Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types

Autor: Chi Wai Yip, Chung-Chau Hon, Kayoko Yasuzawa, Divya M. Sivaraman, Jordan A. Ramilowski, Youtaro Shibayama, Saumya Agrawal, Anika V. Prabhu, Callum Parr, Jessica Severin, Yan Jun Lan, Josée Dostie, Andreas Petri, Hiromi Nishiyori-Sueki, Michihira Tagami, Masayoshi Itoh, Fernando López-Redondo, Tsukasa Kouno, Jen-Chien Chang, Joachim Luginbühl, Masaki Kato, Mitsuyoshi Murata, Wing Hin Yip, Xufeng Shu, Imad Abugessaisa, Akira Hasegawa, Harukazu Suzuki, Sakari Kauppinen, Ken Yagi, Yasushi Okazaki, Takeya Kasukawa, Michiel de Hoon, Piero Carninci, Jay W. Shin

Publikováno v: Yip, C W, Hon, C-C, Yasuzawa, K, Sivaraman, D M, Ramilowski, J A, Shibayama, Y, Agrawal, S, Prabhu, A V, Parr, C, Severin, J, Lan, Y J, Dostie, J, Petri, A, Nishiyori-Sueki, H, Tagami, M, Itoh, M, López-Redondo, F, Kouno, T, Chang, J-C, Luginbühl, J, Kato, M, Murata, M, Yip, W H, Shu, X, Abugessaisa, I, Hasegawa, A, Suzuki, H, Kauppinen, S, Yagi, K, Okazaki, Y, Kasukawa, T, de Hoon, M, Carninci, P & Shin, J W 2022, ' Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types ', Cell reports, vol. 41, no. 13, 111893 . https://doi.org/10.1016/j.celrep.2022.111893

Within the scope of the FANTOM6 consortium, we perform a large-scale knockdown of 200 long non-coding RNAs (lncRNAs) in human induced pluripotent stem cells (iPSCs) and systematically characterize their roles in self-renewal and pluripotency. We find

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d15a652955f06a58b1c97bd8ea86768f
https://vbn.aau.dk/da/publications/57100123-2566-469a-9534-0fbe9f544bdc

Development of human cartilage circadian rhythm in a stem cell-chondrogenesis model

Autor: Naven, Mark A, Zeef, Leo A H, Li, Shiyang, Humphreys, Paul A, Smith, Christopher A, Pathiranage, Dharshika, Cain, Stuart, Woods, Steven, Bates, Nicola, Au, Manting, Wen, Chunyi, Kimber, Susan J, Meng, Qing-Jun

Publikováno v: Naven, M, Zeef, L, Li, S, Humphreys, P, Smith, C, Pathiranage, D, Cain, S, Woods, S, Bates, N, Au, M, Wen, C, Kimber, S & Meng, Q-J 2022, ' Development of human cartilage circadian rhythm in a stem cell-chondrogenesis model ', Theranostics . https://doi.org/10.7150/thno.70893
Naven, M A, Zeef, L A H, Li, S, Humphreys, P A, Smith, C A, Pathiranage, D, Cain, S, Woods, S, Bates, N, Au, M, Wen, C, Kimber, S J & Meng, Q-J 2022, ' Development of human cartilage circadian rhythm in a stem cell-chondrogenesis model ', Theranostics, vol. 12, no. 9, pp. 3963-3976 . https://doi.org/10.7150/THNO.70893

The circadian clock in murine articular cartilage is a critical temporal regulatory mechanism for tissue homeostasis and osteoarthritis. However, translation of these findings into humans has been hampered by the difficulty in obtaining circadian tim

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b5b565669b29e54ac28073736385b2c1
https://pubmed.ncbi.nlm.nih.gov/35664072

Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets

Autor: Fatin N. Zainul Abidin, David R. Westhead, Salam A. Assi, Rebecca Hannah, Constanze Bonifer, Debbie K. Goode, Nadine Obier, Georges Lacaud, M. S. Vijayabaskar, Amber M L Emmett, Nisar A. Shar, Monika Lichtinger, Valerie Kouskoff, Berthold Göttgens, Michael Lie-A-Ling

Publikováno v: PLoS Computational Biology
PLoS Computational Biology, Vol 15, Iss 11, p e1007337 (2019)
Vijayabaskar, M S, Goode, D K, Obier, N, Lichtinger, M, Emmett, A M L, Abidin, F N Z, Shar, N, Hannah, R, Assi, S A, Lie-A-Ling, M, Gottgens, B, Lacaud, G, Kouskoff, V, Bonifer, C & Westhead, D R 2019, ' Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells : An integrative approach using high-throughput datasets ', PLoS computational biology, vol. 15, no. 11, pp. e1007337 . https://doi.org/10.1371/journal.pcbi.1007337

Gene expression governs cell fate, and is regulated via a complex interplay of transcription factors and molecules that change chromatin structure. Advances in sequencing-based assays have enabled investigation of these processes genome-wide, leading

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ad63bce7b85c00e7164b22b42317509e
http://europepmc.org/articles/PMC6855567

Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus

Autor: Anna Griego, Francesco Aulicino, Antonio del Sol, Aniello Cerrato, Maria Pia Cosma, Gökhan Ertaylan, Anchel de Jaime-Soguero, Frederic Lluis, Aravind Tallam

Publikováno v: PLoS Genetics, Vol 13, Iss 3, p e1006682 (2017)
PLOS genetics (Online) 13 (2017). doi:10.1371/journal.pgen.1006682
info:cnr-pdr/source/autori:De Jaime-Soguero A.; Aulicino F.; Ertaylan G.; Griego A.; Cerrato A.; Tallam A.; del Sol A.; Cosma M.P.; Lluis F./titolo:Wnt%2FTcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4%2FArf locus/doi:10.1371%2Fjournal.pgen.1006682/rivista:PLOS genetics (Online)/anno:2017/pagina_da:/pagina_a:/intervallo_pagine:/volume:13
PLoS Genetics
Recercat. Dipósit de la Recerca de Catalunya
instname
Plos Genetics, 13(3):e1006682. Public Library of Science
De Jaime-Soguero, A, Aulicino, F, Ertaylan, G, Griego, A, Cerrato, A, Tallam, A, Del Sol, A, Cosma, M P & Lluis, F 2017, ' Wnt/Tcf1 pathway restricts embryonic stem cell cycle through activation of the Ink4/Arf locus ', PLoS Genetics, vol. 13, no. 3, e1006682 . https://doi.org/10.1371/journal.pgen.1006682

Understanding the mechanisms regulating cell cycle, proliferation and potency of pluripotent stem cells guarantees their safe use in the clinic. Embryonic stem cells (ESCs) present a fast cell cycle with a short G1 phase. This is due to the lack of e

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0baf0be0d381ed144c662e251481d377
https://lirias.kuleuven.be/handle/123456789/629757

Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction

Autor: Sebastian Dümcke, Johannes Bräuer, Rainer Spang, Niko Beerenwinkel, Achim Tresch, Benedict Anchang

Publikováno v: Bioinformatics, 30 (3)

Bioinformatics, 30 (3)
ISSN:1367-4803
ISSN:1460-2059

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2bfc25d7d219db441bf113956e2d47f7
https://doi.org/10.1093/bioinformatics/btt696