组蛋白变体H2A.Z的转录调控功能与动态作用机制

H2A.Z是组蛋白H2A常见的组蛋白变体。近年来,人们通过多学科手段探究了H2A.Z对于基因转录的激活或抑制作用。本文在概述组蛋白变体和H2A.Z发展史的基础上,重点阐述了H2A.Z不同亚型、不同翻译后修饰和基因组分布在转录调控过程中的作用,明确了其生物学意义和在肿瘤发生发展、神经系统分化发育过程中的病理生理学意义,并总结了H2A.Z在染色质沉积或者移除的动态调控机制方面的研究进展,以期为深入了解组蛋白变体的多样性,并为寻找相关疾病诊疗的新靶点提供参考。

H3K36me3 and H2A.Z coordinately modulate flowering time in Arabidopsis

Flowering time is a vital aspect of the plant life cycle which signifies the transition from the growth stage to the reproductive stage.To ensure the reproductive success and survival of a species,this narrow window must coincide with various environmental factors including pollinator presence,adequate temperature,and availability of nutrients and water.

Scientists Reveal Mechanism Behind Preferential Recognition of H2A.Z Nucleosome during DNA Replication Initiation

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.

小鼠原始生殖细胞迁移过程中H2A.Z的表达

小鼠原始生殖细胞(PGCs)迁移、增殖、性别分化都受着基因组和DNA表观遗传修饰的调控,H2A.Z与转录激活有关,可能与表观遗传修饰存在联系,通过PGCs单细胞及组织石蜡切片的免疫荧光方法进行研究。结果表明,PGCs在迁移过程中,8.5 dpc时PGCs中不存在H2A.Z;迁移至生殖嵴时H2A.Z主要集中于细胞核,11.5dpc整个PGCs细胞核和细胞质都存在;13.5 dpc雌性的卵母细胞中H2A.Z主要集中于细胞质,而精原细胞中H2A.Z偏向集中于细胞核。综合基因组和DNA表观遗传修饰分析,H2A.Z的表达与其有密不可分的联系。

盐离子作用下组蛋白变体H2A.Z增强核小体结构的稳定性

真核生物染色质的基本结构组成单元是核小体,基因组DNA被压缩在染色质中,核小体的存在通常会抑制转录、复制、修复和重组等发生在DNA模板上的生物学过程。组蛋白变体H2A.Z可以调控染色质结构进而影响基因的转录过程,但其详细的调控机制仍未研究清楚。为了比较含有组蛋白变体H2A.Z的核小体和常规核小体在盐离子作用下的稳定性差异,本文采用F rster共振能量转移的方法检测氯化钠、氯化钾、氯化锰、氯化钙、氯化镁等离子对核小体的解聚影响。实验对Widom 601 DNA序列进行双荧光Cy3和Cy5标记,通过荧光信号值的变化来反映核小体的解聚变化。F rster共振能量转移检测结果显示:在氯化钠、氯化钾、氯化锰、氯化钙和氯化镁作用下,含有组蛋白变体H2A.Z的核小体解聚速度相比于常规核小体要慢,且氯化钙、氯化锰和氯化镁的影响更明显。电泳分析结果表明,在75℃条件下含有组蛋白变体H2A.Z的核小体的解聚速率明显低于常规核小体。采用荧光热漂移检测(fluorescence thermal shift analysis,FTS)进一步分析含有组蛋白变体H2A.Z核小体的稳定性,发现两类核小体的荧光信号均呈现2个明显的增长期,含有组蛋白变体H2A.Z核小体的第1个荧光信号增速期所对应的温度明显高于常规核小体,表明核小体中H2A.Z/H2B二聚体的解聚变性温度要高于常规的H2A/H2B二聚体,含有组蛋白变体H2A.Z核小体的热稳定性高。研究结果均表明,含有组蛋白变体H2A.Z的核小体的结构比常规核小体的结构稳定。

The hist one varia nt SI_H2A.Z regulates carote noid biosynthesis and gene expression during tomato fruit ripening

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.

