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CRISPR-Based Interrogation of 4-Dimensional Genome Dynamics

Led by  Hanhui Ma in our lab, this project applies his innovative CRISPR-based fluorescent labeling of discrete genomic loci in human cells, to investigate interphase chromosome dynamics with reference to progression through the cell cycle (Ma et al., J. Cell Biol. 18:1467-1477, 2019).  In a new project, we have collaborated with Hanhui, (now directing his own group at ShanghaiTech University) to deploy a CRISPR-based, genome site-specific strategy to investigate the process of heterochromatin formation (bioRxiv…).  We are also collaborating with Paul Kaufman (MCCB) on novel microRNAs in the nucleoli of murine embryonic stems cells, James Cleaver (UCSF) on the DNA repair protein UVSSA, and Sui Huang (Northwestern) on an apparent homeostatic network among the nucleous, PML bodies and Cajal bodies.

Novel Roles of the Nucleolus


Our laboratory was the first to discover a role for the nucleolus beyond the synthesis of ribosomes, viz. assembly of the signal recognition particle. More recently we discovered the presence of both specific microRNAs and messenger RNAs in the nucleoli of myogenic cells, with strong base-pairing potential between the two classes (as shown at the left). From these results we have erected the exciting (but daring) hypothesis that the nucleolus can serve as a staging center for the assembly of certain microRNA:messenger RNA complexes, which are then exported to the cytoplasm in either a pre-suppressed, or conceivably pre-activated, translational state. This hypothesis forms the basis of the second major focus of our lab.

Meet the Lab



Genome architecture and expression, 2019-2020: the transition phase. 
Pederson, T. 
Curr. Opin. Genetics & Dev., 2020, in press.

The 50th anniversary of reverse transcriptase-and its ironic legacy in the time of coronavirus.
Pederson T.
FASEB J. 2020 Jun;34(6):7219-7221. doi: 10.1096/fj.202001010. 

Meeting report - Nuclear and cytoplasmic molecular machines at work.
Bullock SL, Visa N, Pederson T.
J Cell Sci. 2020 Apr 6;133(7):jcs245134. doi: 10.1242/jcs.245134. 

STRIDE-a fluorescence method for direct, specific in situ detection of individual single- or double-strand DNA breaks in fixed cells.
Kordon MM, Zarębski M, Solarczyk K, Ma H, Pederson T, Dobrucki JW.
Nucleic Acids Res. 2020 Feb 20;48(3):e14. doi: 10.1093/nar/gkz1118. 

Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region. 
Ma, H, Tu, L.C., Chung, Y.C., Naseri, A., Grunwald, D., Zhang, A. and Pederson, T. 
J. Cell Biol. 18:1467-1477, 2019

All Publications


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Contact Us

Lazare Research Building 821
Campus Map (pdf)

508-856-8667 (office)


Mailing Address:
University of Massachusetts Medical School
Attn: Dr. Thoru Pederson - BMP Department
364 Plantation St LRB-821
Worcester, MA 01605

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Undergraduates interested in pursuing a PhD at UMass Medical School should apply directly to the Graduate School of Biomedical Sciences Program.