Genome-wide association studies meta-analysis uncovers NOJO and SGS3 novel genes involved in Arabidopsis thaliana primary root development and plasticity.

Background: Arabidopsis thaliana primary root growth has become a model for evo-devo studies due to its simplicity and facility to record cell proliferation and differentiation. To identify new genetic components relevant to primary root growth, we used a Genome-Wide Association Studies (GWAS) meta-analysis approach using data published in the last decade. In this work, we performed intra and inter-studies analyses to discover new genetic components that could participate in primary root growth.

HDACs MADS-domain protein interaction: a case study of HDA15 and XAL1 in .

Cellular behavior, cell differentiation and ontogenetic development in eukaryotes result from complex interactions between epigenetic and classic molecular genetic mechanisms, with many of these interactions still to be elucidated. Histone deacetylase enzymes (HDACs) promote the interaction of histones with DNA by compacting the nucleosome, thus causing transcriptional repression. MADS-domain transcription factors are highly conserved in eukaryotes and participate in controlling diverse developmental processes in animals and plants, as well as regulating stress responses in plants.

ULTRAPETALAs in action: Unraveling their role in root development.

The epigenetic complex Trithorax (TrxG) regulates gene transcription through post-translational histone modifications and is involved in a wide range of developmental processes. ULTRAPETALA1 (ULT1) is a SAND domain plant-exclusive TrxG protein that regulates the H3K4me3 active mark to counteract PcG repression. ULT1 has been identified to be involved in multiple tissue-specific processes.

Reveals an Additional Level of Flowering Regulation in the Shoot Apical Meristem in Response to Light and Increased Temperature in Arabidopsis.

Light and photoperiod are environmental signals that regulate flowering transition. In plants like , this regulation relies on CONSTANS, a transcription factor that is negatively posttranslational regulated by phytochrome B during the morning, while it is stabilized by PHYA and cryptochromes 1/2 at the end of daylight hours. CO induces the expression of , whose protein travels from the leaves to the apical meristem, where it binds to FD to regulate some flowering genes.

A Green Light to Switch on Genes: Revisiting Trithorax on Plants.

The Trithorax Group (TrxG) is a highly conserved multiprotein activation complex, initially defined by its antagonistic activity with the PcG repressor complex. TrxG regulates transcriptional activation by the deposition of H3K4me3 and H3K36me3 marks. According to the function and evolutionary origin, several proteins have been defined as TrxG in plants; nevertheless, little is known about their interactions and if they can form TrxG complexes.

Combined Approach of GWAS and Phylogenetic Analyses to Identify New Candidate Genes That Participate in Primary Root Development Using Cellular Measurements and Primary Root Length.

Genome-wide association studies (GWAS) have allowed the identification of different loci associated with primary root (PR) growth, and Arabidopsis is an excellent model for these studies. The PR length is controlled by cell proliferation, elongation, and differentiation; however, the specific contribution of proliferation and differentiation in the control of PR growth is still poorly studied. To this end, we analyzed 124 accessions and used a GWAS approach to identify potential causal genomic regions related to four traits: PR length, growth rate, cell proliferation and cell differentiation.

The flowering transition pathways converge into a complex gene regulatory network that underlies the phase changes of the shoot apical meristem in .

Post-embryonic plant development is characterized by a period of vegetative growth during which a combination of intrinsic and extrinsic signals triggers the transition to the reproductive phase. To understand how different flowering inducing and repressing signals are associated with phase transitions of the Shoot Apical Meristem (SAM), we incorporated available data into a gene regulatory network model for . This Flowering Transition Gene Regulatory Network (FT-GRN) formally constitutes a system-level mechanism based on more than three decades of experimental data on flowering.

Live Plant Cell Tracking: Fiji plugin to analyze cell proliferation dynamics and understand morphogenesis.

Arabidopsis (Arabidopsis thaliana) primary and lateral roots (LRs) are well suited for 3D and 4D microscopy, and their development provides an ideal system for studying morphogenesis and cell proliferation dynamics. With fast-advancing microscopy techniques used for live-imaging, whole tissue data are increasingly available, yet present the great challenge of analyzing complex interactions within cell populations. We developed a plugin "Live Plant Cell Tracking" (LiPlaCeT) coupled to the publicly available ImageJ image analysis program and generated a pipeline that allows, with the aid of LiPlaCeT, 4D cell tracking and lineage analysis of populations of dividing and growing cells.

Unraveling the role of epigenetic regulation in asymmetric cell division during plant development.

Asymmetric cell divisions are essential to generate different cellular lineages. In plants, asymmetric cell divisions regulate the correct formation of the embryo, stomatal cells, apical and root meristems, and lateral roots. Current knowledge of regulation of asymmetric cell divisions suggests that, in addition to the function of key transcription factor networks, epigenetic mechanisms play crucial roles.

Beyond the Genetic Pathways, Flowering Regulation Complexity in .

Flowering is one of the most critical developmental transitions in plants' life. The irreversible change from the vegetative to the reproductive stage is strictly controlled to ensure the progeny's success. In , seven flowering genetic pathways have been described under specific growth conditions.

Integrative Roles of Phytohormones on Cell Proliferation, Elongation and Differentiation in the Primary Root.

The growth of multicellular organisms relies on cell proliferation, elongation and differentiation that are tightly regulated throughout development by internal and external stimuli. The plasticity of a growth response largely depends on the capacity of the organism to adjust the ratio between cell proliferation and cell differentiation. The primary root of offers many advantages toward understanding growth homeostasis as root cells are continuously produced and move from cell proliferation to elongation and differentiation that are processes spatially separated and could be studied along the longitudinal axis.

