Ctcf mediated functional chromatin interactome in pluripotent cells pdf

Transcriptional repressor ctcf also known as 11zinc finger protein or ccctcbinding factor is a transcription factor that in humans is encoded by the ctcf gene. Furthermore, ctcfrelated chromatin reorganization contributes to the myocardial stressgene response. We propose a deep learning method, deepmilo, to predict the effects of variants on ctcf cohesin mediated insulator loops. Control of distalless expression in the drosophila appendages by functional 30 enhancers. L handoko, h xu, g li, cy ngan, e chew, m schnapp, cwh lee, c ye. Activation of protooncogenes by disruption of chromosome.

Ctcf mediated chromatin interactions are pervasive across the entire genome in the four tested human cell lines figure s2a. In the domain barrier model, ctcf binding is proposed to function as a buffer from the effects caused by the adjacent chromatin. A positive correlation has been reported between ctcfl and ers in breast tumors and there also exists a coordinated interaction between ctcf and ers in breast cancer cells. The cancertestis antigen boris phenocopies the tumor suppressor. A computational intersection of the genomicbinding sites of ctcf assessed by genomewide chip with a genomewide dna contact map generated by hic suggested that ctcf is involved in chromatin interactions between and within chromosomes across the genome. Functional interplay between myod and ctcf in regulating. Overexpression of ctcf dramatically elevates the heart weight and ejection fraction, and implantation of the therapeutic device can improve cardiac dysthythmia and bring the ctcf back to normal level. Chromatin immunoprecipitation analysis of a human hepatoma cell line revealed that chd8 was present at ctcf target sites, such as the differentially methylated region of h19, the locus control region of betaglobin, and the promoter regions of the brca1 1705 and myc genes.

Their framework of cohesinassociated ctcf loops, and the cohesinassociated enhancerpromoter loops within them, provides a reference map for future interrogation of regulatory interactions. The nature and distribution of histone tail posttranslational modifications as well as dna methylation patterns largely distinguish embryonic stem cells from somatic cell types. Yet, little is known about ctcfassociated higher order chromatin structures at a global scale. Ctcf site longrange interactions surrounding the bglobin locus are primarily cell type specific in a previous study, we used chromatin immunoprecipitation combined with microarray analysis chipchip and chip and qpcr to survey and validate ctcf sites up and downstream of the bglobin locus on human chromosome 11 in k562 cells, where the. Pdf ctcfmediated functional chromatin interactome in. Application of deepmilo on variants from wholegenome sequences of 1834 patients of twelve cancer types revealed 672 insulator loops disrupted in at least. Ctcf, the most characterized insulatorbinding protein, has been implicated as a key genome organizer. At many genomic sites in es cells, dnabound ctcf cohesin can recruit the core promoter factor taf3 and mediate its contact with promoters through taf3dependent loop formation liu et al. The organization of higher order chromatin is an emerging epigenetic mechanism for understanding development and disease. Extensive chromatin and transcriptional reorganization occurs on pluripotent. Lats kinasemediated ctcf phosphorylation and selective loss. Ctcf regulates foxo signalling pathway to affect the proliferation of prostate cancer.

Nucleic acids research ctcfmediated transcriptional regulation through cell typespecific chromosome organization in the bglobin locus ivan junier 0 1 2 ryan k. Aug 14, 20 recent studies suggested that humanmammalian genomes are divided into large, discrete domains that are units of chromosome organization. A recent genomewide ctcf mediated chromatin interactome map in mouse embryonic stem cells described a 314 kb intrachromosomal loop connecting a ctcf binding site located in the second intron of kcnq1 to a ctcf binding site 3. A growing body of evidence suggests that insulators have a primary role in orchestrating the topological arrangement of higherorder chromatin architecture. Genome compaction is a universal feature of cells and has emerged as a global regulator of gene expression. This unique capacity of escs and ipscs to form all cell lineages is termed pluripotency. Despite an identical genotype, each cell type displays a distinct gene expression pro. Ctcf regulates the human p53 gene through direct interaction.

