scholarly journals The chromatin landscape of primary synovial sarcoma organoids is linked to specific epigenetic mechanisms and dependencies

2020 ◽  
Vol 4 (2) ◽  
pp. e202000808
Author(s):  
Gaylor Boulay ◽  
Luisa Cironi ◽  
Sara P Garcia ◽  
Shruthi Rengarajan ◽  
Yu-Hang Xing ◽  
...  
Keyword(s):  
Synovial Sarcoma ◽  
Chromatin Remodeling ◽  
De Novo ◽  
Gene Activation ◽  
Tumor Development ◽  
Chromosomal Translocation ◽  
Regulatory Elements ◽  
Baf Complex ◽  
Genome Wide ◽  
Core Member

Synovial sarcoma (SyS) is an aggressive mesenchymal malignancy invariably associated with the chromosomal translocation t(X:18; p11:q11), which results in the in-frame fusion of the BAF complex gene SS18 to one of three SSX genes. Fusion of SS18 to SSX generates an aberrant transcriptional regulator, which, in permissive cells, drives tumor development by initiating major chromatin remodeling events that disrupt the balance between BAF-mediated gene activation and polycomb-dependent repression. Here, we developed SyS organoids and performed genome-wide epigenomic profiling of these models and mesenchymal precursors to define SyS-specific chromatin remodeling mechanisms and dependencies. We show that SS18-SSX induces broad BAF domains at its binding sites, which oppose polycomb repressor complex (PRC) 2 activity, while facilitating recruitment of a non-canonical (nc)PRC1 variant. Along with the uncoupling of polycomb complexes, we observed H3K27me3 eviction, H2AK119ub deposition and the establishment of de novo active regulatory elements that drive SyS identity. These alterations are completely reversible upon SS18-SSX depletion and are associated with vulnerability to USP7 loss, a core member of ncPRC1.1. Using the power of primary tumor organoids, our work helps define the mechanisms of epigenetic dysregulation on which SyS cells are dependent.

scholarly journals A Specificity and Targeting Subunit of a Human SWI/SNF Family-Related Chromatin-Remodeling Complex

2000 ◽  
Vol 20 (23) ◽  
pp. 8879-8888 ◽  
Author(s):  
Zuqin Nie ◽  
Yutong Xue ◽  
Dafeng Yang ◽  
Sharleen Zhou ◽  
Bonnie J. Deroo ◽  
...  
Keyword(s):  
Glucocorticoid Receptor ◽  
Chromatin Remodeling ◽  
Protein Interactions ◽  
Transcriptional Activation ◽  
Gene Activation ◽  
Dna Interaction ◽  
Protein Protein Interactions ◽  
Baf Complex ◽  
Chromatin Remodeling Complexes

ABSTRACT The SWI/SNF family of chromatin-remodeling complexes facilitates gene activation by assisting transcription machinery to gain access to targets in chromatin. This family includes BAF (also called hSWI/SNF-A) and PBAF (hSWI/SNF-B) from humans and SWI/SNF and Rsc fromSaccharomyces cerevisiae. However, the relationship between the human and yeast complexes is unclear because all human subunits published to date are similar to those of both yeast SWI/SNF and Rsc. Also, the two human complexes have many identical subunits, making it difficult to distinguish their structures or functions. Here we describe the cloning and characterization of BAF250, a subunit present in human BAF but not PBAF. BAF250 contains structural motifs conserved in yeast SWI1 but not in any Rsc components, suggesting that BAF is related to SWI/SNF. BAF250 is also a homolog of the Drosophila melanogaster Osa protein, which has been shown to interact with a SWI/SNF-like complex in flies. BAF250 possesses at least two conserved domains that could be important for its function. First, it has an AT-rich DNA interaction-type DNA-binding domain, which can specifically bind a DNA sequence known to be recognized by a SWI/SNF family-related complex at the β-globin locus. Second, BAF250 stimulates glucocorticoid receptor-dependent transcriptional activation, and the stimulation is sharply reduced when the C-terminal region of BAF250 is deleted. This region of BAF250 is capable of interacting directly with the glucocorticoid receptor in vitro. Our data suggest that BAF250 confers specificity to the human BAF complex and may recruit the complex to its targets through either protein-DNA or protein-protein interactions.

