ABSTRACT
WRKY transcription factors in plants are known to be able to mediate either transcriptional activation or repression, but the mechanism regulating their transcriptional activity is largely unclear. We found that group IId WRKY transcription factors interact with OBERON (OBE) proteins, forming redundant WRKY-OBE complexes in Arabidopsis thaliana. The coiled-coil domain of WRKY transcription factors binds to OBE proteins and is responsible for target gene selection and transcriptional repression. The PHD finger of OBE proteins binds to both histones and WRKY transcription factors. WRKY-OBE complexes repress the transcription of numerous stress-responsive genes and are required for maintaining normal plant growth. Several WRKY and OBE mutants show reduced plant size and increased drought tolerance, accompanied by increased expression of stress-responsive genes. Moreover, expression levels of most of these WRKY and OBE genes are reduced in response to drought stress, revealing a previously uncharacterized regulatory mechanism of the drought stress response. These results suggest that WRKY-OBE complexes repress transcription of stress-responsive genes, and thereby balance plant growth and stress tolerance.
Subject(s)
Arabidopsis , Transcription Factors , Transcription Factors/genetics , Transcription Factors/metabolism , Histones/genetics , Histones/metabolism , Plant Proteins/metabolism , Stress, Physiological , Gene Expression Regulation, Plant , Plants, Genetically Modified , PhylogenyABSTRACT
Early embryonic development is a finely orchestrated process that requires precise regulation of gene expression coordinated with morphogenetic events. TATA-box binding protein-associated factors (TAFs), integral components of transcription initiation coactivators like TFIID and SAGA, play a crucial role in this intricate process. Here we show that disruptions in TAF5, TAF12 and TAF13 individually lead to embryonic lethality in the mouse, resulting in overlapping yet distinct phenotypes. Taf5 and Taf12 mutant embryos exhibited a failure to implant post-blastocyst formation, and Taf5 mutants have aberrant lineage specification within the inner cell mass. In contrast, Taf13 mutant embryos successfully implant and form egg-cylinder stages but fail to initiate gastrulation. Strikingly, we observed a depletion of pluripotency factors in TAF13-deficient embryos, including OCT4, NANOG and SOX2, highlighting an indispensable role of TAF13 in maintaining pluripotency. Transcriptomic analysis revealed distinct gene targets affected by the loss of TAF5, TAF12 and TAF13. Thus, we propose that TAF5, TAF12 and TAF13 convey locus specificity to the TFIID complex throughout the mouse genome.
Subject(s)
Embryonic Development , Gene Expression Regulation, Developmental , TATA-Binding Protein Associated Factors , Animals , TATA-Binding Protein Associated Factors/metabolism , TATA-Binding Protein Associated Factors/genetics , Mice , Embryonic Development/genetics , Transcription Factor TFIID/metabolism , Transcription Factor TFIID/genetics , Female , Blastocyst/metabolism , Octamer Transcription Factor-3/metabolism , Octamer Transcription Factor-3/genetics , Gastrulation/genetics , SOXB1 Transcription Factors/metabolism , SOXB1 Transcription Factors/genetics , Nanog Homeobox Protein/metabolism , Nanog Homeobox Protein/genetics , Embryo, Mammalian/metabolismABSTRACT
Deposition of H2A.Z in chromatin is known to be mediated by a conserved SWR1 chromatin-remodeling complex in eukaryotes. However, little is known about whether and how the SWR1 complex cooperates with other chromatin regulators. Using immunoprecipitation followed by mass spectrometry, we found all known components of the Arabidopsis thaliana SWR1 complex and additionally identified the following three classes of previously uncharacterized plant-specific SWR1 components: MBD9, a methyl-CpG-binding domain-containing protein; CHR11 and CHR17 (CHR11/17), ISWI chromatin remodelers responsible for nucleosome sliding; and TRA1a and TRA1b, accessory subunits of the conserved NuA4 histone acetyltransferase complex. MBD9 directly interacts with CHR11/17 and the SWR1 catalytic subunit PIE1, and is responsible for the association of CHR11/17 with the SWR1 complex. MBD9, TRA1a, and TRA1b function as canonical components of the SWR1 complex to mediate H2A.Z deposition. CHR11/17 are not only responsible for nucleosome sliding but also involved in H2A.Z deposition. These results indicate that the association of the SWR1 complex with CHR11/17 may facilitate the coupling of H2A.Z deposition with nucleosome sliding, thereby co-regulating gene expression, development, and flowering time.
Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/metabolism , DNA-Binding Proteins/metabolism , Histones/metabolism , Adenosine Triphosphatases/metabolism , Chromatin/metabolism , Chromatin Assembly and Disassembly , Histone Acetyltransferases/metabolism , Nucleosomes/metabolism , Protein Interaction Maps , Transcription Factors/metabolismABSTRACT
Gene expression is regulated at multiple levels, including RNA processing and DNA methylation/demethylation. How these regulations are controlled remains unclear. Here, through analysis of a suppressor for the OsEIN2 over-expressor, we identified an RNA recognition motif protein SUPPRESSOR OF EIN2 (SOE). SOE is localized in nuclear speckles and interacts with several components of the spliceosome. We find SOE associates with hundreds of targets and directly binds to a DNA glycosylase gene DNG701 pre-mRNA for efficient splicing and stabilization, allowing for subsequent DNG701-mediated DNA demethylation of the transgene promoter for proper gene expression. The V81M substitution in the suppressor mutant protein mSOE impaired its protein stability and binding activity to DNG701 pre-mRNA, leading to transgene silencing. SOE mutation enhances grain size and yield. Haplotype analysis in c. 3000 rice accessions reveals that the haplotype 1 (Hap 1) promoter is associated with high 1000-grain weight, and most of the japonica accessions, but not indica ones, have the Hap 1 elite allele. Our study discovers a novel mechanism for the regulation of gene expression and provides an elite allele for the promotion of yield potentials in rice.
Subject(s)
Gene Expression Regulation, Plant , Gene Silencing , Oryza , Plant Proteins , Transgenes , Oryza/genetics , Plant Proteins/genetics , Plant Proteins/metabolism , Promoter Regions, Genetic/genetics , Mutation/genetics , Protein Domains , Haplotypes/genetics , DNA Methylation/genetics , Protein Binding , Plants, Genetically Modified , AllelesABSTRACT
In the INO80 chromatin remodeling complex, all of the accessory subunits are assembled on the following three domains of INO80: N-terminal domain (NTD), HSA domain, and ATPase domain. Although the ATPase and HSA domains and their interacting accessory subunits are known to be responsible for chromatin remodeling, it is largely unknown how the accessory subunits that interact with the INO80 NTD regulate chromatin status. Here, we identify both conserved and nonconserved accessory subunits that interact with the three domains in the INO80 complex in Arabidopsis thaliana. While the accessory subunits that interact with all the three INO80 domains can mediate transcriptional repression, the INO80 NTD and the accessory subunits interact with it can contribute to transcriptional activation even when the ATPase domain is absent, suggesting that INO80 has an ATPase-independent role. A subclass of the COMPASS histone H3K4 methyltransferase complexes interact with the INO80 NTD in the INO80 complex and function together with the other accessory subunits that interact with the INO80 NTD, thereby facilitating H3K4 trimethylation and transcriptional activation. This study suggests that the opposite effects of the INO80 complex on transcription are required for the balance between vegetative growth and flowering under diverse environmental conditions.
