{"lab": {"uuid": "b2c2deeb-e883-4ac0-b9e2-906e598884d6", "title": "Andrew Belmont, ILLINOIS", "@type": ["Lab", "Item"], "@id": "/labs/andrew-belmont-lab/", "correspondence": [{"contact_email": "YXNiZWxAaWxsaW5vaXMuZWR1", "@id": "/users/92f90aed-7df1-4bd9-9e74-a472cb50d663/", "display_title": "Andrew Belmont"}], "display_title": "Andrew Belmont, ILLINOIS", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b2c2deeb-e883-4ac0-b9e2-906e598884d6"]}}, "award": {"center_title": "NOFIC - Belmont", "@id": "/awards/1U54DK107965-01/", "status": "current", "@type": ["Award", "Item"], "project": "4DN", "display_title": "COMBINED CYTOLOGICAL, GENOMIC, AND FUNCTIONAL MAPPING OF NUCLEAR GENOME ORGANIZATION", "description": "NOFIC: Decades of microscopy have revealed that the nucleus is not a homogeneous organelle, but rather consists of distinct compartments such as nucleoli, nuclear speckles, the nuclear lamina, among other structures. Increasing evidence indicates that specific genomic regions each associate with these compartments. This genome compartmentalization has been linked to various functions, but these links are still poorly understood. Interestingly, Lamina Associated Domains (LADs) share specific heterochromatin marks, defining chromatin domains with distinct genetic and epigenetic properties. Genomic regions associating with other nuclear compartments may similarly define distinct classes of chromatin domains. One major bottleneck towards a deeper understanding of nuclear organization has been the inability to convert microscopy views of nuclear compartments into genome-wide maps that show which loci are associated with which compartment, and how the chromosomal fiber traverses between compartments. In addition, there is an urgent need for more efficient methods to dissect the mechanisms by which large genomic regions are targeted to specific nuclear compartments. Finally, there is an urgent need for high-throughput approaches that query the functional relevance of genome compartmentalization. For this Center grant, we propose to meet these needs through the following Aims: 1. Develop a strategy that connects microscopy views to genome-wide maps that, together with modeling, reveal the localization and dynamics of genomic regions relative to all major nuclear compartments. 2. Develop methods for efficient manipulation of the genome in order to elucidate mechanisms that target loci to specific compartments. 3. Develop methods to measure, model, and validate the functional relevance of nuclear compartments. The combined results of these approaches will reveal causal relationships now hidden among entangled genomic, epigenetic, and nuclear organization features. Deliverables of this proposal include a wide range of structural and functional maps of nuclear organization, reagents for visualizing endogenous chromosome loci, a powerful pipeline for synthesis of ~100kb DNA fragments, and cell lines facilitating repeated, high-fidelity insertio of these large fragments back into selected sites in the genome. These resources will provide a powerful complement to other 4D Nucleome Consortium efforts. A key strength of this Center proposal is the experience and complementary research capabilities of its five Investigators. Together they will pool their expertise for a concerted investigation into the biological functions of nuclear compartmentalization.", "name": "1U54DK107965-01", "uuid": "91b694c3-f4d7-4ddd-8278-16f94e15c1c5", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"file_type": "reads", "status": "released", "@id": "/files-fastq/4DNFIJ4SWBI3/", "accession": "4DNFIJ4SWBI3", "file_type_detailed": "reads (fastq)", "uuid": "db9e9cf8-5b57-466e-8905-cad7da4f7999", "upload_key": "db9e9cf8-5b57-466e-8905-cad7da4f7999/4DNFIJ4SWBI3.fastq.gz", "display_title": "4DNFIJ4SWBI3.fastq.gz", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "href": "/files-fastq/4DNFIJ4SWBI3/@@download/4DNFIJ4SWBI3.fastq.gz", "file_size": 