Clinical and molecular spectrum of Wiedemann-Steiner syndrome, an emerging member of the chromatinopathy family

Wiedemann-Steiner syndrome(OMIM#605130)is a rare congenital malformation syndrome characterized by hypertrichosis cubiti associated with short stature;consistent facial features,including long eyelashes,thick or arched eyebrows with a lateral flare,wide nasal bridge,and downslanting and vertically narrow palpebral fissures;mild to moderate intellectual disability;behavioral difficulties;and hypertrichosis on the back.It is caused by heterozygous pathogenic variants in KMT2A.This gene has an established role in histone methylation,which explains the overlap of Wiedemann-Steiner syndrome with other chromatinopathies,a heterogeneous group of syndromic conditions that share a common trigger:The disruption of one of the genes involved in chromatin modification,leading to dysfunction of the epigenetic machinery.

SLIDE, the Protein Interacting Domain of Imitation Switch Remodelers, Binds DDT-Domain Proteins of Different Subfamilies in Chromatin Remodeling Complexes

The Imitation Switch （ISWI） type adenosine triphosphate （ATP）-dependent chromatin remodeling factors are conserved proteins in eukaryotes, and some of them are known to form stable remodeling complexes with members from a family of proteins, termed DDT-domain proteins. Although it is well documented that ISWIs play important roles in different biological processes in many eukaryotic species, the molecular basis for protein interactions in ISWI complexes has not been fully addressed. Here, we report the identification of interaction domains for both ISWI and DDT-domain proteins. By analyzing CHROMATIN REMODELING11 （CH R11） and RINGLET1 （RLT1）, an Arabidopsis thaliana ISWI （AtlSWI） and AtDDT-domain protein, respectively, we show that the SLIDE domain of CHR11 and the DDT domain together with an adjacent sequence of RLT1 are responsible for their binding. The Arabidopsis genome contains at least 12 genes that encode DDT-domain proteins, which could be grouped into five subfamilies based on the sequence similarity. The SLIDE domain of AtlSWI is able to bind members from different AtDDT subfamilies. Moreover, a human ISWI protein SNF2H is capable of binding AtDDT-domain proteins through its SLIDE domain, suggesting that binding to DDT-domain proteins is a conserved biochemical function for the SLIDE domain of ISWIs in eukaryotes.

Epigenetics of gastroenteropancreatic neuroendocrine tumors:A clinicopathologic perspective

Gastroenteropancreatic neuroendocrine tumors(GEP-NETs) are a heterogeneous group of rare tumors whose site-specific tumor incidence and clinical behavior vary widely. Genetic alterations associated with familial inherited syndromes have been well defined; however, the genetic profile of sporadic tumors is less clear as their tumorigenesis does not appear to be controlled by classic oncogenes such as P53, RB, or KRAS. Even within GEP-NETs, there are no common oncogenic drivers; for example, DAXX/ATRX mutations are strongly implicated in the tumorigenesis of pancreatic but not small bowel NETs. Accordingly, the dysregulation of epigenetic mechanisms has been hypothesized as a potential regulator of GEPNET tumorigenesis and has become a major focus of recent studies. Despite the heterogeneity of tumor cohorts evaluated in these studies, it is obvious that there are methylation patterns, chromatin remodeling alterations, and microR NA and long non-coding RNA(lncR NA) differential expression profiles that are distinctive of GEPNETs, some of which are correlated with significant differences in clinical outcomes. Several translational studies have provided convincing data identifying potential prognostic biomarkers, and some of these have demonstrated preliminary success as serum biomarkers that can be used clinically. Nevertheless, there are many opportunities to further define the mechanisms by which these epigenetic modifications influence tumorigenesis, and this will provide better insight into their prognostic and therapeutic utility. Furthermore, these findings form the foundation for future studies evaluating the clinical efficacy of epigenetic modifications as prognostic biomarkers, as well as potential therapeutic targets.

