CTCF Loss Research Articles

375-OR: Epigenetic Control of Beta-Cell Stress Response and Senescence

Both type 1 and type 2 diabetes (T1D and T2D) result from chronic insulin insufficiency due to progressive dysfunction and loss of beta cells, driven by cellular stress. Beta cell failure in both forms of diabetes involves defective stress-response and the onset of premature senescence, an irreversible form of cell-cycle arrest induced by chronic stress. However, the mechanisms by which cellular stress triggers beta cell senescence are not clear. We now show that CTCF, a stress-sensitive epigenetic regulator, controls the beta cell stress-response and senescence programs during beta cell maturation process along with the cohesin Smc3. Chromatin immunoprecipitation data suggest that CTCF and Smc3 differentially occupy genes associated with stress and DNA damage responses, functional maturation, and senescence in neonatal versus adult beta cells. Our data show that CTCF and cohesin Smc3 dependent control protects replicating beta cells from DNA damage, and is especially critical during the neonatal growth phase marked by high rates of replication. Beta cell specific loss of CTCF triggers a p53/p21 dependent senescence program, followed by beta cell dysfunction and eventual beta cell failure with advancing age. We further demonstrate that reduced CTCF levels in beta cells lead to adaptive failure in response to a high fat diet challenge, and recapitulate a neonatal beta cell like epigenetic landscape. Notably, CTCF levels are reduced in beta cells in T1D and T2D in mice and humans, and lead to reduced occupancy of CTCF and Smc3 at genes involved in senescence, DNA damage response, and beta cell function. Our data show that CTCF and cohesin collectively protect against senescence and govern beta cell function and fitness through a program established in the neonatal maturation phase. Disclosure S.S.Varghese: None. N.Parveen: None. J.K.Wang: Employee; Pfizer Inc., Johnson & Johnson. A.G.Hernandez-de la pena: None. S.Dhawan: None. Funding National Institutes of Health (R01DK120253)

Elevated Enhancer-Oncogene Contacts and Higher Oncogene Expression Levels By Recurrent CTCF inactivating Mutations in T Cell Acute Lymphoblastic Leukemia

