{"lab": {"correspondence": [{"contact_email": "dmFoZWRpQHBlbm5tZWRpY2luZS51cGVubi5lZHU=", "@id": "/users/a44efbbf-7993-4258-b1ed-88045387e8ba/", "display_title": "Golnaz Vahedi"}], "uuid": "fedfc81d-f1ce-4203-9c87-bc0b6eb2bfc3", "status": "current", "display_title": "Golnaz Vahedi, UPENN", "@type": ["Lab", "Item"], "title": "Golnaz Vahedi, UPENN", "@id": "/labs/golnaz-vahedi-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fedfc81d-f1ce-4203-9c87-bc0b6eb2bfc3"]}}, "award": {"display_title": "SINGLE-CELL DISSECTION OF CHROMATIN ARCHITECTURE MECHANISMS CONNECTING PATHOLOGIC INSTABILITY AND TRANSCRIPTIONAL SILENCING", "status": "current", "name": "1U01DA052715-01", "project": "4DN", "description": "OFHHD: Short tandem repeat regions (STR) are distributed evenly across the human genome, and recent genome-wide studies have demonstrated that STRs are polymorphic across individuals and linked to gene expression levels. STR instability at key genomic loci has been causally linked to disease pathophysiology in a range of expansion disorders. We recently demonstrated that nearly all disease-associated STRs co-localize with boundaries demarcating topologically associated domains (TADs). Moreover, we have observed that pathologic STR instability and transcriptional silencing can destroy the associated boundary and shift genomic loci to the nuclear periphery. These results now open critical unanswered questions regarding whether and how STR expansion and pathologic alterations in gene expression are functionally linked to boundary integrity and radial positioning. Here, we focus on the prototypic repeat expansion disorder Friedreich\u2019s ataxia (FRDA) in which expansion of a GAA STR in the first intron of the FRATAXIN (FXN) gene results in cardiac and neuronal pathology. The cardiac pathology, specifically hypertrophy, fibrosis, and occasional dilation of the ventricle, is the etiology of significant FRDA mortality. GAA expansion is associated with the silencing of FXN transcription and a repositioning of the locus to the nuclear periphery. However, it remains unclear if the change in genome folding, radial positioning, or reduced expression drives STR expansion or vice versa. A major technical barrier contributing to this knowledge gap is that STR instability and genome folding are classically evaluated in bulk populations, however they exhibit tremendous variation across individual somatic cells of the same subtype and among cell types within a pathologically affected tissue. Here, we seek to decipher the causal link among STR instability, transcription, radial positioning, and genome folding. Our central hypothesis is that disruption of long-range loops is the initial event triggered by STR expansion leading to a cascade of heterochromatin spreading, silencing, and loss of radial positioning. We will test our hypothesis by generating genome-wide, single-cell maps of chromatin accessibility, expression, and the repressive H3K9me3 heterochromatin mark in GAA-expanded and control iPS cells and iPS-derived cardiomyocytes. We will integrate genomics data with single-cell sequential Oligopaints/OligoSTORM imaging of TADs and local chromatin structure, as well as single molecule RNA FISH for FXN expression. We will implement multiple genome engineering strategies, including dCas9-VP64 FXN activation and dCas9-CTCF loop re-engineering in FRDA GAA-iPS cells, and dCas9-Krab-Dnmt3a FXN silencing and dCas9-Krab CTCF-mediated loop disruption in healthy iPS cells. We will assay the effect of genome engineering approaches on TADs, radial positioning, STR length, and FXN expression in single cells. Successful completion of the proposed work will shed light on the pathophysiological mechanisms underlying repeat expansion disorders by deciphering the cause-and-effect relationships among genome folding, radial positioning, transcription, and STR expansion.", "@type": ["Award", "Item"], "uuid": "8c9d595e-2809-4779-ae6e-305341f695ff", "@id": "/awards/1U01DA052715-01/", "center_title": "OFHHD - Phillips-Cremins", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "files": [{"accession": "4DNFICUODAOX", "file_size": 47935559617, "upload_key": "57d3f864-4d77-428b-8804-88370c33967b/4DNFICUODAOX.fastq.gz", "display_title": "4DNFICUODAOX.fastq.gz", "status": "released", "href": "/files-fastq/4DNFICUODAOX/@@download/4DNFICUODAOX.fastq.gz", "file_classification": "raw file", "file_type": "reads", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFICUODAOX/", "dbxrefs": ["SRA:SRR17681899"], "uuid": 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"condition": "Cre+ induced mice (control)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "double-positive, alpha-beta thymocyte", "lab_name": "4DN DCIC, HMS"}}], "title": "HiC Processing Pipeline - v0.3.0", "description": "These are files generated using the updated Hi-C processing pipeline. They should be largely similar to those available in the Processed Files tab, which were generated with the previous version of the standard pipeline.  