
Javier F PalatnikInstituto de Biología Molecular y Celular de Rosario
Javier F Palatnik
PhD
About
117
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Introduction
Additional affiliations
January 2016 - present
June 2001 - October 2002
August 2008 - October 2010
Publications
Publications (117)
Growth-regulating factors (GRFs) belong to a plant-specific family of transcription factors which display important roles in plant growth and development. GRF transcriptional activity is finely tuned by regulatory processes involving post-transcriptional silencing exerted by miRNA396, and protein-protein interactions involving a family of co-transc...
MicroRNAs (miRNAs) are essential regulators of gene expression, defined by their unique biogenesis, which requires the precise excision of the small RNA from an imperfect fold-back precursor. Unlike their animal counterparts, plant miRNA precursors exhibit variations in sizes and shapes. Plant MIRNAs can undergo processing in a base-to-loop or loop...
The Growth-Regulating Factor (GRF) family of transcriptional factors are involved in the control of leaf size and senescence, inflorescence and root growth, grain size, and plant regeneration. However, there is limited information about the genes regulated by these transcriptional factors, which are in turn responsible for their functions. Using a...
Key message
Proper root growth depends on the clearance of TCP transcripts from the root apical meristem by microRNA miR319.
Abstract
The evolutionarily conserved microRNA miR319 regulates genes encoding TCP transcription factors in angiosperms. The miR319-TCP module controls cell proliferation and differentiation in leaves and other aerial organs...
Significance
The mitotic cell cycle (MCC) sustains plant organ growth by producing new cells in the meristems. Multiple mechanisms of gene expression regulation determine the dynamics of gene expression across the successive phases of the cell cycle. At the transcriptional level, only E2F and MYB3R transcription factors (TFs) have been identified a...
Members of the GROWTH REGULATING FACTOR (GRF) family of transcription factors play key roles in the promotion of plant growth and development. Many GRFs are post-transcriptionally repressed by microRNA (miRNA) miR396, an evolutionarily conserved small RNA, which restricts their expression to proliferative tissue. We performed a comprehensive analys...
The potential of genome editing to improve the agronomic performance of crops is often limited by low plant regeneration efficiencies and few transformable genotypes. Here, we show that expression of a fusion protein combining wheat GROWTH-REGULATING FACTOR 4 (GRF4) and its cofactor GRF-INTERACTING FACTOR 1 (GIF1) substantially increases the effici...
Genome editing allows precise DNA manipulation, but its potential is limited in many crops by low regeneration efficiencies and few transformable genotypes. Here, we show that expression of a chimeric protein including wheat GROWTH-REGULATING FACTOR 4 (GRF4) and its cofactor GRF-INTERACTING FACTOR 1 (GIF1) dramatically increases the efficiency and...
Seeds germinating underground display a specific developmental program, termed skotomorphogenesis, to ensure survival of the emerging seedlings until they reach the light. They rapidly elongate the hypocotyl and maintain the cotyledons closed, forming a hook with the hypocotyl in order to protect apical meristematic cells from mechanical damage. Su...
MicroRNAs (miRNAs) are major regulators of gene expression in multicellular organisms. Many of the evolutionarily conserved miRNAs in plants are encoded by small gene families. The miR159/miR319 family has six members of similar sequences sharing 17 nucleotides in Arabidopsis thaliana. The members of this miRNA family regulate genes encoding TCP (T...
MicroRNAs are small RNA molecules with big impact in many eukaryotic biological processes. In plants, their role as regulators of important developmental programs such as leaf size and shape, flower organs or phase transitions, among others, have been evidenced by mutants in specific miRNAs and by mutants in components of their biogenesis. However,...
MicroRNAs (miRNA) are small RNAs of 20–22 nt that regulate diverse biological pathways through the modulation of gene expression. miRNAs recognize target RNAs by base complementarity and guide them to degradation or translational arrest. They are transcribed as longer precursors with extensive secondary structures. In plants, these precursors are p...
Many evolutionarily conserved microRNAs (miRNAs) in plants regulate transcription factors with key functions in development. Hence, mutations in the core components of the miRNA biogenesis machinery cause strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from its precursor. In plants, miRNA prec...
An increase in crop yield is essential to reassure food security to meet the accelerating global demand. Several genetic modifications can increase organ size, which in turn might boost crop yield. Still, only in a few cases their performance has been evaluated under stress conditions. MicroRNA miR396 repress the expression of GROWTH-REGULATING FAC...