Immunolocalization assessment of metastasis-associated protein I in human and mouse mature testes and its association with spermatogenesis

Aim： To investigate the stage-specific localization of metastasis-associated protein 1 （MTA1） during spermatogenesis in adult human and mouse testis. Methods： The immunolocalization of MTA1 was studied by immunohistochemistry and Western blot analysis. The distribution pattern of MTA1 in mouse testis was confirmed by using quantitative analysis of purified spermatogenic cells. Results： The specificity of polyclonal antibody was confirmed by Western blot analysis. MTA1 was found expressed in the nucleus of germ cells, except elongate spermatids, and in the cytoplasm of Sertoli cells; Leydig cells did not show any specific reactivity. MTA1 possessed different distribution patterns in the two species： in humans, the most intensive staining was found in the nucleus of round spermatids and of primary spermatocytes while in mice, the most intense MTA 1 staining was in the nucleus of leptotene, zygotene and pachytene spermatocytes. In both species the staining exhibited a cyclic pattern. Conclusion： The present communication initially provides new evidence for the potential role of MTA1 in mature testis. In addition, its distinctive expression in germ cells suggests a regulatory role of the peptide during spermatogenesis.

Genetics and genomics of prostate cancer

Prostate cancer （PCa） is one of the most common malignancies in the world with over 890 000 cases and over 258 000 deaths worldwide each year. Nearly all mortalities from PCa are due to metastatic disease, typically through tumors that evolve to be hormone-refractory or castrate-resistant. Despite intensive epidemiological study, there are few known environmental risk factors, and age and family history are the major determinants. However, there is extreme heterogeneity in PCa incidence worldwide, suggesting that major determining factors have not been described. Genome-wide association studies have been performed and a considerable number of significant, but low-risk loci have been identified. In addition, several groups have analyzed PCa by determination of genomic copy number, fusion gene generation and targeted resequencing of candidate genes, as well as exome and whole genome sequencing. These initial studies have examined both primary and metastatic tumors as well as murine xenografts and identified somatic alterations in TP53and other potential driver genes, and the disturbance of androgen response and cell cycle pathways. It is hoped that continued characterization of risk factors as well as gene mutation and misregulation in tumors will aid in understanding, diagnosing and better treating PCa.

Recent advances in prostate cancer: WNT signaling, chromatin regulation, and transcriptional coregulators

Prostate cancer is one of the most common diseases in men worldwide.Surgery,radiation therapy,and hormonal therapy are effective treatments for early-stage prostate cancer.However,the development of castration-resistant prostate cancer has increased the mortality rate of prostate cancer.To develop novel drugs for castration-resistant prostate cancer,the molecular mechanisms of prostate cancer progression must be elucidated.Among the signaling pathways regulating prostate cancer development,recent studies have revealed the importance of noncanonical wingless-type MMTV integration site family(WNT)signaling pathways,mainly that involving WNT5A,in prostate cancer progression and metastasis;however,its role remains controversial.Moreover,chromatin remodelers such as the switch/sucrose nonfermentable(SWI/SNF)complex and chromodomain helicase DNA-binding proteins 1 also play important roles in prostate cancer progression through genome-wide gene expression changes.Here,we review the roles of noncanonical WNT signaling pathways,chromatin remodelers,and epigenetic enzymes in the development and progression of prostate cancer.

Chromatin Remodeling Factor SMARCA5 is Essential for Hippocampal Memory Maintenance via Metabolic Pathways in Mice

Gene transcription and new protein synthesis regulated by epigenetics play integral roles in the formation of new memories.However,as an important part of epigenetics,the function of chromatin remodeling in learning and memory has been less studied.Here,we showed that SMARCA5(SWI/SNF related,matrix-associated,actin-dependent regulator of chromatin,subfamily A,member 5),a critical chromatin remodeler,was responsible for hippocampus-dependent memory maintenance and neurogenesis.Using proteomics analysis,we found protein expression changes in the hippocampal dentate gyrus(DG)after the knockdown of SMARCA5 during contextual fear conditioning(CFC)memory maintenance in mice.Moreover,SMARCA5 was revealed to participate in CFC memory maintenance via modulating the proteins of metabolic pathways such as nucleoside diphosphate kinase-3(NME3)and aminoacylase 1(ACY1).This work is the first to describe the role of SMARCA5 in memory maintenance and to demonstrate the involvement of metabolic pathways regulated by SMARCA5 in learning and memory.