One potential difference of note is that the version of cooler used to generate the mcool file has a bug fix to prevent a pixel duplication issue which is observed in some files generated by the previous version of the pipeline.  Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation."}], "biosample_quantity_units": "cells", "fragment_size_selection_method": "SPRI beads", "@id": "/experiments-hi-c/4DNEX3QS8YI4/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "58daa1d7-aa79-4d96-b614-dfb0c3a5f14a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ Hi-C on double-positive, alpha-beta thymocyte with Arima - A1, A2 - 4DNEX3QS8YI4", "external_references": [{"ref": "GEO:GSM5827706", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5827706"}, {"ref": "SRA:SRX13845183", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX13845183"}], "experiment_sets": [{"display_title": "4DNES9GX32AL", "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES9GX32AL/", "accession": "4DNES9GX32AL", "status": "released", "uuid": "127333c3-0033-4f8b-8e36-6614e0820a6c", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"journal": "Nature immunology", "authors": ["Wang W", "Chandra A", "Goldman N", "Yoon S", "Ferrari EK", "Nguyen SC", "Joyce EF", "Vahedi G"], "@type": ["Publication", "Item"], "title": "TCF-1 promotes chromatin interactions across topologically associating domains in  T cell progenitors.", "date_published": "2022-07", "@id": "/publications/e4a9ada3-ab33-4fee-aba5-7f39c8205b00/", "uuid": "e4a9ada3-ab33-4fee-aba5-7f39c8205b00", "abstract": "The high mobility group (HMG) transcription factor TCF-1 is essential for early T  cell development. Although in vitro biochemical assays suggest that HMG proteins  can serve as architectural elements in the assembly of higher-order nuclear  organization, the contribution of TCF-1 on the control of three-dimensional (3D)  genome structures during T cell development remains unknown. Here, we  investigated the role of TCF-1 in 3D genome reconfiguration. Using gain- and  loss-of-function experiments, we discovered that the co-occupancy of TCF-1 and  the architectural protein CTCF altered the structure of topologically associating  domains in T cell progenitors, leading to interactions between previously  insulated regulatory elements and target genes at late stages of T cell  development. The TCF-1-dependent gain in long-range interactions was linked to  deposition of active enhancer mark H3K27ac and recruitment of the cohesin-loading  factor NIPBL at active enhancers. These data indicate that TCF-1 has a role in  controlling global genome organization during T cell development.", "short_attribution": "Wang W et al. (2022)", "status": "current", "ID": "PMID:35726060", "display_title": "Wang W et al. (2022) PMID:35726060", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"ID": "PMID:35726060", "short_attribution": "Wang W et al. (2022)", "date_published": "2022-07", "display_title": "Wang W et al. (2022) PMID:35726060", "status": "current", "@id": "/publications/e4a9ada3-ab33-4fee-aba5-7f39c8205b00/", "authors": ["Wang W", "Chandra A", "Goldman N", "Yoon S", "Ferrari EK", "Nguyen SC", "Joyce EF", "Vahedi G"], "title": "TCF-1 promotes chromatin interactions across topologically associating domains in  T cell progenitors.", "uuid": "e4a9ada3-ab33-4fee-aba5-7f39c8205b00", "journal": "Nature immunology", "@type": ["Publication", "Item"], "abstract": "The high mobility group (HMG) transcription factor TCF-1 is essential for early T  cell development. Although in vitro biochemical assays suggest that HMG proteins  can serve as architectural elements in the assembly of higher-order nuclear  organization, the contribution of TCF-1 on the control of three-dimensional (3D)  genome structures during T cell development remains unknown. Here, we  investigated the role of TCF-1 in 3D genome reconfiguration. Using gain- and  loss-of-function experiments, we discovered that the co-occupancy of TCF-1 and  the architectural protein CTCF altered the structure of topologically associating  domains in T cell progenitors, leading to interactions between previously  insulated regulatory elements and target genes at late stages of T cell  development. The TCF-1-dependent gain in long-range interactions was linked to  deposition of active enhancer mark H3K27ac and recruitment of the cohesin-loading  factor NIPBL at active enhancers. These data indicate that TCF-1 has a role in  controlling global genome organization during T cell development.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "Arima - A1, A2", "combined": "Enzyme: Arima - A1, A2"}, "experiment_summary": "in situ Hi-C on double-positive, alpha-beta thymocyte with Arima - A1, A2", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}