基于DNA弯曲度的H2A.Z核小体定位与修饰研究

在真核生物染色质中,H2A.Z是高度保守的组蛋白变异体,与转录调控、基因组的稳定性密切相关。为了探讨组蛋白修饰、DNA弯曲度与H2A.Z核小体定位三者之间的关联,在得到实验所测的相关数据后,利用MINE算法并结合皮尔逊相关系数在酵母全基因组的转录起始位点周围探讨了三者间的线性与非线性关系。其中MIC算法可以定量的得出数据之间关联度大小的值,用于衡量数据之间是否存在着关联,而皮尔逊相关系数则用于检查是否为线性关联。结果除了发现大部分组蛋白修饰种类和核小体定位之间存在着线性关联外,还探测到有两种组蛋白修饰数据(H4ac修饰与GCN4修饰)和核小体定位数据之间存在着以往未发现的非线性关系(大致呈正余弦函数),并从数据的生物背景(组蛋白修饰与核小体位置)上探讨了出现非线性现象的原因。

PIFs interact with SWI2/SNF2-related 1 complex subunit 6 to regulate H2A.Z deposition and photomorphogenesis in Arabidopsis

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.

基于组蛋白甲基化信息的H2A.Z和H2A核小体识别

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。

Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis

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.

H2A.Z Represses Gene Expression by Modulating Promoter Nucleosome Structure and Enhancer Histone Modifications in Arabidopsis

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.

Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z Deposition at Key Regulatory Genes

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.

The INO80 chromatin remodeling complex promotes thermo-morphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis.

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.

SWR1 Chromatin-Remodeling Complex Subunits and H2A.Z Have Non-overlapping Functions in Immunity and Gene Regulation in Arabidopsis

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.

Phytochrome B interacts with SWC6 and ARP6 to regulate H2A.Z deposition and photomorphogensis in Arabidopsis

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.

NF-YCs modulate histone variant H2A.Z deposition to regulate photomorphogenic growth in Arabidopsis

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.

Histone variant H2A.Z facilitates DNA replication

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.

H2A.Z contributes to trithorax activity at the AGAMOUS locus

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).

组蛋白变异体H2A.Z的研究进展

H2A.Z是组蛋白H2A的变异体之一,是高度保守的组蛋白变异体,参与保护常染色体,防止形成异染色质;并且与转录调节、抗沉默、沉默和基因组稳定性有关。组蛋白变异体H2A.Z可能与染色体形成独立的结构域,从而调节染色质结构功能。但是,H2A.Z对染色体结构功能的作用机制还不是很清楚。组蛋白变异体H2A.Z和它的表观遗传修饰对染色体动态结构和功能起重要的作用。该文将对组蛋白变异体H2A.Z进行综述。

H2A变体在小鼠不同时期雄性生殖细胞核质区的分布

【目的】了解小鼠雄性生殖细胞中macro H2A、H2A.Z和H2A.X 3种组蛋白变体变化与其发育特征间的联系,为揭示原始生殖细胞(PGCs)的发育机理及其分子调控机制奠定基础。【方法】以C57BL/6J小鼠胚胎的中肾和生殖嵴为试验材料,通过免疫荧光染色技术检测11.5dpc、12.5dpc和13.5dpc不同发育时期含有PGCs的组织石蜡切片及单细胞中macro H2A、H2A.X和H2A.Z变体的分布情况。【结果】macro H2A变体在11.5dpc胚胎时主要存在于细胞质中,12.5dpc时在细胞质中的表达增强,但进入生殖嵴后(13.5dpc)表达消失;H2A.X变体在11.5dpc和12.5dpc时存在于PGCs的核质区,13.5dpc时主要存于细胞质,且呈聚集分布;H2A.Z变体在11.5dpc时在PGCs的核质区均有存在,12.5dpc和13.5dpc时主要分布在细胞核,且表达明显增强。【结论】随着PGCs的不断迁移、增殖与分化,macro H2A、H2A.X和H2A.Z 3种组蛋白H2A变体在细胞核质区的分布及表达情况也发生变化,即H2A变体分布特征与PGCs的性别分化及其有丝分裂停止相关。