Gene Regulation and Development Section
Section Chief: Ann Dean, Ph.D.

Publications

A selection of recent and significant publications can be viewed below.

Select Publications

Fetal γ-globin genes are regulated by the BGLT3 long noncoding RNA locus.
Ivaldi MS, Diaz LF, Chakalova L, Lee J, Krivega I, Dean A.
Blood (2018 Nov 1) 132:1963-1973. Abstract/Full Text
The LDB1 Complex Co-opts CTCF for Erythroid Lineage-Specific Long-Range Enhancer Interactions.
Lee J, Krivega I, Dale RK, Dean A.
Cell Rep (2017 Jun 20) 19:2490-2502. Abstract/Full Text
LDB1-mediated enhancer looping can be established independent of mediator and cohesin.
Krivega I, Dean A.
Nucleic Acids Res (2017 Aug 21) 45:8255-8268. Abstract/Full Text
Chromatin looping as a target for altering erythroid gene expression.
Krivega I, Dean A.
Ann N Y Acad Sci (2016 Mar) 1368:31-9. Abstract/Full Text
Role of LDB1 in the transition from chromatin looping to transcription activation.
Krivega I, Dale RK, Dean A.
Genes Dev (2014 Jun 15) 28:1278-90. Abstract/Full Text

Additional Publications

Chromatin Immunoprecipitation (ChIP) with Erythroid Samples.
Krivega I, Dean A.
Methods Mol Biol (2018) 1698:229-236. Abstract/Full Text
Chromosome Conformation Capture (3C and Higher) with Erythroid Samples.
Krivega I, Dean A.
Methods Mol Biol (2018) 1698:237-243. Abstract/Full Text
A tetrad of chromatin interactions for chromosome pairing in X inactivation.
Krivega I, Dean A.
Nat Struct Mol Biol (2017 Aug 3) 24:607-608. Abstract/Full Text
CTCF fences make good neighbours.
Krivega I, Dean A.
Nat Cell Biol (2017 Jul 28) 19:883-885. Abstract/Full Text
Inhibition of G9a methyltransferase stimulates fetal hemoglobin production by facilitating LCR/γ-globin looping.
Krivega I, Byrnes C, de Vasconcellos JF, Lee YT, Kaushal M, Dean A, Miller JL.
Blood (2015 Jul 30) 126:665-72. Abstract/Full Text
Chromosome togetherness at the onset of ESC differentiation.
Krivega I, Dean A.
Cell Stem Cell (2015 Mar 5) 16:213-4. Abstract/Full Text
Reactivation of developmentally silenced globin genes by forced chromatin looping.
Deng W, Rupon JW, Krivega I, Breda L, Motta I, Jahn KS, Reik A, Gregory PD, Rivella S, Dean A, Blobel GA.
Cell (2014 Aug 14) 158:849-860. Abstract/Full Text
Enhancer function: mechanistic and genome-wide insights come together.
Plank JL, Dean A.
Mol Cell (2014 Jul 3) 55:5-14. Abstract/Full Text
The hematopoietic regulator TAL1 is required for chromatin looping between the β-globin LCR and human γ-globin genes to activate transcription.
Yun WJ, Kim YW, Kang Y, Lee J, Dean A, Kim A.
Nucleic Acids Res (2014 Apr) 42:4283-93. Abstract/Full Text
Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation.
Li L, Freudenberg J, Cui K, Dale R, Song SH, Dean A, Zhao K, Jothi R, Love PE.
Blood (2013 May 30) 121:4575-85. Abstract/Full Text
Enhancers: five essential questions.
Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G.
Nat Rev Genet (2013 Apr) 14:288-95. Abstract/Full Text
CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus.
Junier I, Dale RK, Hou C, Képès F, Dean A.
Nucleic Acids Res (2012 Sep) 40:7718-27. Abstract/Full Text
Ldb1 regulates carbonic anhydrase 1 during erythroid differentiation.
Song SH, Kim A, Dale R, Dean A.
Biochim Biophys Acta (2012 Aug) 1819:885-91. Abstract/Full Text
Chromatin loop formation in the β-globin locus and its role in globin gene transcription.
Kim A, Dean A.
Mol Cells (2012 Jul) 34:1-5. Abstract/Full Text
Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor.
Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, Dean A, Blobel GA.
Cell (2012 Jun 8) 149:1233-44. Abstract/Full Text
The hypersensitive sites of the murine β-globin locus control region act independently to affect nuclear localization and transcriptional elongation.
Bender MA, Ragoczy T, Lee J, Byron R, Telling A, Dean A, Groudine M.
Blood (2012 Apr 19) 119:3820-7. Abstract/Full Text
Enhancer and promoter interactions-long distance calls.
Krivega I, Dean A.
Curr Opin Genet Dev (2012 Apr) 22:79-85. Abstract/Full Text
Monitoring the effects of chromatin remodelers on long-range interactions in vivo.
Kiefer CM, Dean A.
Methods Mol Biol (2012) 833:29-45. Abstract/Full Text
Distinct Ldb1/NLI complexes orchestrate γ-globin repression and reactivation through ETO2 in human adult erythroid cells.
Kiefer CM, Lee J, Hou C, Dale RK, Lee YT, Meier ER, Miller JL, Dean A.
Blood (2011 Dec 1) 118:6200-8. Abstract/Full Text
Insulators organize chromatin: emerging rules of the game.
Krivega M, Dean A.
Mol Cell (2011 Oct 7) 44:1-2. Abstract/Full Text
Identification of genetic elements that autonomously determine DNA methylation states.