Introduction. The CCCTC-binding factor (CTCF) regulates the 3D chromatin architecture by facilitating chromosomal loops and forming the boundaries of structural domains. In addition, CTCF is an important transcription factor and regulator of antigen receptor and T cell receptor recombination events. CTCF inactivating events have been found in various human cancers. Loss-of-heterozygosity (LOH) or inactivating missense mutations in specific zinc- fingers have been identified in many human cancers including sporadic breast cancer, prostate cancer, Wilms-tumors and acute lymphoblastic leukemia (ALL). Heterozygous deletions or point mutations have been identified in over half of the patients with breast cancer or uterine endometrial cancers, deregulating global gene expression by altering methylated genomic states and poor survival. Here, we investigated the functional significance and molecular-cytogenetic associations of CTCF aberrations in T-cell acute lymphoblastic leukemia patients.Methods. Biopsies from a cohort of 181 pediatric T-ALL patients who enrolled on DCOG or COALL protocols and/or their derivative patient-derived xenograft models were screened for alterations in global DNA copy number, methylation status, topologically associating domain organization and CTCF and cohesion binding patterns and changes in local TLX3 and BCL11B promoter enhancer loops using array-comparative genomic hybridization, single molecule Molecular Inversion Probe sequencing, targeted locus amplification, gene expression and DNA methylation microarrays, Hi-C sequencing, Chromatin Immunoprecipitation and/or real-time quantitative PCR. Ctcf f/fl mice 1 were crossed on a the Lck-cre transgenic background 2 to study the impact of Ctcf loss during early T-cell development.Results. We here describe that inactivation of CTCF can drive subtle and local genomic effects that elevate oncogene expression levels from driver chromosomal rearrangements. We find that for T cell acute lymphoblastic leukemia (T-ALL), heterozygous CTCF deletions or inactivating mutations are present in nearly 50 percent of t(5;14)(q35;q32.2) rearranged patients that positions the TLX3 oncogene in the vicinity of the BCL11B enhancer. Functional CTCF loss results in diminished expression of the αβ-lineage commitment factor BCL11B from the non-rearranged allele and γδ-lineage development. Unexpectedly, it also drives higher levels of the TLX3 oncogene from the translocated allele. We demonstrate that heterozygous CTCF aberrations specifically occur in TLX3-rearranged patients with distal breakpoints that preserve CTCF bindings sites in the translocation breakpoint areas in between the BCL11B enhancer and the TLX3 oncogene. We show that these intervening CTCF sites insulate TLX3 from the enhancer by forming competitive loops with TLX3. Upon loss of CTCF, or the deletion of the intervening CTCF sites, these competitive loops are weakened and loops with the BCL11B enhancer are stimulated, boosting TLX3 oncogene expression levels and leukemia burden in these T-ALL patients.Conclusions. CTCF aberrations are especially associated with t(5;14)(q35;q32.2) rearranged T-ALL patients who maintain TLX3-proximal CTCF sites reflects a necessity to neutralize these sites in order to topologically enable the distal BCL11B enhancer to interact with the TLX3 oncogene and to boost its expression. Collectively, this provides direct demonstration of a mechanism in which loss of CTCF result in removal of enhancer insulation that facilitates elevated levels of an oncogene in leukemia.References.1. Heath H, Ribeiro de Almeida C, Sleutels F, et al. CTCF regulates cell cycle progression of alphabeta T cells in the thymus. EMBO J. 2008;27(21):2839-2850.2. Lee PP, Fitzpatrick DR, Beard C, et al. A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. Immunity. 2001;15(5):763-774. DisclosuresSplinter: Cergentis BV: Current Employment. Van Eyndhoven: Agilent Technologies Netherland: Current Employment. Van Min: Cergentis BV: Current Employment. Mullighan: Pfizer: Research Funding; Illumina: Membership on an entity's Board of Directors or advisory committees; AbbVie: Research Funding; Amgen: Current equity holder in publicly-traded company.

CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression

Coordinated chromatin interactions between enhancers and promoters are critical for gene regulation. The architectural protein CTCF mediates chromatin looping and is enriched at the boundaries of topologically associating domains (TADs), which are sub-megabase chromatin structures. In vitro CTCF depletion leads to a loss of TADs but has only limited effects over gene expression, challenging the concept that CTCF-mediated chromatin structures are a fundamental requirement for gene regulation. However, how CTCF and a perturbed chromatin structure impacts gene expression during development remains poorly understood. Here we link the loss of CTCF and gene regulation during patterning and organogenesis in a ctcf knockout zebrafish model. CTCF absence leads to loss of chromatin structure and affects the expression of thousands of genes, including many developmental regulators. Our results demonstrate the essential role of CTCF in providing the structural context for enhancer-promoter interactions, thus regulating developmental genes.

CTCF and transcription influence chromatin structure re-configuration after mitosis

During mitosis, transcription is globally attenuated and chromatin architecture is dramatically reconfigured. We exploited the M- to G1-phase progression to interrogate the contributions of the architectural factor CTCF and the process of transcription to genome re-sculpting in newborn nuclei. Depletion of CTCF during the M- to G1-phase transition alters short-range compartmentalization after mitosis. Chromatin domain boundary re-formation is impaired upon CTCF loss, but a subset of boundaries, characterized by transitions in chromatin states, is established normally. Without CTCF, structural loops fail to form, leading to illegitimate contacts between cis-regulatory elements (CREs). Transient CRE contacts that are normally resolved after telophase persist deeply into G1-phase in CTCF-depleted cells. CTCF loss-associated gains in transcription are often linked to increased, normally illegitimate enhancer-promoter contacts. In contrast, at genes whose expression declines upon CTCF loss, CTCF seems to function as a conventional transcription activator, independent of its architectural role. CTCF-anchored structural loops facilitate formation of CRE loops nested within them, especially those involving weak CREs. Transcription inhibition does not significantly affect global architecture or transcription start site-associated boundaries. However, ongoing transcription contributes considerably to the formation of gene domains, regions of enriched contacts along gene bodies. Notably, gene domains emerge in ana/telophase prior to completion of the first round of transcription, suggesting that epigenetic features in gene bodies contribute to genome reconfiguration prior to transcription. The focus on the de novo formation of nuclear architecture during G1 entry yields insights into the contributions of CTCF and transcription to chromatin architecture dynamics during the mitosis to G1-phase progression.

