scholarly journals Auxin methylation is required for differential growth inArabidopsis

2018 ◽  
Vol 115 (26) ◽  
pp. 6864-6869 ◽  
Author(s):  
Mohamad Abbas ◽  
Jorge Hernández-García ◽  
Stephan Pollmann ◽  
Sophia L. Samodelov ◽  
Martina Kolb ◽  
...  
Keyword(s):  
Gene Expression ◽  
Auxin Transport ◽  
Polar Auxin Transport ◽  
Asymmetric Distribution ◽  
Loss Of Function ◽  
Differential Growth ◽  
Specific Expression ◽  
Auxin Homeostasis ◽  
Auxin Distribution ◽  
Gene Expression Levels

Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants inArabidopsis IAA CARBOXYL METHYLTRANSFERASE1(IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase inPINgene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in theiamt1mutant. Gravitropic reorientation in theiamt1mutant could be restored with either endodermis-specific expression ofIAMT1or partial inhibition of polar auxin transport, which also results in normalPINgene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.

scholarly journals Role of auxin homeostasis and response in nitrogen limitation and dark stimulation of adventitious root formation in petunia cuttings

2019 ◽  
Vol 124 (6) ◽  
pp. 1053-1066 ◽  
Author(s):  
Huaiyu Yang ◽  
Yvonne Klopotek ◽  
Mohammad R Hajirezaei ◽  
Siegfried Zerche ◽  
Philipp Franken ◽  
...  
Keyword(s):  
Nitrogen Limitation ◽  
Auxin Transport ◽  
Polar Auxin Transport ◽  
Auxin Homeostasis ◽  
Stem Base ◽  
Auxin Signalling ◽  
Dark Exposure ◽  
Rna Accumulation ◽  
Low Nitrogen ◽  
Stimulation Of

Abstract Background and Aims Adventitious root (AR) formation in Petunia hybrida is inhibited by low nitrogen fertilization of stock plants but promoted by dark incubation of cuttings before planting. We investigated whether the plant hormone auxin is involved in nitrogen- and dark-mediated AR formation. Methods Concentrations of indole-3-acetic acid (IAA) and RNA accumulation of genes controlling auxin homeostasis and function were monitored in the stem base in response to high versus low nitrogen supply to stock plants and to temporal dark vs. light exposure of cuttings by use of GC-MS/MS, a petunia-specific microarray and quantitative RT-PCR. Auxin source capacity, polar auxin transport in cuttings and auxin concentration in the rooting zone were manipulated to investigate the functional contribution of auxin homeostasis and response to the effects of nitrogen fertilization and dark exposure on rooting. Key Results The nitrogen content of cuttings had only a marginal effect on IAA concentration in the stem base. Dark incubation enhanced the accumulation of IAA in the stem base during AR induction independent of nitrogen level. Early IAA accumulation in the dark depended on the upper shoot as an auxin source and was enhanced after apical IAA supply. Dark exposure stimulated RNA accumulation of auxin-related genes. In particular, expression of Ph-PIN1 and of genes controlling auxin signalling, including Ph-IAA14, Ph-ARF8, Ph-ARF10 and Ph-SAUR14, was enhanced, while the latter four were repressed in nitrogen-limited cuttings, particularly in the dark. Dark stimulation of rooting depended on polar auxin transport. Basal auxin application partially substituted the effect of dark exposure on rooting, whereas the auxin response of AR formation was strongly depressed by nitrogen limitation. Conclusions Increased auxin delivery from the upper shoot and enhanced auxin signalling in the stem base contribute to dark-stimulated AR formation, while nitrogen limitation inhibits AR formation downstream of the auxin signal.

