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 of Spatial / Architectural Epigenetics Interest Group

Gerd Blobel, M.D., Ph.D. Frank E. Weise III Professor of Pediatrics; Co-Director of Epigenetics Institute

Interest Group Members

Ben E. Black, Ph.D. Professor of Biochemistry and Biophysics
Maya Capelson, Ph.D. Assistant Professor of Cell and Developmental Biology
Robert Babak Faryabi, Ph.D. Assistant Professor of Pathology and Laboratory Medicine
Matthew C. Good, Ph.D. Assistant Professo of Cell and Developmental Biology
Eric F. Joyce, Ph.D. Assistant Professor of Genetics
Rahul Kohli, M.D., Ph.D. Associate Professor of Medicine and Biochemistry & Biophysics
Paul M. Lieberman, Ph.D. Hillary Koprowski, M.D., Endowed Professor; Professor and Program Leader, Gene Expression and Regulation Program
Stephen A. Liebhaber, M.D. Professor of Genetics
Ronen Marmorstein, Ph.D. George W. Raiziss Professor and Vice-Chair, Professor, Department of Biochemistry and Biophysics Investigator, Abramson Family Cancer Research Institute
Warren S. Pear, M.D., Ph.D. Gaylord P. and Mary Louise Harnwell Professor
Jennifer E. Phillips-Cremins, Ph.D. Associate Professor of Bioengineering
Arjun Raj, Ph.D. Assistant Professor Bioengineering
Kai Tan, Ph.D. Professor of Pediatrics
Matthew Weitzman, Ph.D. Professor in Pathology and Laboratory Medicine


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.

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.

Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancers-Promoter Contacts. Pascual-Garcia P, Debo B, Aleman JR, Talamas JA, Lan Y, Nguyen NH, Won KJ, Capelson M. “Molecular cell”> Mol Cell. 2017 Apr 6;66(1):63-76.e6. doi: 10.1016/j.molcel.2017.02020. Epub 2017 Mar 30

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

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.

Visualizing allele-specific expression in single cells reveal epigenetic mosaicism in an H19 loss-of-imprinting mutant. Ginart P, Kalish JM, Jiang CL, Yu AC, Bartolomei MS, Raj A. Genes Dev. 2016 Mar 1;30(5):567-78. doi: 10.1101/gad.275958.115.