{"lab": {"display_title": "Bing Ren, UCSD", "@id": "/labs/bing-ren-lab/", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "title": "Bing Ren, UCSD", "status": "current", "correspondence": [{"contact_email": "YmlyZW5AdWNzZC5lZHU=", "@id": "/users/e3159ffc-a5a9-43a1-8cfa-90b776c39788/", "display_title": "Bing Ren"}], "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "award": {"name": "1U54DK107977-01", "description": "NOFIC: The complete sequencing of the human genome has provided an unprecedented opportunity for the study of the structure and function of the human genome. While our genome has historically been viewed as a linear sequence of bases, it has progressively become clear that this is an inadequate way to represent our genetic information. Notably, research over the last 30 years has begun to shed light on the fact that the higher-order, 3-dimensional organization of our genome plays a critical role in the interpretation of the genetic information encoded in our genome. The structure of our genome in the nucleus has been clearly demonstrated to play influential roles in diverse nuclear processes including DNA replication and gene expression. Despite this, our understanding of the structure of our genome within the nucleus remains incomplete. The reasons for this include limitations in the resolution and throughput of existing tools in chromatin topology mapping, a scarcity of the analytical tools for studying genome structure datasets, and the difficulty to relate the nuclear structure to function. Due to recent advancements in molecular methods based on high-throughput DNA sequencing, single cell analytical approaches, and high-resolution microscopy, the time for breaking through these previous limitations has come. We will establish a highly collaborative, innovative team in order to develop the tools necessary to transform our understanding of chromatin architecture and function in mammalian cells. We will begin by developing datasets that establish gold standards for the study of nuclear structure and function using genetic, biochemical and imaging approaches. We will optimize current existing technologies for mapping genome wide chromatin interactions, while also developing novel, complementary approaches for studying chromatin structure. We will also develop innovative analytical methods to interpret the chromatin structural data, unraveling principles of structural- and temporal- chromatin organization. Our highly collaborative team will draw on the diverse experiences of its members to provide a synergistic environment to push the limits of our understanding of nuclear structure. We expect that the tools and datasets generated through the proposed research will dramatically advance our understanding of the chromatin structure and function in human cells.", "@id": "/awards/1U54DK107977-01/", "project": "4DN", "status": "current", "@type": ["Award", "Item"], "uuid": "4871e338-b07d-4665-a00a-357648e5bad6", "display_title": "SAN DIEGO CENTER FOR 4D NUCLEOME RESEARCH", "center_title": "NOFIC - Ren", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "pi": {"error": "no view permissions"}}, "files": [{"accession": "4DNFIR3JMCWW", "file_size": 1025037516, "status": "released", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIR3JMCWW.fastq.gz", "@id": "/files-fastq/4DNFIR3JMCWW/", "paired_end": "1", "file_classification": "raw file", "dbxrefs": ["SRA:SRR12102247"], "href": "/files-fastq/4DNFIR3JMCWW/@@download/4DNFIR3JMCWW.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "46643b43-d323-475c-a655-c671dd4e3499", "upload_key": "46643b43-d323-475c-a655-c671dd4e3499/4DNFIR3JMCWW.fastq.gz", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/0d302e0c-2e19-4185-94f5-e43db76ec665/", "display_title": "QualityMetricFastqc from 2020-08-20", "Sequence length": "35-75", "uuid": "0d302e0c-2e19-4185-94f5-e43db76ec665", "overall_quality_status": "PASS", "Total Sequences": 22253398, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIR3JMCWW/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "fastq", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "paired_end": "2", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIT2652OA", "status": "released", "display_title": "4DNFIT2652OA.fastq.gz", "@id": "/files-fastq/4DNFIT2652OA/", "uuid": "0585c1b9-59a4-418b-b600-ddc1284ce643", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR12102247", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR12102247"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"accession": "4DNFIT2652OA", "file_size": 1084100086, "status": "released", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIT2652OA.fastq.gz", "@id": "/files-fastq/4DNFIT2652OA/", "paired_end": "2", "file_classification": "raw file", "dbxrefs": ["SRA:SRR12102247"], "href": "/files-fastq/4DNFIT2652OA/@@download/4DNFIT2652OA.