Acute depletion of CTCF rewires genome-wide chromatin accessibility

BackgroundThe transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studies. However, acute depletion of CTCF globally reduces chromatin interactions but does not significantly alter transcription.ResultsHere, we systematically integrate multi-omics data including ATAC-seq, RNA-seq, WGBS, Hi-C, Cut&Run, and CRISPR-Cas9 survival dropout screens, and time-solved deep proteomic and phosphoproteomic analyses in cells carrying auxin-induced degron at endogenous CTCF locus. Acute CTCF protein degradation markedly rewires genome-wide chromatin accessibility. Increased accessible chromatin regions are frequently located adjacent to CTCF-binding sites at promoter regions and insulator sites associated with enhanced transcription of nearby genes. In addition, we use CTCF-associated multi-omics data to establish a combinatorial data analysis pipeline to discover CTCF co-regulatory partners. We successfully identify 40 candidates, including multiple established partners. Interestingly, many CTCF co-regulators that have alterations of their respective downstream gene expression do not show changes of their own expression levels across the multi-omics measurements upon acute CTCF loss, highlighting the strength of our system to discover hidden co-regulatory partners associated with CTCF-mediated transcription.ConclusionsThis study highlights that CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role in transcriptional regulation.

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

Vertebrate genomes are partitioned into contact domains defined by enhanced internal contact frequency and formed by two principal mechanisms: compartmentalization of transcriptionally active and inactive domains, and stalling of chromosomal loop-extruding cohesin by CTCF bound at domain boundaries. While Drosophila has widespread contact domains and CTCF, it is currently unclear whether CTCF-dependent domains exist in flies. We genetically ablate CTCF in Drosophila and examine impacts on genome folding and transcriptional regulation in the central nervous system. We find that CTCF is required to form a small fraction of all domain boundaries, while critically controlling expression patterns of certain genes and supporting nervous system function. We also find that CTCF recruits the pervasive boundary-associated factor Cp190 to CTCF-occupied boundaries and co-regulates a subset of genes near boundaries together with Cp190. These results highlight a profound difference in CTCF-requirement for genome folding in flies and vertebrates, in which a large fraction of boundaries are CTCF-dependent and suggest that CTCF has played mutable roles in genome architecture and direct gene expression control during metazoan evolution.

The Myc-associated zinc finger protein (MAZ) works together with CTCF to control cohesin positioning and genome organization

The Myc-associated zinc finger protein (MAZ) is often found at genomic binding sites adjacent to CTCF, a protein which affects large-scale genome organization through its interaction with cohesin. We show here that, like CTCF, MAZ physically interacts with a cohesin subunit and can arrest cohesin sliding independently of CTCF. It also shares with CTCF the ability to independently pause the elongating form of RNA polymerase II, and consequently affects RNA alternative splicing. CTCF/MAZ double sites are more effective at sequestering cohesin than sites occupied only by CTCF. Furthermore, depletion of CTCF results in preferential loss of CTCF from sites not occupied by MAZ. In an assay for insulation activity like that used for CTCF, binding of MAZ to sites between an enhancer and promoter results in down-regulation of reporter gene expression, supporting a role for MAZ as an insulator protein. Hi-C analysis of the effect of MAZ depletion on genome organization shows that local interactions within topologically associated domains (TADs) are disrupted, as well as contacts that establish the boundaries of individual TADs. We conclude that MAZ augments the action of CTCF in organizing the genome, but also shares properties with CTCF that allow it to act independently.