Many evolutionarily conserved microRNAs (miRNAs) in plants regulate transcription factors with key functions in development. Hence, mutations in the core components of the miRNA biogenesis machinery cause strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from its precursor. In plants, miRNA prec...
The regulatory mechanisms involved in plant development include many signals, some of them acting as graded positional cues regulating gene expression in a concentration-dependent manner. These regulatory molecules, that can be considered similar to animal morphogens, control cell behavior in developing organs. A suitable experimental approach to s...
MicroRNAs (miRNAs) are endogenous small RNAs that recognize target sequences by base complementarity and play a role in the regulation of target gene expression. They are processed from longer precursor molecules that harbor a fold-back structure. Plant miRNA precursors are quite variable in size and shape, and are recognized by the processing mach...
MicroRNAs (miRNAs) are endogenous small RNAs that recognize target sequences by base complementarity. They are processed from longer precursors that harbor a fold-back structure. Plant miRNA precursors are quite variable in size and shape, and are recognized by the processing machinery in different ways. However, ancient miRNAs and their binding si...
The GROWTH-REGULATING FACTOR (GRF) family of transcription factors (TFs) is a small gene family found in land plants and is defined by the presence of two highly conserved protein domains: WRC (Trp–Arg–Cys) and QLQ (Gln–Leu–Gln). The WRC domain contains a nuclear localization signal and a zinc (Zn) finger motif involved in DNA binding. The QLQ doma...
Plants have the ability to generate different and new organs throughout their life cycle. Organ growth is mostly determined by the combinatory effects of cell proliferation and cell expansion. Still, organ size and shape are adjusted constantly by environmental conditions and developmental timing. The plasticity of plant development is further illu...
The combinatory effects of cell proliferation and cell elongation determines the rate at which organs growth. In the root meristematic zone cells both divide and expand, while post-mitotic cells in the elongation zone only expands until they reach their final size. The transcription factors of the GROWTH-REGULATING FACTOR (GRF) class promote cell p...
To ensure an adequate organ mass, the daughters of stem cells progress through a transit-amplifying phase displaying rapid cell division cycles before differentiating. Here, we show that Arabidopsis thaliana microRNA miR396 regulates the transition of root stem cells into transit-amplifying cells by interacting with GROWTH-REGULATING FACTORs (GRFs)...
MicroRNAs have turned out to be important regulators of gene expression. These molecules originate from longer transcripts that are processed by ribonuclease III (RNAse III) enzymes. Dicer proteins are essential RNAse III enzymes that are involved in the generation of microRNAs (miRNAs) and other small RNAs. The correct function of Dicer relies on...
Leaf development has been extensively studied on a genetic level. However, little is known about the interplay between the developmental regulators and the cell cycle machinery, a link that ultimately affects leaf form and size. MiR319 is a conserved microRNA that regulates TCP transcription factors involved in multiple developmental pathways, incl...
Plants produce new organs throughout their life span. Leaves first initiate as rod‐like structures protruding from the shoot apical meristem, while they need to pass through different developmental stages to become the flat organ specialized in photosynthesis. Leaf morphogenesis is an active process regulated by many genes and pathways that can gen...
The Growth Regulating Factors (GRFs) are plant specific transcription factors. They form complexes with GRF Interacting Factors (GIFs), a small family of transcriptional co-activators. In Arabidopsis thaliana, seven out of the nine GRFs are controlled by microRNA miR396. Analysis of Arabidopsis plants carrying a GRF3 allele insensitive to miR396 re...
MicroRNAs (miRNAs) are major regulators of gene expression in plants and animals. They recognize their target mRNAs by sequence complementarity and guide them to cleavage or translational arrest. So far, the prediction of plant miRNA-target pairs generally relies on the use of empirical parameters deduced from known miRNA-target interactions.
We de...
Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression o...
MicroRNAs are small RNA molecules that post-transcriptionally regulate gene expression. MicroRNA-122 is the most abundant and specific liver microRNA. Hepatotoxicity involves a significant alteration of liver gene expression. The aim of this work was to evaluate the microRNA-122 regulatory network in models of hepatotoxicity induced by thioacetamid...
Because of their sessile lifestyle, plants are continuously exposed to solar UV-B radiation. Inhibition of leaf growth is one of the most consistent responses of plants upon exposure to UV-B radiation. In this work, we investigated the role of GROWTH-REGULATING FACTORs (GRFs) and of microRNA miR396 in UV-B-mediated inhibition of leaf growth in Arab...