scholarly journals Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem

2019 ◽  
Vol 70 (15) ◽  
pp. 3867-3879 ◽  
Author(s):  
Anneke Frerichs ◽  
Julia Engelhorn ◽  
Janine Altmüller ◽  
Jose Gutierrez-Marcos ◽  
Wolfgang Werr
Keyword(s):  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Gene Activation ◽  
Regulatory Elements ◽  
Inflorescence Meristem ◽  
Genome Wide ◽  
A Genome ◽  
Hypersensitive Sites ◽  
Lateral Organ ◽  
Founder Cells

Abstract Fluorescence-activated cell sorting (FACS) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) were combined to analyse the chromatin state of lateral organ founder cells (LOFCs) in the peripheral zone of the Arabidopsis apetala1-1 cauliflower-1 double mutant inflorescence meristem. On a genome-wide level, we observed a striking correlation between transposase hypersensitive sites (THSs) detected by ATAC-seq and DNase I hypersensitive sites (DHSs). The mostly expanded DHSs were often substructured into several individual THSs, which correlated with phylogenetically conserved DNA sequences or enhancer elements. Comparing chromatin accessibility with available RNA-seq data, THS change configuration was reflected by gene activation or repression and chromatin regions acquired or lost transposase accessibility in direct correlation with gene expression levels in LOFCs. This was most pronounced immediately upstream of the transcription start, where genome-wide THSs were abundant in a complementary pattern to established H3K4me3 activation or H3K27me3 repression marks. At this resolution, the combined application of FACS/ATAC-seq is widely applicable to detect chromatin changes during cell-type specification and facilitates the detection of regulatory elements in plant promoters.

scholarly journals Dynamic regulation of chromatin topology and transcription by inverted repeat-derived small RNAs in sunflower

2019 ◽  
Vol 116 (35) ◽  
pp. 17578-17583 ◽  
Author(s):  
Delfina Gagliardi ◽  
Damian A. Cambiagno ◽  
Agustin L. Arce ◽  
Ariel H. Tomassi ◽  
Jorge I. Giacomelli ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Inverted Repeat ◽  
Small Rnas ◽  
Rna Silencing ◽  
De Novo ◽  
Epigenetic Modification ◽  
Regulatory Elements ◽  
Dynamic Regulation ◽  
Transposon Activity ◽  
De Novo Methylation

Transposable elements (TEs) are extremely abundant in complex plant genomes. siRNAs of 24 nucleotides in length control transposon activity in a process that involves de novo methylation of targeted loci. Usually, these epigenetic modifications trigger nucleosome condensation and a permanent silencing of the affected loci. Here, we show that a TE-derived inverted repeat (IR) element, inserted near the sunflower HaWRKY6 locus, dynamically regulates the expression of the gene by altering chromatin topology. The transcripts of this IR element are processed into 24-nt siRNAs, triggering DNA methylation on its locus. These epigenetic marks stabilize the formation of tissue-specific loops in the chromatin. In leaves, an intragenic loop is formed, blocking HaWRKY6 transcription. While in cotyledons (Cots), formation of an alternative loop, encompassing the whole HaWRKY6 gene, enhances transcription of the gene. The formation of this loop changes the promoter directionality, reducing IR transcription, and ultimately releasing the loop. Our results provide evidence that TEs can act as active and dynamic regulatory elements within coding loci in a mechanism that combines RNA silencing, epigenetic modification, and chromatin remodeling machineries.

Human IL-12(p35) gene activation involves selective remodeling of a single nucleosome within a region of the promoter containing critical Sp1-binding sites

Blood ◽  
2003 ◽  
Vol 101 (12) ◽  
pp. 4894-4902 ◽  
Author(s):  
Stanislas Goriely ◽  
Dominique Demonté ◽  
Séverine Nizet ◽  
Dominique De Wit ◽  
Fabienne Willems ◽  
...  
Keyword(s):  
Cell Line ◽  
Chromatin Remodeling ◽  
Binding Sites ◽  
Gene Activation ◽  
Regulatory Elements ◽  
Micrococcal Nuclease ◽  
Interleukin 12 ◽  
P35 Gene ◽  
Free Region ◽  
Ifn Γ