1870252760, "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJ4SWBI3/fastqc_report.html", "display_title": "QualityMetricFastqc from 2019-01-02", "Sequence length": "100", "Total Sequences": 31710773, "status": "released", "overall_quality_status": "PASS", "@id": "/quality-metrics-fastqc/f6498ad6-3e38-429c-850a-abce0c9ec244/", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "f6498ad6-3e38-429c-850a-abce0c9ec244", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/fastq/", "file_format": "fastq", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": []}], "notes": "Old Target: d0b4af26-246f-424a-a853-469eefc11aa3", "status": "released", "aliases": ["belmont-lab:sc35-tsa-seq-v1-cond1-yc-201712"], "dbxrefs": ["GEO:GSM3111194"], "antibody": {"@type": ["Antibody", "Item"], "status": "released", "antibody_product_no": "S4045", "@id": "/antibodys/anti-pSC35-S4045/", "uuid": "a4bac461-d1a1-46ba-9775-1fe62c065e74", "display_title": "anti-pSC35 (Millipore Sigma, S4045)", "antibody_name": "anti-pSC35", "antibody_vendor": {"status": "released", "uuid": "255e81a2-6654-4d8b-8359-59f87c071d65", "@type": ["Vendor", "Item"], "@id": "/vendors/millipore-sigma/", "display_title": "Millipore Sigma", "title": "Millipore Sigma", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "protocol": {"status": "released", "@type": ["Protocol", "Item"], "uuid": "379bc6d4-e881-4cfd-9b2f-363648e3627c", "display_title": "TSAseqv1_Method_Protocol_draft.pdf", "@id": "/protocols/379bc6d4-e881-4cfd-9b2f-363648e3627c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEX3PNLGUI", "biosample": {"modifications_summary": "None", "status": "released", "uuid": "854defbe-cb89-47ea-aab3-e1205357a245", "treatments_summary": "None", "@id": "/biosamples/4DNBSNRI1NBL/", "biosample_type": "immortalized cells", "biosource_summary": "K562 (Tier 2)", "@type": ["Biosample", "Item"], "accession": "4DNBSNRI1NBL", "display_title": "4DNBSNRI1NBL", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "biosource": [{"lab": {"@type": ["Lab", "Item"], "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://www.atcc.org/products/all/CCL-243.aspx", "award": {"uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "status": "current", "@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"@id": "/ontology-terms/CL:0000081/", "display_title": "blood cell", "slim_terms": [{"display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "status": "current", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "term_id": "CL:0000081", "@type": ["OntologyTerm", "Item"], "uuid": "0d64fbe2-ed5c-43cd-a30d-d9f0320d27ed", "preferred_name": "blood cell", "term_name": "blood cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:K562T2", "4dn-dcic-lab:K562T2"], "accession": "4DNSRWQFKJYO", "cell_line": {"@id": "/ontology-terms/EFO:0002067/", "status": "released", "term_id": "EFO:0002067", "preferred_name": "K562", "@type": ["OntologyTerm", "Item"], "term_name": "K562", "synonyms": ["K562 cell", "K-562", "K-562 cell"], "uuid": "0f1257b4-30e2-4c34-b8a3-e564c65ec55a", "slim_terms": [{"@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "status": "current", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "status": "released", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "display_title": "K562", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"@type": ["IndividualHuman", "Individual", "Item"], "@id": "/individuals-human/4DNIN4YSFWCS/", "protected_data": false, "display_title": "4DNIN4YSFWCS", "uuid": "2a0c64b1-25f1-44c1-88c3-7da6291f5b69", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "K562 (CCL-243)", "date_created": "2017-04-10T01:14:06.383509+00:00", "submitted_by": {"error": "no view permissions"}, "SOP_cell_line": {"@id": "/protocols/d6eb1886-6427-4083-a05c-9268730f5ed6/", "@type": ["Protocol", "Item"], "uuid": "d6eb1886-6427-4083-a05c-9268730f5ed6", "display_title": "4DN_K562_SOP_170314.pdf", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-05T14:31:58.118863+00:00"}, "modifications": [], "biosource_type": "immortalized cell