The SWi2/SNF2 Chromatin-Remodeling ATPase BRAHMA Regulates Chlorophyll Biosynthesis in Arabidopsis

Chlorophyll biosynthesis is critical for chloroplast development and photosynthesis in plants. Although reactions in the chlorophyll biosynthetic pathway have been largely known, little is known about the regu-latory mechanisms of this pathway. In this study, we found that the dark-grown knockout and knockdown mutants as well as RNA-interference transgenic seedlings of BRAHMA （BRM）, which encodes an SWI2/ SNF2 chromatin-remodeling ATPase, had iligher greening rates, accumulated less protochlorophyllide, and produced less reactive oxygen species than Arabidopsis wild-type plants did upon light exposure. The expression of NADPH：protochlorophyilide oxidoreductase A （PORA）, PORB, and PORC, which catalyze a key step in chlorophyll biosynthesis, was increased in the brm mutants. We found that BRM physically interacted with the bHLH transcription factor PHYTOCHRONIE-iNTERACTING FACTOR 1 （PIF1） through its N-terminal domains. Furthermore, we demonstrated that BRM was directly recruited to the cis-regula-tory regions of PORC, but not of PORA and PORB, at least partially in a PIF1-dependent manner and the level of histone H3 lysine 4 tri-methylation （H3K4me3） at PORC loci was increased in the brm mutant. Taken together, our data indicate that the chromatino-remodeling enzyme BRM modulates PORC expression through interacting with PIF1, providing a novel regulatory mechanism by which plants fine-tune chloro-phyll biosynthesis during the transition from heterotrophic to autotrophic growth.

A Direct Link between Abscisic Acid Sensing and the Chromatin-Remodeling ATPase BRAHMA via Core ABA Signaling Pathway ComDonents

Optimal response to drought is critical for plant survival and will affect biodiversity and crop performance during climate change. Mitotically heritable epigenetic or dynamic chromatin state changes have been implicated in the plant response to the drought stress hormone abscisic acid （ABA）. The Arabidopsis SWI/SNF chromatin-remodeling ATPase BRAHMA （BRM） modulates response to ABA by preventing pre- mature activation of stress response pathways during germination. We show that core ABA signaling pathway components physically interact with BRM and post-translationally modify BRM by phosphoryla- tion/dephosphorylation. Genetic evidence suggests that BRM acts downstream of SnRK2.2/2.3 kinases, and biochemical studies identified phosphorylation sites in the C-terminal region of BRM at SnRK2 target sites that are evolutionarUy conserved. Finally, the phosphomimetic BRMs17s^D S1762D mutant displays ABA hypersensitivity. Prior studies showed that BRM resides at target loci in the ABA pathway in the presence and absence of the stimulus, but is only active in the absence of ABA. Our data suggest that SnRK2- dependent phosphorylation of BRM leads to its inhibition, and PP2CA-mediated dephosphorylation of BRM restores the ability of BRM to repress ABA response. These findings point to the presence of a rapid phosphorylation-based switch to control BRM activity; this property could be potentially harnessed to improve drought tolerance in plants.

Chromatin remodeling factors regulate environmental stress responses in plants

Environmental stress from climate change and agricultural activity threatens global plant biodiversity as well as crop yield and quality.As sessile organisms,plants must maintain the integrity of their genomes and adjust gene expression to adapt to various environmental changes.In eukaryotes,nucleosomes are the basic unit of chromatin around which genomic DNA is packaged by condensation.To enable dynamic access to packaged DNA,eukaryotes have evolved Snf2(sucrose nonfermenting 2)family proteins as chromatin remodeling factors(CHRs)that modulate the position of nucleosomes on chromatin.During plant stress responses,CHRs are recruited to specific genomic loci,where they regulate the distribution or composition of nucleosomes,which in turn alters the accessibility of these loci to general transcription or DNA damage repair machinery.Moreover,CHRs interplay with other epigenetic mechanisms,including DNA methylation,histone modifications,and deposition of histone variants.CHRs are also involved in RNA processing at the posttranscriptional level.In this review,we discuss major advances in our understanding of the mechanisms by which CHRs function during plants’response to environmental stress.