AbstractTo get insight into the regulation of human interleukin-12 (IL-12) synthesis, we determined the chromatin organization of the IL-12(p35) promoter region. First, we determined positioning of nucleosomes within the IL-12(p35) promoter using the indirect end-labeling technique in the THP-1 monocytic cell line. On stimulation with bacterial lipopolysaccharide (LPS) and interferon-γ (IFN-γ), hypersensitivity to digestion with DNase I, micrococcal nuclease, and specific restriction enzymes was detected in the region encompassing nucleotide (nt) –310 to –160, indicating selective inducible chromatin remodeling involving disruption of a single nucleosome (named nuc-2). Using p35 promoter deletion mutants and reporter gene assays, we demonstrated that the –396/–241 region contained critical cis-acting elements. Within this latter region, we characterized physically and functionally 2 Sp1-binding sites, which were acting as key regulatory elements for both basal and LPS/IFN-γ–inducible p35 gene expression: Sp1#1 lies within the remodeled nuc-2 region and Sp1#2 is located in the nucleosome-free region immediately upstream of nuc-2. Finally, we extended the chromatin structure analysis to dendritic cells (DCs) derived from human monocytes and observed the same nucleosomal organization and remodeling as in the THP-1 cell line. Moreover, we found that in DCs, LPS and IFN-γ synergized in the induction of nucleosomal remodeling and that chromatin remodeling at the p35 locus immediately preceded IL-12(p35) mRNA synthesis. Taken together, our results demonstrate that IL-12(p35) gene activation in the course of DC maturation involves selective and rapid remodeling of a single positioned nucleosome within a region of the promoter containing critical Sp1-binding sites.

scholarly journals Genome wide efficiency profiling reveals modulation of maintenance and de novo methylation by Tets

2020 ◽  
Author(s):  
Pascal Giehr ◽  
Charalampos Kyriakopoulos ◽  
Karl Nordström ◽  
Abduhlrahman Salhab ◽  
Fabian Müller ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Epigenetic Modification ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
Sequencing Data ◽  
Reduced Representation ◽  
Genome Wide ◽  
Global And Local

AbstractBackgroundDNA methylation is an essential epigenetic modification which is set and maintained by DNA methyl transferases (Dnmts) and removed via active and passive mechanisms involving Tet mediated oxidation. While the molecular mechanisms of these enzymes are well studied, their interplay on shaping cell specific methylomes remains less well understood. In our work we model the activities of Tets and Dnmts at single CpGs across the genome using a novel type of high resolution sequencing data.ResultsTo accurately measure 5mC and 5hmC levels at single CpGs we developed RRHPoxBS, a reduced representation hairpin oxidative bisulfite sequencing approach. Using this method we mapped the methylomes and hydroxymethylomes of wild type and Tet triple knockout mouse embryonic stem cells. These comprehensive datasets were then used to develop an extended Hidden Markov model allowing us i) to determine the symmetrical methylation and hydroxymethylation state at millions of individual CpGs, ii) infer the maintenance and de novo methylation efficiencies of Dnmts and the hydroxylation efficiencies of Tets at individual CpG positions. We find that Tets exhibit their highest activity around unmethylated regulatory elements, i.e. active promoters and enhancers. Furthermore, we find that Tets’ presence has a profound effect on the global and local maintenance and de novo methylation activities by the Dnmts, not only substantially contributing to a universal demethylation of the genome but also shaping the overall methylation landscape.ConclusionsOur analysis demonstrates that a fine tuned and locally controlled interplay between Tets and Dnmts is important to modulate de novo and maintenance activities of Dnmts across the genome. Tet activities contribute to DNA methylation patterning in the following ways: They oxidize 5mC, they locally shield DNA from accidental de novo methylation and at the same time modulate maintenance and de novo methylation efficiencies of Dnmts across the genome.

scholarly journals Chromosomal Elements Regulate Gene Activity and Chromatin Structure of the Human Serpin Gene Cluster at 14q32.1

2003 ◽  
Vol 23 (10) ◽  
pp. 3516-3526 ◽  
Author(s):  
Mark D. Marsden ◽  
R. E. K. Fournier
Keyword(s):  
Gene Cluster ◽  
Chromatin Remodeling ◽  
Gene Activation ◽  
Serine Protease Inhibitor ◽  
Regulatory Elements ◽  
Human Chromosomes ◽  
Functional Tests ◽  
Serpin Gene ◽  
Hepatic Cells ◽  
Number Of Genes

ABSTRACT The human serine protease inhibitor (serpin) gene cluster at 14q32.1 contains a number of genes that are specifically expressed in hepatic cells. Cell-specific enhancers have been identified in several of these genes, but elements involved in locus-wide gene and chromatin control have yet to be defined. To identify regulatory elements in this region, we prepared a series of mutant chromosomal alleles by homologous recombination and transferred the specifically modified human chromosomes to hepatic cells for functional tests. We report that deletion of an 8-kb DNA segment upstream of the human α1-antitrypsin gene yields a mutant serpin allele that fails to be activated in hepatic cells. Within this region, a 2.3-kb DNA segment between kb −8.1 and −5.8 contains a previously unrecognized control region that is required not only for serpin gene activation but also for chromatin remodeling of the entire locus.