Znf143 is involved in ctcfmediated chromatin interactions. The genome of higher eukaryotes exhibits a patchwork of inactive and active genes. Handoko l, xu h, li g, ngan cy, chew e, schnapp m, lee cw, ye c, ping jl, mulawadi f, wong e, sheng j, zhang y, poh t, chan cs, kunarso g, shahab a, bourque g, cacheuxrataboul v, sung wk, ruan y, wei cl. Ctcfbased chromatin loops differ between k562 cells and 293t cells. Exploring the changing landscape of celltocell variation. The chromatin insulator ctcf and the emergence of metazoan. Ctcf mediated functional chromatin interactome in pluripotent cells lusy handoko 1, han xu 1, guoliang li 1, chew yee ngan 1, elaine chew 1, marie schnapp 1, charlie wah heng lee 1, chaopeng ye 1, joanne lim hui ping, fabianus mulawadi 1, eleanor. Direct integration of hox and segmentation gene inputs during drosophila development. Ctcfmediated functional chromatin interactome in pluripotent cells lusy handoko1, han xu1, guoliang li1, chew yee ngan1, elaine chew1, marie schnapp1, charlie wah heng lee1, chaopeng ye1. Our data suggest that deregulated function of dna loops mediated by p63 and ctcf represents an additional layer to the disease mechanism fig. The concept of pluripotent capacity may rely on the interplay between the different individual cells in a pluripotent embryo, which might be reflected in the cell.

Ctcf is involved in many cellular processes, including transcriptional regulation, insulator activity, vdj recombination and regulation of chromatin architecture. Several lines of evidence support a role for these modifications in ctcf function. Oct 23, 2012 although functional data are available so far only from mice and d. We and others have previously observed dynamic changes during differentiation and oncogenesis in large heterochromatin domains such as large organized chromatin k lysine modifications locks, of histone h3 lysine9 dimethylation h3k9me2 or other. To address the functional relevance of wrap53 rnactcf interactions in vivo, we generated an inducible cell system in which endogenous ctcf is depleted by shrna knockdown and the ctcfdeficient cells are rescued with hatagged versions of ctcf, either wild type hactcf wt or mutant in rna binding hactcf. The efficient reoccupancy by ctcf cohesin and inheritance of flanking hemimethylation during dna replication, and the colocalization with mbd proteins, support a model suggesting that ctcf sites actively engaged in chromatin interactions are marked by hemicpgs shortly after passage of the local replication forks, which may facilitate timely. B hic interaction map, tads defined in human embryonic stem cells h1, cohesin chiapet interactions intensity of blue arc represents interaction significance, ctcf and h3k27ac chromatin immunoprecipitation sequencing chipseq profiles and peaks, and rnaseq in jurkat cells at the cd3d locus. Jul 23, 2015 pluripotent cells, which consist of embryonic stem es cells and their reprogrammed counterparts, induced pluripotent stem ips cells, are one of the most wellcharacterized cellular systems to study the connection between chromatin organization and cell identity.

Pluripotent cells, which consist of embryonic stem es cells and their reprogrammed counterparts, induced pluripotent stem ips cells. Here we applied chromatin interaction analysis by pairedend tag chiapet sequencing to elucidate the ctcfchromatin interactome in pluripotent cells. Jun 19, 2011 chialin wei, yijun ruan and colleagues used chromatin interaction analysis by pairedend tag sequencing chiapet to determine the ctcfchromatin interactome in mouse embryonic stem cells. Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation.

To analyze chromatin looping mediated by ctcf, we first defined the genomewide occupancy of ctcf. Ctcfs exact function at a given genomic site is unpredictable. Pluripotent cells, which consist of embryonic stem es cells and their reprogrammed counterparts, induced pluripotent stem ips cells, are one of the most wellcharacterized cellular systems to study the connection between chromatin organization and cell identity 3. Cohesin bound to chromatin extrudes a loop and continues until it reaches a. Nascent dna methylome mapping reveals inheritance of. These functions of ctcf all involve ctcfmediated longrange chromatin organization, which can be manifest intra or interchromosomally 11, 12.

Compaction is maintained by a multitude of architectural proteins, long noncoding rnas lncrnas, and regulatory dna. Ctcf mediated functional chromatin interactome in pluripotent cells l handoko, h xu, g li, cy ngan, e chew, m schnapp, cwh lee, c ye. Based on the ctcf interaction clustering scheme, we identified 53,741 high quality ctcf mediated interactions in gm12878 cells. Pairwise interaction frequencies detected by 3c are shown by arcs for k562 red, k562 ctcf rnai knockdown green and 293t blue cells. We knocked down ctcf in el4 cells using shrna, and conducted single cell rnaseq on both wild type wt cells and ctcfknockdown ctcfkd cells using fluidigm c1 system. Involvement of ctcfmediated chromatin loop structure in. Tissuespecific ctcfcohesinmediated chromatin architecture. Znf143 is a ubiquitously expressed transcription factor conserved in vertebrates and might regulate the expression of numerous genes. When an extra copy of hs5 was placed between the locus control region lcr. Crisprcas9 mediated deletion in hek293t cells of a 25kb segment encompassing the insulated neighborhood boundary ctcf site and two additional ctcf sites that could act as boundary elements caused a factor of 2 increase in the lmo2 transcript fig. Here, we report that lats kinases phosphorylated ctcf in the zinc finger zf linkers and. Genomewide studies of ccctcbinding factor ctcf and. Here we discuss higherorder chromatin organization as a unifying.