line", "cell_line_tier": "Tier 2", "public_release": "2017-09-05", "schema_version": "2", "project_release": "2017-09-05", "biosource_vendor": {"@type": ["Vendor", "Item"], "uuid": "7a6f2efe-5be8-4db2-afa8-d82e9b4ad254", "display_title": "American Type Culture Collection", "status": "released", "@id": "/vendors/american-type-culture-collection/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRWQFKJYO/", "@type": ["Biosource", "Item"], "uuid": "1032c021-c18a-49ab-90d2-fd2cc5a8e1b7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "K562 (Tier 2) - 4DNSRWQFKJYO", "external_references": [], "biosource_name": "K562 (Tier 2)", "biosource_category": ["Tier 2"], "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "name": "human", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "status": "released", "@id": "/organisms/9606/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "badges": [{"messages": ["Biosample missing culture_harvest_date", "Biosample missing doubling_number", "Biosample missing passage_number", "Biosample missing culture_duration", "Biosample missing morphology_image"], "badge": {"badge_classification": "Warning", "display_title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "badge_icon": "/static/img/badges/biosample-icon.svg", "status": "released", "warning": "Biosample Metadata Incomplete", "@id": "/badges/biosample-metadata-incomplete/", "title": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}]}, "documents": [{"uuid": "eea2ccee-2fad-4723-9bbb-f013ab43e760", "display_title": "expt_details_tsaseq_sc35_cond1_yc_201712.xlsx", "status": "released", "@id": "/documents/eea2ccee-2fad-4723-9bbb-f013ab43e760/", "@type": ["Document", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "pcr_cycles": 12, "resolution": "Low", "description": "pSC35 TSA-seq version 1 Reaction Condition 1 (PBS) 10 minute Reaction on K562 cells replicate 2", "follows_sop": "No", "sop_mapping": {"has_sop": "No"}, "date_created": "2018-12-20T19:15:53.040500+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-05-09T17:05:52.299521+00:00"}, "reaction_time": 10.0, "public_release": "2019-04-04", "schema_version": "3", "affinity_rounds": 1, "antibody_lot_id": "021M4845", "experiment_type": {"experiment_category": "Sequencing", "display_title": "TSA-seq", "assay_subclass_short": "Proximity-seq", "@id": "/experiment-types/tsa-seq/", "status": "released", "uuid": "75d7181c-e329-463e-b776-a467433aa4db", "title": "TSA-seq", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"upload_key": "9da9f0f9-fd49-4641-8792-15958c17bc7d/4DNFI15NFNCU.bw", "notes_to_tsv": ["This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available."], "href": "/files-processed/4DNFI15NFNCU/@@download/4DNFI15NFNCU.bw", "accession": "4DNFI15NFNCU", "file_size": 1103960, "@type": ["FileProcessed", "File", "Item"], "file_type_detailed": "normalized counts (bw)", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9da9f0f9-fd49-4641-8792-15958c17bc7d/4DNFI15NFNCU.bw", "file_format": {"display_title": "bw", "@type": ["FileFormat", "Item"], "file_format": "bw", "@id": "/file-formats/bw/", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type": "normalized counts", "file_classification": "processed file", "status": "released", "display_title": "4DNFI15NFNCU.bw", "@id": "/files-processed/4DNFI15NFNCU/", "uuid": "9da9f0f9-fd49-4641-8792-15958c17bc7d", "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/429271df-3067-46a2-9dc9-7a21b11c5c7c/", "display_title": "4DNFI15NFNCU - Higlass Viewconfig", "status": "released", "uuid": "429271df-3067-46a2-9dc9-7a21b11c5c7c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}}], "track_and_facet_info": {"experimental_lab": "Andrew Belmont, ILLINOIS", "experiment_type": "TSA-seq", "experiment_bucket": "processed file", "assay_info": "SC35 protein with Phosphorylation", "dataset": "TSA-seq v1 pSC35 in K562", "condition": "10 min reaction - condition 1 - anti-phosphoSC35", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "K562 (Tier 2)", "lab_name": "Andrew