{"lab": {"title": "Ana Pombo, MDC", "@id": "/labs/ana-pombo-lab/", "@type": ["Lab", "Item"], "display_title": "Ana Pombo, MDC", "status": "current", "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "correspondence": [{"contact_email": "YW5hLnBvbWJvQG1kYy1iZXJsaW4uZGU=", "@id": "/users/bce4f2b5-9a2a-4db2-9dd6-7d61f19025c1/", "display_title": "Ana Pombo"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "award": {"status": "current", "@type": ["Award", "Item"], "@id": "/awards/1U54DK107977-01/", "display_title": "SAN DIEGO CENTER FOR 4D NUCLEOME RESEARCH", "center_title": "NOFIC - Ren", "uuid": "4871e338-b07d-4665-a00a-357648e5bad6", "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.", "project": "4DN", "name": "1U54DK107977-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["ana-pombo-lab:gam_CA1_PGNs"], "accession": "4DNES43FS97D", "condition": "Pyramidal neurons from hippocampus CA1 region", "description": "Replicates of GAM on mouse pyramidal glutamatergic neurons from cornus ammonis 1 region of the hippocampus from C57BL/6J Floxed-Satb2 background mouse", "date_created": "2020-08-18T21:50:20.894048+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "GAM on mouse brain cell types", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-05-19T22:48:54.457947+00:00"}, "public_release": "2021-02-09", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "9c061f8f-328e-4dc9-bb89-7639ecbc18c3", "display_title": "GAM on CA1 field of hippocampus - 4DNEXV4EFZV8", "accession": "4DNEXV4EFZV8", "status": "released", "@id": "/experiments-seq/4DNEXV4EFZV8/", "@type": ["ExperimentSeq", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"uuid": "3f165767-0b00-4c05-92bb-b8b046a8e7d3", "display_title": "GAM on CA1 field of hippocampus - 4DNEXXCYTAMT", "accession": "4DNEXXCYTAMT", "status": "released", "@id": "/experiments-seq/4DNEXXCYTAMT/", "@type": ["ExperimentSeq", "Experiment", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_headers": [{"lab": {"@id": "/labs/ana-pombo-lab/", "display_title": "Ana Pombo, MDC", "uuid": "cf5abe29-1cf9-4413-b02e-664b47a6d53d", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.cf5abe29-1cf9-4413-b02e-664b47a6d53d"]}}, "body": "**NOTE** The excel workbooks available from the following links - one file per replicate contain information that can be used to evaluate the quality of the GAM libraries linked to this dataset.\n\n[**Replicate 1 downloadable from here**](https://data.4dnucleome.org/documents/a9391285-5fef-4c0d-884f-5625623f74c1/)\n\n[**Replicate 2 downloadable from here**](https://data.4dnucleome.org/documents/20357ac1-82c5-4483-8b9c-c8afd4068adf/)\n\nEach workbook consists of 2 sheets. The first provides descriptions and terms used in the second and highlights those that may be used to evaluate quality of the libraries. The second sheet provides information on each individual GAM library linked to this dataset. Each library corresponds to a single FastQ file that can be identified using the provided Sample_ID in the first column.", "name": "neuroGAM-PGN-set-QC-info-notice", "award": {"status": "current", "@id": "/awards/2U01CA200059-06/", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Batch Quality Information for GAM libraries (NP fastq files) in this Dataset", "status": "released", "aliases": ["4dn-dcic-lab:neuroGAM_PGN_set_QC_info_notice"], "options": {"filetype": "md", "collapsible": false, "default_open": true}, "date_created": "2021-05-19T21:09:45.027955+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-05-19T21:09:45.037123+00:00"}, "schema_version": "2", "@id": "/static-sections/fe4ec4a9-0e5c-441d-9f7c-6a7256c1ab06/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "fe4ec4a9-0e5c-441d-9f7c-6a7256c1ab06", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267227777"]}, "display_title": "Batch Quality Information for GAM libraries (NP fastq files) in this Dataset", "external_references": [], "content": "**NOTE** The excel workbooks available from the following links - one file per replicate contain information that can be used to evaluate the quality of the GAM libraries linked to this dataset.\n\n[**Replicate 1 downloadable from here**](https://data.4dnucleome.org/documents/a9391285-5fef-4c0d-884f-5625623f74c1/)\n\n[**Replicate 2 downloadable from here**](https://data.4dnucleome.org/documents/20357ac1-82c5-4483-8b9c-c8afd4068adf/)\n\nEach workbook consists of 2 sheets. The first provides descriptions and terms used in the second and highlights those that may be used to evaluate quality of the libraries. The second sheet provides information on each individual GAM library linked to this dataset. Each library corresponds to a single FastQ file that can be identified using the provided Sample_ID in the first column.", "filetype": "md", "content_as_html": "

NOTE The excel workbooks available from the following links - one file per replicate contain information that can be used to evaluate the quality of the GAM libraries linked to this dataset.

