Actin-Related Protein 4 Interacts with PIE1 and Regulates Gene Expression in Arabidopsis

As essential structural components of ATP-dependent chromatin-remodeling complex, the nucleolus-localized actin-related proteins (ARPs) play critical roles in many biological processes. Among them, ARP4 is identified as an integral subunit of chromatin remodeling complex SWR1, which is conserved in yeast, humans and plants. It was shown that RNAi mediated knock-down of Arabidopsis thaliana ARP4 (AtARP4) could affect plant development, specifically, leading to early flowering. However, so far, little is known about how ARP4 functions in the SWR1 complex in plant. Here, we identified a loss-of-function mutant of AtARP4 with a single nucleotide change from glycine to arginine, which had significantly smaller leaf size. The results from the split luciferase complementation imaging (LCI) and yeast two hybrid (Y2H) assays confirmed its physical interaction with the scaffold and catalytic subunit of SWR1 complex, photoperiod-independent early flowering 1 (PIE1). Furthermore, mutation of AtARP4 caused altered transcription response of hundreds of genes, in which the number of up-regulated differentially expressed genes (DEGs) was much larger than those down-regulated. Although most DEGs in atarp4 are related to plant defense and response to hormones such as salicylic acid, overall, it has less overlapping with other swr1 mutants and the hta9 hta11 double-mutant. In conclusion, our results reveal that AtARP4 is important for plant growth and such an effect is likely attributed to its repression on gene expression, typically at defense-related loci, thus providing some evidence for the coordination of plant growth and defense, while the regulatory patterns and mechanisms are distinctive from other SWR1 complex components.

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The SWI/SNF Chromatin Remodeling Complex Regulates Myocardin-Induced Smooth Muscle–Specific Gene Expression

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvbaha.109.187229 ◽

2009 ◽

Vol 29 (6) ◽

pp. 921-928 ◽

Cited By ~ 54

Author(s):

Jiliang Zhou ◽

Min Zhang ◽

Hong Fang ◽

Omar El-Mounayri ◽

Jennifer M. Rodenberg ◽

...

Keyword(s):

Gene Expression ◽

Smooth Muscle ◽

Chromatin Remodeling ◽

Specific Gene ◽

Specific Gene Expression ◽

Chromatin Remodeling Complex

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LFR Physically and Genetically Interacts With SWI/SNF Component SWI3B to Regulate Leaf Blade Development in Arabidopsis

Frontiers in Plant Science ◽

10.3389/fpls.2021.717649 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiaowei Lin ◽

Can Yuan ◽

Bonan Zhu ◽

Tingting Yuan ◽

Xiaorong Li ◽

...

Keyword(s):

Chromatin Remodeling ◽

Apical Meristem ◽

Peripheral Zone ◽

Transcriptional Expression ◽

Loss Of Function ◽

Leaf Lamina ◽

Protein Protein Interaction ◽

Chromatin Remodeling Complex ◽

Leaf Phenotype ◽

Metabolism Enzyme

Leaves start to develop at the peripheral zone of the shoot apical meristem. Thereafter, symmetric and flattened leaf laminae are formed. These events are simultaneously regulated by auxin, transcription factors, and epigenetic regulatory factors. However, the relationships among these factors are not well known. In this study, we conducted protein-protein interaction assays to show that our previously reported Leaf and Flower Related (LFR) physically interacted with SWI3B, a component of the ATP-dependent chromatin remodeling SWI/SNF complex in Arabidopsis. The results of truncated analysis and transgenic complementation showed that the N-terminal domain (25–60 amino acids) of LFR was necessary for its interaction with SWI3B and was crucial for LFR functions in Arabidopsis leaf development. Genetic results showed that the artificial microRNA knockdown lines of SWI3B (SWI3B-amic) had a similar upward-curling leaf phenotype with that of LFR loss-of-function mutants. ChIP-qPCR assay was conducted to show that LFR and SWI3B co-targeted the promoters of YABBY1/FILAMENTOUS FLOWER (YAB1/FIL) and IAA carboxyl methyltransferase 1 (IAMT1), which were misexpressed in lfr and SWI3B-amic mutants. In addition, the association between LFR and the FIL and IAMT1 loci was partly hampered by the knockdown of SWI3B. These data suggest that LFR interacts with the chromatin-remodeling complex component, SWI3B, and influences the transcriptional expression of the important transcription factor, FIL, and the auxin metabolism enzyme, IAMT1, in flattened leaf lamina development.