Genome-Wide Analysis of NOTCH1, ETS Family Factors, and RUNX1 Binding in Human T Lymphoblastic Leukemia Cells Reveals Distinct Regulatory Elements

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1277-1277
Author(s):  
Hongfang Wang ◽  
Chongzhi Zang ◽  
Len Taing ◽  
Hoifung Wong ◽  
Yumi Yashiro-Ohtani ◽  
...  
Keyword(s):  
Binding Sites ◽  
Motif Discovery ◽  
De Novo ◽  
Conflicts Of Interest ◽  
Lymphoblastic Leukemia ◽  
Regulatory Elements ◽  
Motif Analysis ◽  
Binding Motifs ◽  
Genome Wide ◽  
Ets Factors

Abstract Abstract 1277 NOTCH1 regulates gene expression by forming transcription activation complexes with the DNA-binding factor RBPJ and gain-of-function NOTCH1 mutations are common in human and murine T lymphoblastic leukemia/lymphoma (T-LL). Via ChIP-seq studies of T-LL cells with constitutive Notch activation, we previously showed that NOTCH1/RBPJ binding sites in T-LL genomes are highly enriched for motifs corresponding to Ets factors and Runx factors. In this study, we determined the relationship of NOTCH1, RBPJ, ETS1, GABPA and RUNX1 binding sites in human T-LL cells by performing ChIP-Seq for each of these factors, as well as the chromatin marks H3K4me1, H3K4me3, and H3K27me3, and aligning the resulting sequences to human genome reference hg19 using programs available through Cistrome. Peak calling was performed with MACS2, and motif analysis was performed using SeqPos, which relies on JASPAR, TRANSFAC, Protein Binding Microarray (PBM), Yeast-1-hybrid (y1h), and human protein-DNA interaction (hPDI) databases to find known motifs and can also perform de novo motif discovery. Our analysis showed even more pervasive overlap of NOTCH1/RBPJ binding with ETS1/GABPA and RUNX1 factor binding than was predicted by motif analysis, in part due to binding of Ets factors and RUNX1 to non-canonical sequences. Heat-map analysis with K-means clustering on NOTCH1 binding regions identified three major classes of RBPJ/NOTCH1: class 1, characterized by high NOTCH/RBPJ signals, binding of the cofactors ZNF143, ETS1 and GABPA, high H3K4me3 signals, localization to promoters, and binding motifs for ZNF143; class 2, characterized by low NOTCH/RBPJ signals, binding of the cofactors ETS1, GABPA and RUNX1, high H3K4me3 signals, and Ets factor and CREB binding motifs; and class 3, characterized by high NOTCH/RBPJ signals, binding of RUNX1 and ETS1 cofactors, high H3K4me1 signals, intergenic localization (consistent with enhancers), and motifs for RUNX factors, ETS factors, and RBPJ. Of note, the nearest binding sites to the most responsive NOTCH1 target genes (defined as >2 fold stimulation when NOTCH1 was activated following release of gamma-secretase inhibitor (GSI) blockade by drug washout) were preferentially associated with Class 3 sites. Furthermore, shRNA knockdown of Ets factors and RUNX1 in T-LL cell lines induced apoptosis and reduced cell proliferation, implicating these factors in maintenance of T-LL growth and survival. Combination of knockdown of either Ets factors or RUNX1 with GSI treatment resulted in more severe phenotype in terms of apoptosis and cell growth compared to the knockdown or GSI treatment alone. In summary, our studies represent a step forward towards genome-wide understanding of how Notch works in concerts with other transcription factors to regulate the transcriptome of T-LL cells. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Global Chromatin Changes Resulting from Single-Gene Inactivation—The Role of SMARCB1 in Malignant Rhabdoid Tumor

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2561
Author(s):  
Colin Kenny ◽  
Elaine O’Meara ◽  
Mevlüt Ulaş ◽  
Karsten Hokamp ◽  
Maureen J. O’Sullivan
Keyword(s):  
Chromatin Remodeling ◽  
Human Cancer ◽  
Single Gene ◽  
Gene Activation ◽  
Suppressor Gene ◽  
Rhabdoid Tumor ◽  
Malignant Rhabdoid Tumor ◽  
Complex Activity ◽  
Baf Complex ◽  
Chromatin Remodeling Complex

