular dedifferentiation and regeneration. Changes in epigenetic landscapes accompany the cell fate transition. Notably, modifications of chromatin structure occur primarily during callus formation via an in vitro tissue culture process and, thus, pluripotent callus cells have unique epigenetic signatures. Here, we highlight the latest progress in epigenetic regulation of callus formation in plants, which addresses fundamental questions related to cell fate changes and pluripotency establishment. Global and local modifications of chromatin structure underlie callus formation, and the combination and sequence of epigenetic modifications further shape intricate cell fate changes. This review illustrates how a series of chromatin marks change dynamically during callus formation and their biological relevance in plant regeneration.

Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation

Cellular dedifferentiation, the transition of differentiated somatic cells to pluripotent stem cells, ensures developmental plasticity and contributes to wound healing in plants. Wounding induces cells to form a mass of unorganized pluripotent cells called callus at the wound site. Explanted cells can also form callus tissues in vitro. Reversible cellular differentiation-dedifferentiation processes in higher eukaryotes are controlled mainly by chromatin modifications. We demonstrate that ARABIDOPSIS TRITHORAX-RELATED 2 (ATXR2), a histone lysine methyltransferase that promotes the accumulation of histone H3 proteins that are trimethylated on lysine 36 (H3K36me3) during callus formation, promotes early stages of cellular dedifferentiation through activation of LATERAL ORGAN BOUNDARIES DOMAIN (LBD) genes. The LBD genes of Arabidopsis thaliana are activated during cellular dedifferentiation to enhance the formation of callus. Leaf explants from Arabidopsis atxr2 mutants exhibited a reduced ability to form callus and a substantial reduction in LBD gene expression. ATXR2 bound to the promoters of LBD genes and was required for the deposition of H3K36me3 at these promoters. ATXR2 was recruited to LBD promoters by the transcription factors AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19. Leaf explants from arf7-1arf19-2 double mutants were defective in callus formation and showed reduced H3K36me3 accumulation at LBD promoters. Genetic analysis provided further support that ARF7 and ARF19 were required for the ability of ATXR2 to promote the expression of LBD genes. These observations indicate that the ATXR2-ARF-LBD axis is key for the epigenetic regulation of callus formation in Arabidopsis.

High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis

The auxin-brassinosteroid interaction involving the BIN2-ARF-LBD axis plays a key role in temperature-dependent callus formation in Arabidopsis. An extensive web of multiple hormone signaling pathways underlies callus formation. Here, we report that a brassinosteroid (BR) signaling component, BR-INSENSITIVE 2 (BIN2), positively regulates callus formation. The BIN2 kinase promotes transcriptional activities of AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 and subsequently activates expression of LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) and LBD29 during callus formation. Consistently, the BIN2 activity is dependent on ARFs in the control of callus formation. Notably, this auxin-BR interaction is particularly relevant in temperature-dependent callus formation. Misexpression of BIN2 and ARFs resulted in the temperature insensitivity of callus formation. These results indicate that the BIN2-ARF-LBD axis plays a key role in temperature-dependent callus formation in Arabidopsis.

Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants

Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants. Recent discoveries have advanced our understanding of the orchestration of plant developmental switches by transcriptional master regulators, chromatin state changes, and hormone response pathways. Here, we review these recent advances with emphasis on the earliest stages of plant development and on the switch from pluripotency to differentiation in different plant organ systems.