Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes

Autor: Chirag Nepal, Jesper B. Andersen

Publikováno v: Nepal, C & Andersen, J B 2023, ' Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes ', Nature Communications, vol. 14, 2712 . https://doi.org/10.1038/s41467-023-38272-4

Transcriptional regulation is commonly governed by alternative promoters. However, the regulatory architecture in alternative and reference promoters, and how they differ, remains elusive. In 100 CAGE-seq libraries from hepatocellular carcinoma patie

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a40d8087079cfd0f686daad42602d97b
https://curis.ku.dk/ws/files/346531529/s41467_023_38272_4.pdf

DNA methylation signature of chronic low-grade inflammation and its role in cardio-respiratory diseases

Autor: Wielscher, Matthias, Mandaviya, Pooja R, Kuehnel, Brigitte, Joehanes, Roby, Mustafa, Rima, Robinson, Oliver, Zhang, Yan, Bodinier, Barbara, Walton, Esther, Mishra, Pashupati P, Schlosser, Pascal, Wilson, Rory, Tsai, Pei-Chien, Palaniswamy, Saranya, Marioni, Riccardo E, Fiorito, Giovanni, Cugliari, Giovanni, Karhunen, Ville, Ghanbari, Mohsen, Psaty, Bruce M, Loh, Marie, Bis, Joshua C, Lehne, Benjamin, Sotoodehnia, Nona, Deary, Ian J, Chadeau-Hyam, Marc, Brody, Jennifer A, Cardona, Alexia, Selvin, Elizabeth, Smith, Alicia K, Miller, Andrew H, Torres, Mylin A, Marouli, Eirini, Gào, Xin, Van Meurs, Joyce BJ, Graf-Schindler, Johanna, Rathmann, Wolfgang, Koenig, Wolfgang, Peters, Annette, Weninger, Wolfgang, Farlik, Matthias, Zhang, Tao, Chen, Wei, Xia, Yujing, Teumer, Alexander, Nauck, Matthias, Grabe, Hans J, Doerr, Macus, Lehtimäki, Terho, Guan, Weihua, Milani, Lili, Tanaka, Toshiko, Fisher, Krista, Waite, Lindsay L, Kasela, Silva, Vineis, Paolo, Verweij, Niek, Van Der Harst, Pim, Iacoviello, Licia, Sacerdote, Carlotta, Panico, Salvatore, Krogh, Vittorio, Tumino, Rosario, Tzala, Evangelia, Matullo, Giuseppe, Hurme, Mikko A, Raitakari, Olli T, Colicino, Elena, Baccarelli, Andrea A, Kähönen, Mika, Herzig, Karl-Heinz, Li, Shengxu, BIOS Consortium, Conneely, Karen N, Kooner, Jaspal S, Köttgen, Anna, Heijmans, Bastiaan T, Deloukas, Panos, Relton, Caroline, Ong, Ken K, Bell, Jordana T, Boerwinkle, Eric, Elliott, Paul, Brenner, Hermann, Beekman, Marian, Levy, Daniel, Waldenberger, Melanie, Chambers, John C, Dehghan, Abbas, Järvelin, Marjo-Riitta

Publikováno v: Nature Communications, 13(1). NATURE PORTFOLIO
Nat. Commun. 13:2408 (2022)
Nature Communications, 13:2408. Nature Publishing Group
Nature Communications
Nature Communications, 13(1):2408. Nature Publishing Group
Wielscher, M, Mandaviya, P R, Kuehnel, B, Joehanes, R, Mustafa, R, Robinson, O, Zhang, Y, Bodinier, B, Walton, E, Mishra, P P, Schlosser, P, Wilson, R, Tsai, P-C, Palaniswamy, S, Marioni, R E, Fiorito, G, Cugliari, G, Karhunen, V, Ghanbari, M, Psaty, B M, Loh, M, Bis, J C, Lehne, B, Sotoodehnia, N, Deary, I J, Chadeau-Hyam, M, Brody, J A, Cardona, A, Selvin, E, Smith, A K, Miller, A H, Torres, M A, Marouli, E, Gào, X, van Meurs, J B J, Graf-Schindler, J, Rathmann, W, Koenig, W, Peters, A, Weninger, W, Farlik, M, Zhang, T, Chen, W, Xia, Y, Teumer, A, Nauck, M, Grabe, H J, Doerr, M, Lehtimäki, T, Guan, W, Milani, L, Tanaka, T, Fisher, K, Waite, L L, Kasela, S, Vineis, P, Verweij, N, van der Harst, P, Iacoviello, L, Sacerdote, C, Panico, S, Krogh, V, Tumino, R, Tzala, E, Matullo, G, Hurme, M A, Raitakari, O T, Colicino, E, Baccarelli, A A, Kähönen, M, Herzig, K-H, Li, S, Conneely, K N, Kooner, J S, Köttgen, A, Heijmans, B T, Deloukas, P, Relton, C, Ong, K K, Bell, J T, Boerwinkle, E, Elliott, P, Brenner, H, Beekman, M, Levy, D, Waldenberger, M, Chambers, J C, Dehghan, A & Järvelin, M-R 2022, ' DNA methylation signature of chronic low-grade inflammation and its role in cardio-respiratory diseases ', Nature Communications, vol. 13, 2408 . https://doi.org/10.1038/s41467-022-29792-6

