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Items: 1 to 20 of 32

1.

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states.

Fabre PJ, Benke A, Joye E, Nguyen Huynh TH, Manley S, Duboule D.

Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):13964-9. doi: 10.1073/pnas.1517972112. Epub 2015 Oct 26.

2.

Analysis methods for studying the 3D architecture of the genome.

Ay F, Noble WS.

Genome Biol. 2015 Sep 2;16:183. doi: 10.1186/s13059-015-0745-7.

3.

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C.

Ay F, Vu TH, Zeitz MJ, Varoquaux N, Carette JE, Vert JP, Hoffman AR, Noble WS.

BMC Genomics. 2015 Feb 25;16:121. doi: 10.1186/s12864-015-1236-7.

4.

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization.

Williamson I, Berlivet S, Eskeland R, Boyle S, Illingworth RS, Paquette D, Dostie J, Bickmore WA.

Genes Dev. 2014 Dec 15;28(24):2778-91. doi: 10.1101/gad.251694.114.

5.
6.

A variably occupied CTCF binding site in the ultrabithorax gene in the Drosophila bithorax complex.

Magbanua JP, Runneburger E, Russell S, White R.

Mol Cell Biol. 2015 Jan;35(1):318-30. doi: 10.1128/MCB.01061-14. Epub 2014 Nov 3.

7.

CTCF controls HOXA cluster silencing and mediates PRC2-repressive higher-order chromatin structure in NT2/D1 cells.

Xu M, Zhao GN, Lv X, Liu G, Wang LY, Hao DL, Wang J, Liu DP, Liang CC.

Mol Cell Biol. 2014 Oct;34(20):3867-79. doi: 10.1128/MCB.00567-14. Epub 2014 Aug 18.

8.

Classifying leukemia types with chromatin conformation data.

Rousseau M, Ferraiuolo MA, Crutchley JL, Wang XQ, Miura H, Blanchette M, Dostie J.

Genome Biol. 2014 Apr 30;15(4):R60. doi: 10.1186/gb-2014-15-4-r60.

9.

Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci.

Noordermeer D, Leleu M, Schorderet P, Joye E, Chabaud F, Duboule D.

Elife. 2014 Apr 29;3:e02557. doi: 10.7554/eLife.02557.

10.

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts.

Ay F, Bailey TL, Noble WS.

Genome Res. 2014 Jun;24(6):999-1011. doi: 10.1101/gr.160374.113. Epub 2014 Feb 5.

11.

Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs.

Berlivet S, Paquette D, Dumouchel A, Langlais D, Dostie J, Kmita M.

PLoS Genet. 2013;9(12):e1004018. doi: 10.1371/journal.pgen.1004018. Epub 2013 Dec 26.

12.

Hox in motion: tracking HoxA cluster conformation during differentiation.

Rousseau M, Crutchley JL, Miura H, Suderman M, Blanchette M, Dostie J.

Nucleic Acids Res. 2014 Feb;42(3):1524-40. doi: 10.1093/nar/gkt998. Epub 2013 Oct 29.

13.

Conserved chromosome 2q31 conformations are associated with transcriptional regulation of GAD1 GABA synthesis enzyme and altered in prefrontal cortex of subjects with schizophrenia.

Bharadwaj R, Jiang Y, Mao W, Jakovcevski M, Dincer A, Krueger W, Garbett K, Whittle C, Tushir JS, Liu J, Sequeira A, Vawter MP, Gardner PD, Casaccia P, Rasmussen T, Bunney WE Jr, Mirnics K, Futai K, Akbarian S.

J Neurosci. 2013 Jul 17;33(29):11839-51. doi: 10.1523/JNEUROSCI.1252-13.2013.

14.

Chromatin insulators: linking genome organization to cellular function.

Phillips-Cremins JE, Corces VG.

Mol Cell. 2013 May 23;50(4):461-74. doi: 10.1016/j.molcel.2013.04.018. Review.

15.

Chromatin organization and global regulation of Hox gene clusters.

Montavon T, Duboule D.

Philos Trans R Soc Lond B Biol Sci. 2013 May 6;368(1620):20120367. doi: 10.1098/rstb.2012.0367. Print 2013. Review.

16.

Vertebrate GAGA factor associated insulator elements demarcate homeotic genes in the HOX clusters.

Srivastava S, Puri D, Garapati HS, Dhawan J, Mishra RK.

Epigenetics Chromatin. 2013 Apr 22;6(1):8. doi: 10.1186/1756-8935-6-8.

17.

The properties of genome conformation and spatial gene interaction and regulation networks of normal and malignant human cell types.

Wang Z, Cao R, Taylor K, Briley A, Caldwell C, Cheng J.

PLoS One. 2013;8(3):e58793. doi: 10.1371/journal.pone.0058793. Epub 2013 Mar 11.

18.

Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia.

Wang E, Kawaoka S, Yu M, Shi J, Ni T, Yang W, Zhu J, Roeder RG, Vakoc CR.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3901-6. doi: 10.1073/pnas.1301045110. Epub 2013 Feb 14.

19.

Upstream distal regulatory elements contact the Lmo2 promoter in mouse erythroid cells.

Bhattacharya A, Chen CY, Ho S, Mitchell JA.

PLoS One. 2012;7(12):e52880. doi: 10.1371/journal.pone.0052880. Epub 2012 Dec 21.

20.

From cells to chromatin: capturing snapshots of genome organization with 5C technology.

Ferraiuolo MA, Sanyal A, Naumova N, Dekker J, Dostie J.

Methods. 2012 Nov;58(3):255-67. doi: 10.1016/j.ymeth.2012.10.011. Epub 2012 Nov 5.

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