In higher eukaryotes,DNA replication ensures precise transmission of genetic information from parental DNA to progeny,and the correct selection of replication origins is a critical step in this process.A very recent s...In higher eukaryotes,DNA replication ensures precise transmission of genetic information from parental DNA to progeny,and the correct selection of replication origins is a critical step in this process.A very recent study has shown that nucleosomes containing histone variant H2A.Z recruit SUV420H1,a histone H4 lysine 20 specific methyltransferase.Moreover,SUV420H1 promotes the H4K20 dimethylation,which can recruit the origin recognition complex to fulfill the selection and licensing of the replication origins.展开更多
The conserved histone variant H2A.Z is essential for transcriptional regulation;defense responses;and various biological processes in plants,such as growth,development,and flowering.However,little is known about how H...The conserved histone variant H2A.Z is essential for transcriptional regulation;defense responses;and various biological processes in plants,such as growth,development,and flowering.However,little is known about how H2A.Z affects the developmental process and ripening of tomato fruits.Here,we utilized the CRISPR/Cas9 gene-editing system to generate a sl_hta9 sl_hta11 double-mutant,designated sl_h2az,and found that these two mutations led to a signi fi cant reduction in the fresh weight of tomato fruits.Subsequent messenger RNA(mRNA)-seq results showed that dysfunction of SI_H2A.Z has profound effects on the reprogramming of genome-wide gene expression at different developmental stages of tomato fruits,indicating a ripening-dependent correlation between SI_H2A.Z and gene expression regulation in tomato fruits.In addition,the expression of three genes,SIPSY1,SlPDS,and SlVDE,encoding the key enzymes in the biosynthesis pathway of carotenoids,was signi fi cantly upregulated in the later ripening stages,which was consistent with the increased contents of carotenoids in sl_h2a.z double-mutant fruits.Overall,our study reveals a role of SI_H2A.Z in the regulation of carotenoids and provides a resource for the study of SI_H2A.Z-dependent gene expression regulation.Hence,our results provide a link between epigenetic regulation via histone variants and fruit development,suggesting a conceptual framework to understand how histone variants regulate tomato fruit quality.展开更多
Light is an essential environmental signal perceived by a broad range of photoreceptors in plants. Among them, the red/far-red light receptor phytochromes function to promote photomorphogenesis, which is critical to t...Light is an essential environmental signal perceived by a broad range of photoreceptors in plants. Among them, the red/far-red light receptor phytochromes function to promote photomorphogenesis, which is critical to the survival of seedlings after seeds germination. The basic-helix-loop-helix transcription factors phytochrome-interacting factors (PIFs) are the pivotal direct downstream components of phytochromes. H2A.Z is a highly conserved histone variant regulating gene transcription, and its incorporation into nucleosomes is catalyzed by SWI2/SNF2-related 1 complex, in which SWI2/SNF2-related 1 complex subunit 6 (SWC6) and actin-related protein 6 (ARP6) serve as core subunits. Here, we show that PIFs physically interact with SWC6 in vitro and in vivo, leading to the disassociation of HY5 from SWC6. SWC6 and ARP6 regulate hypocotyl elongation partly through PIFs in red light. PIFs and SWC6 coregulate the expression of auxin-responsive genes such as IAA6, IAA19, IAA20, and IAA29 and repress H2A.Z deposition at IAA6 and IAA19 in red light. Based on previous studies and our findings, we propose that PIFs inhibit photomorphogenesis, at least in part, through repression of H2A.Z deposition at auxin-responsive genes mediated by the interactions of PIFs with SWC6 and promotion of their expression in red light.展开更多
组蛋白H2A的变体H2A.Z在基因的表达过程中发挥着重要的作用。根据H2A.Z和H2A核小体中组蛋白甲基化修饰方式的不同,作者应用多样性增量二次判别方法(increment of diversity with quadratic discriminant,IDQD)成功地对H2A.Z和H2A核小体...组蛋白H2A的变体H2A.Z在基因的表达过程中发挥着重要的作用。根据H2A.Z和H2A核小体中组蛋白甲基化修饰方式的不同,作者应用多样性增量二次判别方法(increment of diversity with quadratic discriminant,IDQD)成功地对H2A.Z和H2A核小体进行了识别,说明了以组蛋白甲基化信息作为特征参数的IDQD模型对H2A.Z和H2A核小体识别的有效性。通过计算DNA序列的柔性,发现H2A.Z核小体对应的DNA序列的平均柔性比常规H2A核小体对应的DNA序列的平均柔性弱。展开更多
