Search Results - "Downes, Damien"

Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus by Downes, Damien J., Cross, Amy R., Hua, Peng, Roberts, Nigel, Schwessinger, Ron, Cutler, Antony J., Munis, Altar M., Brown, Jill, Mielczarek, Olga, de Andrea, Carlos E., Melero, Ignacio, Gill, Deborah R., Hyde, Stephen C., Knight, Julian C., Todd, John A., Sansom, Stephen N., Issa, Fadi, Davies, James O. J., Hughes, Jim R.

“…The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) disease (COVID-19) pandemic has caused millions of deaths worldwide. Genome-wide association…”
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Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo by Hanssen, Lars L. P., Kassouf, Mira T., Oudelaar, A. Marieke, Biggs, Daniel, Preece, Chris, Downes, Damien J., Gosden, Matthew, Sharpe, Jacqueline A., Sloane-Stanley, Jacqueline A., Hughes, Jim R., Davies, Benjamin, Higgs, Douglas R.

“…The genome is organized via CTCF–cohesin-binding sites, which partition chromosomes into 1–5 megabase (Mb) topologically associated domains (TADs), and further…”
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Hypoxia Induces Transcriptional and Translational Downregulation of the Type I IFN Pathway in Multiple Cancer Cell Types by Miar, Ana, Arnaiz, Esther, Bridges, Esther, Beedie, Shaunna, Cribbs, Adam P, Downes, Damien J, Beagrie, Robert A, Rehwinkel, Jan, Harris, Adrian L

“…Hypoxia is a common phenomenon in solid tumors and is strongly linked to hallmarks of cancer. Recent evidence has shown that hypoxia promotes local immune…”
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DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation by Godfrey, Laura, Crump, Nicholas T., Thorne, Ross, Lau, I-Jun, Repapi, Emmanouela, Dimou, Dimitra, Smith, Alastair L., Harman, Joe R., Telenius, Jelena M., Oudelaar, A. Marieke, Downes, Damien J., Vyas, Paresh, Hughes, Jim R., Milne, Thomas A.

“…Enhancer elements are a key regulatory feature of many important genes. Several general features including the presence of specific histone modifications are…”
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Defining genome architecture at base-pair resolution by Hua, Peng, Badat, Mohsin, Hanssen, Lars L. P., Hentges, Lance D., Crump, Nicholas, Downes, Damien J., Jeziorska, Danuta M., Oudelaar, A. Marieke, Schwessinger, Ron, Taylor, Stephen, Milne, Thomas A., Hughes, Jim R., Higgs, Doug R., Davies, James O. J.

“…In higher eukaryotes, many genes are regulated by enhancers that are 10 4 –10 6  base pairs (bp) away from the promoter. Enhancers contain…”
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Natural and Experimental Rewiring of Gene Regulatory Regions by Downes, Damien J, Hughes, Jim R

“…The successful development and ongoing functioning of complex organisms depend on the faithful execution of the genetic code. A critical step in this process…”
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Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis by Gillespie, Mark A., Palii, Carmen G., Sanchez-Taltavull, Daniel, Shannon, Paul, Longabaugh, William J.R., Downes, Damien J., Sivaraman, Karthi, Espinoza, Herbert M., Hughes, Jim R., Price, Nathan D., Perkins, Theodore J., Ranish, Jeffrey A., Brand, Marjorie

“…Dynamic cellular processes such as differentiation are driven by changes in the abundances of transcription factors (TFs). However, despite years of studies,…”
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Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains by Oudelaar, A. Marieke, Davies, James O. J., Hanssen, Lars L. P., Telenius, Jelena M., Schwessinger, Ron, Liu, Yu, Brown, Jill M., Downes, Damien J., Chiariello, Andrea M., Bianco, Simona, Nicodemi, Mario, Buckle, Veronica J., Dekker, Job, Higgs, Douglas R., Hughes, Jim R.

“…The promoters of mammalian genes are commonly regulated by multiple distal enhancers, which physically interact within discrete chromatin domains. How such…”
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LanceOtron: a deep learning peak caller for genome sequencing experiments by Hentges, Lance D, Sergeant, Martin J, Cole, Christopher B, Downes, Damien J, Hughes, Jim R, Taylor, Stephen

“…Abstract Motivation Genome sequencing experiments have revolutionized molecular biology by allowing researchers to identify important DNA-encoded elements…”
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The chromatin remodeller ATRX facilitates diverse nuclear processes, in a stochastic manner, in both heterochromatin and euchromatin by Truch, Julia, Downes, Damien J., Scott, Caroline, Gür, E. Ravza, Telenius, Jelena M., Repapi, Emmanouela, Schwessinger, Ron, Gosden, Matthew, Brown, Jill M., Taylor, Stephen, Cheong, Pak Leng, Hughes, Jim R., Higgs, Douglas R., Gibbons, Richard J.

“…The chromatin remodeller ATRX interacts with the histone chaperone DAXX to deposit the histone variant H3.3 at sites of nucleosome turnover. ATRX is known to…”
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A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker by Bozhilov, Yavor K., Downes, Damien J., Telenius, Jelena, Marieke Oudelaar, A., Olivier, Emmanuel N., Mountford, Joanne C., Hughes, Jim R., Gibbons, Richard J., Higgs, Douglas R.