Belmont, ILLINOIS", "track_title": "normalized counts for K562 (Tier 2) TSA-seq SC35 protein with Phosphorylation"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "external_references": []}], "project_release": "2019-04-04", "reaction_buffer": "Standard", "targeted_factor": [{"@type": ["BioFeature", "Item"], "@id": "/bio-features/2285a2c6-c8e8-45fc-803d-185909374503/", "uuid": "2285a2c6-c8e8-45fc-803d-185909374503", "status": "released", "display_title": "SC35 protein with Phosphorylation", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "protocol_version": "1.0", "antibody_dilution": "1:500", "biosample_quantity": 326000000.0, "secondary_antibody": {"@type": ["Antibody", "Item"], "antibody_product_no": "115-035-062", "status": "released", "@id": "/antibodys/goat-anti-mouse-IgG-115-035-062/", "antibody_name": "goat anti-mouse IgG", "uuid": "9cadcc23-d29a-40cf-80c1-937b2477fe10", "display_title": "goat anti-mouse IgG (Jackson ImmunoResearch, 115-035-062)", "antibody_vendor": {"uuid": "295a05e5-fa7c-498d-9cd6-fa0586d430b9", "@type": ["Vendor", "Item"], "@id": "/vendors/jackson-immunoresearch/", "status": "released", "title": "Jackson ImmunoResearch", "display_title": "Jackson ImmunoResearch", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "authentication_docs": [{"status": "released", "display_title": "image-yc-201712.pdf", "@id": "/protocols/28d87d08-afea-430a-a2b1-ca31c145d523/", "@type": ["Protocol", "Item"], "uuid": "28d87d08-afea-430a-a2b1-ca31c145d523", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "sc35-lmnac-dot-blot-yc-2017.pdf", "@id": "/protocols/4e73ce1c-4173-4cc2-9816-319005c8f1b1/", "@type": ["Protocol", "Item"], "uuid": "4e73ce1c-4173-4cc2-9816-319005c8f1b1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_relation": [{"experiment": {"uuid": "fabdb08c-ca66-41e6-a76e-aba9b784e1fb", "@type": ["ExperimentTsaseq", "Experiment", "Item"], "status": "released", "@id": "/experiments-tsaseq/4DNEXXIZBV5L/", "display_title": "TSA-seq on K562 (Tier 2) - 4DNEXXIZBV5L", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "controlled by"}, {"experiment": {"uuid": "aaf0a62c-2330-4df3-92c5-eb5604cec856", "@type": ["ExperimentTsaseq", "Experiment", "Item"], "status": "released", "@id": "/experiments-tsaseq/4DNEX82FPIKJ/", "display_title": "TSA-seq against SC35 protein with Phosphorylation on K562 (Tier 2) - 4DNEX82FPIKJ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "has input"}], "fragment_size_range": "100-500", "fragmentation_method": "sonication", "reaction_temperature": 25.0, "average_fragment_size": 250, "other_processed_files": [{"type": "preliminary", "files": [{"error": "no view permissions"}, {"error": "no view permissions"}], "title": "Repli-Seq Pipeline - Preliminary Files"}], "tyramide_concentration": "1:10000", "biosample_quantity_units": "cells", "library_preparation_date": "2017-11-03", "biotinylated_spikein_source": "drosophila_48E12_L_BiodT_primer: GAAACATCGC/iBiodT/GCCCATAAT--AGAAGCAGCTACGCTCCTCA", "secondary_antibody_dilution": "1:1000", "biotinylated_spikein_sequences": {"status": "released", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFIQ3495RN/", "uuid": "bf96e7b1-d2e1-4758-8a31-7549f72f3c59", "display_title": "4DNFIQ3495RN.fasta", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "fragment_size_selection_method": "none", "@id": "/experiments-tsaseq/4DNEX3PNLGUI/", "@type": ["ExperimentTsaseq", "Experiment", "Item"], "uuid": "c23a4bc6-d25c-4a39-856e-0a36c1216900", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "TSA-seq against SC35 protein with Phosphorylation on K562 (Tier 2) - 4DNEX3PNLGUI", "external_references": [{"ref": "GEO:GSM3111194", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3111194"}], "experiment_sets": [{"@id": "/experiment-set-replicates/4DNESNER8V11/", "status": "released", "uuid": "aa11eefb-3112-4d70-93af-703999849135", "accession": "4DNESNER8V11", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESNER8V11", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"@type": ["Publication", "Item"], "uuid": "0cbf34ae-fd3e-4b9d-a02f-cc80f1f8a872", "title": "Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as  