Temperature influences the distribution, range, and phenology of plants. The key transcriptional activators of heat shock response in eukaryotes, the heat shock factors （HSFs）, have undergone large-scale gene amplif...Temperature influences the distribution, range, and phenology of plants. The key transcriptional activators of heat shock response in eukaryotes, the heat shock factors （HSFs）, have undergone large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in the response to ambient temperature changes is less well understood. We show here that the warm ambient temperature transcriptome is dependent upon the HSFA1 clade ofArabidopsis HSFs, which cause a rapid and dynamic eviction of H2A.Z nucleosomes at target genes. A transcriptional cascade results in the activation of multiple downstream stress-responsive transcription factors, triggering large-scale changes to the transcriptome in response to elevated temperature. H2A.Z nucleosomes are enriched at temperature-responsive genes at non-inducible temperature, and thus likely confer inducibility of gene expression and higher responsive dynamics. We propose that the antagonistic effects of H2A.Z and HSF1 provide a mechanism to activate gene expression rapidly and precisely in response to temperature, while preventing leaky transcription in the absence of an activation signal.展开更多
Deposition of the histone variant H2A.Z at gene bodies regulates transcription by modifying chromatin accessibility in plants. However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear, and...Deposition of the histone variant H2A.Z at gene bodies regulates transcription by modifying chromatin accessibility in plants. However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear, and how H2A.Z interacts with other mechanisms of chromatin modification to regulate gene expression remains obscure. Here, we mapped genome-wide H2A.Z, H3K4me3, H3K27me3, Pol II, and nucleosome occupancy in Arabidopsis inflorescence. We showed that H2A.Z preferentially associated with H3K4me3 at promoters, while it was found with H3K27me3 at enhancers, and that H2A.Z deposition negatively correlated with gene expression. In addition, we demonstrated that H2A.Z represses gene expression by establishing low gene accessibility at ＋1 nucleosome and maintaining high gene accessibility at -1 nucleosome. We further showed that the high measures of gene responsiveness correlate with the H2A.Z-associated closed ＋1 nucleosome structure. Moreover, we found that H2A.Z represses enhancer activity by promoting H3K27me3 and preventing H3K4me3 histone modifications. This study provides a framework for future studies of H2A.Z functions and opens up new aspects for decoding the interplay between chromatin modification and histone variants in transcrip- tional control.展开更多
Deposition of the H2A.Z histone variant by the SWR1 complex （SWRI-C） in regulatory regions of specific loci modulates transcription. Characterization of mutations in Arabidopsis thaliana homologs of yeast SWRI-C has...Deposition of the H2A.Z histone variant by the SWR1 complex （SWRI-C） in regulatory regions of specific loci modulates transcription. Characterization of mutations in Arabidopsis thaliana homologs of yeast SWRI-C has revealed a role for H2A.Z exchange in a variety of developmental processes. Nevertheless, the exact composition of plant SWRI-C and how it is recruited to target genes remains to be established. Here we show that SWC4, the Arabidopsis homolog of yeast SANT domain protein Swc4/Eaf2, is a DNA-binding protein that interacts with SWR1-C subunits. We demonstrate that the swc4-1 knockout mutant is embryo- lethal, while SWC4 RNAi knockdown lines display pleiotropic phenotypic alterations in vegetative and repro- ductive traits, including acceleration of flowering time, indicating that SWC4 controls post-embryonic processes. Transcriptomic analyses and genome-wide profiling of H2A.Z indicate that SWC4 represses tran- scription of a number of genes, including the floral integrator FT and key transcription factors, mainly by modulating H2A.Z deposition. Interestingly, SWC4 silencing does not affect H2A.Z deposition at the FLC locus nor expression of this gene, a master regulator of flowering previously shown to be controlled by SWR1-C. Importantly, we find that SWC4 recognizes specific AT-rich DNA elements in the chromatin regions of target genes and that SWC4 silencing impairs SWRI-C binding at FT. Collectively, our data suggest that SWC4 regulates plant growth and development by aiding SWR1-C recruitment and modulating H2A.Z deposition.展开更多