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Frameshift Variant in ARID2 in a Chilean Individual with Coffin–Siris Syndrome Phenotype

Journal of Pediatric Genetics ◽

10.1055/s-0041-1740531 ◽

2021 ◽

Author(s):

Fernanda Martin Merlez ◽

María González Zalazar ◽

Silvia Castillo Taucher

Keyword(s):

Chromatin Remodeling ◽

Scalp Hair ◽

Case Reports ◽

Regulation Of Gene Expression ◽

Loss Of Function ◽

Disease Mechanism ◽

Chromatin Remodeling Complex ◽

Behavioral Abnormalities ◽

Whole Exome ◽

First Time

AbstractCoffin–Siris syndrome (CSS) is one of the several causes of intellectual disability (ID) and, since its first description, has posed diagnostic challenges given its variability and phenotypic overlap with other alterations of chromatin-remodeling-associated syndromes. It is genetically heterogeneous, and causative mutations are detected in less than 70% of cases. The different subtypes of the syndrome described to date are caused by mutations in genes that encode subunits of the SWI/SNF chromatin-remodeling complex, which plays an essential role in the regulation of gene expression during embryogenesis. Whole exome sequencing (WES) has allowed the identification of pathogenic mutations in these genes, including ARID2. ARID2 is one of the primary components of the SWI/SNF complex and has been associated with ID and phenotypes similar to CSS for the first time in 2015. Fifteen published case reports have identified loss-of-function mutations, suggesting that the underlying pathogenic disease mechanism is haploinsufficiency of ARID2.We herein presented the case of an 8-year-old Chilean girl with clinical suspicion of CSS, in whom a novel frameshift variant in ARID2 was identified by WES. She was the first reported case in Latin America to our knowledge and her phenotype displays the main clinical features suggestive of CSS described in other patients with ARID2 variants. However, she did not present behavioral abnormalities, a characteristic frequently reported in the majority of patients with ARID2 variants, and also had some features, such as sparse scalp hair, which is frequently reported as a manifestation of CSS, but is uncommon in this new group of patients.

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Akirin Is Required for Muscle Function and Acts Through the TGF-β Sma/Mab Signaling Pathway in Caenorhabditis elegans Development

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400377 ◽

2019 ◽

Vol 10 (1) ◽

pp. 387-400 ◽

Cited By ~ 1

Author(s):

Richard Bowman ◽

Nathan Balukoff ◽

Amy Clemons ◽

Emily Koury ◽

Talitha Ford ◽

...

Keyword(s):

Body Size ◽

Caenorhabditis Elegans ◽

Signaling Pathway ◽

Chromatin Remodeling ◽

Muscle Development ◽

The Body ◽

Model Systems ◽

Loss Of Function ◽

C Elegans ◽

Chromatin Remodeling Complex

Akirin, a conserved metazoan protein, functions in muscle development in flies and mice. However, this was only tested in the rodent and fly model systems. Akirin was shown to act with chromatin remodeling complexes in transcription and was established as a downstream target of the NFκB pathway. Here we show a role for Caenorhabditis elegans Akirin/AKIR-1 in the muscle and body length regulation through a different pathway. Akirin localizes to somatic tissues throughout the body of C. elegans, including muscle nuclei. In agreement with its role in other model systems, Akirin loss of function mutants exhibit defects in muscle development in the embryo, as well as defects in movement and maintenance of muscle integrity in the C. elegans adult. We also have determined that Akirin acts downstream of the TGF-β Sma/Mab signaling pathway in controlling body size. Moreover, we found that the loss of Akirin resulted in an increase in autophagy markers, similar to mutants in the TGF-β Sma/Mab signaling pathway. In contrast to what is known in rodent and fly models, C. elegans Akirin does not act with the SWI/SNF chromatin-remodeling complex, and is instead involved with the NuRD chromatin remodeling complex in both movement and regulation of body size. Our studies define a novel developmental role (body size) and a new pathway (TGF-β Sma/Mab) for Akirin function, and confirmed its evolutionarily conserved function in muscle development in a new organism.

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The chromatin remodeling complex subunit Baf60c regulates essential gene expression programs in heart development

Developmental Biology ◽

10.1016/j.ydbio.2011.05.645 ◽

2011 ◽

Vol 356 (1) ◽

pp. 174

Author(s):

Xin Sun ◽

John Wylie ◽

Yuqing Zhou ◽

Danos Christodoulou ◽

Christine E. Seidman ◽

...

Keyword(s):

Gene Expression ◽

Chromatin Remodeling ◽

Heart Development ◽

Essential Gene ◽

Chromatin Remodeling Complex

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Wongabel Rhabdovirus Accessory Protein U3 Targets the SWI/SNF Chromatin Remodeling Complex

Journal of Virology ◽

10.1128/jvi.02010-14 ◽

2014 ◽

Vol 89 (2) ◽

pp. 1377-1388

Author(s):

D. Albert Joubert ◽

Julio Rodriguez-Andres ◽

Paul Monaghan ◽

Michelle Cummins ◽

William J. McKinstry ◽

...