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "uuid": "0585c1b9-59a4-418b-b600-ddc1284ce643", "upload_key": "0585c1b9-59a4-418b-b600-ddc1284ce643/4DNFIT2652OA.fastq.gz", "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "@id": "/quality-metrics-fastqc/2ce83b24-cf03-4579-8df6-ac43aa794326/", "display_title": "QualityMetricFastqc from 2020-08-20", "Sequence length": "35-75", "uuid": "2ce83b24-cf03-4579-8df6-ac43aa794326", "overall_quality_status": "PASS", "Total Sequences": 22253398, "status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIT2652OA/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"status": "released", "@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "fastq", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"file_type": "reads", "file_type_detailed": "reads (fastq)", "paired_end": "1", "@type": ["FileFastq", "File", "Item"], "accession": "4DNFIR3JMCWW", "status": "released", "display_title": "4DNFIR3JMCWW.fastq.gz", "@id": "/files-fastq/4DNFIR3JMCWW/", "uuid": "46643b43-d323-475c-a655-c671dd4e3499", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR12102247", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR12102247"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "aliases": ["bing-ren-lab:experiment_chip-seq_against_ctcf_on_f123_cells_nbd_syn15_B1_T1"], "dbxrefs": ["GEO:GSM4643783"], "antibody": {"status": "released", "uuid": "3be6dc52-30b5-49d0-9d7a-1709435923ec", "antibody_name": "anti-CTCF", "@type": ["Antibody", "Item"], "display_title": "anti-CTCF (Abcam, ab70303)", "@id": "/antibodys/anti-CTCF-ab70303/", "antibody_product_no": "ab70303", "antibody_vendor": {"display_title": "Abcam", "@type": ["Vendor", "Item"], "status": "released", "@id": "/vendors/abcam/", "uuid": "13540f71-312d-441e-a2dc-ea0dfa7e0841", "title": "Abcam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "protocol": {"@type": ["Protocol", "Item"], "status": "released", "display_title": "Ren Lab ChIP-seq protocol", "@id": "/protocols/f4c7c9ca-0d94-4114-891d-ed3604c08e8d/", "uuid": "f4c7c9ca-0d94-4114-891d-ed3604c08e8d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEX3EQDIG6", "biosample": {"status": "released", "biosample_type": "stem cells", "modifications_summary": "RMCE replacement", "@type": ["Biosample", "Item"], "accession": "4DNBSLA64OHQ", "@id": "/biosamples/4DNBSLA64OHQ/", "uuid": "da81c4b7-8843-445d-bdda-c597ad9d13bd", "display_title": "4DNBSLA64OHQ", "treatments_summary": "None", "biosource_summary": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE", "badges": [{"messages": ["Biosample missing Cell Culture Details"], "badge": {"@id": "/badges/biosample-metadata-incomplete/", "title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "status": "released", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "warning": "Biosample Metadata Incomplete", "@type": ["Badge", "Item"], "display_title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "badge_icon": "/static/img/badges/biosample-icon.svg", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "modifications": [{"@type": ["Modification", "Item"], "display_title": "RMCE replacement", "genomic_change": "replacement", "status": "released", "modification_type": "RMCE", "description": "Insertion of fifteen tandemly arrayed synthetic non-boundary CTCF binding sites between the Sox2 gene and its super-enhancer", "uuid": "af651d48-2e51-41e5-8446-af2c84e42dde", "@id": "/modifications/af651d48-2e51-41e5-8446-af2c84e42dde/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource": [{"lab": {"status": "current", "uuid": "795847de-20b6-4f8c-ba8d-185215469cbf", "display_title": "Bing Ren, UCSD", "@type": ["Lab", "Item"], "@id": "/labs/bing-ren-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.795847de-20b6-4f8c-ba8d-185215469cbf"]}}, "award": {"@type": ["Award", "Item"], "uuid": "4871e338-b07d-4665-a00a-357648e5bad6", "display_title": "SAN DIEGO CENTER FOR 4D NUCLEOME RESEARCH", "@id": "/awards/1U54DK107977-01/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"display_title": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@id": "/ontology-terms/CL:0000034/", "synonyms": ["animal stem cell"], "slim_terms": [{"@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "preferred_name": "stem cell", "term_name": "stem cell", "@type": ["OntologyTerm", "Item"], "term_id": "CL:0000034", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["bing-ren-lab:f123-sox2-cast-egfp-btw-hytk-frt-s129-mcherry"], "accession": "4DNSR9TIV5EV", "cell_line": {"@type": ["OntologyTerm", "Item"], "slim_terms": [{"status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "display_title": "F123-CASTx129", "uuid": "b75930ee-182a-4f7a-8360-ecd6b7ac532f", "synonyms": ["F123"], "term_id": "EFO:0009319", "preferred_name": "F123-CASTx129", "term_name": "F123-CASTx129", "status": "released", "@id": "/ontology-terms/EFO:0009319/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"display_title": "4DNINWEP34C1", "status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "uuid": "9eb64afa-705f-4710-a298-32ad67764d14", "@id": "/individuals-mouse/4DNINWEP34C1/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "A mouse embryonic cell line derived from the F123-CASTXs129 F1 hybrid line engineered with