Subject(s)
Adenosine Triphosphatases/genetics , Arabidopsis Proteins/genetics , Arabidopsis/genetics , DNA-Binding Proteins/genetics , Histones/metabolism , Adenosine Triphosphatases/metabolism , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , DNA-Binding Proteins/metabolism , MethylationABSTRACT
DNA methylation is a conserved epigenetic mark in plants and mammals. In Arabidopsis, DNA methylation can be triggered by small interfering RNAs (siRNAs) through an RNA-directed DNA methylation (RdDM) pathway. Here, we report the identification of an RdDM effector, KTF1. Loss-of-function mutations in KTF1 reduce DNA methylation and release the silencing of RdDM target loci without abolishing the siRNA triggers. KTF1 has similarity to the transcription elongation factor SPT5 and contains a C-terminal extension rich in GW/WG repeats. KTF1 colocalizes with ARGONAUTE 4 (AGO4) in punctate nuclear foci and binds AGO4 and RNA transcripts. Our results suggest KTF1 as an adaptor protein that binds scaffold transcripts generated by Pol V and recruits AGO4 and AGO4-bound siRNAs to form an RdDM effector complex. The dual interaction of an effector protein with AGO and small RNA target transcripts may be a general feature of RNA-silencing effector complexes.
Subject(s)
Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , DNA Methylation , Transcription Factors/genetics , Transcription Factors/metabolism , Argonaute Proteins , Binding Sites , DNA, Plant/metabolism , DNA-Directed RNA Polymerases/metabolism , Mutation , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Protein Binding , RNA Interference , RNA, Small Interfering , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolismABSTRACT
DNA methylation directed by 24-nucleotide (nt) small interfering RNAs (siRNAs) plays critical roles in gene regulation and transposon silencing in Arabidopsis. 24-nt siRNAs are known to be processed from double-stranded RNAs by Dicer-like 3 (DCL3) and loaded into the effector Argonaute 4 (AGO4). Here we report a distinct class of siRNAs independent of DCLs (sidRNAs). sidRNAs are present as ladders of â¼ 20-60 nt in length, often having the same 5' ends but differing in 3' ends by 1-nt steps. We further show that sidRNAs are associated with AGO4 and capable of directing DNA methylation. Finally we show that sidRNA production depends on distributive 3'-5' exonucleases. Our findings suggest an alternative route for siRNA biogenesis. Precursor transcripts are bound by AGO4 and subsequently subjected to 3'-5' exonucleolytic trimming for maturation. We propose that sidRNAs generated through this route are the initial triggers of de novo DNA methylation.
Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/genetics , DNA Methylation , RNA, Small Interfering/biosynthesis , Arabidopsis Proteins/genetics , Argonaute Proteins/metabolism , Base Sequence , Genome, Plant , Molecular Sequence Data , Mutation/genetics , RNA, Plant/genetics , RNA-Dependent RNA Polymerase/genetics , Seedlings/geneticsABSTRACT
BACKGROUND: To explore a method for screening and diagnosing neonatal congenital heart disease (CHD) applicable to grassroots level, evaluate the prevalence of CHD, and establish a hierarchical management system for CHD screening and treatment at the grassroots level. METHODS: A total of 24,253 newborns born in Tang County between January 2016 and December 2020 were consecutively enrolled and screened by trained primary physicians via the "twelve-section ultrasonic screening and diagnosis method" (referred to as the "twelve-section method"). Specialized staff from the CHD Screening and Diagnosis Center of Hebei Children's Hospital regularly visited the local area for definite diagnosis of CHD in newborns who screened positive. Newborns with CHD were managed according to the hierarchical management system. RESULTS: The centre confirmed that, except for 2 newborns with patent ductus arteriosus missed in the diagnosis of ventricular septal defect combined with severe pulmonary hypertension, newborns with other isolated or concomitant simple CHDs were identified at the grassroots level. The sensitivity, specificity and diagnostic coincidence rate of the twelve-section method for screening complex CHD were 92%, 99.6% and 84%, respectively. A total of 301 children with CHD were identified. The overall CHD prevalence was 12.4. According to the hierarchical management system, 113 patients with simple CHD recovered spontaneously during local follow-up, 48 patients continued local follow-up, 106 patients were referred to the centre for surgery (including 17 patients with severe CHD and 89 patients with progressive CHD), 1 patient died without surgery, and 8 patients were lost to follow-up. Eighteen patients with complex CHD were directly referred to the centre for surgery, 3 patients died without surgery, and 4 patients were lost to follow-up. Most patients who received early intervention achieved satisfactory results. The mortality rate of CHD was approximately 28.86 per 100,000 children. CONCLUSIONS: The "twelve-section method" is suitable for screening neonatal CHD at the grassroots level. The establishment of a hierarchical management system for CHD screening and treatment is conducive to the scientific management of CHD, which has important clinical and social significance for early detection, early intervention, reduction in mortality and improvement of the prognosis of complex and severe CHDs.