Keyword(s):

Gene Expression ◽

Viral Replication ◽

Chromatin Remodeling ◽

Unknown Function ◽

Host Response ◽

Accessory Protein ◽

Accessory Proteins ◽

Content Type ◽

Chromatin Remodeling Complex ◽

Regulated Expression

ABSTRACTWongabel virus (WONV) is an arthropod-borne rhabdovirus that infects birds. It is one of the growing array of rhabdoviruses with complex genomes that encode multiple accessory proteins of unknown function. In addition to the five canonical rhabdovirus structural protein genes (N, P, M, G, and L), the 13.2-kb negative-sense single-stranded RNA (ssRNA) WONV genome contains five uncharacterized accessory genes, one overlapping the N gene (Nx or U4), three located between the P and M genes (U1 to U3), and a fifth one overlapping the G gene (Gx or U5). Here we show that WONV U3 is expressed during infection in insect and mammalian cells and is required for efficient viral replication. A yeast two-hybrid screen against a mosquito cell cDNA library identified that WONV U3 interacts with the 83-amino-acid (aa) C-terminal domain of SNF5, a component of the SWI/SNF chromatin remodeling complex. The interaction was confirmed by affinity chromatography, and nuclear colocalization was established by confocal microscopy. Gene expression studies showed that SNF5 transcripts are upregulated during infection of mosquito cells with WONV, as well as West Nile virus (Flaviviridae) and bovine ephemeral fever virus (Rhabdoviridae), and that SNF5 knockdown results in increased WONV replication. WONV U3 also inhibits SNF5-regulated expression of the cytokine geneCSF1. The data suggest that WONV U3 targets the SWI/SNF complex to block the host response to infection.IMPORTANCEThe rhabdoviruses comprise a large family of RNA viruses infecting plants, vertebrates, and invertebrates. In addition to the major structural proteins (N, P, M, G, and L), many rhabdoviruses encode a diverse array of accessory proteins of largely unknown function. Understanding the role of these proteins may reveal much about host-pathogen interactions in infected cells. Here we examine accessory protein U3 of Wongabel virus, an arthropod-borne rhabdovirus that infects birds. We show that U3 enters the nucleus and interacts with SNF5, a component of the chromatin remodeling complex that is upregulated in response to infection and restricts viral replication. We also show that U3 inhibits SNF5-regulated expression of the cytokine colony-stimulating factor 1 (CSF1), suggesting that it targets the chromatin remodeling complex to block the host response to infection. This study appears to provide the first evidence of a virus targeting SNF5 to inhibit host gene expression.

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CHD8 Regulates Cellular Homeostasis and Neuronal Function Genes Across Multiple Models of CHD8 Haploinsufficiency

10.1101/375238 ◽

2018 ◽

Author(s):

A. Ayanna Wade ◽

Kenneth Lim ◽

Rinaldo Catta-Preta ◽

Alex S. Nord

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Chromatin Remodeling ◽

De Novo ◽

Autism Spectrum ◽

Loss Of Function ◽

Cell Functions ◽

High Affinity

ABSTRACTThe packaging of DNA into chromatin determines the transcriptional potential of cells and is central to eukaryotic gene regulation. Recent sequencing of patient mutations has linked de novo loss-of-function mutations to chromatin remodeling factors with specific, causal roles in neurodevelopmental disorders. Characterizing cellular and molecular phenotypes arising from haploinsufficiency of chromatin remodeling factors could reveal convergent mechanisms of pathology. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeling factor gene and has among the highest de novo loss-of-function mutations rates in patients with autism spectrum disorder (ASD). Mutations to CHD8 are expected to drive neurodevelopmental pathology through global disruptions to gene expression and chromatin state, however, mechanisms associated with CHD8 function have yet to be fully elucidated. We analyzed published transcriptomic and epigenomic data across CHD8 in vitro and in vivo knockdown and knockout models to identify convergent mechanisms of gene regulation by CHD8. We found reproducible high-affinity interactions of CHD8 near promoters of genes necessary for basic cell functions and gene regulation, especially chromatin organization and RNA processing genes. Overlap between CHD8 interaction and differential expression suggests that reduced dosage of CHD8 directly relates to decreased expression of these genes. In addition, genes important for neuronal development and function showed consistent dysregulation, though there was a reduced rate and decreased affinity for CHD8 interactions near these genes. This meta-analysis verifies CHD8 as a critical regulator of gene expression and reveals a consistent set of high affinity CHD8 interaction targets observed across human and mouse in vivo and in vitro studies. Our findings highlight novel core functions of CHD8 and indicate direct and downstream gene regulatory impacts that are likely to be associated with neuropathology underlying CHD8-associated neurodevelopmental disorder.

