{"lab": {"title": "Yijun Ruan, JAX", "uuid": "abd48785-b0e5-4453-be14-30d37a516bf3", "correspondence": [{"contact_email": "eWlqdW4ucnVhbkBqYXgub3Jn", "@id": "/users/d8ac229e-ec08-4411-be38-dc779520ea62/", "display_title": "Yijun Ruan"}], "@type": ["Lab", "Item"], "display_title": "Yijun Ruan, JAX", "status": "current", "@id": "/labs/yijun-ruan-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.abd48785-b0e5-4453-be14-30d37a516bf3"]}}, "award": {"@id": "/awards/1U54DK107967-01/", "uuid": "029a2578-43dc-4343-8f41-694518cce304", "status": "current", "project": "4DN", "description": "NOFIC: This proposal seeks to fulfill a community need for a comprehensive, high-resolution genome-mapping platform that will enable investigation of the structural, functional and spatiotemporal organization of the human genome. Our ultimate goal is to deliver complex chromatin interaction network maps in the context of 3D genome structures from which the dynamics of individual genomic elements can be monitored and referenced. Here, we propose to develop a Nucleome Positioning System (NPS)-comprised of 1) a robust genome- wide mapping technology platform, 2) advanced computational modeling algorithms and 3) state-of-the-art nuclear imaging methods-that will allow users community-wide to uncover the regulatory functions of 3D genome organization in human cells. NPS will be based upon the established ChIA-PET method (1,2), enhanced by process optimizations-i.e., microfluidic-based miniaturization and Tn5-transposase-based library preparation-to facilitate the study of chromatin interactions mediated by protein factors across a broader range of human cell types (Aim 1, see also Mapping Technology Development Component). We will also optimize RICh-PET for the comprehensive mapping of chromatin interactions mediated by non-coding RNAs (Aim 1). The high-quality mapping data generated through these optimization efforts will be analyzed by a new computational platform (Three-Dimensional Nucleome Modeling Engine, or 3D-NOME) that makes use of hierarchical multi-scaling to model 3D genome structures (Aim 2, Data Analysis and Modeling component). We will also complement the 3D modeling with transcriptome, epigenome and SNP data associated with genetic diseases (GWAS) to provide functional annotation to structural units (Aim 2). We will continue by developing strategies to validate the nucleome geometry predicted by 3D-NOME both structurally, using new nuclear imaging technologies, and functionally, using cutting-edge genome- and epigenome-editing approaches, in both human cell lines and mouse models (Aim 3, Biological Validation Component). Finally, we will implement NPS to generate pilot 3D genome maps from a wide range of human cell lines and primary immune cells sorted from whole blood, to elucidate the spatiotemporal dynamics of human genome organization over major developmental and hematopoietic cell lineages, as well as among differentiating lymphocytes involved in the immune response (Aim 4, Data Generation Component). Together, these efforts will yield a powerful set of sophisticated, high-quality tools and mapping data for the larger research community, and will help establish the standards for future 3D/4D nucleome studies. They will also provide insights into the broad mechanisms that organize the structure and regulate the function of the human genome, as well as the specific mechanisms by which immune responses are regulated at the nuclear level.", "center_title": "NOFIC - Ruan", "display_title": "NUCLEOME POSITIONING SYSTEM FOR SPATIOTEMPORAL GENOME ORGANIZATION AND REGULATION", "@type": ["Award", "Item"], "name": "1U54DK107967-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"uuid": "06935c07-6e86-4a6e-ac89-f4e030b207c5", "display_title": "4DNFIEUZOSRY.fastq.gz", "accession": "4DNFIEUZOSRY", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "href": "/files-fastq/4DNFIEUZOSRY/@@download/4DNFIEUZOSRY.fastq.gz", "file_classification": "raw file", "file_type_detailed": "reads (fastq)", "upload_key": "06935c07-6e86-4a6e-ac89-f4e030b207c5/4DNFIEUZOSRY.fastq.gz", "status": "released", "file_type": "reads", "file_size": 6255540029, "@id": "/files-fastq/4DNFIEUZOSRY/", "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIKQCX7PD", "display_title": "4DNFIKQCX7PD.fastq.gz", "uuid": "32266380-a6d3-4ef4-a1d6-1ee4defdf93f", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIKQCX7PD/", "file_type_detailed": "reads (fastq)", "paired_end": "2", "file_type": "reads", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "be15f8b0-e696-4c10-b80a-7d02d67b0958", "display_title": "QualityMetricFastqc from 2019-12-17", "Sequence