Global warming imposes a major threat to plant growth and crop production. In some plants including Arabidopsis thaliana, elevated temperatures induce a series of morphological and developmental adjustments, termed th...Global warming imposes a major threat to plant growth and crop production. In some plants including Arabidopsis thaliana, elevated temperatures induce a series of morphological and developmental adjustments, termed thermomorphogenesis to facilitate plant cooling under high-temperature conditions. Plant thermal response is suppressed by histone variant H2A.Z. At warm temperatures, H2A.Z is evicted from nucleosomes at thermo-responsive genes, resulting in their expression changes. However, the mechanisms that regulate H2A.Z eviction and subsequent transcription changes are largely unknown. Here, we show that the INO80 chromatin remodeling complex (INO80-C) promotes thermomorphogenesis and activates the expression of thermo-responsive and auxin-related genes. INO80-C associates with PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), a potent regulator in thermomorphogenesis, and mediates temperature-induced H2A.Z eviction at PIF4 targets. Moreover, INO80-C directly interacts with COMPASS-like and transcription elongation factors to promote active histone modification Histone H3 lysine 4 trimethylation (H3K4me3) and RNA Polymerase II (RNA Pol II) elongation, leading to the thermal induction of transcription. Notably, transcription elongation factors SPT4 and SPT5 are required for the H2A.Z eviction at PIF4 targets, suggesting the cooperation of INO80-C and transcription elongation in H2A.Z removal. Our results demonstrate that the (PIF4)-(INO80-C)-(COMPASS-like)-(transcription elongator) module controls plant thermal response, and establish a link between H2A.Z eviction and active transcription.展开更多
Incorporation of the histone variant H2A.Z into nucleosomes by the SWR1 chromatin remodeling complex is a critical step in eukaryotic gene regulation. In Arabidopsis, SWRlc and H2A.Z have been shown to con- trol gene ...Incorporation of the histone variant H2A.Z into nucleosomes by the SWR1 chromatin remodeling complex is a critical step in eukaryotic gene regulation. In Arabidopsis, SWRlc and H2A.Z have been shown to con- trol gene expression underlying development and environmental responses. Although they have been implicated in defense, the specific roles of the complex subunits and H2A.Z in immunity are not well under- stood. In this study, we analyzed the roles of the SWRlc subunits, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 （PIE1）, ACTIN-RELATED PROTEIN6 （ARP6）, and SWR1 COMPLEX 6 （SWC6）, as well as H2A.Z, in defense and gene regulation. We found that SWRlc components play different roles in resistance to different pathogens. Loss of PIE1 and SWC6 function as well as depletion of H2A.Z led to reduced basal resistance, while loss of ARP6 fucntion resulted in enhanced resistance. We found that mutations in PIE1 and SWC6 resulted in impaired effector-triggered immunity. Mutation in SWRlc components and H2A.Z also resulted in compromised jasmonic acid/ethylene-mediated immunity. Genome-wide expres- sion analyses similarly reveal distinct roles for H2A.Z and SWRlc components in gene regulation, and sug- gest a potential role for PIE1 in the regulation of the cross talk between defense signaling pathways. Our data show that although they are part of the same complex, Arabidopsis SWRlc components could have non-redundant functions in plant immunity and gene regulation.展开更多