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.

Chromatin Remodeling in Stem Cell Maintenance in Arabidopsis thaliana

Pluripotent stem cells are able to both self-renew and generate undifferentiated cells for the formation of new tissues and organs. In higher plants, stem cells found in the shoot apical meristem （SAM） and the root apical meristem （RAM） are origins of organogenesis occurring post-embryonically. It is important to understand how the regulation of stem cell fate is coordinated to enable the meristem to constantly generate different types of lateral organs. Much knowledge has accumulated on specific transcription factors controlling SAM and RAM activity. Here, we review recent evidences for a role of chromatin remodeling in the maintenance of stable expression states of transcription factor genes and the control of stem cell activity in Arabidopsis.

The chromatin remodeling complex imitation of switch controls stamen filament elongation by promoting jasmonic acid biosynthesis in Arabidopsis

Plant reproduction requires the coordinated development of both male and female reproductive organs.Jasmonic acid(JA)plays an essential role in stamen filament elongation.However,the mechanism by which the JA biosynthesis genes are regulated to promote stamen elongation remains unclear.Here,we show that the chromatin remodeling complex Imitation of Switch(ISWI)promotes stamen filament elongation by regulating JA biosynthesis.We show that AT-Rich Interacting Domain 5(ARID5)interacts with CHR11,CHR17,and RLT1,several known subunits of ISWI.Mutations in ARID5 and RLTs caused a reduced seed set due to greatly shortened stamen filaments.RNA-seq analyses reveal that the expression of key genes responsible for JA biosynthesis is significantly down-regulated in the arid5 and rlt mutants.Consistently,the JA levels are drastically decreased in both arid5 and rlt mutants.Chromatin immunoprecipitationquantitative PCR analyses further show that ARID5 is recruited to the chromatin of JA biosynthesis genes.Importantly,exogenous JA treatments can fully rescue the defects of stamen filament elongation in both arid5 and rlt mutants,leading to the partial recovery of fertility.Our results provide a clue how JA biosynthesisis positively regulated by the chromatin remodeling complex ISWI,thereby promoting stamen filament elongation in Arabidopsis.

Chromatin-remodeling complexes:Conserved and plant-specific subunits in Arabidopsis

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 chromatinremodeling complexes function in plants.

KDM2B promotes IL-6 production and inflammatory responses through Brg1-mediated chromatin remodeling

IL-6 plays important and pleiotropic roles in infection and inflammatory diseases,and its production needs to be tightly regulated.However,the epigenetic mechanism underlying Il6 gene transcription remains to be fully elucidated.Here,we report that lysine-specific demethylase 2b(KDM2B),which demethylates H3K4me3 and H3K36me2,is required in macrophages and dendritic cells for the induction of IL-6 but not TNF-α,IL-1,and IFN-β.Compared to wild-type mice,KDM2B-deficient mice were more resistant to endotoxin shock and colitis,with a less severe inflammatory pathogenesis phenotype and decreased IL-6 production in sera.KDM2B selectively bound the Il6 promoter but did not alter histone demethylation;instead,KDM2B interacted with Brahma-related gene 1(Brg1),the core ATPase subunit of SWI/SNF chromatin remodeling complexes,to facilitate chromatin accessibility of the Il6 promoter.Furthermore,KDM2B directly recruited RNA Polymerase II to further initiate and promote Il6 transcription.Thus,our finding identifies a novel nonclassical function of KDM2B in gene-specific transcription initiation and enhancement of Il6 independent of its demethylase activity and adds new insight into the specific epigenetic modification mechanism of inflammatory immune responses.