length": "151", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIEUZOSRY/fastqc_report.html", "@id": "/quality-metrics-fastqc/be15f8b0-e696-4c10-b80a-7d02d67b0958/", "Total Sequences": 69463568, "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "32266380-a6d3-4ef4-a1d6-1ee4defdf93f", "display_title": "4DNFIKQCX7PD.fastq.gz", "accession": "4DNFIKQCX7PD", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "href": "/files-fastq/4DNFIKQCX7PD/@@download/4DNFIKQCX7PD.fastq.gz", "file_classification": "raw file", "file_type_detailed": "reads (fastq)", "upload_key": "32266380-a6d3-4ef4-a1d6-1ee4defdf93f/4DNFIKQCX7PD.fastq.gz", "status": "released", "file_type": "reads", "file_size": 6905826151, "@id": "/files-fastq/4DNFIKQCX7PD/", "related_files": [{"relationship_type": "paired with", "file": {"accession": "4DNFIEUZOSRY", "display_title": "4DNFIEUZOSRY.fastq.gz", "uuid": "06935c07-6e86-4a6e-ac89-f4e030b207c5", "@type": ["FileFastq", "File", "Item"], "@id": "/files-fastq/4DNFIEUZOSRY/", "file_type_detailed": "reads (fastq)", "paired_end": "1", "file_type": "reads", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "2b306564-b18d-4e52-8777-efd0c3b79f88", "display_title": "QualityMetricFastqc from 2019-12-17", "Sequence length": "151", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKQCX7PD/fastqc_report.html", "@id": "/quality-metrics-fastqc/2b306564-b18d-4e52-8777-efd0c3b79f88/", "Total Sequences": 69463568, "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [], "file_format": {"@id": "/file-formats/fastq/", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "file_format": "fastq", "@type": ["FileFormat", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "aliases": ["ruan-lab:experiment_GM12878-ctcf-chiadrop_B4_T1"], "antibody": {"status": "released", "@id": "/antibodys/anti-CTCF-A1133/", "antibody_product_no": "A1133", "uuid": "61dd9472-c5c4-4675-a659-feec8f5031b7", "antibody_name": "anti-CTCF", "display_title": "anti-CTCF (ABclonal, A1133)", "@type": ["Antibody", "Item"], "antibody_vendor": {"@id": "/vendors/abclonal/", "display_title": "ABclonal", "status": "released", "@type": ["Vendor", "Item"], "title": "ABclonal", "uuid": "1d670510-5106-4dd4-8390-23c548bd36cc", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "protocol": {"display_title": "4DN_ChIA-Drop_protocol_Ruan_Lab_20191127.pdf", "uuid": "3a2a4b6a-aa3e-4c66-b2cf-c25e52d27c4f", "@type": ["Protocol", "Item"], "status": "released", "@id": "/protocols/3a2a4b6a-aa3e-4c66-b2cf-c25e52d27c4f/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEX2FMPU1P", "biosample": {"modifications_summary": "None", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "accession": "4DNBSNOGVYAB", "display_title": "4DNBSNOGVYAB", "treatments_summary": "None", "biosource_summary": "GM12878", "@id": "/biosamples/4DNBSNOGVYAB/", "uuid": "c14dc59d-9077-42d0-8e6b-87b75af279d6", "status": "released", "badges": [{"messages": ["Biosample missing passage_number", "Biosample missing morphology_image"], "badge": {"badge_icon": "/static/img/badges/biosample-icon.svg", "display_title": "Biosample Metadata Incomplete", "badge_classification": "Warning", "status": "released", "title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "@id": "/badges/biosample-metadata-incomplete/", "@type": ["Badge", "Item"], "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "biosource": [{"lab": {"@type": ["Lab", "Item"], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "url": "https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC", "award": {"@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_name": "lymphocyte of B lineage", "term_id": "CL:0000945", "@type": ["OntologyTerm", "Item"], "slim_terms": [{"@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/UBERON:0002405/", "display_title": "immune system", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "111133bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "preferred_name": "B-lymphocyte", "status": "released", "display_title": "B-lymphocyte", "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "@id": "/ontology-terms/CL:0000945/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:gm12878", "4dn-dcic-lab:gm12878"], "accession": "4DNSRVWZS4XO", "cell_line": {"display_title": "GM12878", "status": "released", "term_name": "GM12878", "preferred_name": "GM12878", "term_id": "EFO:0002784", "slim_terms": [{"display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "current", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "@type": ["OntologyTerm", "Item"], "status": "released", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@type": ["OntologyTerm", "Item"], "uuid": "b9668b9a-be39-47de-8eab-5bf1b0854417", "@id": "/ontology-terms/EFO:0002784/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"uuid": "3ec2ff42-6f8c-42e9-a1f0-0fa69f482b85", "@id": "/individuals-human/4DNINGWYEI15/", "status": "released", "@type": ["IndividualHuman", "Individual", "Item"], "display_title": "4DNINGWYEI15", "protected_data": false, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "Homo