“…Many single nucleotide variants (SNVs) associated with human traits and genetic diseases are thought to alter the activity of existing regulatory elements…”
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Comparing the two leading erythroid lines BEL-A and HUDEP-2 by Daniels, Deborah E, Downes, Damien J, Ferrer-Vicens, Ivan, Ferguson, Daniel C J, Singleton, Belinda K, Wilson, Marieangela C, Trakarnsanga, Kongtana, Kurita, Ryo, Nakamura, Yukio, Anstee, David J, Frayne, Jan

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Enhancers predominantly regulate gene expression during differentiation via transcription initiation by Larke, Martin S.C., Schwessinger, Ron, Nojima, Takayuki, Telenius, Jelena, Beagrie, Robert A., Downes, Damien J., Oudelaar, A. Marieke, Truch, Julia, Graham, Bryony, Bender, M.A., Proudfoot, Nicholas J., Higgs, Douglas R., Hughes, Jim R.

“…Gene transcription occurs via a cycle of linked events, including initiation, promoter-proximal pausing, and elongation of RNA polymerase II (Pol II). A key…”
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Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture by Downes, Damien J., Smith, Alastair L., Karpinska, Magdalena A., Velychko, Taras, Rue-Albrecht, Kevin, Sims, David, Milne, Thomas A., Davies, James O. J., Oudelaar, A. Marieke, Hughes, Jim R.

“…Chromosome conformation capture (3C) methods measure the spatial proximity between DNA elements in the cell nucleus. Many methods have been developed to sample…”
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High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale by Downes, Damien J., Beagrie, Robert A., Gosden, Matthew E., Telenius, Jelena, Carpenter, Stephanie J., Nussbaum, Lea, De Ornellas, Sara, Sergeant, Martin, Eijsbouts, Chris Q., Schwessinger, Ron, Kerry, Jon, Roberts, Nigel, Shivalingam, Arun, El-Sagheer, Afaf, Oudelaar, A. Marieke, Brown, Tom, Buckle, Veronica J., Davies, James O. J., Hughes, Jim R.

“…Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods generally provide either…”
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Erratum to: Comparing the two leading erythroid lines BEL-A and HUDEP-2 by Daniels, Deborah E, Downes, Damien J, Ferrer-Vicens, Ivan, Ferguson, Daniel C J, Singleton, Belinda K, Wilson, Marieangela C, Trakarnsanga, Kongtana, Kurita, Ryo, Nakamura, Yukio, Anstee, David J, Frayne, Jan

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Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development by Owens, Dominic D. G., Anselmi, Giorgio, Oudelaar, A. Marieke, Downes, Damien J., Cavallo, Alessandro, Harman, Joe R., Schwessinger, Ron, Bucakci, Akin, Greder, Lucas, de Ornellas, Sara, Jeziorska, Danuta, Telenius, Jelena, Hughes, Jim R., de Bruijn, Marella F. T. R.

“…The transcription factor RUNX1 is a critical regulator of developmental hematopoiesis and is frequently disrupted in leukemia. Runx1 is a large, complex gene…”
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Impaired DNA demethylation of C/EBP sites causes premature aging by Schäfer, Andrea, Mekker, Bernadette, Mallick, Medhavi, Vastolo, Viviana, Karaulanov, Emil, Sebastian, Dominik, von der Lippen, Carina, Epe, Bernd, Downes, Damien J, Scholz, Carola, Niehrs, Christof

“…Changes in DNA methylation are among the best-documented epigenetic alterations accompanying organismal aging. However, whether and how altered DNA methylation…”
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Editing an α-globin enhancer in primary human hematopoietic stem cells as a treatment for β-thalassemia by Mettananda, Sachith, Fisher, Chris A., Hay, Deborah, Badat, Mohsin, Quek, Lynn, Clark, Kevin, Hublitz, Philip, Downes, Damien, Kerry, Jon, Gosden, Matthew, Telenius, Jelena, Sloane-Stanley, Jackie A., Faustino, Paula, Coelho, Andreia, Doondeea, Jessica, Usukhbayar, Batchimeg, Sopp, Paul, Sharpe, Jacqueline A., Hughes, Jim R., Vyas, Paresh, Gibbons, Richard J., Higgs, Douglas R.

“…β-Thalassemia is one of the most common inherited anemias, with no effective cure for most patients. The pathophysiology reflects an imbalance between α- and…”
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Reactivation of a developmentally silenced embryonic globin gene by King, Andrew J., Songdej, Duantida, Downes, Damien J., Beagrie, Robert A., Liu, Siyu, Buckley, Megan, Hua, Peng, Suciu, Maria C., Marieke Oudelaar, A., Hanssen, Lars L. P., Jeziorska, Danuta, Roberts, Nigel, Carpenter, Stephanie J., Francis, Helena, Telenius, Jelena, Olijnik, Aude-Anais, Sharpe, Jacqueline A., Sloane-Stanley, Jacqueline, Eglinton, Jennifer, Kassouf, Mira T., Orkin, Stuart H., Pennacchio, Len A., Davies, James O. J., Hughes, Jim R., Higgs, Douglas R., Babbs, Christian

“…The α- and β-globin loci harbor developmentally expressed genes, which are silenced throughout post-natal life. Reactivation of these genes may offer…”
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