MicroRNAs (miRNAs) derive from longer precursors with fold-back structures. While animal miRNA precursors have homogenous structures, plant precursors comprise a collection of fold-backs with variable size and shape. Here, we design an approach to systematically analyze miRNA processing intermediates and characterize the biogenesis of most of the e...
The root system is crucial for the acquisition of resources from the soil. In legumes, the efficiency of mineral and water uptake by the roots may be reinforced due to the establishment of symbiotic relationships with mycorrhizal fungi and interactions with soil rhizobia. Here, we investigated the role of miR396 in regulating the architecture of th...
Dicer-like ribonuclease III enzymes are involved in different paths related to RNA silencing in plants. Little is known about the structural aspects of these processes. Here we present a structural characterization of the second double-stranded RNA binding domain (dsRBD) of DCL1, which is presumed to participate in pri-micro-RNA recognition and sub...
MicroRNAs are endogenous small RNAs known to be key regulators of gene expression in animals and plants. They are defined
by their specific biogenesis which involves the precise excision from an imperfect fold-back precursor. These precursors contain
structural determinants required for their correct processing. Still, there are significant differe...
The microRNA (miRNA) miR396 regulates GROWTH-REGULATING FACTORs (GRFs), a plant specific family of transcription factors. Overexpression of miR396 causes a decrease in the GRFs that has been shown to affect cell proliferation in the meristem and developing leaves. To bring further insights into the function of the miR396 regulatory network we perfo...
MicroRNAs (miRNAs) are major regulators of gene expression in multicellular organisms. They recognize their targets by sequence
complementarity and guide them to cleavage or translational arrest. It is generally accepted that plant miRNAs have extensive
complementarity to their targets and their prediction usually relies on the use of empirical par...
Hepatotoxicity is associated with major changes in liver gene expression induced by xenobiotic exposure. Understanding the underlying mechanisms is critical for its clinical diagnosis and treatment. MicroRNAs are key regulators of gene expression that control mRNA stability and translation, during normal development and pathology. The canonical tec...
Representative amplification and melt-curve profiles of Real-Time qPCR assays.
(PDF)
Normality assessment of log-transformed expression data of candidate reference genes by Shapiro-Wilk test.
(PDF)
Experimental validation of all expression data of ribosomal genes evaluating their inclusion within the dynamic range of RT-qPCR.
(PDF)
Checklist MIQE.
(PDF)
qPCR raw data in RDML language.
(RAR)
Outputs of geNorm, NormFinder, BestKeeper and RankAggreg.
(PDF)
Example of calculation of the Normalization efficiency index (NEI) for different normalization methods in an study of liver gene expression between control and carbon tetrachloride (CT) treated rats.
(XLS)
Study of normalization efficiency of candidate reference genes for microRNA and mRNA in differents models of hepatotoxicity.
(PDF)
Originally identified in a genetic screen, microRNA miR319 regulates transcription factors of the TCP family. The balance between miR319 and its targets controls leaf morphogenesis and several other plant developmental processes. High levels of miR319 or low TCP activity causes an excess of cell proliferation that generates a crinkled simple leaf i...
MicroRNAs (miRNAs) are ∼21 nt small RNAs that regulate gene expression in animals and plants. They can be grouped into families comprising different genes encoding similar or identical mature miRNAs. Several miRNA families are deeply conserved in plant lineages and regulate key aspects of plant development, hormone signaling, and stress response. T...
Effects of high expression levels of bHLH74 on Arabidopsis thaliana development. (A) Schematic representation of the 35S:bHLH74 and 35S:rbHLH74 constructs. (B) Phenotypes observed in 12-day old T1 seedlings overexpressing bHLH74 or rbHLH74. Phenotypes were classified according to their strength (numbers 1 to 4). Arrowheads indicate the elongated co...
Interaction of the bHLH74 target site with (A) Arabidopsis miR396a and (B) the monocot-specific variant (miR396_7-8insG).
(TIF)
Expression of different miR396 variants in publicly available small RNA sequencing libraries.
(DOC)
Small RNA blot of miR396. Small RNA blot showing miR396 levels in control plants (transformed with an empty vector) and transgenic plants expressing Arabidopsis miR396b or miR396_7-8insG displaying an intermediate phenotype (see Figure 6F). A locked nucleic acid (LNA) probe against miR396b was used.