Subject(s)
Heart Defects, Congenital , Neonatal Screening , Humans , Heart Defects, Congenital/epidemiology , Heart Defects, Congenital/diagnostic imaging , Infant, Newborn , China/epidemiology , Neonatal Screening/methods , Female , Male , Prevalence , Sensitivity and SpecificityABSTRACT
Although previous studies have identified several autonomous pathway components that are required for the promotion of flowering, little is known about how these components cooperate. Here, we identified an autonomous pathway complex (AuPC) containing both known components (FLD, LD and SDG26) and previously unknown components (EFL2, EFL4 and APRF1). Loss-of-function mutations of all of these components result in increased FLC expression and delayed flowering. The delayed-flowering phenotype is independent of photoperiod and can be overcome by vernalization, confirming that the complex specifically functions in the autonomous pathway. Chromatin immunoprecipitation combined with sequencing indicated that, in the AuPC mutants, the histone modifications (H3Ac, H3K4me3 and H3K36me3) associated with transcriptional activation are increased, and the histone modification (H3K27me3) associated with transcriptional repression is reduced, suggesting that the AuPC suppresses FLC expression at least partially by regulating these histone modifications. Moreover, we found that the AuPC component SDG26 associates with FLC chromatin via a previously uncharacterized DNA-binding domain and regulates FLC expression and flowering time independently of its histone methyltransferase activity. Together, these results provide a framework for understanding the molecular mechanism by which the autonomous pathway regulates flowering time.
Subject(s)
Arabidopsis Proteins , Arabidopsis , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , Flowers/genetics , Flowers/metabolism , Gene Expression Regulation, Plant , MADS Domain Proteins/genetics , MADS Domain Proteins/metabolism , MutationABSTRACT
Chromatin remodeling and histone modifications are important for development and floral transition in plants. However, it is largely unknown whether and how these two epigenetic regulators coordinately regulate the important biological processes. Here, we identified three types of Imitation Switch (ISWI) chromatin-remodeling complexes in Arabidopsis (Arabidopsis thaliana). We found that AT-RICH INTERACTING DOMAIN5 (ARID5), a subunit of a plant-specific ISWI complex, can regulate development and floral transition. The ARID-PHD dual domain cassette of ARID5 recognizes both the H3K4me3 histone mark and AT-rich DNA. We determined the ternary complex structure of the ARID5 ARID-PHD cassette with an H3K4me3 peptide and an AT-containing DNA. The H3K4me3 peptide is combinatorially recognized by the PHD and ARID domains, while the DNA is specifically recognized by the ARID domain. Both PHD and ARID domains are necessary for the association of ARID5 with chromatin. The results suggest that the dual recognition of AT-rich DNA and H3K4me3 by the ARID5 ARID-PHD cassette may facilitate the association of the ISWI complex with specific chromatin regions to regulate development and floral transition.
