Taking the Wheel - de novo DNA Methylation as a Driving Force of Plant Embryonic Development

Dynamics of DNA methylation and its impact on plant embryogenesis

Flowering plants exhibit unique DNA methylation dynamics during development. Particular attention can be focused on seed development and the embryo, which represents the starting point of the sporophytic life cycle. A build-up of CHH methylation is now recognized as highly characteristic of embryo development. This process is thought to occur in order to silence potentially harmful transposable element expression, though roles in promoting seed dormancy and dessication tolerance have also been revealed. Recent studies show that increased CHH methylation in embryos inhabits both novel loci, unmethylated elsewhere in the plant, as well as shared loci, exhibiting more dense methylation. The role of DNA methylation in cis-regulatory gene regulation in plants is less well established compared to mammals, and here we discuss both transposable element regulation and the potential role of DNA methylation in dynamic gene expression.

Epigenetic modifications and miRNAs determine the transition of somatic cells into somatic embryos

KEY MESSAGE

This review discusses the epigenetic changes during somatic embryo (SE) development, highlights the genes and miRNAs involved in the transition of somatic cells into SEs as a result of epigenetic changes, and draws insights on biotechnological opportunities to study SE development. Somatic embryogenesis from somatic cells occurs in a series of steps. The transition of somatic cells into somatic embryos (SEs) is the most critical step under genetic and epigenetic regulations. Major regulatory genes such as SERK, WUS, BBM, FUS3/FUSA3, AGL15, and PKL, control SE steps and development by turning on and off other regulatory genes. Gene transcription profiles of somatic cells during SE development is the result of epigenetic changes, such as DNA and histone protein modifications, that control and decide the fate of SE formation. Depending on the type of somatic cells and the treatment with plant growth regulators, epigenetic changes take place dynamically. Either hypermethylation or hypomethylation of SE-related genes promotes the transition of somatic cells. For example, the reduced levels of DNA methylation of SERK and WUS promotes SE initiation. Histone modifications also promote SE induction by regulating SE-related genes in somatic cells. In addition, miRNAs contribute to the various stages of SE by regulating the expression of auxin signaling pathway genes (TIR1, AFB2, ARF6, and ARF8), transcription factors (CUC1 and CUC2), and growth-regulating factors (GRFs) involved in SE formation. These epigenetic and miRNA functions are unique and have the potential to regenerate bipolar structures from somatic cells when a pluripotent state is induced. However, an integrated overview of the key regulators involved in SE development and downstream processes is lacking. Therefore, this review discusses epigenetic modifications involved in SE development, SE-related genes and miRNAs associated with epigenetics, and common cis-regulatory elements in the promoters of SE-related genes. Finally, we highlight future biotechnological opportunities to alter epigenetic pathways using the genome editing tool and to study the transition mechanism of somatic cells.

An insight into the roles of regulatory ncRNAs in plants: An abiotic stress and developmental perspective

Different environmental cues lead to changes in physiology, biochemistry and molecular status of plant's growth. Till date, various genes have been accounted for their role in regulating plant development and response to abiotic stress. Excluding genes that code for a functional protein in a cell, a large chunk of the eukaryotic transcriptome consists of non-coding RNAs (ncRNAs) which lack protein coding capacity but are still functional. Recent advancements in Next Generation Sequencing (NGS) technology have led to the unearthing of different types of small and large non-coding RNAs in plants. Non-coding RNAs are broadly categorised into housekeeping ncRNAs and regulatory ncRNAs which work at transcriptional, post-transcriptional and epigenetic levels. Diverse ncRNAs play different regulatory roles in nearly all biological processes including growth, development and response to changing environments. This response can be perceived and counteracted by plants using diverse evolutionarily conserved ncRNAs like miRNAs, siRNAs and lncRNAs to participate in complex molecular regimes by activating gene-ncRNA-mRNA regulatory modules to perform the downstream function. Here, we review the current understanding with a focus on recent advancements in the functional studies of the regulatory ncRNAs at the nexus of abiotic stresses and development. Also, the potential roles of ncRNAs in imparting abiotic stress tolerance and yield improvement in crop plants are also discussed with their future prospects.

Epigenetic Regulation of Nitrogen Signaling and Adaptation in Plants

Nitrogen (N) is a crucial nutrient that plays a significant role in enhancing crop yield. Its availability, including both supply and deficiency, serves as a crucial signal for plant development. However, excessive N use in agriculture leads to environmental and economic issues. Enhancing nitrogen use efficiency (NUE) is, therefore, essential to minimize negative impacts. Prior studies have investigated the genetic factors involved in N responses and the process of low-nitrogen (LN) adaptation. In this review, we discuss recent advances in understanding how epigenetic modifications, including DNA methylation, histone modification, and small RNA, participate in the regulation of N response and LN adaptation. We highlight the importance of decoding the epigenome at various levels to accelerate the functional study of how plants respond to N availability. Understanding the epigenetic control of N signaling and adaptation can lead to new strategies to improve NUE and enhance crop productivity sustainably.

Precise Regulation of the TAA1/TAR-YUCCA Auxin Biosynthesis Pathway in Plants

The indole-3-pyruvic acid (IPA) pathway is the main auxin biosynthesis pathway in the plant kingdom. Local control of auxin biosynthesis through this pathway regulates plant growth and development and the responses to biotic and abiotic stresses. During the past decades, genetic, physiological, biochemical, and molecular studies have greatly advanced our understanding of tryptophan-dependent auxin biosynthesis. The IPA pathway includes two steps: Trp is converted to IPA by TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS/TRYPTOPHAN AMINOTRANSFERASE RELATED PROTEINs (TAA1/TARs), and then IPA is converted to IAA by the flavin monooxygenases (YUCCAs). The IPA pathway is regulated at multiple levels, including transcriptional and post-transcriptional regulation, protein modification, and feedback regulation, resulting in changes in gene transcription, enzyme activity and protein localization. Ongoing research indicates that tissue-specific DNA methylation and miRNA-directed regulation of transcription factors may also play key roles in the precise regulation of IPA-dependent auxin biosynthesis in plants. This review will mainly summarize the regulatory mechanisms of the IPA pathway and address the many unresolved questions regarding this auxin biosynthesis pathway in plants.

Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity

Both phytohormone signaling and epigenetic mechanisms have long been known to play crucial roles in plant development and plasticity in response to ambient stimuli. Indeed, diverse signaling pathways mediated by phytohormones and epigenetic processes integrate multiple upstream signals to regulate various plant traits. Emerging evidence indicates that phytohormones and epigenetic processes interact at multiple levels. In this review, we summarize the current knowledge of the interplay between phytohormones and epigenetic processes from the perspective of phytohormone biology. We also review chemical regulators used in epigenetic studies and propose strategies for developing novel regulators using multidisciplinary approaches.

DNA Methylation in Algae and Its Impact on Abiotic Stress Responses

Epigenetics, referring to heritable gene regulatory information that is independent of changes in DNA sequences, is an important mechanism involved both in organism development and in the response to environmental events. About the epigenetic marks, DNA methylation is one of the most conserved mechanisms, playing a pivotal role in organism response to several biotic and abiotic stressors. Indeed, stress can induce changes in gene expression through hypo- or hyper-methylation of DNA at specific loci and/or in DNA methylation at the genome-wide level, which has an adaptive significance and can direct genome evolution. Exploring DNA methylation in responses to abiotic stress could have important implications for improving stress tolerance in algae. This article summarises the DNA methylation pattern in algae and its impact on abiotic stress, such as heavy metals, nutrients and temperature. Our discussion provides information for further research in algae for a better comprehension of the epigenetic response under abiotic stress, which could favour important implications to sustain algae growth under abiotic stress conditions, often related to high biosynthesis of interesting metabolites.

stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences

The enzyme Dicer is a component of many small RNA (sRNA) pathways involved in RNA processing for post-transcriptional regulation, anti-viral response and control of transposable elements. Cleavage of double-stranded RNA by Dicer produces a signature overhanging sequence at the 3’ end of the sRNA sequence relative to a complementary passenger strand in a RNA duplex. There is a need for reliable tools to computationally search for Dicer cleavage signatures to help characterise families of sRNAs. This is increasingly important due to the rising popularity of sRNA sequencing, especially in non-model organisms. Here, we present stepRNA, a fast, local tool that identifies (i) overhang signatures strongly indicative of Dicer cleavage in RNA sequences, and (ii) the length of the passenger strand in sRNAs duplexes. We demonstrate the use of stepRNA with simulated and biological datasets to detect Dicer cleavage signatures in experimentally validated examples. Compared to currently available tools, stepRNA is more accurate, requires only sRNA sequence data rather than a reference genome, and provides information about other important features such as passenger strand length. stepRNA is freely available at https://github.com/Vicky-Hunt-Lab/stepRNA and is easily installable.

Chromatin during plant regeneration: Opening towards root identity?

Plants show exceptional developmental plasticity and the ability to reprogram cell identities during regeneration. Although regeneration has been used in plant propagation for decades, we only recently gained detailed cellular and molecular insights into this process. Evidently, not all cell types have the same regeneration potential, and only a subset of regeneration-competent cells reach pluripotency. Pluripotent cells exhibit transcriptional similarity to root stem cells. In different plant regeneration systems, transcriptional reprogramming involves transient release of chromatin repression during pluripotency establishment and its restoration during organ or embryo differentiation. Incomplete resetting of the epigenome leads to somaclonal variation in regenerated plants. As single-cell technologies advance, we expect novel, exciting insights into epigenome dynamics during the establishment of pluripotency.

New Wine in an Old Bottle: Utilizing Chemical Genetics to Dissect Apical Hook Development

The apical hook is formed by dicot seedlings to protect the tender shoot apical meristem during soil emergence. Regulated by many phytohormones, the apical hook has been taken as a model to study the crosstalk between individual signaling pathways. Over recent decades, the roles of different phytohormones and environmental signals in apical hook development have been illustrated. However, key regulators downstream of canonical hormone signaling have rarely been identified via classical genetics screening, possibly due to genetic redundancy and/or lethal mutation. Chemical genetics that utilize small molecules to perturb and elucidate biological processes could provide a complementary strategy to overcome the limitations in classical genetics. In this review, we summarize current progress in hormonal regulation of the apical hook, and previously reported chemical tools that could assist the understanding of this complex developmental process. We also provide insight into novel strategies for chemical screening and target identification, which could possibly lead to discoveries of new regulatory components in apical hook development, or unidentified signaling crosstalk that is overlooked by classical genetics screening.

The roles of epigenetic modifications in the regulation of auxin biosynthesis

Auxin is one of the most important plant growth regulators of plant morphogenesis and response to environmental stimuli. Although the biosynthesis pathway of auxin has been elucidated, the mechanisms regulating auxin biosynthesis remain poorly understood. The transcription of auxin biosynthetic genes is precisely regulated by complex signaling pathways. When the genes are expressed, epigenetic modifications guide mRNA synthesis and therefore determine protein production. Recent studies have shown that different epigenetic factors affect the transcription of auxin biosynthetic genes. In this review, we focus our attention on the molecular mechanisms through which epigenetic modifications regulate auxin biosynthesis.