Light serves as a crucial environmental cue which modulates plant growth and development, and which is controlled by multiple photoreceptors including the primary red light photoreceptor,phytochrome B(phyB). The signa...Light serves as a crucial environmental cue which modulates plant growth and development, and which is controlled by multiple photoreceptors including the primary red light photoreceptor,phytochrome B(phyB). The signaling mechanism of phyB involves direct interactions with a group of basic helix-loop-helix(bHLH) transcription factors, PHYTOCHROME-INTERACTING FACTORS(PIFs), and the negative regulators of photomorphogenesis, COP1 and SPAs. H2 A.Z is an evolutionarily conserved H2 A variant which plays essential roles in transcriptional regulation. The replacement of H2 A with H2 A.Z is catalyzed by the SWR1 complex. Here, we show that the Pfr form of phyB physically interacts with the SWR1 complex subunits SWC6 and ARP6. phyB and ARP6 coregulate numerous genes in the same direction,some of which are associated with auxin biosynthesis and response including YUC9, which encodes a rate-limiting enzyme in the tryptophandependent auxin biosynthesis pathway. Moreover,phyB and HY5/HYH act to inhibit hypocotyl elongation partially through repression of auxin biosynthesis. Based on our findings and previous studies, we propose that phyB promotes H2 A.Z deposition at YUC9 to inhibit its expression through direct phyB-SWC6/ARP6 interactions,leading to repression of auxin biosynthesis, and thus inhibition of hypocotyl elongation in red light.展开更多
Inplants,lightsignalstriggeraphotomorphogenic program involving transcriptome changes, epigenetic regulation, and inhibited hypocotyl elongation. The evolutionarily conserved histone variant H2 A.Z, which functions in...Inplants,lightsignalstriggeraphotomorphogenic program involving transcriptome changes, epigenetic regulation, and inhibited hypocotyl elongation. The evolutionarily conserved histone variant H2 A.Z, which functions in transcriptional regulation, is deposited in chromatin by the SWI2/SNF2-RELATED 1 complex(SWR1 c). However, the role of H2 A.Z in photomorphogenesis and its deposition mechanism remain unclear. Here, we show that in Arabidopsis thaliana, H2 A.Z deposition at its target loci is induced by light irradiation via NUCLEAR FACTOR-Y, subunit C(NF-YC) proteins, thereby inhibiting photomorphogenic growth. NF-YCs physically interact with ACTIN-RELATED PROTEIN6(ARP6), a key component of the SWR1 c that is essential for depositing H2 A.Z, in a lightdependent manner. NF-YCs and ARP6 function together as negative regulators of hypocotyl growth by depositing H2 A.Z at their target genes during photomorphogenesis. Our findings reveal an important role for the histone variant H2 A.Z in photomorphogenic growth and provide insights into a novel transcription regulatory node that mediates H2 A.Z deposition to control plant growth in response to changing light conditions.展开更多
In eukaryotes,DNA wraps around the histone octamer to form nucleosomes,which are further compacted into the chromosome structure.The chromosome contains multiple replication origins that are regulated by both DNA sequ...In eukaryotes,DNA wraps around the histone octamer to form nucleosomes,which are further compacted into the chromosome structure.The chromosome contains multiple replication origins that are regulated by both DNA sequence and epigenetic features.展开更多
Dear Editor,In multicellular eukaryotes,Polycomb repression heritably si-lences gene expression programs not needed or detrimental for a given developmental stage or tissue(Schuettengruber et al.,2017).During cell fat...Dear Editor,In multicellular eukaryotes,Polycomb repression heritably si-lences gene expression programs not needed or detrimental for a given developmental stage or tissue(Schuettengruber et al.,2017).During cell fate reprogramming,Polycomb silencing can be overcome by the combined activity of multiple Trithorax group(TrxG)proteins(Wu et al.,2012;Liang et al.,2015;Schuettengruber et al.,2017).TrxG proteins are genetically defined as suppressors of homeotic defects caused by loss of Polycomb function and have diverse enzymatic activities(Schuettengruber et al.,2017).We used a genetic enhancer screen to identify candidate TrxG proteins and uncovered TrxG activity for components of the SWR1 chromatin remodeling complex,which deposits the histone variant H2A.Z(Deal et al.,2007;March-Diaz et al.,2008).展开更多
文摘In higher eukaryotes,DNA replication ensures precise transmission of genetic information from parental DNA to progeny,and the correct selection of replication origins is a critical step in this process.A very recent study has shown that nucleosomes containing histone variant H2A.Z recruit SUV420H1,a histone H4 lysine 20 specific methyltransferase.Moreover,SUV420H1 promotes the H4K20 dimethylation,which can recruit the origin recognition complex to fulfill the selection and licensing of the replication origins.
