{"ID": "PMID:23953119", "lab": {"uuid": "6343d57a-213e-4ac7-89ec-8b5e74c21bd2", "display_title": "Bas van Steensel, NKI", "@id": "/labs/bas-van-steensel-lab/", "status": "current", "correspondence": [{"contact_email": "Yi52LnN0ZWVuc2VsQG5raS5ubA==", "@id": "/users/dd8b1cd6-93cd-41e5-b184-caf1369cb39f/", "display_title": "Bas van Steensel"}], "title": "Bas van Steensel, NKI", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6343d57a-213e-4ac7-89ec-8b5e74c21bd2"]}}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/23953119", "award": {"center_title": "External", "description": "Funding source is from outside 4DN.", "@id": "/awards/external-award/", "display_title": "EXTERNAL AWARD", "status": "current", "project": "External", "name": "external-award", "@type": ["Award", "Item"], "center": "External", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Chromatin position effects assayed by thousands of reporters integrated in parallel.", "status": "current", "aliases": ["4dn-dcic-lab:akhtar_trip_1st_paper"], "authors": ["Akhtar W", "de Jong J", "Pindyurin AV", "Pagie L", "Meuleman W", "de Ridder J", "Berns A", "Wessels LF", "van Lohuizen M", "van Steensel B"], "journal": "Cell", "abstract": "Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here, we describe a multiplexing approach for the parallel monitoring of transcriptional activity of  thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show approximately 1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for crosstalk between neighboring genes and estimate that enhancers can influence gene expression on average over approximately 20 kb. The  multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation.", "categories": ["methods paper"], "date_created": "2019-04-10T17:03:25.187695+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-04-02T20:26:43.036246+00:00"}, "date_published": "2013-08-15", "public_release": "2019-04-10", "schema_version": "2", "project_release": "2019-04-10", "@id": "/publications/04bd379c-aae0-427f-9a71-a1d59fb4752c/", "@type": ["Publication", "Item"], "uuid": "04bd379c-aae0-427f-9a71-a1d59fb4752c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "Akhtar W et al. (2013) PMID:23953119", "external_references": [], "short_attribution": "Akhtar W et al. (2013)", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}