Nuclear Organization

An important goal of the Lakadamyali lab is to reconcile the epigenomic and microscopic views of chromatin organization and determine how chromatin structure regulates gene function. Nuclear organization of the chromatin fiber spans many length-scales and while the nanoscale level organization plays a key role in regulating gene expression, this organization is impossible to visualize using conventional microscopy methods. Lakadamyali lab has been using and further developing quantitative super-resolution microscopy methods to overcome this limitation. We visualized and estimated the number of nucleosomes along the chromatin fiber of different cells at nanoscale resolution. We discovered that nucleosomes are assembled in heterogeneous groups of varying sizes, which we termed “clutches”. Remarkably, the median number of nucleosomes and their packing density inside clutches highly correlated with cellular state, such that clutch size correlates with gene expression and pluripotency grade of iPSCs. This work forms the basis for the current proposal. We are using these studies as a benchmark to gain mechanistic insights into the dynamic nanoscale remodeling of chromatin fiber during the cellular processes of differentiation and reprogramming. 

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Relevant Literature:

Super-resolution microscopy reveals how histone tail acetylation affects DNA compaction within nucleosomes in vivo”, J. Otterstrom, A.C. Garcia, C. Vicario, P.A. Gomez-Garcia, M.P. Cosma, M. Lakadamyali, Nucleic Acids Research,  doi: 10.1093/nar/gkz593 (2019)

“(Po)STAC (Polycistronic SunTAg modified CRISPR) enables live-cell and fixed cell super-resolution imaging of multiple genes”, M. Victoria Neguembor, R, Sebastian-Perez , F, Aulicinio , P. Gomez-Garcia , M. Pia Cosma, M. Lakadamyali, Nucleic Acids Research, doi: 10.1093/nar/gkx1271, (2017)

“Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation”, K.R., Kieffer-Kwon, K. Nimura, S.S.P. Rao, J. Xu, S, Jung, A. Pekowska, M. Dose, E. Stevens, E. Mathe, P. Dong, S.C. Huang, M.A. Ricci, L. Baranello, Y. Zheng, F.T. Ardori, W. Resch, D. Stavreva, S. Nelson, M. McAndrew, A. Casellas, E. Finn, C. Gregory, B.G. St. Hilaire, S.M. Johnson, W. Dubois, M.P. Cosma, E. Batchelor, D. Levens, R.D. Phair, T. Misteli, L. Tessarollo, G. Hager, M. Lakadamyali, Z. Liu, M. Floer, H. Shroff, E.L. Aiden, R. Casellas, Molecular Cell, doi: 10.1016/j.molcel.2017.07.013 (2017).

“Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo”, M. A. Ricci, C. Manzo, M. Garcia-Parajo, M. Lakadamyali†, M. P. Cosma†, (†co-senior authors), Cell, 160, 1145-1158 (2015)