基金the National Key R&D Program of China(2016YFD0101703 and 2017YFD0101902)the Natural ScienCe Foundation of Jiangsu Province(BK20200948)the National Nature ScienCe Foundation of China(32002046).
文摘The conserved histone variant H2A.Z is essential for transcriptional regulation;defense responses;and various biological processes in plants,such as growth,development,and flowering.However,little is known about how H2A.Z affects the developmental process and ripening of tomato fruits.Here,we utilized the CRISPR/Cas9 gene-editing system to generate a sl_hta9 sl_hta11 double-mutant,designated sl_h2az,and found that these two mutations led to a signi fi cant reduction in the fresh weight of tomato fruits.Subsequent messenger RNA(mRNA)-seq results showed that dysfunction of SI_H2A.Z has profound effects on the reprogramming of genome-wide gene expression at different developmental stages of tomato fruits,indicating a ripening-dependent correlation between SI_H2A.Z and gene expression regulation in tomato fruits.In addition,the expression of three genes,SIPSY1,SlPDS,and SlVDE,encoding the key enzymes in the biosynthesis pathway of carotenoids,was signi fi cantly upregulated in the later ripening stages,which was consistent with the increased contents of carotenoids in sl_h2a.z double-mutant fruits.Overall,our study reveals a role of SI_H2A.Z in the regulation of carotenoids and provides a resource for the study of SI_H2A.Z-dependent gene expression regulation.Hence,our results provide a link between epigenetic regulation via histone variants and fruit development,suggesting a conceptual framework to understand how histone variants regulate tomato fruit quality.
基金This work was supported by the National Natural Science Foundation of China(31900609)the National Key Research and Development Program of China(2017YFA0503802)+1 种基金the National Natural Science Foundation of China(31530085,31900207,and 32000183)the Science and Technology Commission of Shanghai Municipality(18DZ2260500).
文摘Light is an essential environmental signal perceived by a broad range of photoreceptors in plants. Among them, the red/far-red light receptor phytochromes function to promote photomorphogenesis, which is critical to the survival of seedlings after seeds germination. The basic-helix-loop-helix transcription factors phytochrome-interacting factors (PIFs) are the pivotal direct downstream components of phytochromes. H2A.Z is a highly conserved histone variant regulating gene transcription, and its incorporation into nucleosomes is catalyzed by SWI2/SNF2-related 1 complex, in which SWI2/SNF2-related 1 complex subunit 6 (SWC6) and actin-related protein 6 (ARP6) serve as core subunits. Here, we show that PIFs physically interact with SWC6 in vitro and in vivo, leading to the disassociation of HY5 from SWC6. SWC6 and ARP6 regulate hypocotyl elongation partly through PIFs in red light. PIFs and SWC6 coregulate the expression of auxin-responsive genes such as IAA6, IAA19, IAA20, and IAA29 and repress H2A.Z deposition at IAA6 and IAA19 in red light. Based on previous studies and our findings, we propose that PIFs inhibit photomorphogenesis, at least in part, through repression of H2A.Z deposition at auxin-responsive genes mediated by the interactions of PIFs with SWC6 and promotion of their expression in red light.