both alleles of the Sox2 gene tagged - CAST allele with eGFP and s129 allele with mCherry and an suicidal fusion gene Tg(CAG-HyTK) flanked by Flippase recognition sites FRT/F3 inserted between Sox2 and it's downstream Super Enhancer to allow insertion of DNA cassettes followed by selection for integration using the RMCE strategy.", "date_created": "2020-07-27T15:19:15.233241+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-09-08T20:33:53.605231+00:00"}, "modifications": [{"status": "released", "@id": "/modifications/8bf623f7-3894-4763-b286-4efed16c1755/", "@type": ["Modification", "Item"], "display_title": "Crispr insertion for Sox2 mouse gene", "uuid": "8bf623f7-3894-4763-b286-4efed16c1755", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/modifications/cb04bb10-77a3-4123-bea1-985e97045cee/", "@type": ["Modification", "Item"], "display_title": "Crispr insertion for Sox2 mouse gene", "uuid": "cb04bb10-77a3-4123-bea1-985e97045cee", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/modifications/b201bb73-137d-4597-bb01-39f99019413c/", "@type": ["Modification", "Item"], "display_title": "Crispr insertion", "uuid": "b201bb73-137d-4597-bb01-39f99019413c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosource_type": "stem cell derived cell line", "cell_line_tier": "Unclassified", "public_release": "2020-09-08", "schema_version": "2", "project_release": "2020-09-08", "biosource_vendor": {"@type": ["Vendor", "Item"], "status": "released", "display_title": "Bing Ren Lab", "@id": "/vendors/bing-ren-lab/", "uuid": "e909af70-74cb-426a-8ecf-1c9100c1ea44", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "override_biosource_name": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE", "@id": "/biosources/4DNSR9TIV5EV/", "@type": ["Biosource", "Item"], "uuid": "c1f610d2-a25d-400a-b807-5306c34fe3fc", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE - 4DNSR9TIV5EV", "external_references": [], "biosource_name": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE", "biosource_category": ["Tier 2", "Mouse stem cell"], "organism": {"uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@id": "/organisms/10090/", "name": "mouse", "display_title": "M. musculus", "@type": ["Organism", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "sop_mapping": {"has_sop": "No"}, "date_created": "2020-08-13T18:15:45.849878+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-02-01T22:10:34.658090+00:00"}, "public_release": "2020-09-08", "schema_version": "5", "experiment_type": {"uuid": "47a593da-c458-422a-a974-82b3302e89cb", "experiment_category": "Sequencing", "display_title": "ChIP-seq", "title": "ChIP-seq", "status": "released", "@id": "/experiment-types/chip-seq/", "@type": ["ExperimentType", "Item"], "assay_subclass_short": "DNA binding", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"upload_key": "9a20a5e9-fa91-4518-85d9-b4729ce44875/4DNFI9STTCVG.bed.gz", "file_type_detailed": "read positions (bed)", "file_format": {"uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@id": "/file-formats/bed/", "display_title": "bed", "@type": ["FileFormat", "Item"], "file_format": "bed", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/files-processed/4DNFI9STTCVG/", "accession": "4DNFI9STTCVG", "uuid": "9a20a5e9-fa91-4518-85d9-b4729ce44875", "file_type": "read positions", "href": "/files-processed/4DNFI9STTCVG/@@download/4DNFI9STTCVG.bed.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/9a20a5e9-fa91-4518-85d9-b4729ce44875/4DNFI9STTCVG.bed.gz", "file_size": 221967392, "file_classification": "processed file", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI9STTCVG.bed.gz", "quality_metric": {"status": "released", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI9STTCVG/qc_report.html", "display_title": "QualityMetricChipseq from 2020-08-29", "overall_quality_status": "PASS", "@type": ["QualityMetricChipseq", "QualityMetric", "Item"], "uuid": "ff53386d-e6f9-4858-a7bf-1f07970e72ac", "@id": "/quality-metrics-chipseq/ff53386d-e6f9-4858-a7bf-1f07970e72ac/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Nonredundant Read Fraction (NRF)", "value": "0.78", "tooltip": "distinct non-mito read pairs / total non-mito read pairs", "numberType": "float"}, {"title": "PCR Bottleneck Coefficient (PBC)", "value": "0.77", "tooltip": "one-read non-mito read pairs / distinct non-mito read pairs", "numberType": "float"}, {"title": "Filtered & Deduped Reads", "value": "12600305", "numberType": "integer"}]}, "track_and_facet_info": {"experimental_lab": "Bing Ren, UCSD", "experiment_type": "ChIP-seq", "experiment_bucket": "processed file", "assay_info": "Ctcf mouse protein", "dataset": "ChIP-seq on tagged Sox2 cells", "condition": "15 syn non-boundary CTCF sites - anti-CTCF", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE", "lab_name": "4DN DCIC, HMS"}, "external_references": [], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "project_release": "2020-09-08", "targeted_factor": [{"display_title": "Ctcf mouse