a cytological ruler.", "journal": "The Journal of cell biology", "status": "current", "abstract": "While nuclear compartmentalization is an essential feature of three-dimensional genome organization, no genomic method exists for measuring chromosome distances  to defined nuclear structures. In this study, we describe TSA-Seq, a new mapping  method capable of providing a \"cytological ruler\" for estimating mean chromosomal distances from nuclear speckles genome-wide and for predicting several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results in K562 cells reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple spatially separated nuclear domains including two types of transcription \"hot zones.\" Transcription hot zones protruding furthest into the nuclear interior and positioning deterministically very close to nuclear speckles have higher numbers  of total genes, the most highly expressed genes, housekeeping genes, genes with low transcriptional pausing, and super-enhancers. Our results demonstrate the capability of TSA-Seq for genome-wide mapping of nuclear structure and suggest a  new model for spatial organization of transcription and gene expression.", "@id": "/publications/0cbf34ae-fd3e-4b9d-a02f-cc80f1f8a872/", "ID": "doi:10.1083/jcb.201807108", "date_published": "2018-11-05", "display_title": "Chen Y et al. (2018) doi:10.1083/jcb.201807108", "authors": ["Chen Y", "Zhang Y", "Wang Y", "Zhang L", "Brinkman EK", "Adam SA", "Goldman R", "van Steensel B", "Ma J", "Belmont AS"], "short_attribution": "Chen Y et al. (2018)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"short_attribution": "Chen Y et al. (2018)", "@type": ["Publication", "Item"], "ID": "doi:10.1083/jcb.201807108", "display_title": "Chen Y et al. (2018) doi:10.1083/jcb.201807108", "abstract": "While nuclear compartmentalization is an essential feature of three-dimensional genome organization, no genomic method exists for measuring chromosome distances  to defined nuclear structures. In this study, we describe TSA-Seq, a new mapping  method capable of providing a \"cytological ruler\" for estimating mean chromosomal distances from nuclear speckles genome-wide and for predicting several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results in K562 cells reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple spatially separated nuclear domains including two types of transcription \"hot zones.\" Transcription hot zones protruding furthest into the nuclear interior and positioning deterministically very close to nuclear speckles have higher numbers  of total genes, the most highly expressed genes, housekeeping genes, genes with low transcriptional pausing, and super-enhancers. Our results demonstrate the capability of TSA-Seq for genome-wide mapping of nuclear structure and suggest a  new model for spatial organization of transcription and gene expression.", "journal": "The Journal of cell biology", "@id": "/publications/0cbf34ae-fd3e-4b9d-a02f-cc80f1f8a872/", "authors": ["Chen Y", "Zhang Y", "Wang Y", "Zhang L", "Brinkman EK", "Adam SA", "Goldman R", "van Steensel B", "Ma J", "Belmont AS"], "uuid": "0cbf34ae-fd3e-4b9d-a02f-cc80f1f8a872", "date_published": "2018-11-05", "title": "Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as  a cytological ruler.", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "SC35 protein with Phosphorylation", "combined": "Target: SC35 protein with Phosphorylation"}, "experiment_summary": "TSA-seq against SC35 protein with Phosphorylation on K562 (Tier 2)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSNRI1NBL/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing culture_harvest_date", "Biosample missing doubling_number", "Biosample missing passage_number", "Biosample missing culture_duration", "Biosample missing morphology_image"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}