Subject(s)
Arabidopsis Proteins/genetics , Arabidopsis/physiology , DNA-Binding Proteins/genetics , Flowers/physiology , Histones/metabolism , Arabidopsis Proteins/metabolism , Chromatin Assembly and Disassembly , Crystallography, X-Ray , DNA, Plant/genetics , DNA, Plant/metabolism , DNA-Binding Proteins/metabolism , Gene Expression Regulation, Plant , Histones/genetics , Multiprotein Complexes/genetics , Multiprotein Complexes/metabolism , Plants, Genetically Modified , Protein DomainsABSTRACT
Kaposiform hemangioendothelioma is a rare tumour of vascular origin that rarely occurs in the heart. We provided a rare case of a 26-day-old infant with tachypnoea. Echocardiography showed a solid tumour in the pericardial cavity and a large amount of pericardial effusion. The solid tumour was confirmed by surgery, and the pathology was kaposiform hemangioendothelioma. We analysed this case and reviewed the related literature to explore the clinical features and echocardiographic manifestations to improve the understanding, diagnosis, and treatment of this disease for clinicians and sonographers.
Subject(s)
Hemangioendothelioma , Kasabach-Merritt Syndrome , Sarcoma, Kaposi , Infant , Humans , Kasabach-Merritt Syndrome/diagnosis , Hemangioendothelioma/diagnosis , Hemangioendothelioma/surgery , Hemangioendothelioma/pathology , Sarcoma, Kaposi/diagnosis , Sarcoma, Kaposi/surgery , Sarcoma, Kaposi/pathology , HeartABSTRACT
Loose-fitting powered air-purifying respirators (LF-PAPRs) are increasingly used in hospitals and coal mines because of their high comfort and protection level, but the utilization faces the challenges of 8-hr continuous high protection requirements in the hospital environment and the coupling effects of high temperature, high humidity, high dust concentration in coal mines. Based on the self-developed powered air-purifying respirator simulation test system, this study explores the 8-hr changes of supplied airflow, the relative air pressure inside the inlet covering (ΔP), and total inward leakage (TIL) of four models of LF-PAPRs in simulated hospital and coal mine environments. Results show that: (1) In a simulated hospital environment, all four LF-PAPRs showed filter cartridge blockage within 5 â¼ 6 hr of continuous operation; while in the simulated coal mine, three models of LF-PAPRs showed filter cartridge blockage within 3 hr. (2) In both the hospital and coal mine environments, there are cases where the supplied airflow of LF-PAPRs dropped below 170 L/min within 3 hr. (3) In a simulated hospital environment, the ΔP of all LF-PAPRs maintained positive within 5-6 hr; while in the simulated coal mine, the ΔP of two LF-PAPRs, respectively, appeared negative after 1 hr and 1.6 hr operation. (4) The maximum TIL of the tested LF-PAPRs, respectively ranged from 0.5-0.9% and 1.4-3% in simulated hospital and coal mine environments. (5) In both hospital and coal mine environments, the supplied airflow and ΔP of each LF-PAPR showed a decreasing trend with increasing test duration, while the TIL significantly increased with testing time. (6) The supplied airflow, ΔP, and TIL of each LF-PAPR in the simulated hospital environment performed better than those in the coal mine. This study evaluated the performance of PAPR under the most severe operating conditions, and respirator performance may differ under in-situ conditions.
Subject(s)
Air Pollutants, Occupational , Occupational Exposure , Respiratory Protective Devices , Air Pollutants, Occupational/analysis , Occupational Exposure/prevention & control , Occupational Exposure/analysis , Aerosols/analysis , Hospitals , CoalABSTRACT
Association of RNA polymerase V (Pol V) with chromatin is a critical step for RNA- directed DNA methylation (RdDM) in plants. Although the methylated DNA-binding proteins SUVH2 and SUVH9 and the chromatin remodeler-containing complex DRD1-DMS3-RDM1 are known to be required for the association of Pol V with chromatin, the molecular mechanisms underlying the association of Pol V with different chromatin environments remain largely unknown. Here we found that SUVH9 interacts with FVE, a homolog of the mammalian retinoblastoma-associated protein, which has been previously identified as a shared subunit of the histone deacetylase complex and the polycomb-type histone H3K27 trimethyltransferase complex. We demonstrated that FVE facilitates the association of Pol V with chromatin and thus contributes to DNA methylation at a substantial subset of RdDM target loci. Compared with FVE-independent RdDM target loci, FVE-dependent RdDM target loci are more abundant in gene-rich chromosome arms than in pericentromeric heterochromatin regions. This study contributes to our understanding of how the association of Pol V with chromatin is regulated in different chromatin environments.