\n

Replicate 1 downloadable from here

\n

Replicate 2 downloadable from here

\n

Each workbook consists of 2 sheets. The first provides descriptions and terms used in the second and highlights those that may be used to evaluate quality of the libraries. The second sheet provides information on each individual GAM library linked to this dataset. Each library corresponds to a single FastQ file that can be identified using the provided Sample_ID in the first column.

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(2021)", "ID": "PMID:34789882", "status": "current", "@id": "/publications/613340da-ecdc-44bd-ae74-437b2ad65ac6/", "uuid": "613340da-ecdc-44bd-ae74-437b2ad65ac6", "journal": "Nature", "date_published": "2021-11", "url": "https://www.ncbi.nlm.nih.gov/pubmed/34789882", "display_title": "Winick-Ng W et al. (2021) PMID:34789882", "abstract": "The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function(1-3). Methods based on chromatin conformation capture have mapped chromatin structures in neuronal systems such as in vitro differentiated neurons, neurons isolated through fluorescence-activated cell sorting from cortical tissues pooled from different animals and from dissociated whole hippocampi(4-6). However, changes in chromatin organization captured by imaging, such as the relocation of Bdnf away from the nuclear periphery after activation(7), are invisible with such approaches(8). Here we developed immunoGAM, an extension of genome architecture mapping (GAM)(2,9), to map 3D chromatin topology genome-wide in specific brain cell types, without tissue disruption, from single animals. GAM is a ligation-free technology that maps genome topology by sequencing the DNA content from thin (about 220 nm) nuclear cryosections. Chromatin interactions are identified from the increased probability of co-segregation of contacting loci across a collection of nuclear slices. ImmunoGAM expands the scope of GAM to enable the selection of specific cell types using low cell numbers (approximately 1,000 cells) within a complex tissue and avoids tissue dissociation(2,10). We report cell-type specialized 3D chromatin structures at multiple genomic scales that relate to patterns of gene expression. We discover extensive 'melting' of long genes when they are highly expressed and/or have high chromatin accessibility. The contacts most specific of neuron subtypes contain genes associated with specialized processes, such as addiction and synaptic plasticity, which harbour putative binding sites for neuronal transcription factors within accessible chromatin regions. Moreover, sensory receptor genes are preferentially found in heterochromatic compartments in brain cells, which establish strong contacts across tens of megabases. Our results demonstrate that highly specific chromatin conformations in brain cells are tightly related to gene regulation mechanisms and specialized functions.", "@type": ["Publication", "Item"], "title": "Cell-type specialization is encoded by specific chromatin topologies.", "authors": ["Winick-Ng W", "Kukalev A", "Harabula I", "Zea-Redondo L", "Szabo D", "Meijer M", "Serebreni L", "Zhang Y", "Bianco S", "Chiariello AM", "Irastorza-Azcarate I", "Thieme CJ", "Sparks TM", "Carvalho S", "Fiorillo L", "Musella F", "Irani E", "Triglia ET", "Kolodziejczyk AA", "Abentung A", "Apostolova G", "Paul EJ", "Franke V", "Kempfer R", "Akalin A", "Teichmann SA", "Dechant G", "Ungless MA", "Nicodemi M", "Welch L", "Castelo-Branco G", "Pombo A"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [{"display_title": "Szabo D et al. (2024) PMID:38766140", "status": "current", "uuid": "53947f85-e28f-405f-b92e-92ca7bdb2aea", "@type": ["Publication", "Item"], "@id": "/publications/53947f85-e28f-405f-b92e-92ca7bdb2aea/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "publications_of_set": [{"title": "Cell-type specialization is encoded by specific chromatin topologies.", "display_title": "Winick-Ng W et al. (2021) PMID:34789882", "date_published": "2021-11", "ID": "PMID:34789882", "authors": ["Winick-Ng W", "Kukalev A", "Harabula I", "Zea-Redondo L", "Szabo D", "Meijer M", "Serebreni L", "Zhang Y", "Bianco S", "Chiariello AM", "Irastorza-Azcarate I", "Thieme CJ", "Sparks TM", "Carvalho S", "Fiorillo L", "Musella F", "Irani E", "Triglia ET", "Kolodziejczyk AA", "Abentung A", "Apostolova G", "Paul EJ", "Franke V", "Kempfer R", "Akalin A", "Teichmann SA", "Dechant G", "Ungless MA", "Nicodemi M", "Welch L", "Castelo-Branco G", "Pombo