Spatial / Architectural Epigenetics

Members of the Spatial/Architectural Epigenetics Interest Group Section are interested in the following questions: How is the genome is configured at various length scales?  How is chromosomal topology influenced by chromatin modification and nuclear factors? Conversely, how does chromosomal topology impact transcription factor function, gene expression, and other nuclear processes? How are genes positioned within the nucleus with regards to nuclear landmarks, and what is the mutual relationship with gene expression? We use genomic tools, various imaging technologies as well as genome and epi genome editing in diverse cell systems and organisms to address these questions.

Director

Interest Group Members

Publications

From Jennifer Phillips-Cremins Lab

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. Beagan JA, Duong MT, Titus KR, Zhou L, Cao Z, Ma J, Lachanski CV, Gillis DR, Phillips-Cremins JE.  Genome Res. 2017 Jul;27(7):1139-1152.

From Gerd Blobel Lab

The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. Hsu SC, Gilgenast TG, Bartman CR, Edwards CR, Stonestrom AJ, Huang P, Emerson DJ, Evans P, Werner MT, Keller CA, Giardine B, Hardison RC, Raj A, Phillips-Cremis JE, Blobel GA. Mol Cell. 2017 Apr 6;66(1):102-116.e7. doi: 10.1016/j.molcel.2017.02.027.

From Maya Capelson Lab

Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts  Pascual-Garcia P, Debo B, Aleman JR, Talamas JA, Lan Y, Nguyen NH, Won KJ, Capelson M.  Mol Cell. 2017 Apr 6;66(1):63-76.e6. doi: 10.1016/j.molcel.2017.02.020. Epub 2017 Mar 30.
 

From Jennifer Phillips-Cremins Lab

Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. Beagan JA1, Gilgenast TG1, Kim J1, Plona Z1, Norton HK1, Hu G1, Hsu SC2, Shields EJ2, Lyu X3, Apostolou E4, Hochedlinger K4, Corces VG3, Dekker J5, Phillips Cremins JE6. Cell Stem Cell. 2016 May 5; 18(5):611-24. doi: 10.1016/j.stem.2016.04.004

From Ben Black Lab

CENP-C directs a structural transition of CENP-A nucleosomes mainly through sliding of DNA gyres.  Falk SJ, Lee J, Sekulic N, Sennett MA, Lee TH, Black BE.  Nat Struct Mol Biol. 2016 Mar;23(3):204-208. doi: 10.1038/nsmb.3175. Epub 2016 Feb 15.

From Arjun Raj Lab

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss of imprinting mutant. Ginard, P., Kalish, J.M., Jiang, C.L., Yu, A.C., Bartolomei, M.S.* and A. Raj*. (2016). Genes and Development, 30:567-578