Subject(s)
Arabidopsis Proteins/physiology , Chromatin/metabolism , DNA Methylation , DNA-Directed RNA Polymerases/metabolism , Transcription Factors/physiology , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , Immunoprecipitation , RNA Interference , Seedlings/metabolism , Transcription Factors/metabolismABSTRACT
In eukaryotes, heterochromatin regions are typically subjected to transcriptional silencing. DNA methylation has an important role in such silencing and has been studied extensively. However, little is known about how methylated heterochromatin regions are subjected to silencing. We conducted a genetic screen and identified an epcr (enhancer of polycomb-related) mutant that releases heterochromatin silencing in Arabidopsis thaliana We demonstrated that EPCR1 functions redundantly with its paralog EPCR2 and interacts with PWWP domain-containing proteins (PWWPs), AT-rich interaction domain-containing proteins (ARIDs), and telomere repeat binding proteins (TRBs), thus forming multiple functionally redundant protein complexes named PEAT (PWWPs-EPCRs-ARIDs-TRBs). The PEAT complexes mediate histone deacetylation and heterochromatin condensation and thereby facilitate heterochromatin silencing. In heterochromatin regions, the production of small interfering RNAs (siRNAs) and DNA methylation is repressed by the PEAT complexes. The study reveals how histone deacetylation, heterochromatin condensation, siRNA production, and DNA methylation interplay with each other and thereby maintain heterochromatin silencing.
Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/metabolism , Gene Expression Regulation, Plant/physiology , Gene Silencing/physiology , Heterochromatin/metabolism , Histones/metabolism , Multiprotein Complexes/metabolism , Acetylation , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Heterochromatin/genetics , Histones/genetics , Multiprotein Complexes/geneticsABSTRACT
FLOWERING LOCUS M (FLM) is a well-known MADS-box transcription factor that is required for preventing early flowering under low temperatures in Arabidopsis thaliana. Alternative splicing of FLM is involved in the regulation of temperature-responsive flowering. However, how the basic transcript level of FLM is regulated is largely unknown. Here, we conducted forward genetic screening and identified a previously uncharacterized flowering repressor gene, UBA2c. Genetic analyses indicated that UBA2c represses flowering at least by promoting FLM transcription. We further demonstrated that UBA2c directly binds to FLM chromatin and facilitates FLM transcription by inhibiting histone H3K27 trimethylation, a histone marker related to transcriptional repression. UBA2c encodes a protein containing two putative RNA recognition motifs (RRMs) and one prion-like domain (PrLD). We found that UBA2c forms speckles in the nucleus and that both the RRMs and PrLD are required not only for forming the nuclear speckles but also for the biological function of UBA2c. These results identify a previously unknown flowering repressor and provide insights into the regulation of flowering time.
Subject(s)
Arabidopsis Proteins , Arabidopsis , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Flowers/physiology , Gene Expression Regulation, Plant , MADS Domain Proteins/genetics , MADS Domain Proteins/metabolism , RNA Recognition MotifABSTRACT
Adenosine triphosphate-dependent chromatin remodeling complexes are important for the regulation of transcription, DNA replication, and genome stability in eukaryotes. Although genetic studies have illustrated various biological functions of core and accessory subunits of chromatin-remodeling complexes in plants, the identification and characterization of chromatin-remodeling complexes in plants is lagging behind that in yeast and animals. Recent studies determined whether and how the Arabidopsis SWI/SNF, ISWI, INO80, SWR1, and CHD chromatin remodelers function in multi-subunit complexes in Arabidopsis. Both conserved and plant-specific subunits of chromatin-remodeling complexes have been identified and characterized. These findings provide a basis for further studies of the molecular mechanisms by which the chromatin-remodeling complexes function in plants.