Abstract 15945: Temporal Analyses of Chromatin Accessibility, Dna Methylation and Epigenomic Structure Identify Mechanisms of Locus-specific Regulation in the Heart

Heart failure can be induced or ameliorated in animal models by regulation of chromatin modifying enzymes, yet the chromatin level actions of these enzymes during pathogenesis is unknown. Because many histone modifiers and transcription factors regulate gene expression, we sought to directly measure chromatin accessibility through an unbiased method (ATAC-seq) that reports the status of a given locus at any time—the sum total of all epigenetic modifiers—in a mouse model of pressure overload hypertrophy. Early compensation of pressure overload at 3 days was associated with widespread changes in chromatin accessibility and DNA methylation, primarily in noncoding regions. The majority of changes that persisted to the decompensated phase (3weeks) were already established at the earlier time point, revealing a temporal nature of epigenomic compensation to pathologic stimuli. A cardiac-specific CTCF depletion model was used to examine basal cardiac chromatin function and revealed that disruption of this structure by loss of CTCF causes widespread changes in accessibility and methylation distinct from those in pressure overload. Less than half of the gene expression changes occurring at either time point after pressure overload were explained by DNA methylation alone and accessibility was likewise an imperfect predictor of transcription. Distal enhancers were paired with genes based on chromatin structural data and the regulatory actions of these elements examined in the context of DNA methylation and accessibility: enhancer actions require specific combinations of transcription factors and histone modifications at different stages of disease and to execute aspecific transcriptional event (methylation or accessibility alone was insufficient to predict the behavior). For example, the subset of differentially accessible enhancers in both 3 weeks TACand CTCF depletion significantly overlaps with cardiac transcription factors Gata4 (p=4.13x10 -6 ),Nkx2-5 (p=2.49x10 -5 ) and P300 (p=8.38x10 -7 ). In summary, these studies characterize the logic employed at coding, regulatory, and noncoding regions to regulate chromatin accessibility and transcription, providing a resource of epigenomic data at distinct temporal stages of heart failure.

The Myc-Associated Zinc Finger Protein (MAZ) Works Both Independently and Together with CTCF to Control Cohesin Positioning and Genome Organization

The Myc-associated zinc finger protein, MAZ, is often found at genomic binding sites adjacent to CTCF, a protein which affects large scale genome organization through its interaction with cohesin. We show here that, like CTCF, MAZ physically interacts with a cohesin subunit and can arrest cohesin sliding independently of CTCF. It also shares with CTCF the ability to independently pause the elongating form of RNA polymerase II 2. CTCF/MAZ double sites are more effective at sequestering cohesin than sites occupied only by CTCF. Furthermore, depletion of CTCF results in preferential loss of CTCF from sites not occupied by MAZ. In an assay for insulation activity like that used for CTCF, binding of MAZ to sites between an enhancer and promoter results in downregulation of reporter gene expression, consistent with insulator activity. Hi-C analysis of the effect of MAZ depletion on genome organization shows that local interactions within TADs are disrupted, as well as contacts that establish the boundaries of individual TADs. We conclude that MAZ augments the action of CTCF in organizing the genome, but also shares properties with CTCF that allow it to act independently.

Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping.

Numerous pieces of evidence support the complex, 3D spatial organization of the genome dictates gene expression. CTCF is essential to define topologically associated domain boundaries and to facilitate the formation of insulated chromatin loop structures. To understand CTCF’s direct role in global transcriptional regulation, we integrated the miniAID-mClover3 cassette to the endogenous CTCF locus in a human pediatric B-ALL cell line, SEM, and an immortal erythroid precursor cell line, HUDEP-2, to allow for acute depletion of CTCF protein by the auxin-inducible degron system. In SEM cells, CTCF loss notably disrupted intra-TAD loops and TAD integrity in concurrence with a reduction in CTCF-binding affinity, while showing no perturbation to nuclear compartment integrity. Strikingly, the overall effect of CTCF’s loss on transcription was minimal. Whole transcriptome analysis showed hundreds of genes differentially expressed in CTCF-depleted cells, among which MYC and a number of MYC target genes were specifically downregulated. Mechanically, acute depletion of CTCF disrupted the direct interaction between the MYC promoter and its distal enhancer cluster residing ∼1.8 Mb downstream. Notably, MYC expression was not profoundly affected upon CTCF loss in HUDEP-2 cells suggesting that CTCF could play a B-ALL cell line specific role in maintaining MYC expression.

DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries.

Coordinated changes of DNA (de)methylation, nucleosome positioning, and chromatin binding of the architectural protein CTCF play an important role for establishing cell-type–specific chromatin states during differentiation. To elucidate molecular mechanisms that link these processes, we studied the perturbed DNA modification landscape in mouse embryonic stem cells (ESCs) carrying a double knockout (DKO) of the Tet1 and Tet2 dioxygenases. These enzymes are responsible for the conversion of 5-methylcytosine (5mC) into its hydroxymethylated (5hmC), formylated (5fC), or carboxylated (5caC) forms. We determined changes in nucleosome positioning, CTCF binding, DNA methylation, and gene expression in DKO ESCs and developed biophysical models to predict differential CTCF binding. Methylation-sensitive nucleosome repositioning accounted for a significant portion of CTCF binding loss in DKO ESCs, whereas unmethylated and nucleosome-depleted CpG islands were enriched for CTCF sites that remained occupied. A number of CTCF sites also displayed direct correlations with the CpG modification state: CTCF was preferentially lost from sites that were marked with 5hmC in wild-type (WT) cells but not from 5fC-enriched sites. In addition, we found that some CTCF sites can act as bifurcation points defining the differential methylation landscape. CTCF loss from such sites, for example, at promoters, boundaries of chromatin loops, and topologically associated domains (TADs), was correlated with DNA methylation/demethylation spreading and can be linked to down-regulation of neighboring genes. Our results reveal a hierarchical interplay between cytosine modifications, nucleosome positions, and DNA sequence that determines differential CTCF binding and regulates gene expression.

CTCF Regulates Otic Neurogenesis via Histone Modification in the Neurog1 Locus.

The inner ear is a complex sensory organ responsible for hearing and balance. Formation of the inner ear is dependent on tight regulation of spatial and temporal expression of genes that direct a series of developmental processes. Recently, epigenetic regulation has emerged as a crucial regulator of the development of various organs. However, what roles higher-order chromatin organization and its regulator molecules play in inner ear development are unclear. CCCTC-binding factor (CTCF) is a highly conserved 11-zinc finger protein that regulates the three-dimensional architecture of chromatin, and is involved in various gene regulation processes. To delineate the role of CTCF in inner ear development, the present study investigated inner ear-specific Ctcf knockout mouse embryos (Pax2-Cre; Ctcffl/fl). The loss of Ctcf resulted in multiple defects of inner ear development and severely compromised otic neurogenesis, which was partly due to a loss of Neurog1 expression. Furthermore, reduced Neurog1 gene expression by CTCF knockdown was found to be associated with changes in histone modification at the gene’s promoter, as well as its upstream enhancer. The results of the present study demonstrate that CTCF plays an essential role in otic neurogenesis by modulating histone modification in the Neurog1 locus.

