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Robust CRISPR/Cas9 Genome Editing of the HUDEP-2 Erythroid Precursor Line Using Plasmids and Single-Stranded Oligonucleotide Donors.

Moir-Meyer G, Cheong PL, Olijnik AA, Brown J, Knight S, King A, Kurita R, Nakamura Y, Gibbons RJ, Higgs DR, Buckle VJ, Babbs C.

Methods Protoc. 2018 Jul 30;1(3). pii: E28. doi: 10.3390/mps1030028.


The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist.

van Bemmel JG, Galupa R, Gard C, Servant N, Picard C, Davies J, Szempruch AJ, Zhan Y, Żylicz JJ, Nora EP, Lameiras S, de Wit E, Gentien D, Baulande S, Giorgetti L, Guttman M, Hughes JR, Higgs DR, Gribnau J, Heard E.

Nat Genet. 2019 Jun;51(6):1024-1034. doi: 10.1038/s41588-019-0412-0. Epub 2019 May 27.


Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate.

Palii CG, Cheng Q, Gillespie MA, Shannon P, Mazurczyk M, Napolitani G, Price ND, Ranish JA, Morrissey E, Higgs DR, Brand M.

Cell Stem Cell. 2019 May 2;24(5):812-820.e5. doi: 10.1016/j.stem.2019.02.006. Epub 2019 Mar 14.


Potential new approaches to the management of the Hb Bart's hydrops fetalis syndrome: the most severe form of α-thalassemia.

King AJ, Higgs DR.

Hematology Am Soc Hematol Educ Program. 2018 Nov 30;2018(1):353-360. doi: 10.1182/asheducation-2018.1.353. Review.


Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains.

Oudelaar AM, Davies JOJ, Hanssen LLP, Telenius JM, Schwessinger R, Liu Y, Brown JM, Downes DJ, Chiariello AM, Bianco S, Nicodemi M, Buckle VJ, Dekker J, Higgs DR, Hughes JR.

Nat Genet. 2018 Dec;50(12):1744-1751. doi: 10.1038/s41588-018-0253-2. Epub 2018 Oct 29.


A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions.

Brown JM, Roberts NA, Graham B, Waithe D, Lagerholm C, Telenius JM, De Ornellas S, Oudelaar AM, Scott C, Szczerbal I, Babbs C, Kassouf MT, Hughes JR, Higgs DR, Buckle VJ.

Nat Commun. 2018 Sep 21;9(1):3849. doi: 10.1038/s41467-018-06248-4.


How to Tackle Challenging ChIP-Seq, with Long-Range Cross-Linking, Using ATRX as an Example.

Truch J, Telenius J, Higgs DR, Gibbons RJ.

Methods Mol Biol. 2018;1832:105-130. doi: 10.1007/978-1-4939-8663-7_6.


Molecular Basis and Genetic Modifiers of Thalassemia.

Mettananda S, Higgs DR.

Hematol Oncol Clin North Am. 2018 Apr;32(2):177-191. doi: 10.1016/j.hoc.2017.11.003. Review.


Phenotypic and molecular characterization of a serum-free miniature erythroid differentiation system suitable for high-throughput screening and single-cell assays.

Mettananda S, Clark K, Fisher CA, Sloane-Stanley JA, Gibbons RJ, Higgs DR.

Exp Hematol. 2018 Apr;60:10-20. doi: 10.1016/j.exphem.2018.01.001. Epub 2018 Jan 9.


Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C.

Oudelaar AM, Davies JOJ, Downes DJ, Higgs DR, Hughes JR.

Nucleic Acids Res. 2017 Dec 15;45(22):e184. doi: 10.1093/nar/gkx1194.


Between form and function: the complexity of genome folding.

Oudelaar AM, Hanssen LLP, Hardison RC, Kassouf MT, Hughes JR, Higgs DR.

Hum Mol Genet. 2017 Oct 1;26(R2):R208-R215. doi: 10.1093/hmg/ddx306. Review.


Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints.

Schwessinger R, Suciu MC, McGowan SJ, Telenius J, Taylor S, Higgs DR, Hughes JR.

Genome Res. 2017 Oct;27(10):1730-1742. doi: 10.1101/gr.220202.117. Epub 2017 Sep 13.


Editing an α-globin enhancer in primary human hematopoietic stem cells as a treatment for β-thalassemia.

Mettananda S, Fisher CA, Hay D, Badat M, Quek L, Clark K, Hublitz P, Downes D, Kerry J, Gosden M, Telenius J, Sloane-Stanley JA, Faustino P, Coelho A, Doondeea J, Usukhbayar B, Sopp P, Sharpe JA, Hughes JR, Vyas P, Gibbons RJ, Higgs DR.

Nat Commun. 2017 Sep 4;8(1):424. doi: 10.1038/s41467-017-00479-7.