Subject(s)
Arabidopsis Proteins , Arabidopsis , Animals , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Chromatin , Chromatin Assembly and Disassembly , Transcription Factors/genetics , Transcription Factors/metabolismABSTRACT
Although the Trithorax histone methyltransferases ATX1-5 are known to regulate development and stress responses by catalyzing histone H3K4 methylation in Arabidopsis thaliana, it is unknown whether and how these histone methyltransferases affect DNA methylation. Here, we found that the redundant ATX1-5 proteins are not only required for plant development and viability but also for the regulation of DNA methylation. The expression and H3K4me3 levels of both RNA-directed DNA methylation (RdDM) genes (NRPE1, DCL3, IDN2, and IDP2) and active DNA demethylation genes (ROS1, DML2, and DML3) were downregulated in the atx1/2/4/5 mutant. Consistent with the facts that the active DNA demethylation pathway mediates DNA demethylation mainly at CG and CHG sites, and that the RdDM pathway mediates DNA methylation mainly at CHH sites, whole-genome DNA methylation analyses showed that hyper-CG and CHG DMRs in atx1/2/4/5 significantly overlapped with those in the DNA demethylation pathway mutant ros1 dml2 dml3 (rdd), and that hypo-CHH DMRs in atx1/2/4/5 significantly overlapped with those in the RdDM mutant nrpe1, suggesting that the ATX paralogues function redundantly to regulate DNA methylation by promoting H3K4me3 levels and expression levels of both RdDM genes and active DNA demethylation genes. Given that the ATX proteins function as catalytic subunits of COMPASS histone methyltransferase complexes, we also demonstrated that the COMPASS complex components function as a whole to regulate DNA methylation. This study reveals a previously uncharacterized mechanism underlying the regulation of DNA methylation.
Subject(s)
Arabidopsis Proteins , Arabidopsis , DNA Glycosylases , Arabidopsis/genetics , Arabidopsis/metabolism , DNA Methylation/genetics , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Protein-Tyrosine Kinases/genetics , Protein-Tyrosine Kinases/metabolism , Histone Methyltransferases/genetics , Histone Methyltransferases/metabolism , Proto-Oncogene Proteins/genetics , Gene Expression Regulation, Plant , Methyltransferases/metabolism , Ribonuclease III/genetics , Ribonuclease III/metabolism , DNA Glycosylases/genetics , DNA Glycosylases/metabolismABSTRACT
Although two Enhancer of Polycomb-like proteins, EPL1A and EPL1B (EPL1A/B), are known to be conserved and characteristic subunits of the NuA4-type histone acetyltransferase complex in Arabidopsis thaliana, the biological function of EPL1A/B and the mechanism by which EPL1A/B function in the complex remain unknown. Here, we report that EPL1A/B are required for the histone acetyltransferase activity of the NuA4 complex on the nucleosomal histone H4 in vitro and for the enrichment of histone H4K5 acetylation at thousands of protein-coding genes in vivo. Our results suggest that EPL1A/B are required for linking the NuA4 catalytic subunits HISTONE ACETYLTRANSFERASE OF THE MYST FAMILY 1ï¼HAM1) and HAM2 with accessory subunits in the NuA4 complex. EPL1A/B function redundantly in regulating plant development especially in chlorophyll biosynthesis and de-etiolation. The EPL1A/B-dependent transcription and H4K5Ac are enriched at genes involved in chlorophyll biosynthesis and photosynthesis. We also find that EAF6, another characteristic subunit of the NuA4 complex, contributes to de-etiolation. These results suggest that the Arabidopsis NuA4 complex components function as a whole to mediate histone acetylation and transcriptional activation specifically at light-responsive genes and are critical for photomorphogenesis.