sapiens\u00a0GM12878 immortalized cell line", "date_created": "2017-04-09T17:24:19.894425+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-04T21:02:03.442329+00:00"}, "modifications": [], "biosource_type": "immortalized cell line", "cell_line_tier": "Unclassified", "public_release": "2017-07-20", "schema_version": "2", "project_release": "2017-07-20", "biosource_vendor": {"@type": ["Vendor", "Item"], "@id": "/vendors/coriell-institute-for-medical-research/", "uuid": "f0e9a370-7451-40e3-9a35-c36d77ebdb4b", "display_title": "Coriell Institute for Medical Research", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRVWZS4XO/", "@type": ["Biosource", "Item"], "uuid": "0f011b1e-b772-4f2a-8c24-cc55de28a994", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "GM12878 - 4DNSRVWZS4XO", "external_references": [], "biosource_name": "GM12878", "biosource_category": ["GM12878", "1000 genomes/Hap Map"], "organism": {"status": "released", "name": "human", "display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pcr_cycles": 8, "sop_mapping": {"has_sop": "No"}, "date_created": "2019-12-16T23:02:03.314507+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-10-07T17:58:41.062678+00:00"}, "digestion_time": 960.0, "public_release": "2020-05-22", "schema_version": "5", "antibody_lot_id": "Lot 0046700301", "experiment_type": {"display_title": "ChIA-Drop", "status": "released", "@type": ["ExperimentType", "Item"], "title": "ChIA-Drop", "uuid": "1b54058e-922a-4caa-9e59-de7e5ef98e59", "assay_subclass_short": "Ligation-free 3C", "@id": "/experiment-types/chia-drop/", "experiment_category": "Sequencing", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "project_release": "2020-05-22", "targeted_factor": [{"@id": "/bio-features/8efeec9a-bea3-4b17-b884-4690d86fc3c7/", "@type": ["BioFeature", "Item"], "uuid": "8efeec9a-bea3-4b17-b884-4690d86fc3c7", "display_title": "CTCF protein", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "@type": ["Enzyme", "Item"], "display_title": "HindIII", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "antibody_dilution": "20 ug per experiment", "biosample_quantity": 10000000.0, "fragmentation_method": "sonication", "average_fragment_size": 600, "digestion_temperature": 37.0, "other_processed_files": [{"type": "supplementary", "files": [{"@type": ["FileProcessed", "File", "Item"], "file_size": 4532788, "accession": "4DNFIZCXNG3D", "display_title": "4DNFIZCXNG3D.txt.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/7cd44be7-7b69-4946-9765-197709509061/4DNFIZCXNG3D.txt.gz", "status": "released", "href": "/files-processed/4DNFIZCXNG3D/@@download/4DNFIZCXNG3D.txt.gz", "file_type_detailed": "long range chromatin interactions (compressed_txt)", "@id": "/files-processed/4DNFIZCXNG3D/", "genome_assembly": "GRCh38", "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."], "uuid": "7cd44be7-7b69-4946-9765-197709509061", "file_type": "long range chromatin interactions", "file_format": {"uuid": "dba26778-f40a-4561-a552-65539702ded4", "file_format": "compressed_txt", "@type": ["FileFormat", "Item"], "display_title": "compressed_txt", "@id": "/file-formats/compressed_txt/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2021-12-16T07:43:37.085588+00:00"}, "track_and_facet_info": {"experimental_lab": "Yijun Ruan, JAX", "experiment_type": "ChIA-Drop", "experiment_bucket": "ChIA-DropBox and MIA-Sig Results", "assay_info": "CTCF protein", "dataset": "ChIA-Drop in GM12878", "condition": "CTCF antibody", "replicate_info": "Biorep 14, Techrep 1", "biosource_name": "GM12878", "lab_name": "Yijun Ruan, JAX"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "title": "ChIA-DropBox and MIA-Sig Results", "description": "ChIA-DropBox was executed by the data submitting lab to obtain intra-chromosomal putative complexes. The entropy-based distance filter in the MIA-Sig package further resolved potential multiplets (e.g., droplets with more than 1 chromatin complex), resulting in confident complexes. A pairwise contact matrix in mcool format was generated by the DCIC for combined replicates. Complexes were processed using a 2/n complex size normalization."