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

Jeziorska DM, Murray RJS, De Gobbi M, Gaentzsch R, Garrick D, Ayyub H, Chen T, Li E, Telenius J, Lynch M, Graham B, Smith AJH, Lund JN, Hughes JR, Higgs DR, Tufarelli C.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):E7526-E7535. doi: 10.1073/pnas.1703087114. Epub 2017 Aug 21.


Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo.

Hanssen LLP, Kassouf MT, Oudelaar AM, Biggs D, Preece C, Downes DJ, Gosden M, Sharpe JA, Sloane-Stanley JA, Hughes JR, Davies B, Higgs DR.

Nat Cell Biol. 2017 Aug;19(8):952-961. doi: 10.1038/ncb3573. Epub 2017 Jul 24.


The chromatin remodelling factor ATRX suppresses R-loops in transcribed telomeric repeats.

Nguyen DT, Voon HPJ, Xella B, Scott C, Clynes D, Babbs C, Ayyub H, Kerry J, Sharpe JA, Sloane-Stanley JA, Butler S, Fisher CA, Gray NE, Jenuwein T, Higgs DR, Gibbons RJ.

EMBO Rep. 2017 Jun;18(6):914-928. doi: 10.15252/embr.201643078. Epub 2017 May 9.


Functional characterisation of cis-regulatory elements governing dynamic Eomes expression in the early mouse embryo.

Simon CS, Downes DJ, Gosden ME, Telenius J, Higgs DR, Hughes JR, Costello I, Bikoff EK, Robertson EJ.

Development. 2017 Apr 1;144(7):1249-1260. doi: 10.1242/dev.147322. Epub 2017 Feb 7.


How best to identify chromosomal interactions: a comparison of approaches.

Davies JO, Oudelaar AM, Higgs DR, Hughes JR.

Nat Methods. 2017 Jan 31;14(2):125-134. doi: 10.1038/nmeth.4146. Review.


An international registry of survivors with Hb Bart's hydrops fetalis syndrome.

Songdej D, Babbs C, Higgs DR; BHFS International Consortium.

Blood. 2017 Mar 9;129(10):1251-1259. doi: 10.1182/blood-2016-08-697110. Epub 2017 Jan 5. Review.


Selective silencing of α-globin by the histone demethylase inhibitor IOX1: a potentially new pathway for treatment of β-thalassemia.

Mettananda S, Fisher CA, Sloane-Stanley JA, Taylor S, Oppermann U, Gibbons RJ, Higgs DR.

Haematologica. 2017 Mar;102(3):e80-e84. doi: 10.3324/haematol.2016.155655. Epub 2016 Nov 3. No abstract available.


Beta thalassaemia intermedia due to co-inheritance of three unique alpha globin cluster duplications characterised by next generation sequencing analysis.

Clark B, Shooter C, Smith F, Brawand D, Steedman L, Oakley M, Rushton P, Rooks H, Wang X, Drousiotou A, Kyrri A, Hadjigavriel M, Will A, Fisher C, Higgs DR, Phylipsen M, Harteveld C, Kleanthous M, Thein SL.

Br J Haematol. 2018 Jan;180(1):160-164. doi: 10.1111/bjh.14294. Epub 2016 Jul 29. No abstract available.


Genetic dissection of the α-globin super-enhancer in vivo.

Hay D, Hughes JR, Babbs C, Davies JOJ, Graham BJ, Hanssen L, Kassouf MT, Marieke Oudelaar AM, Sharpe JA, Suciu MC, Telenius J, Williams R, Rode C, Li PS, Pennacchio LA, Sloane-Stanley JA, Ayyub H, Butler S, Sauka-Spengler T, Gibbons RJ, Smith AJH, Wood WG, Higgs DR.

Nat Genet. 2016 Aug;48(8):895-903. doi: 10.1038/ng.3605. Epub 2016 Jul 4.


MicroRNAs of the miR-290-295 Family Maintain Bivalency in Mouse Embryonic Stem Cells.

Graham B, Marcais A, Dharmalingam G, Carroll T, Kanellopoulou C, Graumann J, Nesterova TB, Bermange A, Brazauskas P, Xella B, Kriaucionis S, Higgs DR, Brockdorff N, Mann M, Fisher AG, Merkenschlager M.

Stem Cell Reports. 2016 May 10;6(5):635-642. doi: 10.1016/j.stemcr.2016.03.005. Epub 2016 Apr 14.


Krüppeling erythropoiesis: an unexpected broad spectrum of human red blood cell disorders due to KLF1 variants.

Perkins A, Xu X, Higgs DR, Patrinos GP, Arnaud L, Bieker JJ, Philipsen S; KLF1 Consensus Workgroup.

Blood. 2016 Apr 14;127(15):1856-62. doi: 10.1182/blood-2016-01-694331. Epub 2016 Feb 22. Review.


Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin.

Masuda T, Wang X, Maeda M, Canver MC, Sher F, Funnell AP, Fisher C, Suciu M, Martyn GE, Norton LJ, Zhu C, Kurita R, Nakamura Y, Xu J, Higgs DR, Crossley M, Bauer DE, Orkin SH, Kharchenko PV, Maeda T.

Science. 2016 Jan 15;351(6270):285-9. doi: 10.1126/science.aad3312.


Understanding α-globin gene regulation and implications for the treatment of β-thalassemia.

Mettananda S, Gibbons RJ, Higgs DR.

Ann N Y Acad Sci. 2016 Mar;1368(1):16-24. doi: 10.1111/nyas.12988. Epub 2015 Dec 22. Review.


Studying epigenomics in single cells: what is feasible and what can we learn?

Wills QF, Higgs DR, Mead AJ.

Epigenomics. 2015;7(8):1231-4. doi: 10.2217/epi.15.93. Epub 2015 Dec 8. No abstract available.


Multiplexed analysis of chromosome conformation at vastly improved sensitivity.

Davies JO, Telenius JM, McGowan SJ, Roberts NA, Taylor S, Higgs DR, Hughes JR.

Nat Methods. 2016 Jan;13(1):74-80. doi: 10.1038/nmeth.3664. Epub 2015 Nov 23.


Suppression of the alternative lengthening of telomere pathway by the chromatin remodelling factor ATRX.

Clynes D, Jelinska C, Xella B, Ayyub H, Scott C, Mitson M, Taylor S, Higgs DR, Gibbons RJ.

Nat Commun. 2015 Jul 6;6:7538. doi: 10.1038/ncomms8538.


An international effort to cure a global health problem: A report on the 19th Hemoglobin Switching Conference.

Blobel GA, Bodine D, Brand M, Crispino J, de Bruijn MF, Nathan D, Papayannopoulou T, Porcher C, Strouboulis J, Zon L, Higgs DR, Stamatoyannopoulos G, Engel JD.

Exp Hematol. 2015 Oct;43(10):821-37. doi: 10.1016/j.exphem.2015.06.008. Epub 2015 Jul 2. Review.


α-Globin as a molecular target in the treatment of β-thalassemia.

Mettananda S, Gibbons RJ, Higgs DR.

Blood. 2015 Jun 11;125(24):3694-701. doi: 10.1182/blood-2015-03-633594. Epub 2015 Apr 13. Review.


ATRX Plays a Key Role in Maintaining Silencing at Interstitial Heterochromatic Loci and Imprinted Genes.

Voon HP, Hughes JR, Rode C, De La Rosa-Velázquez IA, Jenuwein T, Feil R, Higgs DR, Gibbons RJ.

Cell Rep. 2015 Apr 21;11(3):405-18. doi: 10.1016/j.celrep.2015.03.036. Epub 2015 Apr 9.


Considerations when investigating lncRNA function in vivo.

Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W, Higgs DR, Miska EA, Ponting CP.

Elife. 2014 Aug 14;3:e03058. doi: 10.7554/eLife.03058. Review.


Differential regulation of the α-globin locus by Krüppel-like Factor 3 in erythroid and non-erythroid cells.

Funnell AP, Vernimmen D, Lim WF, Mak KS, Wienert B, Martyn GE, Artuz CM, Burdach J, Quinlan KG, Higgs DR, Whitelaw E, Pearson RC, Crossley M.

BMC Mol Biol. 2014 May 16;15:8. doi: 10.1186/1471-2199-15-8.


ATRX dysfunction induces replication defects in primary mouse cells.

Clynes D, Jelinska C, Xella B, Ayyub H, Taylor S, Mitson M, Bachrati CZ, Higgs DR, Gibbons RJ.

PLoS One. 2014 Mar 20;9(3):e92915. doi: 10.1371/journal.pone.0092915. eCollection 2014.


Mutations in Kruppel-like factor 1 cause transfusion-dependent hemolytic anemia and persistence of embryonic globin gene expression.

Viprakasit V, Ekwattanakit S, Riolueang S, Chalaow N, Fisher C, Lower K, Kanno H, Tachavanich K, Bejrachandra S, Saipin J, Juntharaniyom M, Sanpakit K, Tanphaichitr VS, Songdej D, Babbs C, Gibbons RJ, Philipsen S, Higgs DR.

Blood. 2014 Mar 6;123(10):1586-95. doi: 10.1182/blood-2013-09-526087. Epub 2014 Jan 17.


Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment.

Hughes JR, Roberts N, McGowan S, Hay D, Giannoulatou E, Lynch M, De Gobbi M, Taylor S, Gibbons R, Higgs DR.

Nat Genet. 2014 Feb;46(2):205-12. doi: 10.1038/ng.2871. Epub 2014 Jan 12.


Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs.

Marques AC, Hughes J, Graham B, Kowalczyk MS, Higgs DR, Ponting CP.

Genome Biol. 2013 Nov 29;14(11):R131. doi: 10.1186/gb-2013-14-11-r131.


The chromatin remodeller ATRX: a repeat offender in human disease.

Clynes D, Higgs DR, Gibbons RJ.

Trends Biochem Sci. 2013 Sep;38(9):461-6. doi: 10.1016/j.tibs.2013.06.011. Epub 2013 Aug 1. Review.


Causes and consequences of chromatin variation between inbred mice.

Hosseini M, Goodstadt L, Hughes JR, Kowalczyk MS, de Gobbi M, Otto GW, Copley RR, Mott R, Higgs DR, Flint J.

PLoS Genet. 2013 Jun;9(6):e1003570. doi: 10.1371/journal.pgen.1003570. Epub 2013 Jun 13.


Homozygous mutations in a predicted endonuclease are a novel cause of congenital dyserythropoietic anemia type I.

Babbs C, Roberts NA, Sanchez-Pulido L, McGowan SJ, Ahmed MR, Brown JM, Sabry MA; WGS500 Consortium, Bentley DR, McVean GA, Donnelly P, Gileadi O, Ponting CP, Higgs DR, Buckle VJ.

Haematologica. 2013 Sep;98(9):1383-7. doi: 10.3324/haematol.2013.089490. Epub 2013 May 28.


High-resolution analysis of cis-acting regulatory networks at the α-globin locus.

Hughes JR, Lower KM, Dunham I, Taylor S, De Gobbi M, Sloane-Stanley JA, McGowan S, Ragoussis J, Vernimmen D, Gibbons RJ, Higgs DR.

Philos Trans R Soc Lond B Biol Sci. 2013 May 6;368(1620):20120361. doi: 10.1098/rstb.2012.0361. Print 2013.


Analysis of sequence variation underlying tissue-specific transcription factor binding and gene expression.

Lower KM, De Gobbi M, Hughes JR, Derry CJ, Ayyub H, Sloane-Stanley JA, Vernimmen D, Garrick D, Gibbons RJ, Higgs DR.

Hum Mutat. 2013 Aug;34(8):1140-8. doi: 10.1002/humu.22343. Epub 2013 Jun 18.


The molecular basis of α-thalassemia.

Higgs DR.

Cold Spring Harb Perspect Med. 2013 Jan 1;3(1):a011718. doi: 10.1101/cshperspect.a011718.


Nprl3 is required for normal development of the cardiovascular system.

Kowalczyk MS, Hughes JR, Babbs C, Sanchez-Pulido L, Szumska D, Sharpe JA, Sloane-Stanley JA, Morriss-Kay GM, Smoot LB, Roberts AE, Watkins H, Bhattacharya S, Gibbons RJ, Ponting CP, Wood WG, Higgs DR.

Mamm Genome. 2012 Aug;23(7-8):404-15. doi: 10.1007/s00335-012-9398-y. Epub 2012 Apr 27.


Molecular biology: RNA discrimination.

Kowalczyk MS, Higgs DR, Gingeras TR.

Nature. 2012 Feb 15;482(7385):310-1. doi: 10.1038/482310a. No abstract available.


Intragenic enhancers act as alternative promoters.

Kowalczyk MS, Hughes JR, Garrick D, Lynch MD, Sharpe JA, Sloane-Stanley JA, McGowan SJ, De Gobbi M, Hosseini M, Vernimmen D, Brown JM, Gray NE, Collavin L, Gibbons RJ, Flint J, Taylor S, Buckle VJ, Milne TA, Wood WG, Higgs DR.

Mol Cell. 2012 Feb 24;45(4):447-58. doi: 10.1016/j.molcel.2011.12.021. Epub 2012 Jan 19.


An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment.

Lynch MD, Smith AJ, De Gobbi M, Flenley M, Hughes JR, Vernimmen D, Ayyub H, Sharpe JA, Sloane-Stanley JA, Sutherland L, Meek S, Burdon T, Gibbons RJ, Garrick D, Higgs DR.

EMBO J. 2012 Jan 18;31(2):317-29. doi: 10.1038/emboj.2011.399. Epub 2011 Nov 4.



Higgs DR, Engel JD, Stamatoyannopoulos G.

Lancet. 2012 Jan 28;379(9813):373-83. doi: 10.1016/S0140-6736(11)60283-3. Epub 2011 Sep 9. Review.


Polycomb eviction as a new distant enhancer function.

Vernimmen D, Lynch MD, De Gobbi M, Garrick D, Sharpe JA, Sloane-Stanley JA, Smith AJ, Higgs DR.

Genes Dev. 2011 Aug 1;25(15):1583-8. doi: 10.1101/gad.16985411.

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