Expression profiles of metamorphosis-related genes during natural transformations in tadpoles of wild Wood Frogs (Lithobates sylvaticus)

2012 ◽  
Vol 90 (9) ◽  
pp. 1059-1071 ◽  
Author(s):  
Laia Navarro-Martín ◽  
Chantal Lanctôt ◽  
Christopher Edge ◽  
Jeff Houlahan ◽  
Vance L. Trudeau
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Rana Sylvatica ◽  
Fold Increase ◽  
Gonadal Development ◽  
Specific Expression ◽  
Wood Frogs ◽  
Lithobates Sylvaticus ◽  
Expression Levels ◽  
Gene Expression Levels

Numerous studies using laboratory-reared tadpoles have shown the importance of thyroid hormones (TH), thyroid receptors (TR), and deiodinase (Dio) enzymes during anuran metamorphosis. Our study focuses on the analysis of thyroid-related genes in tadpoles of wild Wood Frogs ( Lithobates sylvaticus (LeConte, 1825); also known as Rana sylvatica (Cope, 1889)) during metamorphosis. Results showed that, in concordance with laboratory-reared studies, thyroid receptor beta (trb) gene expression profiles presented the most marked changes. At climax and compared with premetamorphic stages, brains, tails, and gonad–mesonephros complex (GMC) tissues increased trb expression levels 5-, 21-, and 41-fold, respectively (p < 0.05). In addition, gene expression levels of brain deiodinase type II and III showed opposite trends, where 3-fold decrease and 10-fold increase were, respectively, found. This finding supports the idea that thyroid hormone, as it has been demonstrated in laboratory-reared tadpoles, is also involved in natural metamorphosis in wild tadpoles. Interestingly, and contrary to our predictions, we observed that whole brain corticotropin-releasing factor (crf) and crf receptor 1 (crfr1) gene expression levels significantly decrease through metamorphosis in wild L. sylvaticus tadpoles. Further analyses are required to determine if a role of TH in the timing of anuran gonadal development exists, as well as the importance of cell-specific and tissue-specific expression of crf and crfr1 to metamorphosis.

scholarly journals Cis- and Trans-Regulatory Variations in the Domestication of the Chili Pepper Fruit

2020 ◽  
Vol 37 (6) ◽  
pp. 1593-1603 ◽  
Author(s):  
Erik Díaz-Valenzuela ◽  
Ruairidh H Sawers ◽  
Angélica Cibrián-Jaramillo
Keyword(s):  
Gene Expression ◽  
Chili Pepper ◽  
Loss Of Function ◽  
Morphological Transformation ◽  
Specific Expression ◽  
Network Analyses ◽  
Regulatory Variants ◽  
Regulatory Cascades ◽  
In The Wild ◽  
Cis And Trans

Abstract The process of domestication requires the rapid transformation of the wild morphology into the cultivated forms that humans select for. This process often takes place through changes in the regulation of genes, yet, there is no definite pattern on the role of cis- and trans-acting regulatory variations in the domestication of the fruit among crops. Using allele-specific expression and network analyses, we characterized the regulatory patterns and the inheritance of gene expression in wild and cultivated accessions of chili pepper, a crop with remarkable fruit morphological variation. We propose that gene expression differences associated to the cultivated form are best explained by cis-regulatory hubs acting through trans-regulatory cascades. We show that in cultivated chili, the expression of genes associated with fruit morphology is partially recessive with respect to those in the wild relative, consistent with the hybrid fruit phenotype. Decreased expression of fruit maturation and growth genes in cultivated chili suggest that selection for loss-of-function took place in its domestication. Trans-regulatory changes underlie the majority of the genes showing regulatory divergence and had larger effect sizes on gene expression than cis-regulatory variants. Network analysis of selected cis-regulated genes, including ARP9 and MED25, indicated their interaction with many transcription factors involved in organ growth and fruit ripening. Differentially expressed genes linked to cis-regulatory variants and their interactions with downstream trans-acting genes have the potential to drive the morphological differences observed between wild and cultivated fruits and provide an attractive mechanism of morphological transformation during the domestication of the chili pepper.

scholarly journals The genetic architecture of gene expression levels in wild baboons

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Jenny Tung ◽  
Xiang Zhou ◽  
Susan C Alberts ◽  
Matthew Stephens ◽  
Yoav Gilad
Keyword(s):  
Gene Expression ◽  
Genetic Architecture ◽  
Eqtl Mapping ◽  
Rna Seq ◽  
Specific Expression ◽  
Data Set ◽  
Expression Levels ◽  
Trait Locus ◽  
Eqtl Data ◽  
Gene Expression Levels