Abstract 2998: Dynamic 3d chromosomal landscapes in acute leukemia

Abstract T-cell acute lymphoblastic leukemia (T-ALL) accounts for approximately 10-15% of pediatric and 25% of adult ALL cases. Despite improved prognosis driven by the significant advances in the molecular understanding of T-ALL, the outcome of T-ALL patients with primary resistant and relapsed leukemia remains poor. Recent evidences have highlighted a role for changes in 3D chromatin architecture in cancer progression. Herein, for the first time we explored genomewide changes in chromatin organization in primary T-ALL samples relative to T cells from healthy donors. We show how the organization of topologically associated domains (TADs) influences key oncogenic and tumor-suppressive loci by modifying the promoter-enhancer landscape, deregulating the transcriptional program and ultimately causing disease progression. To comprehensively characterize the chromatin landscape of clinically relevant loci in T-ALL, we sought to identify changes in intra-TAD activity and TAD disruptions on a genome-wide scale. We developed and implemented new computational approaches for Hi-C data analysis with a focus on Hi-C data integration with ChIP-Seq and RNA-Seq. We found significant correlations of TAD activity with CTCF occupancy, super-enhancer activity and gene expression of leukemia relevant loci. Furthermore, among the dozens of TAD disruptions we identified, we found a novel TAD “fusion” event around the MYC locus, which allows for chromatin interactions between a recently reported Notch-dependent MYC super-enhancer and promoter to drive overexpression of MYC. This particular TAD fusion is accompanied by a complete CTCF loss in the TAD boundary and increased MYC expression in T-ALL samples. Overall, this study sheds new light into how changes in chromatin architecture influence disease progression by restructuring oncogene and tumor suppressor landscapes. Citation Format: Palaniraja Thandapani, Andreas Kloetgen, Charalampos Lazaris, Xufeng Chen, Panagiotis Ntziachristos, Aristotelis Tsirigos, Iannis Aifantis. Dynamic 3d chromosomal landscapes in acute leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2998.

CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart

Cardiac progenitors are specified early in development and progressively differentiate and mature into fully functional cardiomyocytes. This process is controlled by an extensively studied transcriptional program. However, the regulatory events coordinating the progression of such program from development to maturation are largely unknown. Here, we show that the genome organizer CTCF is essential for cardiogenesis and that it mediates genomic interactions to coordinate cardiomyocyte differentiation and maturation in the developing heart. Inactivation of Ctcf in cardiac progenitor cells and their derivatives in vivo during development caused severe cardiac defects and death at embryonic day 12.5. Genome wide expression analysis in Ctcf mutant hearts revealed that genes controlling mitochondrial function and protein production, required for cardiomyocyte maturation, were upregulated. However, mitochondria from mutant cardiomyocytes do not mature properly. In contrast, multiple development regulatory genes near predicted heart enhancers, including genes in the IrxA cluster, were downregulated in Ctcf mutants, suggesting that CTCF promotes cardiomyocyte differentiation by facilitating enhancer-promoter interactions. Accordingly, loss of CTCF disrupts gene expression and chromatin interactions as shown by chromatin conformation capture followed by deep sequencing. Furthermore, CRISPR-mediated deletion of an intergenic CTCF site within the IrxA cluster alters gene expression in the developing heart. Thus, CTCF mediates local regulatory interactions to coordinate transcriptional programs controlling transitions in morphology and function during heart development.

Abstract 4993: The role of super-enhancers and genetic boundaries in gene regulation

Abstract The purpose of this study was to investigate the role of the Zn finger protein CTCF in the establishment of genetic borders and in controlling spatially-restricted activity of a mammary-specific super-enhancer (SE) known to selectively activate gene expression during pregnancy. CRISPR/Cas9 gene editing was used to generate mice with deletions in CTCF binding sites (CBSs) separating the Wap SE from the Ramp3 gene. ChIP-seq and qRT-PCR were used to investigate protein-DNA interactions and changes in gene expression, respectively. RNA-seq data demonstrated that expression of the mammary-specific Wap and widely-expressed Ramp3 gene was activated in mammary tissue at the onset of lactation. To investigate the possibility that the Wap SE can regulate both genes, mice carrying deletions in the SE were established. In these mice, both Wap and downstream Ramp3 were downregulated to the same extent, supporting the notion that the SE regulates both genes. Given these results, we investigated the contributions of several intervening CBSs in dampening SE activity on Ramp3. Mice harboring individual and combinatorial deletions of three CBSs (A, B and C) between the Wap SE and Ramp3 were generated. While loss of CTCF at site B (ΔB) had no apparent effect, loss of site A (ΔA) led to an expansion of H3K27ac from the adjacent SE in mammary tissue. The site C mutation (ΔC) resulted in a two-fold induction of Ramp3 in mammary tissue. Mice lacking all three binding sites demonstrated a marked increase in Ramp3 expression, which indicates that the CBSs block expression in an additive manner. To test the possible insulator function of these in a tissue with opposing gene expression, cerebellum was chosen as Ramp3 is actively transcribed while Wap is silent. The ΔA and ΔB mice showed no phenotype, but surprisingly ΔC mice demonstrated an 80% reduction in Ramp3 expression. Analysis of ChIP-seq and DNAse-seq demonstrated that site C coincides with a cerebellum-specific enhancer, which appears to regulate Ramp3 expression. These data demonstrate that a SE can activate two genes, albeit to different degrees. Furthermore, we demonstrate that CBSs do not serve as tight genetic boundaries encapsulating transcriptional enhancers and their associated genes, but are porous borders that allow for fine tuning of transcriptional activity. Individual CBSs have a modest ability to insulate genes, but a cluster of CTCF proteins is required to adjust the enhancer activity on genes and prevent deregulation. In addition, we show that CBSs are not restricted to a unique function and can act in a tissue-specific manner to contribute to gene regulation. These data help us to develop a more nuanced understanding of SE function as well as the roles of CTCF in regulating gene expression. Previous studies have shown that SEs and CBSs are mutational hotspots in cancer, implicating them in tumorigenesis. A more complete understanding of their biology will allow a better understanding of their role in cancer. Citation Format: Michaela Willi, Tyler M. Kuhns, Kyung Hyun Yoo, Fabian Reinisch, Christian Reinbold, Teresa Mohr, Chaochen Wang, Lothar Hennighausen. The role of super-enhancers and genetic boundaries in gene regulation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4993. doi:10.1158/1538-7445.AM2017-4993