文摘组蛋白H2A的变体H2A.Z在基因的表达过程中发挥着重要的作用。根据H2A.Z和H2A核小体中组蛋白甲基化修饰方式的不同,作者应用多样性增量二次判别方法(increment of diversity with quadratic discriminant,IDQD)成功地对H2A.Z和H2A核小体进行了识别,说明了以组蛋白甲基化信息作为特征参数的IDQD模型对H2A.Z和H2A核小体识别的有效性。通过计算DNA序列的柔性,发现H2A.Z核小体对应的DNA序列的平均柔性比常规H2A核小体对应的DNA序列的平均柔性弱。
文摘Temperature influences the distribution, range, and phenology of plants. The key transcriptional activators of heat shock response in eukaryotes, the heat shock factors （HSFs）, have undergone large-scale gene amplification in plants. While HSFs are central in heat stress responses, their role in the response to ambient temperature changes is less well understood. We show here that the warm ambient temperature transcriptome is dependent upon the HSFA1 clade ofArabidopsis HSFs, which cause a rapid and dynamic eviction of H2A.Z nucleosomes at target genes. A transcriptional cascade results in the activation of multiple downstream stress-responsive transcription factors, triggering large-scale changes to the transcriptome in response to elevated temperature. H2A.Z nucleosomes are enriched at temperature-responsive genes at non-inducible temperature, and thus likely confer inducibility of gene expression and higher responsive dynamics. We propose that the antagonistic effects of H2A.Z and HSF1 provide a mechanism to activate gene expression rapidly and precisely in response to temperature, while preventing leaky transcription in the absence of an activation signal.
文摘Deposition of the histone variant H2A.Z at gene bodies regulates transcription by modifying chromatin accessibility in plants. However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear, and how H2A.Z interacts with other mechanisms of chromatin modification to regulate gene expression remains obscure. Here, we mapped genome-wide H2A.Z, H3K4me3, H3K27me3, Pol II, and nucleosome occupancy in Arabidopsis inflorescence. We showed that H2A.Z preferentially associated with H3K4me3 at promoters, while it was found with H3K27me3 at enhancers, and that H2A.Z deposition negatively correlated with gene expression. In addition, we demonstrated that H2A.Z represses gene expression by establishing low gene accessibility at ＋1 nucleosome and maintaining high gene accessibility at -1 nucleosome. We further showed that the high measures of gene responsiveness correlate with the H2A.Z-associated closed ＋1 nucleosome structure. Moreover, we found that H2A.Z represses enhancer activity by promoting H3K27me3 and preventing H3K4me3 histone modifications. This study provides a framework for future studies of H2A.Z functions and opens up new aspects for decoding the interplay between chromatin modification and histone variants in transcrip- tional control.
文摘Deposition of the H2A.Z histone variant by the SWR1 complex （SWRI-C） in regulatory regions of specific loci modulates transcription. Characterization of mutations in Arabidopsis thaliana homologs of yeast SWRI-C has revealed a role for H2A.Z exchange in a variety of developmental processes. Nevertheless, the exact composition of plant SWRI-C and how it is recruited to target genes remains to be established. Here we show that SWC4, the Arabidopsis homolog of yeast SANT domain protein Swc4/Eaf2, is a DNA-binding protein that interacts with SWR1-C subunits. We demonstrate that the swc4-1 knockout mutant is embryo- lethal, while SWC4 RNAi knockdown lines display pleiotropic phenotypic alterations in vegetative and repro- ductive traits, including acceleration of flowering time, indicating that SWC4 controls post-embryonic processes. Transcriptomic analyses and genome-wide profiling of H2A.Z indicate that SWC4 represses tran- scription of a number of genes, including the floral integrator FT and key transcription factors, mainly by modulating H2A.Z deposition. Interestingly, SWC4 silencing does not affect H2A.Z deposition at the FLC locus nor expression of this gene, a master regulator of flowering previously shown to be controlled by SWR1-C. Importantly, we find that SWC4 recognizes specific AT-rich DNA elements in the chromatin regions of target genes and that SWC4 silencing impairs SWRI-C binding at FT. Collectively, our data suggest that SWC4 regulates plant growth and development by aiding SWR1-C recruitment and modulating H2A.Z deposition.
