DEEPOMICS FFPE, a deep neural network model, identifies DNA sequencing artifacts from formalin fixed paraffin embedded tissue with high accuracy

Autor: Dong-hyuk Heo, Inyoung Kim, Heejae Seo, Seong-Gwang Kim, Minji Kim, Jiin Park, Hongsil Park, Seungmo Kang, Juhee Kim, Soonmyung Paik, Seong-Eui Hong

Publikováno v: Scientific Reports, Vol 14, Iss 1, Pp 1-12 (2024)

Abstract Formalin-fixed, paraffin-embedded (FFPE) tissue specimens are routinely used in pathological diagnosis, but their large number of artifactual mutations complicate the evaluation of companion diagnostics and analysis of next-generation sequen

Externí odkaz: https://doaj.org/article/da63738b45354260bd937516c2c2f9d1

The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA

Autor: Sina Wittmann, Max Renner, Beth R. Watts, Oliver Adams, Miles Huseyin, Carlo Baejen, Kamel El Omari, Cornelia Kilchert, Dong-Hyuk Heo, Tea Kecman, Patrick Cramer, Jonathan M. Grimes, Lidia Vasiljeva

Publikováno v: Nature Communications, Vol 8, Iss 1, Pp 1-15 (2017)

Termination of RNA polymerase II is a critical step in transcription. Here, the authors provide evidence that the fission yeast CID-RRM protein Seb1 is required for termination of coding and non-coding genes through interaction with both the polymera

Externí odkaz: https://doaj.org/article/ef394db5756b48a9bb4c2015dc21a112

Elongation/Termination Factor Exchange Mediated by PP1 Phosphatase Orchestrates Transcription Termination

Autor: Tea Kecman, Krzysztof Kuś, Dong-Hyuk Heo, Katie Duckett, Adrien Birot, Sabrina Liberatori, Shabaz Mohammed, Lucia Geis-Asteggiante, Carol V. Robinson, Lidia Vasiljeva

Publikováno v: Cell Reports, Vol 25, Iss 1, Pp 259-269.e5 (2018)

Summary: Termination of RNA polymerase II (Pol II) transcription is a key step that is important for 3′ end formation of functional mRNA, mRNA release, and Pol II recycling. Even so, the underlying termination mechanism is not yet understood. Here,

Externí odkaz: https://doaj.org/article/3caa5739608f43eb8617adce3984345a

Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription

Autor: Nikolay Zenkin, Tea Kecman, Søren Nielsen, Krzysztof Kuś, Dong-Hyuk Heo, Adrien Birot, Pawel Grzechnik, Sue Mei Tan-Wong, Lidia Vasiljeva

Publikováno v: Cell Reports
Heo, D H, Kuś, K, Grzechnik, P, Tan-Wong, S M, Birot, A, Kecman, T, Nielsen, S, Zenkin, N & Vasiljeva, L 2021, ' Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription ', Cell Reports, vol. 36, no. 10, 109671 . https://doi.org/10.1016/j.celrep.2021.109671

Summary Phosphorylation of the RNA polymerase II C-terminal domain Y1S2P3T4S5P6S7 consensus sequence coordinates key events during transcription, and its deregulation leads to defects in transcription and RNA processing. Here, we report that the hist

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::752e94ffdeea97dd844ab3b0f80c0038
http://europepmc.org/articles/PMC8441049

Histone deacetylation promotes transcriptional silencing at facultative heterochromatin

Autor: Beth R, Watts, Sina, Wittmann, Maxime, Wery, Camille, Gautier, Krzysztof, Kus, Adrien, Birot, Dong-Hyuk, Heo, Cornelia, Kilchert, Antonin, Morillon, Lidia, Vasiljeva

Publikováno v: Nucleic Acids Research

It is important to accurately regulate the expression of genes involved in development and environmental response. In the fission yeast Schizosaccharomyces pombe, meiotic genes are tightly repressed during vegetative growth. Despite being embedded in

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::4f0951852644c73a4009602e02e3b0a3
https://pubmed.ncbi.nlm.nih.gov/29618061