Hormonal Regulation of Stem Cell Proliferation at the Root Stem Cell Niche.

The root stem cell niche (SCN) of consists of the quiescent center (QC) cells and the surrounding initial stem cells that produce progeny to replenish all the tissues of the root. The QC cells divide rather slowly relative to the initials, yet most root tissues can be formed from these cells, depending on the requirements of the plant. Hormones are fundamental cues that link such needs with the cell proliferation and differentiation dynamics at the root SCN.

The Epigenetic Faces of ULTRAPETALA1.

ULTRAPETALA1 (ULT1) is a versatile plant-exclusive protein, initially described as a trithorax group (TrxG) factor that regulates transcriptional activation and counteracts polycomb group (PcG) repressor function. As part of TrxG, ULT1 interacts with ARABIDOPSIS TRITHORAX1 (ATX1) to regulate H3K4me3 activation mark deposition. However, our recent studies indicate that ULT1 can also act independently of ATX1.

Beyond What Your Retina Can See: Similarities of Retinoblastoma Function between Plants and Animals, from Developmental Processes to Epigenetic Regulation.

The Retinoblastoma protein (pRb) is a key cell cycle regulator conserved in a wide variety of organisms. Experimental analysis of pRb's functions in animals and plants has revealed that this protein participates in cell proliferation and differentiation processes. In addition, pRb in animals and its orthologs in plants (RBR), are part of highly conserved protein complexes which suggest the possibility that analogies exist not only between functions carried out by pRb orthologs themselves, but also in the structure and roles of the protein networks where these proteins are involved.

A system-level mechanistic explanation for asymmetric stem cell fates: Arabidopsis thaliana root niche as a study system.

Asymmetric divisions maintain long-term stem cell populations while producing new cells that proliferate and then differentiate. Recent reports in animal systems show that divisions of stem cells can be uncoupled from their progeny differentiation, and the outcome of a division could be influenced by microenvironmental signals. But the underlying system-level mechanisms, and whether this dynamics also occur in plant stem cell niches (SCN), remain elusive.

ULTRAPETALA1 maintains Arabidopsis root stem cell niche independently of ARABIDOPSIS TRITHORAX1.

During plant development, morphogenetic processes rely on the activity of meristems. Meristem homeostasis depends on a complex regulatory network constituted by different factors and hormone signaling that regulate gene expression to coordinate the correct balance between cell proliferation and differentiation. ULTRAPETALA1, a transcriptional regulatory protein described as an Arabidopsis Trithorax group factor, has been characterized as a regulator of the shoot and floral meristems activity.

MADS-Box Genes Are Key Components of Genetic Regulatory Networks Involved in Abiotic Stress and Plastic Developmental Responses in Plants.

Plants, as sessile organisms, adapt to different stressful conditions, such as drought, salinity, extreme temperatures, and nutrient deficiency, via plastic developmental and growth responses. Depending on the intensity and the developmental phase in which it is imposed, a stress condition may lead to a broad range of responses at the morphological, physiological, biochemical, and molecular levels. Transcription factors are key components of regulatory networks that integrate environmental cues and concert responses at the cellular level, including those that imply a stressful condition.

MADS-box genes underground becoming mainstream: plant root developmental mechanisms.

Plant growth is largely post-embryonic and depends on meristems that are active throughout the lifespan of an individual. Developmental patterns rely on the coordinated spatio-temporal expression of different genes, and the activity of transcription factors is particularly important during most morphogenetic processes. MADS-box genes constitute a transcription factor family in eukaryotes.

Identifying the transition to the maturation zone in three ecotypes of roots.

The (hereafter Arabidopsis) root has become a useful model for studying how organ morphogenesis emerge from the coordination and balance of cell proliferation and differentiation, as both processes may be observed and quantified in the root at different stages of development. Hence, being able to objectively identify and delimit the different stages of root development has been very important. Up to now, three different zones along the longitudinal axis of the primary root of Arabidopsis, have been identified: the root apical meristematic zone (RAM) with two domains [the proliferative (PD) and the transition domain (TD)], the elongation zone (EZ) and the maturation zone (MZ).

The MADS-box XAANTAL1 increases proliferation at the Arabidopsis root stem-cell niche and participates in transition to differentiation by regulating cell-cycle components.

Background Morphogenesis depends on the concerted modulation of cell proliferation and differentiation. Such modulation is dynamically adjusted in response to various external and internal signals via complex transcriptional regulatory networks that mediate between such signals and regulation of cell-cycle and cellular responses (proliferation, growth, differentiation). In plants, which are sessile, the proliferation/differentiation balance is plastically adjusted during their life cycle and transcriptional networks are important in this process.

Root Architecture Diversity and Meristem Dynamics in Different Populations of Arabidopsis thaliana.

Arabidopsis thaliana has been an excellent model system for molecular genetic approaches to development and physiology. More recently, the potential of studying various accessions collected from diverse habitats has been started to exploit. Col-0 has been the best-studied accession but we now know that several traits show significant divergences among them.

The impact of Polycomb group (PcG) and Trithorax group (TrxG) epigenetic factors in plant plasticity.

Current advances indicate that epigenetic mechanisms play important roles in the regulatory networks involved in plant developmental responses to environmental conditions. Hence, understanding the role of such components becomes crucial to understanding the mechanisms underlying the plasticity and variability of plant traits, and thus the ecology and evolution of plant development. We now know that important components of phenotypic variation may result from heritable and reversible epigenetic mechanisms without genetic alterations.