Chronic inflammation, marked by C-reactive protein, has been associated with changes in methylation, but the causal relationship is unclear. Here, the authors perform a Epigenome-wide association meta-analysis for C-reactive protein levels and find t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::daf8cc1ac792293a388782a2252ded72
https://doi.org/10.1038/s41467-022-29792-6

Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin

Autor: Martial Marbouty, Stefano Cairo, Christine Neuveut, Romain Koszul, Agnès Thierry, Gianna Aurora Palumbo, Marc Lavigne, Shogofa Mortaza, Axel Cournac, Pierrick Moreau

Publikováno v: Nature Communications, Vol 9, Iss 1, Pp 1-14 (2018)
Nature Communications
Nature Communications, Nature Publishing Group, 2018, 9 (1), pp.4268. ⟨10.1038/s41467-018-06739-4⟩
Nature Communications, 2018, 9 (1), pp.4268. ⟨10.1038/s41467-018-06739-4⟩

Whether non-integrated viral DNAs distribute randomly or target specific positions within the higher-order architecture of mammalian genomes remains largely unknown. Here we use Hi-C and viral DNA capture (CHi-C) in primary human hepatocytes infected

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b25a01ae3ff182b3c56e2c98435fe5a3
http://link.springer.com/article/10.1038/s41467-018-06739-4

DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease

Autor: Cristina Tufarelli, Ricarda Gaentzsch, Robert J S Murray, Danuta M. Jeziorska, Jim R. Hughes, Bryony Graham, Marco De Gobbi, Jonathan N. Lund, Andrew J.H. Smith, Helena Ayyub, En Li, Magnus D. Lynch, Taiping Chen, Jelena Telenius, Douglas R. Higgs, David Garrick

Publikováno v: Jeziorska, D M, Murray, R J S, De Gobbi, M, Gaentzsch, R, Garrick, D, Ayyub, H, Chen, T, Li, E, Telenius, J, Lynch, M, Graham, B, Smith, A J H, Lund, J N, Hughes, J R, Higgs, D R & Tufarelli, C 2017, ' DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease ', Proceedings of the National Academy of Sciences, vol. 114, no. 36, pp. E7526-E7535 . https://doi.org/10.1073/pnas.1703087114

The human genome contains ∼30,000 CpG islands (CGIs). While CGIs associated with promoters nearly always remain unmethylated, many of the ∼9,000 CGIs lying within gene bodies become methylated during development and differentiation. Both promoter

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2b09643ca63009b33e0f3c4a62192df6

ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection

Autor: Robert J. Klose, Neil P. Blackledge, Hannah K. Long

Publikováno v: Long, H K, Blackledge, N P & Klose, R J 2013, ' ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection ', Biochemical Society Transactions, vol. 41, no. 3, pp. 727-40 . https://doi.org/10.1042/BST20130028
Biochemical Society Transactions

Vertebrate DNA can be chemically modified by methylation of the 5 position of the cytosine base in the context of CpG dinucleotides. This modification creates a binding site for MBD (methyl-CpG-binding domain) proteins which target chromatin-modifyin

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::04d23e5886961723d395fb4798c63f76
https://ora.ox.ac.uk/objects/uuid:194ec326-8549-4a6f-a9fd-66f9001fc79c