Primate evolution has been argued to result, in part, from changes in how genes are regulated. However, we still know little about gene regulation in natural primate populations. We conducted an RNA sequencing (RNA-seq)-based study of baboons from an intensively studied wild population. We performed complementary expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses, discovering substantial evidence for, and surprising power to detect, genetic effects on gene expression levels in the baboons. eQTL were most likely to be identified for lineage-specific, rapidly evolving genes; interestingly, genes with eQTL significantly overlapped between baboons and a comparable human eQTL data set. Our results suggest that genes vary in their tolerance of genetic perturbation, and that this property may be conserved across species. Further, they establish the feasibility of eQTL mapping using RNA-seq data alone, and represent an important step towards understanding the genetic architecture of gene expression in primates.

scholarly journals ATANN3 is involved in extracellular ATP-regulated auxin transport and distribution in Arabidopsis thaliana seedlings

2021 ◽  
Author(s):  
Lijuan Han ◽  
Shuyan Xia ◽  
Jiawei Xu ◽  
Ruojia Zhu ◽  
Zhonglin Shang ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Stress Responses ◽  
Auxin Transport ◽  
Inhibitory Effect ◽  
Extracellular Atp ◽  
Root Tip ◽  
Asymmetric Distribution ◽  
Loss Of Function ◽  
Hypocotyl Growth

Abstract Background Extracellular ATP (eATP) exists in the apoplast of plants and plays multiple roles in growth, development, and stress responses. It has been reported that eATP stimulation suppresses growth rate and alters growth orientation of root and hypocotyls of Arabidopsis thaliana seedlings by affecting auxin accumulation and transport in these organs. However, the mechanism of eATP-stimulated vegetative organ growth remains unclear. Annexins are involved in multiple aspects of plant cellular metabolism, while the role of annexins in response to apoplast signal remains unclear. Here, by using loss-of-function mutants, we investigated the role of several annexins in eATP-regulated root and hypocotyl growth. Since mutant of AtANN3 did not respond to eATP sensitively, the role of AtANN3 in eATP regulated auxin transport was intensively investigated. Results First, the inhibitory effect of eATP on root or hypocotyl elongation was weakened or impaired in AtANN3 null mutants (atann3). Meanwhile, single-, double- or triple-null mutant of AtANN1, AtANN2 or AtANN4 responded to eATP stimulation in same manner and degree with Col-0. The abundance and distribution of Dr5-GUS and Dr5-GFP indicated that eATP-induced accumulation and asymmetric distribution of auxin in root tip or hypocotyl cells, which appeared in wild type controls, were lacking in atann3 seedlings. Further, eATP-induced accumulation and asymmetric distribution of PIN2-GFP in root tip cells or PIN3-GFP in hypocotyl cells were reduced in atann3 seedlings. Conclusions AtANN3 may be involved in eATP-regulated seedling growth through regulating auxin transport and accumulation in vegetative organs.

scholarly journals Auxin perception and polar auxin transport are not always a prerequisite for differential growth

2009 ◽  
Vol 4 (9) ◽  
pp. 899-901 ◽  
Author(s):  
Martijn van Zanten ◽  
Frank F. Millenaar ◽  
Marjolein C.H. Cox ◽  
Ronald Pierik ◽  
Laurentius A.C.J. Voesenek ◽  
...  
Keyword(s):  
Auxin Transport ◽  
Polar Auxin Transport ◽  
Differential Growth

scholarly journals Cis-Repression of Foxq1 Expression Affects Foxf2-Mediated Gene Expression in Palate Development

2021 ◽  
Vol 9 ◽  
Author(s):  
Jingyue Xu ◽  
Han Liu ◽  
Yu Lan ◽  
Rulang Jiang
Keyword(s):  
Gene Expression ◽  
Cleft Palate ◽  
Chromatin Domain ◽  
Loss Of Function ◽  
Specific Expression ◽  
Palate Development ◽  
Domain Specific ◽  
Conditional Allele ◽  
Or Gene ◽  
Conserved Gene