Each component comprises interlinked regulatory circuits that organize the genome in threedimensional 3d space to manage gene expression. Different cells display substantial variation in gene expression and in response to environmental signaling even in an apparently homogeneous. But its function in mediating chromatin interactions remains elusive. Introduction in metazoans, the zygotic genome represents the founding blueprint for all cell types in the developing organism. Jul 24, 2017 rather than acting solely as a barrier to chromatin modification, ctcfcohesin boundaries in this subtad delimit the region of chromatin to which enhancers have access and within which they. Ctcf regulates the foxo signaling pathway to affect the. Ctcf mediates chromatin looping via nterminal domain. Euchromatin islands in large heterochromatin domains are.

Ctcfmediated functional chromatin interactome in pluripotent cells l handoko, h xu, g li, cy ngan, e chew, m schnapp, cwh lee, c ye. Ongoing research by multiple laboratories is expected to soon reveal the significance of preferential ctcf binding sites for the formation of tads, subtads and cell typespecific chromatin loops, enabling prediction of chromatin topology changes during cell fate transitions or upon genetic and epigenetic alterations around ctcf sites. The role of chromatin insulators in nuclear architecture and. Jun 27, 2016 the pluripotencyspecific transcription program is associated with a unique epigenetic landscape. Jun 23, 2016 znf143 is a ubiquitously expressed transcription factor conserved in vertebrates and might regulate the expression of numerous genes. The dnabinding protein ccctcbinding factor ctcf and the cohesin complex function together to establish chromatin loops and regulate gene expression in mammalian cells. Oct 11, 2019 cellular heterogeneity, which was initially defined for tumor cells, is a fundamental property of all cellular systems, ranging from genetic diversity to celltocell variation driven by stochastic molecular interactions involved all cellular processes. Ctcf, a ccctc binding factor, has a diverse role in genome regulation including transcriptional regulation, chromosomeboundary insulation, dna replication, and chromatin packaging. Ctcfmediated chromatin interactome revealed by chiapet. However, the analysis of the ctcf chromatin interactome in embryonic stem cells revealed that only a small percentage of the genomic sites bound by this factor participate in chromatin loops handoko et al. Geneenhancer interactions are accommodated in the same ctcf mediated insulated neighborhoods.

Dec 26, 2019 however, the effect of ctcf on genomewide landscape of celltocell variation remains unclear. Preferential associations between coregulated genes reveal a transcriptional interactome in erythroid cells. We performed chipseq in murine embryonic stem cells escs and neural progenitor cells npcs and found 54,151 and 65,983 bound ctcf sites, respectively. It remains unclear whether a subset of ctcf binding sites plays a functional. B, mtt assay showed that the cell proliferation of lncap and pc. Ctcf binding polarity determines chromatin looping. Ctcfl, a paralogue of the chromatin organizer ctcf, is a potential biomarker of breast cancer, but its expression in this disease is currently controversial. Chromatin topological organization is instrumental in gene transcription. A coordinated interaction between ctcf and er in breast. Ctcfmediated functional chromatin interactome in pluripotent cells. However, little is known about ctcfassociated higherorder chromatin structures at. However, little is known about ctcfassociated higherorder chromatin structures at a global scale. Pluripotencyrelated, valproic acid vpainduced genomewide histone h3 lysine 9 h3k9 acetylation patterns in embryonic stem cells.

This finding calls attention to the importance of ctcf interacting partners in regulating the arrangement of ctcf mediated. However, it remains poorly understood whether and how the 3d genome architecture is dynamically restructured by external signals. The error has been corrected in the html and pdf versions of the article. It has been proposed that the cohesin complex moving bidirectionally along dna extrudes the chromatin fiber and generates chromatin loops when it pauses at ctcf binding sites. Here, we applied chromatin interaction analysis by pairedendtag sequencing to elucidate the ctcfchromatin interactome in pluripotent cells. An initial study in mouse fetal liver using chipchip found 200 methylationfree ctcfbinding sites, many of which functioned as insulators. Thus, we next investigated whether ctcf are also involved in chromatin loop formation around early g1 genes. By integrated analysis of public datasets, we provided evidence that a majority of znf143 binding sites bss were involved in ctcf mediated chromatin interaction networks ctcf cins by. A and b 3c analyses of ctcf anchored chromatin looping at the pfkfb3 gene in mcf7 cells under glucose starvation a and at the axl gene in mcf7 cells following cell detachment b. Ctcfctcf loops appear to function as insulated neighbor. A functionally pluripotent population of cells may be characterized by its highly entropic state, as the open chromatin state offers only weak regulatory constraints. Ctcf mediated human 3d genome architecture reveals chromatin topology for. From this analysis, 1,480 cis and 336 trans interacting loci were identified with high reproducibility and precision.