}], "biosample_quantity_units": "cells", "library_preparation_date": "2018-05-16", "fragment_size_selection_method": "see document", "@id": "/experiments-seq/4DNEX2FMPU1P/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "fed5d2e9-b2b9-41fd-8062-1e95cb590e60", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "ChIA-Drop against CTCF protein on GM12878 - 4DNEX2FMPU1P", "external_references": [], "experiment_sets": [{"status": "released", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESQR3D9XM/", "uuid": "c5f46d18-10a0-487c-b00c-9f6c25b88ba2", "display_title": "4DNESQR3D9XM", "accession": "4DNESQR3D9XM", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"status": "current", "date_published": "2024-03-27", "ID": "doi:10.1101/2024.03.25.586715", "@type": ["Publication", "Item"], "display_title": "Kim M et al. (2024) doi:10.1101/2024.03.25.586715", "journal": "bioRxiv : the preprint server for biology", "authors": ["Kim M", "Wang P", "Clow PA", "Chien IE", "Wang X", "Peng J", "Chai H", "Liu X", "Lee B", "Ngan CY", "Yue F", "Milenkovic O", "Chuang JH", "Wei CL", "Casellas R", "Cheng AW", "Ruan Y"], "abstract": "Cohesin is required for chromatin loop formation. However, its precise role in  regulating gene transcription remains largely unknown. We investigated the  relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule  mapping and live-cell imaging methods in human cells. Cohesin-mediated  transcriptional loops were highly correlated with those of RNAPII and followed  the direction of gene transcription. Depleting RAD21, a subunit of cohesin,  resulted in the loss of long-range (>100 kb) loops between distal  (super-)enhancers and promoters of cell-type-specific genes. By contrast, the  short-range (<50 kb) loops were insensitive to RAD21 depletion and connected  genes that are mostly housekeeping. This result explains why only a small  fraction of genes are affected by the loss of long-range chromatin interactions  due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate  genes located in early initiation zones (EIZ) of DNA replication, and the EIZ  signals were amplified drastically without RAD21. Our results revealed new  mechanistic insights of cohesin's multifaceted roles in establishing  transcriptional loops, preserving long-range chromatin interactions for  cell-specific genes, and maintaining timely order of DNA replication.", "@id": "/publications/a84d089a-b2a0-4da5-a454-07f73987df08/", "uuid": "a84d089a-b2a0-4da5-a454-07f73987df08", "short_attribution": "Kim M et al. (2024)", "title": "Multifaceted roles of cohesin in regulating transcriptional loops.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"abstract": "Cohesin is required for chromatin loop formation. However, its precise role in  regulating gene transcription remains largely unknown. We investigated the  relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule  mapping and live-cell imaging methods in human cells. Cohesin-mediated  transcriptional loops were highly correlated with those of RNAPII and followed  the direction of gene transcription. Depleting RAD21, a subunit of cohesin,  resulted in the loss of long-range (>100 kb) loops between distal  (super-)enhancers and promoters of cell-type-specific genes. By contrast, the  short-range (<50 kb) loops were insensitive to RAD21 depletion and connected  genes that are mostly housekeeping. This result explains why only a small  fraction of genes are affected by the loss of long-range chromatin interactions  due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate  genes located in early initiation zones (EIZ) of DNA replication, and the EIZ  signals were amplified drastically without RAD21. Our results revealed new  mechanistic insights of cohesin's multifaceted roles in establishing  transcriptional loops, preserving long-range chromatin interactions for  cell-specific genes, and maintaining timely order of DNA replication.", "short_attribution": "Kim M et al. (2024)", "ID": "doi:10.1101/2024.03.25.586715", "title": "Multifaceted roles of cohesin in regulating transcriptional loops.", "display_title": "Kim M et al. (2024) doi:10.1101/2024.03.25.586715", "journal": "bioRxiv : the preprint server for biology", "status": "current", "authors": ["Kim M", "Wang P", "Clow PA", "Chien IE", "Wang X", "Peng J", "Chai H", "Liu X", "Lee B", "Ngan CY", "Yue F", "Milenkovic O", "Chuang JH", "Wei CL", "Casellas R", "Cheng AW", "Ruan Y"], "@id": "/publications/a84d089a-b2a0-4da5-a454-07f73987df08/", "@type": ["Publication", "Item"], "date_published": "2024-03-27", "uuid": "a84d089a-b2a0-4da5-a454-07f73987df08", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "CTCF protein", "combined": "Target: CTCF protein"}, "experiment_summary": "ChIA-Drop against CTCF protein on GM12878", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSNOGVYAB/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing passage_number", "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": []}