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CRISPR-Based Interrogation of 4-Dimensional Genome Dynamics

Led by Hanhui Ma in our lab, this project applied 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 .  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.

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. We are pursuing this now in collaboration with Paul Kaufman's laboratory (MCCB).  In a second nucleous-based project, we are collaborating with Sui Huang (Northwestern) and Susan Baserga (Yale) on an unanticipated intranuclear network that links nucleolar homeostasis with the maintenance of Cajal bodies and other nucleolus-distal regions (see link).

DNA Repair

DNA Single- vs. Double-Strand Break Repair Dynamics Imaged in Live Cells, in collaboration with the laboratory of Jurek Drobrucki, Jagellonian University, Krakow, Poland

Using CRISPR Cas9 machinery that induces either a single- or double-strand break at a specific desired site, detected simultaneous by a fluorescent reporter, we are investigating the dynamics of repair factors at the site- each labeled in additional colors.  We believe we have an unprecedented opportunity to track these critical genome-protective events in a live cell context, to complement elegant biochemistry that has been done.

Role of Transcription-Coupled DNA Repair Proteins in the Puzzling Resistance of Cockayne Syndrome Patients to Skin Cancer, in collaboration with James Cleaver, University of California, San Francisco

Transcription-coupled DNA repair is a process in which specific proteins confer RNA polymerase II with the ability to transcribe over a gapped template DNA strand.  Patients with the condition Cockayne Syndrome are deficient in these proteins and also display a relative resistance to skin cancer.  The Cleaver laboratory has undertaken a systematic investigation of this question and we have provided cell lines in which the transcription-coupled DNA repair protein UVSSA has been edited out by CRISPR.




A layperson encounter, on the "modified" RNA world.
Thoru Pederson
Proc Natl Acad Sci U S A. 2021 Nov 16;118(46):e2110706118.  doi:10.1073/pnas.2110706118.

Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription.
Feng Y, Wang Y, Wang X, He X, Yang C, Naseri A, Pederson T, Zheng J, Zhang S, Xiao X, Xie W, Ma H.
Genome Biol. 2020 21:296. doi:10.1186/s13059-020-02201-1

Genome architecture and expression 2019-2020: the transition phase.
Pederson T.
Curr Opin Genet Dev. 2020: 67:1-4.  doi:10.1016/j/gde.2020.09.003

Arthur B. Pardee, 1921-2109.
Pederson T,  Goldberg AL 
Biographical Memoirs of the National Academy of Sciences. 2020. National Academy of Sciences Press, Washington, DC. 

STRIDE- a fluorescence method for direct, specific in situ detection of individual single- or double-strand DNA breaks in fixed cells.
Kordon MA, Zarebski M, Solarczyk K, Ma H, Pederson T, Dobrucki J.
Nucleic Acids Res. 2020. 48:e14.  doi:10.1093/narlgkz1118   

The centriole mystique.
Pederson T.
Trends Cell Biol. 2020. 30:590-593. doi:10.1016/j.tcb.2020.05.001 

Meeting Report: Nuclear and cytoplasmic machines at work.
Bullock SL, Visa N, Pederson T.
Cell Sci. 2020. 133:jcs245134. 

Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region.
Ma H, Tu LC, Chung, Y-C, Naseri A, Grunwald D, Zhang S, Pederson T.
Cell Biol. 2019. 218:1467-1477. 

The sui generis Sydney Brenner.
Pederson T.
Proc. Natl. Acad. Sci. USA. 2019. 116:13155-13157.  doi:10.1073/pnas.1907536116.

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