(TIF)
Predicted targets of miR396 in poplar.
(DOC)
Binary plasmids prepared for this study.
(DOC)
Relevant locus identifiers, mutant alleles and RT-qPCR primers.
(DOC)
Sequence alignment of bHLH74 homologs from several species. Alignment of partial coding sequences for bHLH74. A red box highlights the miR396 target site and a grey box depicts part of the coding sequence of the bHLH domain. Conserved positions across all species are indicated by asterisks. See Table S4 for accession numbers of sequences used.
(TIF...
Predicted targets of miR396 in Arabidopsis thaliana.
(DOC)
Variations in the mature sequence of conserved miRNA families. (A) and (B) Variations in the mature sequence of miRNAs conserved in angiosperms (20 families). Bars represent the nucleotide changes in miRNA obtained for each family from position 1 to 21. Variation for each family was normalized to the number of members so that each family contribute...
Description of the method used to quantify miR396 variants. The retrotranscription reaction was performed using a stem-loop oligo that matches the three miR396 variants. For the qPCR, an equimolar mix of primers matching the miR396 variants was used. PCR efficiencies were checked to be equivalent for the different miRNAs.
(TIF)
Overexpression of miR396_7A>G in Arabidopsis thaliana. (A) Scheme showing the secondary structure of the miRNA-miRNA* region in miR396 precursors from Arabidopsis thaliana, Selaginella moellendorffii and Picea glauca. miR396 sequence is indicated in red. Note that a G-A change in position 7 of the mature miRNA sequence (indicated in light gray) doe...
Predicted targets of miR396 in rice.
(DOC)
Sequences used to analyze the conservation of the miR396 target site.
(DOC)
It has been demonstrated that protein folds can be determined using appropriate computational protocols with NMR chemical shifts as the sole source of experimental restraints. While such approaches are very promising they still suffer from low convergence resulting in long computation times to achieve accurate results. Here we present a suite of ti...
MicroRNAs (miRNAs) are small RNAs of ∼21 nt that regulate multiple biological pathways in complex organisms. They are defined
by their specific biogenesis that involves the precise excision from an imperfect fold-back precursor. In plants, the ribonuclease
III DICER-LIKE1 (DCL1) assisted by accessory proteins cleaves the precursor to release the mi...
The KNOXI transcription factor SHOOT MERISTEMLESS (STM) is required to establish and maintain the Arabidopsis (Arabidopsis thaliana) apical meristem, yet little is known about its direct targets. Using different approaches we demonstrate that the induction of STM causes a significant up-regulation of the organ boundary gene CUP SHAPED COTYLEDON1 (C...
Two Arabidopsis thaliana genes (HCC1 and HCC2), resulting from a duplication that took place before the emergence of flowering plants, encode proteins with homology to
the SCO proteins involved in copper insertion during cytochrome c oxidase (COX) assembly in other organisms. Heterozygote HCC1 mutant plants produce 25% abnormal seeds with defective...
HYL1 is a double-stranded RNA binding protein involved in microRNA processing in plants. HYL1 enhances the efficiency and precision of the RNase III protein DCL1 and participates in microRNA strand selection. In this work, we dissect the contributions of the domains of HYL1 to the binding of RNA targets. We found that the first domain is the main c...
Cell proliferation is an important determinant of plant form, but little is known about how developmental programs control cell division. Here, we describe the role of microRNA miR396 in the coordination of cell proliferation in Arabidopsis leaves. In leaf primordia, miR396 is expressed at low levels that steadily increase during organ development....
MicroRNAs (miRNAs) are widespread posttranscriptional regulators of gene expression. They are processed from longer primary transcripts that contain foldback structures (reviewed in). In animals, a complex formed by Drosha and DGCR8/Pasha recognizes the transition between the single-stranded RNA sequences and the stem loop to produce the first clea...
The first step in microRNA (miRNA) biogenesis usually involves cleavage at the base of its fold-back precursor. Here, we describe a non-canonical processing mechanism for miRNAs miR319 and miR159 in Arabidopsis thaliana. We found that their biogenesis begins with the cleavage of the loop, instead of the usual cut at the base of the stem-loop struct...
A major challenge in structural biology remains the identification of protein constructs amenable to structural characterization. Here, we present a simple method for parallel expression, labeling, and purification of protein constructs (up to 80 kDa) combined with rapid evaluation by NMR spectroscopy. Our approach, which is equally applicable for...