Functional interplay between myod and ctcf in regulating long. Though insulators have been extensively characterized by their ability to influence gene expression in transgenic reporter assays, mapping of insulator proteinbinding sites has allowed recent studies to probe the function of chromatin insulators in their normal context. Extensive chromatin and transcriptional reorganization occurs on. We depleted ctcf in tsft210 cells by sirna and analyzed chromatin structure of. However, the analysis of the ctcfchromatin interactome in embryonic stem cells revealed that only a small percentage of the genomic sites bound by this factor participate in chromatin loops handoko et al. Oct 27, 2011 embryonic stem cells escs and induced pluripotent stem cells ipscs hold tremendous clinical potential because of their ability to selfrenew, and to differentiate into all cell types of the body. The nuclear protein ccctcbinding factor ctcf when bound to insulator sequences can prevent undesirable crosstalk between active and inactive genomic regions, and it can also shield particular genes from enhancer function, a role that has many applications in development.

Many of the shorterrange, ctcfmediated interactions do not conform to this rule. This finding calls attention to the importance of ctcfinteracting partners in regulating the arrangement of ctcfmediated. Cell type specificity of chromatin organization mediated by. Ctcfmediated functional chromatin interactome in pluripotent. Lats kinasemediated ctcf phosphorylation and selective. Our data suggest a positive, protranscriptional role for ctcf in er mediated gene expression in breast cancer cells.

Ctcf inhibits endoplasmic reticulum stress and apoptosis in. We find that ctcf mediated cell typespecific interactions in erythroid cells are organized to favor contacts known to occur in vivo between the. The scissormarked regions c1 and c2 were deleted by crisprmediated deletion. Ctcfmediated functional chromatin interactome in pluripotent cells experimental protocol chromatin interaction analysis coupled with pair end tags of ctcf. Genetic variants within the second intron of the kcnq1. The ctcfctcf loop structures of tads in naive and primed cells were very similar, although there were some instances where a tadspanning loop or an internal loop identified in one of the pluripotent cells was absent in data for the other cell. Insulator mediated longrange interactions can influence the epigenetic status of the genome and, in certain contexts, may have important effects on gene expression. Emerging roles of insulators in nuclear architecture and genome function. While escs and ipscs are pluripotent and remarkably similar in appearance, whether ipscs truly resemble. Journal of computational biology supplementary data. This view is reinforced by recent genomewide chiapet analysis that suggests a global function of ctcf in chromatin organization and transcriptional control through the establishment of distinct chromatin domains. Further support comes from the mapping of ctcf mediated chromatin interaction sites using chiapet, combining chip, proximity ligation, and deep sequencing. Ctcf not only provides boundaries for accessible and protected transcriptional blocks, but may also influence the actual binding of er to the chromatin, thereby modulating the estrogen mediated gene expression changes observed.

Aiguader, 88, 08003 barcelona, spain 1 institute of complex systems, paris, france 2 epigenomics project and institute of systems. Chip using anti ctcf antibody, followed by close proximity ligations. Cellular heterogeneity, which was initially defined for tumor cells, is a fundamental property of all cellular systems, ranging from genetic diversity to cell to cell variation driven by stochastic molecular interactions involved all cellular processes. Noncoding variants have been shown to be related to disease by alteration of 3d genome structures. Given that ctcf binding did not change, it is likely that the looping interactions are static, but the looping is no longer active due to the absence of p63 binding fig. Ctcfmediated transcriptional regulation through cell type. Ctcf mediates formation of chromatin loop and regulates transcription 17, 26. Jun 19, 2011 however, little is known about ctcfassociated higherorder chromatin structures at a global scale. Ctcf mediated functional chromatin interactome in pluripotent cells.

The majority n 37,298 of ctcf sites were found to be conserved between these two cell types. Developmental regulation of chromatin conformation. A different method of identifying paired sites guo et al. This cited by count includes citations to the following articles in scholar.