基金This work was supported by the National Key R&D Program of China(2019YFA0903903)the Strategic Priority Research Program of the Chinese Academy of Sciences(Precision Seed Design and Breeding,XDA24020303)the National Natural Science Foundation of China(31970527).
文摘Global warming imposes a major threat to plant growth and crop production. In some plants including Arabidopsis thaliana, elevated temperatures induce a series of morphological and developmental adjustments, termed thermomorphogenesis to facilitate plant cooling under high-temperature conditions. Plant thermal response is suppressed by histone variant H2A.Z. At warm temperatures, H2A.Z is evicted from nucleosomes at thermo-responsive genes, resulting in their expression changes. However, the mechanisms that regulate H2A.Z eviction and subsequent transcription changes are largely unknown. Here, we show that the INO80 chromatin remodeling complex (INO80-C) promotes thermomorphogenesis and activates the expression of thermo-responsive and auxin-related genes. INO80-C associates with PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), a potent regulator in thermomorphogenesis, and mediates temperature-induced H2A.Z eviction at PIF4 targets. Moreover, INO80-C directly interacts with COMPASS-like and transcription elongation factors to promote active histone modification Histone H3 lysine 4 trimethylation (H3K4me3) and RNA Polymerase II (RNA Pol II) elongation, leading to the thermal induction of transcription. Notably, transcription elongation factors SPT4 and SPT5 are required for the H2A.Z eviction at PIF4 targets, suggesting the cooperation of INO80-C and transcription elongation in H2A.Z removal. Our results demonstrate that the (PIF4)-(INO80-C)-(COMPASS-like)-(transcription elongator) module controls plant thermal response, and establish a link between H2A.Z eviction and active transcription.
文摘Incorporation of the histone variant H2A.Z into nucleosomes by the SWR1 chromatin remodeling complex is a critical step in eukaryotic gene regulation. In Arabidopsis, SWRlc and H2A.Z have been shown to con- trol gene expression underlying development and environmental responses. Although they have been implicated in defense, the specific roles of the complex subunits and H2A.Z in immunity are not well under- stood. In this study, we analyzed the roles of the SWRlc subunits, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 （PIE1）, ACTIN-RELATED PROTEIN6 （ARP6）, and SWR1 COMPLEX 6 （SWC6）, as well as H2A.Z, in defense and gene regulation. We found that SWRlc components play different roles in resistance to different pathogens. Loss of PIE1 and SWC6 function as well as depletion of H2A.Z led to reduced basal resistance, while loss of ARP6 fucntion resulted in enhanced resistance. We found that mutations in PIE1 and SWC6 resulted in impaired effector-triggered immunity. Mutation in SWRlc components and H2A.Z also resulted in compromised jasmonic acid/ethylene-mediated immunity. Genome-wide expres- sion analyses similarly reveal distinct roles for H2A.Z and SWRlc components in gene regulation, and sug- gest a potential role for PIE1 in the regulation of the cross talk between defense signaling pathways. Our data show that although they are part of the same complex, Arabidopsis SWRlc components could have non-redundant functions in plant immunity and gene regulation.
