Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells.

Autor: Ioanna Pavlaki, Michael Shapiro, Giuseppina Pisignano, Stephanie M E Jones, Jelena Telenius, Silvia Muñoz-Descalzo, Robert J Williams, Jim R Hughes, Keith W Vance

Publikováno v: PLoS Genetics, Vol 18, Iss 6, p e1010230 (2022)

Central nervous system-expressed long non-coding RNAs (lncRNAs) are often located in the genome close to protein coding genes involved in transcriptional control. Such lncRNA-protein coding gene pairs are frequently temporally and spatially co-expres

Externí odkaz: https://doaj.org/article/267aa164ac8d4000b31b4e3e36f9ad6c

Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases

Autor: Alistair T. Pagnamenta, Carme Camps, Edoardo Giacopuzzi, John M. Taylor, Mona Hashim, Eduardo Calpena, Pamela J. Kaisaki, Akiko Hashimoto, Jing Yu, Edward Sanders, Ron Schwessinger, Jim R. Hughes, Gerton Lunter, Helene Dreau, Matteo Ferla, Lukas Lange, Yesim Kesim, Vassilis Ragoussis, Dimitrios V. Vavoulis, Holger Allroggen, Olaf Ansorge, Christian Babbs, Siddharth Banka, Benito Baños-Piñero, David Beeson, Tal Ben-Ami, David L. Bennett, Celeste Bento, Edward Blair, Charlotte Brasch-Andersen, Katherine R. Bull, Holger Cario, Deirdre Cilliers, Valerio Conti, E. Graham Davies, Fatima Dhalla, Beatriz Diez Dacal, Yin Dong, James E. Dunford, Renzo Guerrini, Adrian L. Harris, Jane Hartley, Georg Hollander, Kassim Javaid, Maureen Kane, Deirdre Kelly, Dominic Kelly, Samantha J. L. Knight, Alexandra Y. Kreins, Erika M. Kvikstad, Craig B. Langman, Tracy Lester, Kate E. Lines, Simon R. Lord, Xin Lu, Sahar Mansour, Adnan Manzur, Reza Maroofian, Brian Marsden, Joanne Mason, Simon J. McGowan, Davide Mei, Hana Mlcochova, Yoshiko Murakami, Andrea H. Németh, Steven Okoli, Elizabeth Ormondroyd, Lilian Bomme Ousager, Jacqueline Palace, Smita Y. Patel, Melissa M. Pentony, Chris Pugh, Aboulfazl Rad, Archana Ramesh, Simone G. Riva, Irene Roberts, Noémi Roy, Outi Salminen, Kyleen D. Schilling, Caroline Scott, Arjune Sen, Conrad Smith, Mark Stevenson, Rajesh V. Thakker, Stephen R. F. Twigg, Holm H. Uhlig, Richard van Wijk, Barbara Vona, Steven Wall, Jing Wang, Hugh Watkins, Jaroslav Zak, Anna H. Schuh, Usha Kini, Andrew O. M. Wilkie, Niko Popitsch, Jenny C. Taylor

Publikováno v: Genome Medicine, Vol 15, Iss 1, Pp 1-25 (2023)

Abstract Background Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly l

Externí odkaz: https://doaj.org/article/c9f00f4d0c70402d8c69f3f7e4981fbc

Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development

Autor: Dominic D. G. Owens, Giorgio Anselmi, A. Marieke Oudelaar, Damien J. Downes, Alessandro Cavallo, Joe R. Harman, Ron Schwessinger, Akin Bucakci, Lucas Greder, Sara de Ornellas, Danuta Jeziorska, Jelena Telenius, Jim R. Hughes, Marella F. T. R. de Bruijn

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-15 (2022)

RUNX1 is a large and complex gene with two alternative promoters and multiple hematopoietic enhancers. Here the authors show that unlike smaller genes Runx1 becomes sub-compartmentalized during differentiation and gene activation. This subcompartment

Externí odkaz: https://doaj.org/article/2c70bda05c964692b2499b46b84229b8

A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker

Autor: Yavor K. Bozhilov, Damien J. Downes, Jelena Telenius, A. Marieke Oudelaar, Emmanuel N. Olivier, Joanne C. Mountford, Jim R. Hughes, Richard J. Gibbons, Douglas R. Higgs

Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-13 (2021)

The role of promoters as potential insulator elements has been largely unexplored in mammals. Here the authors show that a single nucleotide variant in the α-globin locus forms a new promoter and acts as an orientation-dependent enhancer-blocking in

Externí odkaz: https://doaj.org/article/0f0ac4b4b81348c696127f64ad73d2ae

High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale

Autor: Damien J. Downes, Robert A. Beagrie, Matthew E. Gosden, Jelena Telenius, Stephanie J. Carpenter, Lea Nussbaum, Sara De Ornellas, Martin Sergeant, Chris Q. Eijsbouts, Ron Schwessinger, Jon Kerry, Nigel Roberts, Arun Shivalingam, Afaf El-Sagheer, A. Marieke Oudelaar, Tom Brown, Veronica J. Buckle, James O. J. Davies, Jim R. Hughes

Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-15 (2021)

Current 3C methods generate low-resolution interaction profiles across the genome or high-resolution profiles at a limited number of loci. Here the authors present Nuclear-Titrated Capture-C which produces high-resolution genome-wide interaction prof

Externí odkaz: https://doaj.org/article/0197837fb40c491eb660e62c1a29c968