Human cancer typically results from the stochastic accumulation of multiple oncogene-activating and tumor-suppressor gene-inactivating mutations. However, this process takes time and especially in the context of certain pediatric cancer, fewer but more ‘impactful’ mutations may in short order produce the full-blown cancer phenotype. This is well exemplified by the highly aggressive malignant rhabdoid tumor (MRT), where the only gene classically showing recurrent inactivation is SMARCB1, a subunit member of the BAF chromatin-remodeling complex. This is true of all three presentations of MRT including MRT of kidney (MRTK), MRT of the central nervous system (atypical teratoid rhabdoid tumor—ATRT) and extracranial, extrarenal rhabdoid tumor (EERT). Our reverse modeling of rhabdoid tumors with isogenic cell lines, either induced or not induced, to express SMARCB1 showed widespread differential chromatin remodeling indicative of altered BAF complex activity with ensuant histone modifications when tested by chromatin immunoprecipitation followed by sequencing (ChIP-seq). The changes due to reintroduction of SMARCB1 were preponderantly at typical enhancers with tandem BAF complex occupancy at these sites and related gene activation, as substantiated also by transcriptomic data. Indeed, for both MRTK and ATRT cells, there is evidence of an overlap between SMARCB1-dependent enhancer activation and tissue-specific lineage-determining genes. These genes are inactive in the tumor state, conceivably arresting the cells in a primitive/undifferentiated state. This epigenetic dysregulation from inactivation of a chromatin-remodeling complex subunit contributes to an improved understanding of the complex pathophysiological basis of MRT, one of the most lethal and aggressive human cancers.

scholarly journals Methylated cis-regulatory elements mediate KLF4-dependent gene transactivation and cell migration

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Jun Wan ◽  
Yijing Su ◽  
Qifeng Song ◽  
Brian Tung ◽  
Olutobi Oyinlade ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Chromatin Remodeling ◽  
Molecular Mechanisms ◽  
Biological Function ◽  
Morphological Changes ◽  
Methylation Status ◽  
Gene Activation ◽  
Regulatory Elements ◽  
Binding Activity ◽  
New Paradigm

Altered DNA methylation status is associated with human diseases and cancer; however, the underlying molecular mechanisms remain elusive. We previously identified many human transcription factors, including Krüppel-like factor 4 (KLF4), as sequence-specific DNA methylation readers that preferentially recognize methylated CpG (mCpG), here we report the biological function of mCpG-dependent gene regulation by KLF4 in glioblastoma cells. We show that KLF4 promotes cell adhesion, migration, and morphological changes, all of which are abolished by R458A mutation. Surprisingly, 116 genes are directly activated via mCpG-dependent KLF4 binding activity. In-depth mechanistic studies reveal that recruitment of KLF4 to the methylated cis-regulatory elements of these genes result in chromatin remodeling and transcription activation. Our study demonstrates a new paradigm of DNA methylation-mediated gene activation and chromatin remodeling, and provides a general framework to dissect the biological functions of DNA methylation readers and effectors.

scholarly journals De novo mutations in regulatory elements cause neurodevelopmental disorders

2017 ◽  
Author(s):  
Patrick J. Short ◽  
Jeremy F. McRae ◽  
Giuseppe Gallone ◽  
Alejandro Sifrim ◽  
Hyejung Won ◽  
...  
Keyword(s):  
Neurodevelopmental Disorders ◽  
Developmental Disorders ◽  
De Novo ◽  
Genetic Disorders ◽  
Fetal Brain ◽  
Regulatory Elements ◽  
De Novo Mutations ◽  
Active Elements ◽  
Diagnostic Coding ◽  
Genome Wide

SummaryDe novo mutations in hundreds of different genes collectively cause 25-42% of severe developmental disorders (DD). The cause in the remaining cases is largely unknown. The role of de novo mutations in regulatory elements affecting known DD associated genes or other genes is essentially unexplored. We identified de novo mutations in three classes of putative regulatory elements in almost 8,000 DD patients. Here we show that de novo mutations in highly conserved fetal-brain active elements are significantly and specifically enriched in neurodevelopmental disorders. We identified a significant two-fold enrichment of recurrently mutated elements. We estimate that, genome-wide, de novo mutations in fetaLbrain active elements are likely to be causal for 1-3% of patients without a diagnostic coding variant and that only a small fraction (<2%) of de novo mutations in these elements are pathogenic. Our findings represent a robust estimate of the contribution of de novo mutations in regulatory elements to this genetically heterogeneous set of disorders, and emphasise the importance of combining functional and evolutionary evidence to delineate regulatory causes of genetic disorders.

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