基金supported by The National Natural Science Foundation of China grants to Z.M.(31900609)The National Key Research and Development Program of China grant(2017YFA0503802)+1 种基金The National Natural Science Foundation of China grants to H.Q.Y.(31530085),W.W.(31900207)and T.G.(32000183)The Science and Technology Commission of Shanghai Municipality grant(18DZ2260500)。
文摘Light serves as a crucial environmental cue which modulates plant growth and development, and which is controlled by multiple photoreceptors including the primary red light photoreceptor,phytochrome B(phyB). The signaling mechanism of phyB involves direct interactions with a group of basic helix-loop-helix(bHLH) transcription factors, PHYTOCHROME-INTERACTING FACTORS(PIFs), and the negative regulators of photomorphogenesis, COP1 and SPAs. H2 A.Z is an evolutionarily conserved H2 A variant which plays essential roles in transcriptional regulation. The replacement of H2 A with H2 A.Z is catalyzed by the SWR1 complex. Here, we show that the Pfr form of phyB physically interacts with the SWR1 complex subunits SWC6 and ARP6. phyB and ARP6 coregulate numerous genes in the same direction,some of which are associated with auxin biosynthesis and response including YUC9, which encodes a rate-limiting enzyme in the tryptophandependent auxin biosynthesis pathway. Moreover,phyB and HY5/HYH act to inhibit hypocotyl elongation partially through repression of auxin biosynthesis. Based on our findings and previous studies, we propose that phyB promotes H2 A.Z deposition at YUC9 to inhibit its expression through direct phyB-SWC6/ARP6 interactions,leading to repression of auxin biosynthesis, and thus inhibition of hypocotyl elongation in red light.
基金supported by the National Natural Science Foundation of China(No.32000416)the Natural Science Foundation of Guangdong Province(No.2019A1515110885)。
文摘Inplants,lightsignalstriggeraphotomorphogenic program involving transcriptome changes, epigenetic regulation, and inhibited hypocotyl elongation. The evolutionarily conserved histone variant H2 A.Z, which functions in transcriptional regulation, is deposited in chromatin by the SWI2/SNF2-RELATED 1 complex(SWR1 c). However, the role of H2 A.Z in photomorphogenesis and its deposition mechanism remain unclear. Here, we show that in Arabidopsis thaliana, H2 A.Z deposition at its target loci is induced by light irradiation via NUCLEAR FACTOR-Y, subunit C(NF-YC) proteins, thereby inhibiting photomorphogenic growth. NF-YCs physically interact with ACTIN-RELATED PROTEIN6(ARP6), a key component of the SWR1 c that is essential for depositing H2 A.Z, in a lightdependent manner. NF-YCs and ARP6 function together as negative regulators of hypocotyl growth by depositing H2 A.Z at their target genes during photomorphogenesis. Our findings reveal an important role for the histone variant H2 A.Z in photomorphogenic growth and provide insights into a novel transcription regulatory node that mediates H2 A.Z deposition to control plant growth in response to changing light conditions.
基金supported by the National Natural Science Foundation of China(31972884)1·3·5 Project for Disciplines of Excellence,West China Hospital(ZYGD18003),Sichuan University。
文摘In eukaryotes,DNA wraps around the histone octamer to form nucleosomes,which are further compacted into the chromosome structure.The chromosome contains multiple replication origins that are regulated by both DNA sequence and epigenetic features.
基金funded by National Science Foundation grant MCB1916431 to D.W.
文摘Dear Editor,In multicellular eukaryotes,Polycomb repression heritably si-lences gene expression programs not needed or detrimental for a given developmental stage or tissue(Schuettengruber et al.,2017).During cell fate reprogramming,Polycomb silencing can be overcome by the combined activity of multiple Trithorax group(TrxG)proteins(Wu et al.,2012;Liang et al.,2015;Schuettengruber et al.,2017).TrxG proteins are genetically defined as suppressors of homeotic defects caused by loss of Polycomb function and have diverse enzymatic activities(Schuettengruber et al.,2017).We used a genetic enhancer screen to identify candidate TrxG proteins and uncovered TrxG activity for components of the SWR1 chromatin remodeling complex,which deposits the histone variant H2A.Z(Deal et al.,2007;March-Diaz et al.,2008).
