Cell-type specialization is encoded by specific chromatin topologies
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2021 |
| Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| Texto Completo: | http://hdl.handle.net/10362/142526 |
Resumo: | U54DK107977 1UM1HG011585 IRTG2403 Germany’s Excellence Strategy–EXC-2049–390688087 EPIScOPE no. 681893 no. 2015-03558; 2019-01360 FO2017-0075 2019-0107 JUB2019 P25014-B24 Council (UK) (U120085816 G HP10CYFPS5 HP10CRTY8P ASTF 336-2015 |
| id |
RCAP_85b24c4ecb7a5f5160ddd511a186653b |
|---|---|
| oai_identifier_str |
oai:run.unl.pt:10362/142526 |
| network_acronym_str |
RCAP |
| network_name_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| repository_id_str |
7160 |
| spelling |
Cell-type specialization is encoded by specific chromatin topologiesGeneralU54DK107977 1UM1HG011585 IRTG2403 Germany’s Excellence Strategy–EXC-2049–390688087 EPIScOPE no. 681893 no. 2015-03558; 2019-01360 FO2017-0075 2019-0107 JUB2019 P25014-B24 Council (UK) (U120085816 G HP10CYFPS5 HP10CRTY8P ASTF 336-2015The three-dimensional (3D) structure of chromatin is intrinsically associated with gene regulation and cell function1–3. 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 hippocampi4–6. However, changes in chromatin organization captured by imaging, such as the relocation of Bdnf away from the nuclear periphery after activation7, are invisible with such approaches8. 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 dissociation2,10. 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.UCIBIO - Applied Molecular Biosciences UnitDCV - Departamento de Ciências da VidaRUNWinick-Ng, WarrenKukalev, AlexanderHarabula, IzabelaZea-Redondo, LunaSzabó, DominikMeijer, MandySerebreni, LeonidZhang, YingnanBianco, SimonaChiariello, Andrea M.Irastorza-Azcarate, IbaiThieme, Christoph J.Sparks, Thomas M.Carvalho, SílviaFiorillo, LucaMusella, FrancescoIrani, EhsanTriglia, Elena TorlaiKolodziejczyk, Aleksandra A.Abentung, AndreasApostolova, GalinaPaul, Eleanor J.Franke, VedranKempfer, RiekeAkalin, AltunaTeichmann, Sarah A.Dechant, GeorgUngless, Mark A.Nicodemi, MarioWelch, LonnieCastelo-Branco, GonçaloPombo, Ana2022-07-27T22:26:32Z2021-11-252021-11-25T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article8application/pdfhttp://hdl.handle.net/10362/142526eng0028-0836PURE: 45642673https://doi.org/10.1038/s41586-021-04081-2info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T05:20:17Zoai:run.unl.pt:10362/142526Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:50:22.062450Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
| dc.title.none.fl_str_mv |
Cell-type specialization is encoded by specific chromatin topologies |
| title |
Cell-type specialization is encoded by specific chromatin topologies |
| spellingShingle |
Cell-type specialization is encoded by specific chromatin topologies Winick-Ng, Warren General |
| title_short |
Cell-type specialization is encoded by specific chromatin topologies |
| title_full |
Cell-type specialization is encoded by specific chromatin topologies |
| title_fullStr |
Cell-type specialization is encoded by specific chromatin topologies |
| title_full_unstemmed |
Cell-type specialization is encoded by specific chromatin topologies |
| title_sort |
Cell-type specialization is encoded by specific chromatin topologies |
| author |
Winick-Ng, Warren |
| author_facet |
Winick-Ng, Warren Kukalev, Alexander Harabula, Izabela Zea-Redondo, Luna Szabó, Dominik Meijer, Mandy Serebreni, Leonid Zhang, Yingnan Bianco, Simona Chiariello, Andrea M. Irastorza-Azcarate, Ibai Thieme, Christoph J. Sparks, Thomas M. Carvalho, Sílvia Fiorillo, Luca Musella, Francesco Irani, Ehsan Triglia, Elena Torlai Kolodziejczyk, Aleksandra A. Abentung, Andreas Apostolova, Galina Paul, Eleanor J. Franke, Vedran Kempfer, Rieke Akalin, Altuna Teichmann, Sarah A. Dechant, Georg Ungless, Mark A. Nicodemi, Mario Welch, Lonnie Castelo-Branco, Gonçalo Pombo, Ana |
| author_role |
author |
| author2 |
Kukalev, Alexander Harabula, Izabela Zea-Redondo, Luna Szabó, Dominik Meijer, Mandy Serebreni, Leonid Zhang, Yingnan Bianco, Simona Chiariello, Andrea M. Irastorza-Azcarate, Ibai Thieme, Christoph J. Sparks, Thomas M. Carvalho, Sílvia Fiorillo, Luca Musella, Francesco Irani, Ehsan Triglia, Elena Torlai Kolodziejczyk, Aleksandra A. Abentung, Andreas Apostolova, Galina Paul, Eleanor J. Franke, Vedran Kempfer, Rieke Akalin, Altuna Teichmann, Sarah A. Dechant, Georg Ungless, Mark A. Nicodemi, Mario Welch, Lonnie Castelo-Branco, Gonçalo Pombo, Ana |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
UCIBIO - Applied Molecular Biosciences Unit DCV - Departamento de Ciências da Vida RUN |
| dc.contributor.author.fl_str_mv |
Winick-Ng, Warren Kukalev, Alexander Harabula, Izabela Zea-Redondo, Luna Szabó, Dominik Meijer, Mandy Serebreni, Leonid Zhang, Yingnan Bianco, Simona Chiariello, Andrea M. Irastorza-Azcarate, Ibai Thieme, Christoph J. Sparks, Thomas M. Carvalho, Sílvia Fiorillo, Luca Musella, Francesco Irani, Ehsan Triglia, Elena Torlai Kolodziejczyk, Aleksandra A. Abentung, Andreas Apostolova, Galina Paul, Eleanor J. Franke, Vedran Kempfer, Rieke Akalin, Altuna Teichmann, Sarah A. Dechant, Georg Ungless, Mark A. Nicodemi, Mario Welch, Lonnie Castelo-Branco, Gonçalo Pombo, Ana |
| dc.subject.por.fl_str_mv |
General |
| topic |
General |
| description |
U54DK107977 1UM1HG011585 IRTG2403 Germany’s Excellence Strategy–EXC-2049–390688087 EPIScOPE no. 681893 no. 2015-03558; 2019-01360 FO2017-0075 2019-0107 JUB2019 P25014-B24 Council (UK) (U120085816 G HP10CYFPS5 HP10CRTY8P ASTF 336-2015 |
| publishDate |
2021 |
| dc.date.none.fl_str_mv |
2021-11-25 2021-11-25T00:00:00Z 2022-07-27T22:26:32Z |
| dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
| dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10362/142526 |
| url |
http://hdl.handle.net/10362/142526 |
| dc.language.iso.fl_str_mv |
eng |
| language |
eng |
| dc.relation.none.fl_str_mv |
0028-0836 PURE: 45642673 https://doi.org/10.1038/s41586-021-04081-2 |
| dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
| eu_rights_str_mv |
openAccess |
| dc.format.none.fl_str_mv |
8 application/pdf |
| dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
| instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
| instacron_str |
RCAAP |
| institution |
RCAAP |
| reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
| repository.mail.fl_str_mv |
|
| _version_ |
1799138100660666368 |