Subject(s)
Arabidopsis , Saccharomyces cerevisiae Proteins , Acetylation , Arabidopsis/genetics , Arabidopsis/metabolism , Chlorophyll , Histone Acetyltransferases/genetics , Histone Acetyltransferases/metabolism , Histones/metabolism , Photosynthesis/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolismABSTRACT
Small interfering RNAs (siRNAs) are responsible for establishing and maintaining DNA methylation through the RNA-directed DNA methylation (RdDM) pathway in plants. Although siRNA biogenesis is well known, it is relatively unclear about how the process is regulated. By a forward genetic screen in Arabidopsis thaliana, we identified a mutant defective in NOT1 and demonstrated that NOT1 is required for transcriptional silencing at RdDM target genomic loci. We demonstrated that NOT1 is required for Pol IV-dependent siRNA accumulation and DNA methylation at a subset of RdDM target genomic loci. Furthermore, we revealed that NOT1 is a constituent of a multi-subunit CCR4-NOT deadenylase complex by immunoprecipitation combined with mass spectrometry and demonstrated that the CCR4-NOT components can function as a whole to mediate chromatin silencing. Therefore, our work establishes that the CCR4-NOT complex regulates the biogenesis of Pol IV-dependent siRNAs, and hence facilitates DNA methylation and transcriptional silencing in Arabidopsis.
Subject(s)
Arabidopsis Proteins/metabolism , DNA Methylation , DNA-Directed RNA Polymerases/metabolism , RNA, Small Interfering/metabolism , Repressor Proteins/metabolism , Transcription Factors/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/physiology , DNA-Directed RNA Polymerases/physiology , Repressor Proteins/genetics , Repressor Proteins/physiology , Transcription Factors/physiologyABSTRACT
BACKGROUND: The purpose of this study was to explore echocardiographic views and methods of aortic arch anomalies in infants, so as to improve the screening sensitivity and diagnostic accuracy. METHODS: 140 children with abnormal aortic arch diagnosed by ultrasound in Children's Hospital of Hebei Province from January 2014 to December 2019 were selected for retrospective analysis. All were confirmed by surgery or/and computerized tomography angiography. Series of views for aortic arch (the three-vessel and tracheal view, aortic arch short axis view, left aortic arch long axis view, aortic arch long axis continuous scan views) were performed in all cases on the basis of the routine views of echocardiography. The screening sensitivity and diagnostic coincidence rate of different echocardiographic views for aortic arch anomalies were analyzed. RESULTS: Among the 140 infants, right aortic arch were 21 cases (6/21 were accompanied by mirror branch and 15/21 were with aberrant left subclavian artery). Left aortic arch with aberrant right subclavian artery were 2 cases, and double aortic arch with both arches open were 20 cases. Double aortic arch with left arch atresia were 2 cases, and atresia of the proximal aorta with aortic arch dysplasia was 1 case. Coarctation of the aorta were 67 cases, and interruption of aortic arch were 27 cases. All the patients were correctly diagnosed except that 2 infants with interruption of aortic arch were incorrectly diagnosed as coarctation of the aorta, and 1 infant with coarctation of the aorta was misdiagnosed as interruption of aortic arch by echocardiography. The screening sensitivities of four views and four-view combination for abnormal aortic arch were 99.3, 73.6, 87.1, 99.3, and 100%; the diagnostic coincidence rates were 85.7, 27.1,66.4, 95.0%, and 97.9% respectively. On the basis of traditional left aortic long axis view, other three views had their own advantages. The screening sensitivity and diagnostic coincidence rate of four-view combination were significantly improved. CONCLUSIONS: The three-vessel trachea view is simple and feasible, which is suitable for screening abnormal aortic arch. The combination of four views conduces to improving screening sensitivity and diagnostic accuracy of aortic arch abnormalities.