Disruption of FOXF2, encoding a member of the Forkhead family transcription factors, has been associated with cleft palate in humans and mice. FOXF2 is located in a conserved gene cluster containing FOXQ1, FOXF2, and FOXC1. We found that expression of Foxq1 is dramatically upregulated in the embryonic palatal mesenchyme in Foxf2–/– mouse embryos. We show here that the Foxf2 promoter-deletion mutation caused dramatically increased expression of the cis-linked Foxq1 allele but had little effect on the Foxq1 allele in trans. We analyzed effects of the Foxf2 mutation on the expression of other neighboring genes and compared those effects with the chromatin domain structure and recently identified enhancer-promoter associations as well as H3K27ac ChIP-seq data. We show that the Foxf2 mutation resulted in significantly increased expression of the Foxq1 and Exoc2 genes located in the same topologically associated domain with Foxf2 but not the expression of the Foxc1 and Gmds genes located in the adjacent chromatin domain. We inactivated the Foxq1 gene in mice homozygous for a Foxf2 conditional allele using CRISPR genome editing and generated (Foxf2/Foxq1)+/– mice with loss-of-function mutations in Foxf2 and Foxq1 in cis. Whereas the (Foxf2/Foxq1)–/– mice exhibited cleft palate at birth similar as in the Foxf2–/– mice, systematic expression analyses of a large number of Foxf2-dependent genes revealed that the (Foxf2/Foxq1)–/– embryos exhibited distinct effects on the domain-specific expression of several important genes, including Foxf1, Shox2, and Spon1, in the developing palatal shelves compared with Foxf2–/– embryos. These results identify a novel cis-regulatory effect of the Foxf2 mutation and demonstrate that cis-regulation of Foxq1 contributed to alterations in palatal gene expression in Foxf2–/– embryos. These results have important implications for interpretation of results and mechanisms from studies of promoter- or gene-deletion alleles. In addition, the unique mouse lines generated in this study provide a valuable resource for understanding the cross-regulation and combinatorial functions of the Foxf2 and Foxq1 genes in development and disease.

scholarly journals The Arabidopsis R-SNARE VAMP714 is essential for polarization of PIN proteins in the establishment and maintenance of auxin gradients

2019 ◽  
Author(s):  
Xiaoyan Gu ◽  
Kumari Fonseka ◽  
Stuart A. Casson ◽  
Andrei Smertenko ◽  
Guangqin Guo ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Auxin Transport ◽  
Protein Localization ◽  
Adaptor Protein ◽  
Dominant Negative ◽  
Endocytic Pathway ◽  
Asymmetric Distribution ◽  
List Type ◽  
Loss Of Function ◽  
Regulatory Loop

SummaryThe plant hormone auxin and its directional intercellular transport plays a major role in diverse aspects of plant growth and development. The establishment of auxin gradients in plants requires asymmetric distribution of members of the auxin efflux carrier PIN-FORMED (PIN) protein family to the plasma membrane. An endocytic pathway regulates the recycling of PIN proteins between the plasma membrane and endosomes, providing a mechanism for dynamic localization.N-ethylmaleimide-sensitive factor adaptor protein receptors (SNAP receptors, SNAREs) mediate fusion between vesicles and target membranes and are classed as Q- or R-SNAREs based on their sequence. We analysed gain- and loss-of-function mutants, dominant negative transgenics and protein localization of the Arabidopsis R-SNARE VAMP714 to understand its function.We demonstrate that VAMP714 is essential for the insertion of PINs into the plasmamembrane, for polar auxin transport, and for root gravitropism and morphogenesis. VAMP714 gene expression is upregulated by auxin, and the VAMP714 protein co-localizes with ER and Golgi vesicles and with PIN proteins at the plasma membrane.It is proposed that VAMP714 mediates the delivery of PIN-carrying vesicles to the plasma membrane, and that this forms part of a positive regulatory loop in which auxin activates a VAMP714-dependent PIN/auxin transport system to control development.

scholarly journals Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Matthew Jensen ◽  
Anastasia Tyryshkina ◽  
Lucilla Pizzo ◽  
Corrine Smolen ◽  
Maitreya Das ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Delay ◽  
Gene Networks ◽  
Phenotypic Variability ◽  
Specific Interaction ◽  
Loss Of Function ◽  
Specific Expression ◽  
Second Hit ◽  
Complex Disorders ◽  
Variable Expressivity