protein", "@id": "/bio-features/66c1edc2-fed0-4ed0-a1b8-5d64f9a3ebd1/", "uuid": "66c1edc2-fed0-4ed0-a1b8-5d64f9a3ebd1", "status": "released", "@type": ["BioFeature", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "library_prep_kit": "In-house protocol", "antibody_dilution": "5\u03bcg", "biosample_quantity": 3000000.0, "experiment_relation": [{"experiment": {"@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "b924e616-fa27-4e84-898c-8d132eb4e8c1", "@id": "/experiments-seq/4DNEX948JUMI/", "display_title": "ChIP-seq on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE - 4DNEX948JUMI", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relationship_type": "controlled by"}], "fragment_size_range": "300-500", "fragmentation_method": "sonication", "average_fragment_size": 500, "biosample_quantity_units": "cells", "library_preparation_date": "2020-06-22", "fragment_size_selection_method": "SPRI beads", "@id": "/experiments-seq/4DNEX3EQDIG6/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "c705d87e-06fe-48a9-af82-5432df8af911", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "ChIP-seq against Ctcf mouse protein on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE - 4DNEX3EQDIG6", "external_references": [{"ref": "GEO:GSM4643783", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4643783"}], "experiment_sets": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESOTGY25S/", "uuid": "84e61bdb-54ca-4c72-ae79-4e02950be858", "display_title": "4DNESOTGY25S", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "accession": "4DNESOTGY25S", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"abstract": "Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here we  explore the sequence requirements of CTCF-mediated transcriptional insulation using a sensitive insulator reporter in mouse embryonic stem cells. We find that  insulation potency depends on the number of CTCF-binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on upstream flanking sequences at its binding sites. CTCF-binding sites at topologically associating domain boundaries are more likely to function as insulators than those outside topologically associating domain boundaries, independently of binding strength. We demonstrate that insulators form local chromatin domain boundaries and weaken  enhancer-promoter contacts. Taken together, our results provide genetic, molecular and structural evidence connecting chromatin topology to the action of  insulators in the mammalian genome.", "@type": ["Publication", "Item"], "@id": "/publications/4f766397-5ead-416e-b891-1c95391dcd77/", "journal": "Nature genetics", "authors": ["Huang H", "Zhu Q", "Jussila A", "Han Y", "Bintu B", "Kern C", "Conte M", "Zhang Y", "Bianco S", "Chiariello AM", "Yu M", "Hu R", "Tastemel M", "Juric I", "Hu M", "Nicodemi M", "Zhuang X", "Ren B"], "status": "current", "uuid": "4f766397-5ead-416e-b891-1c95391dcd77", "title": "CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.", "display_title": "Huang H et al. (2021) PMID:34002095", "date_published": "2021-07", "ID": "PMID:34002095", "short_attribution": "Huang H et al. (2021)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"abstract": "Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here we  explore the sequence requirements of CTCF-mediated transcriptional insulation using a sensitive insulator reporter in mouse embryonic stem cells. We find that  insulation potency depends on the number of CTCF-binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on upstream flanking sequences at its binding sites. CTCF-binding sites at topologically associating domain boundaries are more likely to function as insulators than those outside topologically associating domain boundaries, independently of binding strength. We demonstrate that insulators form local chromatin domain boundaries and weaken  enhancer-promoter contacts. Taken together, our results provide genetic, molecular and structural evidence connecting chromatin topology to the action of  insulators in the mammalian genome.", "@id": "/publications/4f766397-5ead-416e-b891-1c95391dcd77/", "status": "current", "title": "CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.", "authors": ["Huang H", "Zhu Q", "Jussila A", "Han Y", "Bintu B", "Kern C", "Conte M", "Zhang Y", "Bianco S", "Chiariello AM", "Yu M", "Hu R", "Tastemel M", "Juric I", "Hu M", "Nicodemi M", "Zhuang X", "Ren B"], "journal": "Nature genetics", "date_published": "2021-07", "short_attribution": "Huang H et al. (2021)", "ID": "PMID:34002095", "@type": ["Publication", "Item"], "uuid": "4f766397-5ead-416e-b891-1c95391dcd77", "display_title": "Huang H et al. (2021) PMID:34002095", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "Ctcf mouse protein", "combined": "Target: Ctcf mouse protein"}, "experiment_summary": "ChIP-seq against Ctcf mouse protein on F123-CASTx129 with Sox2 tags and RMCE site between Sox2 and its SE", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSLA64OHQ/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing Cell Culture Details"], "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": []}