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Molecular mechanisms of Evening Complex activity in Arabidopsis

10.1101/584854 ◽

2019 ◽

Cited By ~ 1

Author(s):

Catarina S. Silva ◽

Aditya Nayak ◽

Xuelei Lai ◽

Veronique Hugouvieux ◽

Jae-Hoon Jung ◽

...

Keyword(s):

Gene Expression ◽

Dna Binding ◽

Plant Growth ◽

Circadian Clock ◽

Binding Affinity ◽

Growth And Development ◽

Molecular Mechanisms ◽

Early Flowering ◽

Dna Binding Domain

AbstractThe Evening Complex (EC), composed of the DNA-binding protein LUX ARRHYTHMO (LUX) and two additional proteins, EARLY FLOWERING 3 (ELF3) and ELF4, is a transcriptional repressor complex and a core component of the plant circadian clock. In addition to maintaining oscillations in clock gene expression, the EC also participates in temperature and light entrainment and regulates important clock output genes such asPHYTOCHROME INTERACTING FACTOR 4(PIF4), a key transcription factor involved in temperature dependent plant growth. These properties make the EC an attractive target for altering plant development through targeted mutations to the complex. However, the molecular basis for EC function was not known. Here we show that binding of the EC requires all three proteins and that ELF3 decreases the ability of LUX to bind DNA whereas the presence of ELF4 restores interaction with DNA. To be able to manipulate this complex, we solved the structure of the DNA-binding domain of LUX bound to DNA. Using structure-based design, a LUX variant was constructed that showed decreasedin vitrobinding affinity but retained specificity for its cognate sequences. This designed LUX allele modulates hypocotyl elongation and flowering. These results demonstrate that modifying the DNA-binding affinity of LUX can be used to titrate the repressive activity of the entire EC, tuning growth and development in a predictable manner.Significance StatementCircadian gene expression oscillates over a 24 hr. period and regulates many genes critical for growth and development. In plants, the Evening Complex (EC), a three-protein repressive complex made up of LUX ARRYTHMO, EARLY FLOWERING 3 and EARLY FLOWERING 4, acts as a key component of the circadian clock and is a regulator of thermomorphogenic growth. However, the molecular mechanisms of complex formation and DNA-binding have not been identified. Here we determine the roles of each protein in the complex and present the structure of the LUX DNA-binding domain in complex with DNA. Based on these data, we used structure-based protein engineering to produce a version of the EC with alteredin vitroandin vivoactivity. These results demonstrate that the EC can be modified to alter plant growth and development at different temperatures in a predictable manner.

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A trans-acting long non-coding RNA represses flowering in Arabidopsis

10.1101/2021.11.15.468639 ◽

2021 ◽

Author(s):

Yu Jin ◽

Maxim Ivanov ◽

Anna Nelson Dittrich ◽

Andrew Nelson ◽

Sebastian Marquardt

Keyword(s):

Gene Expression ◽

Functional Characterization ◽

Early Flowering ◽

Differentially Expressed ◽

Loss Of Function ◽

Allelic Series ◽

Non Coding Rna ◽

Genome Wide ◽

Genomic Regions ◽

Early Flowering Phenotype

Eukaryotic genomes give rise to thousands of long non-coding RNAs (lncRNAs), yet the purpose of lncRNAs remains largely enigmatic. Functional characterization of lncRNAs is challenging due to multiple orthogonal hypothesis for molecular activities of lncRNA loci. Here, we identified a flowering associated intergenic lncRNA (FLAIL) that represses flowering in Arabidopsis. An allelic series of flail loss-of-function mutants generated by CRISPR/Cas9 and T-DNA mutagenesis showed an early flowering phenotype. Gene expression analyses in flail mutants revealed differentially expressed genes linked to the regulation of flowering. A genomic rescue fragment of FLAIL introduced in flail mutants complemented gene expression defects and early flowering, consistent with trans-acting effects of the FLAIL RNA. Knock-down of FLAIL RNA levels using the artificial microRNA approach revealed an early flowering phenotype shared with genomic mutations, indicating a trans-acting role of FLAIL RNA in the repression of flowering time. Genome-wide detection of FLAIL-DNA interactions by ChIRP-seq suggested that FLAIL may directly bind genomic regions. FLAIL bound to genes involved in regulation of flowering that were differentially expressed in flail, consistent with the interpretation of FLAIL as a trans-acting lncRNA directly shaping gene expression. Our findings highlight FLAIL as a trans-acting lncRNA that affects flowering in Arabidopsis, likely through mediating transcriptional regulation of genes directly bound by FLAIL.

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