The Evening Complex and the Chromatin-Remodeling Factor PICKLE Coordinately Control Seed Dormancy by Directly Repressing DOG1 in Arabidopsis

Primary seed dormancy is acquired during seed development and maturation,which is important for plant fitness and survival.DELAY OF GERMINATION1(DOG1)plays a critical role in inducing seed dormancy.DOG1 expression increases rapidly during seed development,but the precise mechanism underlying this process remains elusive.In this study,we showed that mutants with a loss or reduced function of the chromatin-remodeling factor PICKLE(PKL)exhibit increased seed dormancy.PKL associates with DOG1 chromatin and inhibits its transcription.We found that PKL physically interacts with LUX ARRHYTHMO(LUX),a member of the evening complex(EC)of the circadian clock.Furthermore,LUX directly binds to a specific coding sequence of DOG1,and DOG1 acts genetically downstream of PKL and LUX.Mutations in either LUX or EARLY FLOWERING3(ELF3)encoding another member of the EC led to increased DOG1 expression and enhanced seed dormancy.Surprisingly,these phenotypes were abolished when the parent plants were grown under continuous light.In addition,we observed that loss of function of either PKL or LUX decreased H3K27me3 levels at the DOG1 locus.Taken together,our study reveals a regulatory mechanism in which EC proteins coordinate with PKL to transmit circadian signals for directly regulating DOG1 expression and seed dormancy during seed development.

Adaptor protein APPL1 links neuronal activity to chromatin remodeling in cultured hippocampal neurons

Local signaling events at synapses or axon terminals are communicated to the nucleus to elicit transcriptional responses,and thereby translate information about the external environment into internal neuronal representations.This retrograde signaling is critical to dendritic growth,synapse development,and neuronal plasticity.Here,we demonstrate that neuronal activity induces retrograde translocation and nuclear accumulation of endosomal adaptor APPL1.Disrupting the interaction of APPL1 with Importin ocl abolishes nuclear accumulation of APPL1,which in turn decreases the levels of histone acetylation.We further demonstrate that retrograde translocation of APPL1 is required for the regulation of gene transcription and then maintenance of hippocampal late-phase long-term potentiation.Thus,these results illustrate an APPLl-mediated pathway that contributes to the modulation of synaptic plasticity via coupling neuronal activity with chromatin remodeling.

Multiple functions of SWI/SNF chromatin remodeling complex in plant-pathogen interactions

The SWI/SNF chromatin remodeling complex utilizes the energy of ATP hydrolysis to facilitate chromatin access and plays essential roles in DNA-based events.Studies in animals,plants and fungi have uncovered sophisticated regulatory mechanisms of this complex that govern development and various stress responses.In this review,we summarize the composition of SWI/SNF complex in eukaryotes and discuss multiple functions of the SWI/SNF complex in regulating gene transcription,mRNA splicing,and DNA damage response.Our review further highlights the importance of SWI/SNF complex in regulating plant immunity responses and fungal pathogenesis.Finally,the potentials in exploiting chromatin remodeling for management of crop disease are presented.

Mechanism of chromatin remodeling revealed by the Snf2-nucleosome structure

Subject Code:C05With the support from the National Natural Science Foundation of China,a collaborative study by the research teams led by Chen Zhucheng(陈柱成)and Li Xueming(李雪明)at the School of Life Sciences,Tsinghua University,recently reported their work,titled“Mechanism of chromatin remodeling revealed

Structure and regulation of the chromatin remodeller ISWI

Subject Code:C05With the support by the National Natural Science Foundation of China,the research team led by Dr.Chen Zhucheng(陈柱成)at the School of Life Science,Tsinghua University,Beijing,recently reported their work,titled'Structure and regulation of the chromatin remodeller ISWI',in Nature(2016,540:466—469).Chromatin is the life blueprint of eukaryotes.Chromatin remodellers utilize the energy of ATP hydrolysis to move,destabilize,eject,or restructure nucleosomes,building and rebuilding the blueprint