Lienert F, Wirbelauer C, Som I, Dean A, Mohn F, Schübeler D.
Nat Genet (2011 Oct 2) 43:1091-7. Abstract/Full Text
In the loop: long range chromatin interactions and gene regulation.
Dean A.
Brief Funct Genomics (2011 Jan) 10:3-10. Abstract/Full Text
A requirement for Lim domain binding protein 1 in erythropoiesis.
Li L, Lee JY, Gross J, Song SH, Dean A, Love PE.
J Exp Med (2010 Nov 22) 207:2543-50. Abstract/Full Text
Multiple functions of Ldb1 required for beta-globin activation during erythroid differentiation.
Song SH, Kim A, Ragoczy T, Bender MA, Groudine M, Dean A.
Blood (2010 Sep 30) 116:2356-64. Abstract/Full Text
Cell type specificity of chromatin organization mediated by CTCF and cohesin.
Hou C, Dale R, Dean A.
Proc Natl Acad Sci U S A (2010 Feb 23) 107:3651-6. Abstract/Full Text
Cytokine-mediated increases in fetal hemoglobin are associated with globin gene histone modification and transcription factor reprogramming.
Sripichai O, Kiefer CM, Bhanu NV, Tanno T, Noh SJ, Goh SH, Russell JE, Rognerud CL, Ou CN, Oneal PA, Meier ER, Gantt NM, Byrnes C, Lee YT, Dean A, Miller JL.
Blood (2009 Sep 10) 114:2299-306. Abstract/Full Text
Short-chain fatty acid-mediated effects on erythropoiesis in primary definitive erythroid cells.
Bhatia H, Hallock JL, Dutta A, Karkashon S, Sterner LS, Miyazaki T, Dean A, Little JA.
Blood (2009 Jun 18) 113:6440-8. Abstract/Full Text
BRG1 requirement for long-range interaction of a locus control region with a downstream promoter.
Kim SI, Bultman SJ, Kiefer CM, Dean A, Bresnick EH.
Proc Natl Acad Sci U S A (2009 Feb 17) 106:2259-64. Abstract/Full Text
CTCF-dependent enhancer-blocking by alternative chromatin loop formation.
Hou C, Zhao H, Tanimoto K, Dean A.
Proc Natl Acad Sci U S A (2008 Dec 23) 105:20398-403. Abstract/Full Text
Epigenetics of beta-globin gene regulation.
Kiefer CM, Hou C, Little JA, Dean A.
Mutat Res (2008 Dec 1) 647:68-76. Abstract/Full Text
The role of transcriptional activator GATA-1 at human beta-globin HS2.
Cho Y, Song SH, Lee JJ, Choi N, Kim CG, Dean A, Kim A.
Nucleic Acids Res (2008 Aug) 36:4521-8. Abstract/Full Text
A positive role for NLI/Ldb1 in long-range beta-globin locus control region function.
Song SH, Hou C, Dean A.
Mol Cell (2007 Dec 14) 28:810-22. Abstract/Full Text
Beta-globin intergenic transcription and histone acetylation dependent on an enhancer.
Kim A, Zhao H, Ifrim I, Dean A.
Mol Cell Biol (2007 Apr) 27:2980-6. Abstract/Full Text
Distinctive signatures of histone methylation in transcribed coding and noncoding human beta-globin sequences.
Kim A, Kiefer CM, Dean A.
Mol Cell Biol (2007 Feb) 27:1271-9. Abstract/Full Text
Nucleosome and transcription activator antagonism at human beta-globin locus control region DNase I hypersensitive sites.
Kim A, Song SH, Brand M, Dean A.
Nucleic Acids Res (2007) 35:5831-8. Abstract/Full Text
Enhancer blocking by chicken beta-globin 5'-HS4: role of enhancer strength and insulator nucleosome depletion.
Zhao H, Kim A, Song SH, Dean A.
J Biol Chem (2006 Oct 13) 281:30573-80. Abstract/Full Text
On a chromosome far, far away: LCRs and gene expression.
Dean A.
Trends Genet (2006 Jan) 22:38-45. Abstract/Full Text
Organizing the genome: enhancers and insulators.
Zhao H, Dean A.
Biochem Cell Biol (2005 Aug) 83:516-24. Abstract/Full Text
An insulator blocks spreading of histone acetylation and interferes with RNA polymerase II transfer between an enhancer and gene.
Zhao H, Dean A.
Nucleic Acids Res (2004) 32:4903-19. Abstract/Full Text
Developmental stage differences in chromatin subdomains of the beta-globin locus.
Kim A, Dean A.
Proc Natl Acad Sci U S A (2004 May 4) 101:7028-33. Abstract/Full Text
Chromatin remodelling and the interaction between enhancers and promoters in the beta-globin locus.
Dean A.
Brief Funct Genomic Proteomic (2004 Feb) 2:344-54. Abstract/Full Text
A human globin enhancer causes both discrete and widespread alterations in chromatin structure.
Kim A, Dean A.
Mol Cell Biol (2003 Nov) 23:8099-109. Abstract/Full Text
A major role for the TATA box in recruitment of chromatin modifying complexes to a globin gene promoter.
Gui CY, Dean A.
Proc Natl Acad Sci U S A (2003 Jun 10) 100:7009-14. Abstract/Full Text
Beta-globin locus control region HS2 and HS3 interact structurally and functionally.
Jackson DA, McDowell JC, Dean A.
Nucleic Acids Res (2003 Feb 15) 31:1180-90. Abstract/Full Text
Acetylation of a specific promoter nucleosome accompanies activation of the epsilon-globin gene by beta-globin locus control region HS2.
Gui CY, Dean A.
Mol Cell Biol (2001 Feb) 21:1155-63. Abstract/Full Text