A"], "abstract": "The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function(1-3). Methods based on chromatin conformation capture have mapped chromatin structures in neuronal systems such as in vitro differentiated neurons, neurons isolated through fluorescence-activated cell sorting from cortical tissues pooled from different animals and from dissociated whole hippocampi(4-6). However, changes in chromatin organization captured by imaging, such as the relocation of Bdnf away from the nuclear periphery after activation(7), are invisible with such approaches(8). Here we developed immunoGAM, an extension of genome architecture mapping (GAM)(2,9), to map 3D chromatin topology genome-wide in specific brain cell types, without tissue disruption, from single animals. GAM is a ligation-free technology that maps genome topology by sequencing the DNA content from thin (about 220 nm) nuclear cryosections. Chromatin interactions are identified from the increased probability of co-segregation of contacting loci across a collection of nuclear slices. ImmunoGAM expands the scope of GAM to enable the selection of specific cell types using low cell numbers (approximately 1,000 cells) within a complex tissue and avoids tissue dissociation(2,10). We report cell-type specialized 3D chromatin structures at multiple genomic scales that relate to patterns of gene expression. We discover extensive 'melting' of long genes when they are highly expressed and/or have high chromatin accessibility. The contacts most specific of neuron subtypes contain genes associated with specialized processes, such as addiction and synaptic plasticity, which harbour putative binding sites for neuronal transcription factors within accessible chromatin regions. Moreover, sensory receptor genes are preferentially found in heterochromatic compartments in brain cells, which establish strong contacts across tens of megabases. Our results demonstrate that highly specific chromatin conformations in brain cells are tightly related to gene regulation mechanisms and specialized functions.", "uuid": "613340da-ecdc-44bd-ae74-437b2ad65ac6", "journal": "Nature", "@id": "/publications/613340da-ecdc-44bd-ae74-437b2ad65ac6/", "status": "current", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"title": "A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons.", "display_title": "Szabo D et al. (2024) PMID:38766140", "date_published": "2024-05-12", "ID": "PMID:38766140", "authors": ["Szabo D", "Franke V", "Bianco S", "Batiuk MY", "Paul EJ", "Kukalev A", "Pfisterer UG", "Irastorza-Azcarate I", "Chiariello AM", "Demharter S", "Zea-Redondo L", "Lopez-Atalaya JP", "Nicodemi M", "Akalin A", "Khodosevich K", "Ungless MA", "Winick-Ng W", "Pombo A"], "abstract": "Midbrain dopamine neurons (DNs) respond to a first exposure to addictive drugs and play key roles in chronic drug usage (1-3) . As the synaptic and transcriptional changes that follow an acute cocaine exposure are mostly resolved within a few days (4,5) , the molecular changes that encode the long-term cellular memory of the exposure within DNs remain unknown. To investigate whether a single cocaine exposure induces long-term changes in the 3D genome structure of DNs, we applied Genome Architecture Mapping and single nucleus transcriptomic analyses in the mouse midbrain. We found extensive rewiring of 3D genome architecture at 24 hours past exposure which remains or worsens by 14 days, outlasting transcriptional responses. The cocaine-induced chromatin rewiring occurs at all genomic scales and affects genes with major roles in cocaine-induced synaptic changes. A single cocaine exposure triggers extensive long-lasting changes in chromatin condensation in post-synaptic and post-transcriptional regulatory genes, for example the unfolding of Rbfox1 which becomes most prominent 14 days post exposure. Finally, structurally remodeled genes are most expressed in a specific DN sub-type characterized by low expression of the dopamine auto-receptor Drd2 , a key feature of highly cocaine-sensitive cells. These results reveal an important role for long-lasting 3D genome remodelling in the cellular memory of a single cocaine exposure, providing new hypotheses for understanding the inception of drug addiction and 3D genome plasticity.", "uuid": "53947f85-e28f-405f-b92e-92ca7bdb2aea", "journal": "bioRxiv : the preprint server for biology", "@id": "/publications/53947f85-e28f-405f-b92e-92ca7bdb2aea/", "status": "current", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 2, "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}