Abstract A12: CTCF facilitates DNA double-strand break repair by homologous recombination

Abstract The repair of DNA double strand breaks (DSB) is mediated via two major pathways, non-homologous end joining (NHEJ) or homologous recombination repair (HRR). Such repair is critical for cell survival and genome stability. Here, we report a new role for the multifunctional protein CTCF in facilitating the repair of DSB via the HRR pathway. CTCF is recruited to DSB through its zinc finger domain independently of poly(ADP-ribose) polymers catalyzed by PARP-1. CTCF ensures proper DSB repair kinetics in response to gamma-irradiation, and potentiates activation of the G2/M checkpoint. We find that CTCF regulates HRR through facilitating the recruitment of BRCA2, which is dependent on CTCF PARylation. In contrast, CTCF does not influence the recruitment, or retention, of the NHEJ protein 53BP1 to DSB. We also see that loss of CTCF is associated with hypersensitivity to DNA damaging inducing agents and inhibitors of PARP-1. Taken together, our findings establish for the first time that CTCF is an important regulator of the HRR pathway and indicate that tumors harboring hypo-PARylated CTCF may show elevated sensitivity to PARP inhibition. Citation Format: Khalid Hilmi, Chenxi Zhang, Zhenbao Yu, Amine Saad, Stephane Richard, Luke McCaffrey, Moulay A. Alaoui-Jamali, Michael Witcher. CTCF facilitates DNA double-strand break repair by homologous recombination [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr A12.

Erythroid specific activator GATA-1-dependent interactions between CTCF sites around the β-globin locus

CTCF sites (binding motifs for CCCTC-binding factor, an insulator protein) are located considerable distances apart on genomes but are closely positioned in organized chromatin. The close positioning of CTCF sites is often cell type or tissue specific. Here we analyzed chromatin organization in eight CTCF sites around the β-globin locus by 3C assay and explored the roles of erythroid specific transcription activator GATA-1 and KLF1 in it. It was found five CTCF sites convergent to the locus interact with each other in erythroid K562 cells but not in non-erythroid 293 cells. The interaction was decreased by depletion of GATA-1 or KLF1. It accompanied reductions of CTCF and Rad21 occupancies and loss of active chromatin structure at the CTCF sites. Furthermore Rad21 occupancy was reduced in the β-globin locus control region (LCR) hypersensitive sites (HSs) by the depletion of GATA-1 or KLF1. The role of GATA-1 in interaction between CTCF sites was revealed by its ectopic expression in 293 cells and by deletion of a GATA-1 site in the LCR HS2. These findings indicate that erythroid specific activator GATA-1 acts at CTCF sites around the β-globin locus to establish tissue-specific chromatin organization.