Abstract Background Recent studies have suggested that individual variants do not sufficiently explain the variable expressivity of phenotypes observed in complex disorders. For example, the 16p12.1 deletion is associated with developmental delay and neuropsychiatric features in affected individuals, but is inherited in > 90% of cases from a mildly-affected parent. While children with the deletion are more likely to carry additional “second-hit” variants than their parents, the mechanisms for how these variants contribute to phenotypic variability are unknown. Methods We performed detailed clinical assessments, whole-genome sequencing, and RNA sequencing of lymphoblastoid cell lines for 32 individuals in five large families with multiple members carrying the 16p12.1 deletion. We identified contributions of the 16p12.1 deletion and “second-hit” variants towards a range of expression changes in deletion carriers and their family members, including differential expression, outlier expression, alternative splicing, allele-specific expression, and expression quantitative trait loci analyses. Results We found that the deletion dysregulates multiple autism and brain development genes such as FOXP1, ANK3, and MEF2. Carrier children also showed an average of 5323 gene expression changes compared with one or both parents, which matched with 33/39 observed developmental phenotypes. We identified significant enrichments for 13/25 classes of “second-hit” variants in genes with expression changes, where 4/25 variant classes were only enriched when inherited from the noncarrier parent, including loss-of-function SNVs and large duplications. In 11 instances, including for ZEB2 and SYNJ1, gene expression was synergistically altered by both the deletion and inherited “second-hits” in carrier children. Finally, brain-specific interaction network analysis showed strong connectivity between genes carrying “second-hits” and genes with transcriptome alterations in deletion carriers. Conclusions Our results suggest a potential mechanism for how “second-hit” variants modulate expressivity of complex disorders such as the 16p12.1 deletion through transcriptomic perturbation of gene networks important for early development. Our work further shows that family-based assessments of transcriptome data are highly relevant towards understanding the genetic mechanisms associated with complex disorders.

scholarly journals Threshold Levels of Hepatocyte Nuclear Factor 6 (HNF-6) Acting in Synergy with HNF-4 and PGC-1α Are Required for Time-Specific Gene Expression during Liver Development

2006 ◽  
Vol 26 (16) ◽  
pp. 6037-6046 ◽  
Author(s):  
Jean-Bernard Beaudry ◽  
Christophe E. Pierreux ◽  
Graham P. Hayhurst ◽  
Nicolas Plumb-Rudewiez ◽  
Mary C. Weiss ◽  
...  
Keyword(s):  
Gene Expression ◽  
Specific Gene ◽  
Liver Development ◽  
Nuclear Factor ◽  
Hepatocyte Nuclear Factor ◽  
Loss Of Function ◽  
Specific Expression ◽  
Threshold Levels ◽  
Time Specific

ABSTRACT During liver development, hepatocytes undergo a maturation process that leads to the fully differentiated state. This relies at least in part on the coordinated action of liver-enriched transcription factors (LETFs), but little is known about the dynamics of this coordination. In this context we investigate here the role of the LETF hepatocyte nuclear factor 6 (HNF-6; also called Onecut-1) during hepatocyte differentiation. We show that HNF-6 knockout mouse fetuses have delayed expression of glucose-6-phosphatase (g6pc), which catalyzes the final step of gluconeogenesis and is a late marker of hepatocyte maturation. Using a combination of in vivo and in vitro gain- and loss-of-function approaches, we demonstrate that HNF-6 stimulates endogenous g6pc gene expression directly via a synergistic and interdependent action with HNF-4 and that it involves coordinate recruitment of the coactivator PGC-1α. The expression of HNF-6, HNF-4, and PGC-1α rises steadily during liver development and precedes that of g6pc. We provide evidence that threshold levels of HNF-6 are required to allow synergism between HNF-6, HNF-4, and PGC-1α to induce time-specific expression of g6pc. Our observations on the regulation of g6pc by HNF-6 provide a model whereby synergism, interdependency, and threshold concentrations of LETFs and coactivators determine time-specific expression of genes during liver development.

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