Abstract 4434: CTCF acts as a master regulator to direct epigenetic events important for tumor development and progression

Abstract Intro Epigenetic changes, including altered DNA methylation, underlie the development and progression of prostate cancer (PCa). DNA methylation events are frequently seen in PCa, however, how these methylation changes are directed locally and regionally remain an important question. CTCF is a widely expressed chromatin insulator protein which plays important roles in transcriptional regulation, chromatin architecture, and the conservation of epigenetic marks. Previous work has shown that CTCF expression declines in the aging mouse prostate and in human metastatic prostate samples. It is our hypothesis that CTCF loss directs DNA methylation increases at specific loci resulting in gene expression and phenotypic advantages in cancer cells. Methods Cell lines with inducible shRNA expression targeting CTCF were created using 9E6/E7 human prostate epithelial cells and PPC1 and LNCaP cancer lines. Knockdowns were confirmed by qPCR and western blotting. DNA methylation was analyzed using MeDIP-chip, utilizing the Affymetrix Cytoscan HD Array and RNA expression analyzed using Affymetrix Human Transcriptome 2.0 Array. Bioinformatic analysis was performed in R 3.2.1 and Bioconductor 3.0. Motif analysis was performed using HOMER. Cell stress included exposure to H2O2 and CoCl2. Results We detected 9811 probes with differential methylation after CTCF knockdown (with P<0.01), of which 5,968 probes (60.1%) were hypermethylated. Of the hypermethylated probes, 417 (7%) were near gene transcription start sites and 3,361 (56.3%) were located within transcribed loci. Motif analysis indicated that CTCF target sequences were enriched in regions developing hypermethylation (P<0.01). Pyrosequencing confirmed methylation increases. RNA expression analysis with CTCF knockdown identified 1,394 transcribed loci with significantly altered expression (FDR<0.1). One-third of genes with altered transcriptional levels also contained a differentially methylated probe in its promoter or transcribed region (459/1394; 32.9%). We confirmed numerous genes with promoter hypermethylation corresponding to decreased RNA expression including CASP14, EDN1, EL, FSTL1, and WIPI1. Gene ontology indicates enrichment for anti-apoptotic genes. CTCF knockdown in epithelial and cancer cell lines led to a significantly increased survival of cells faced with hypoxia or oxidative stress. Conclusion Reduction of CTCF, an alteration that occurs in the development of advanced PCa, directs the hypermethylation of loci containing CTCF binding sites. These hypermethylated regions correspond to the transcriptional downregulation of genes involved in metabolism, ER stress, and apoptosis. CTCF knockdown results in resistance to hypoxia or oxidative stress. This study demonstrates, for the first time that CTCF acts as a master regulator to direct epigenetic events important for tumor development and progression and is a target for therapy. Citation Format: Nathan A. Damaschke, Bing Yang, Anastasia Montgomery, John Svaren, Avtar Roopra, Jianhua Luo, Sunduz Keles, David Jarrard. CTCF acts as a master regulator to direct epigenetic events important for tumor development and progression. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4434.

CTCF loss results in fate change of Lhx6-positive Interneurons

CTCF loss results in fate change of Lhx6-positive Interneurons

The insulator protein CTCF regulates Drosophila steroidogenesis.

ABSTRACTThe steroid hormone ecdysone is a central regulator of insect development. In this report we show that CTCF expression in the prothoracic gland is required for full transcriptional activation of the Halloween genes spookier, shadow and noppera-bo, which encode ecdysone biosynthetic enzymes, and for proper timing of ecdysone-responsive gene expression. Loss of CTCF results in delayed and less synchronized larval development that can only be rescued by feeding larvae with both, the steroid hormone 20-hydroxyecdysone and cholesterol. Moreover, CTCF-knockdown in prothoracic gland cells leads to increased lipid accumulation. In conclusion, the insulator protein CTCF is required for Halloween gene expression and cholesterol homeostasis in ecdysone-producing cells controlling steroidogenesis.