Nicholas Fuda - Post-Doctoral Scholar

131 Koshland Hall
(510) 643-5583

Mailing Address:
University of California Berkeley
16 Barker Hall, MC 3204
Berkeley, CA 94720-3204









Research Summary

Caenorhabditis elegans is an ideal model organism for studying development. The complete cell lineage has allowed the design of genetic screens that uncover factors controlling specific cell fates. These factors have been assembled into the regulatory networks governing cell-type specifications, and biochemical methods are identifying the downstream target genes via transcription factor localization using ChIP and expression changes in animals with impaired regulatory factor expression using RNase-seq. Thus, we have well-defined pathways that mediate specific cell fates and expression profiles.

Although there is extensive information about C. elegans gene expression and the factors that regulate it, surprisingly little research has investigated the basic transcriptional mechanisms of the worm and the interactions between regulatory factors and the transcriptional machinery. In particular, two unique characteristics of worm gene expression have impeded identification of transcription start sites and the promoters controlling initiation. First, the majority of transcripts trans-splice a 5’UTR, removing transcription start site information. Second, many genes are transcribed in polycistronic RNAs that are co-transcriptionally processed to form mRNAs for individual genes. Therefore, more research implementing alternative strategies is needed to identify transcription start sites in worms, and define their promoters.

Our lab studies dosage compensation to elucidate the mechanisms that regulate expression of X chromosome genes during development. The Dosage Compensation Complex (a condensin complex) controls this regulation by binding to the X chromosome and reducing expression on the hermaphrodite X chromosomes about 2-fold. Recent results indicate that this reduced X chromosome expression in hermaphrodites is achieved through reduced RNA polymerase recruitment or initiation, but the mechanisms behind this regulation are still a mystery. I’m investigating the localization of basal transcription machinery within C. elegans genome to define the sites of initiation and the promoters that guide initiation. I’m performng these experiments in wild type and DCC mutants to investigate how dosage compensation alters initiation and localization initiation factors. This information will be informative for dosage compensation and transcriptional regulation of development.


Fuda NJ, Core LJ, Waters CT, Lis JT. GAGA Factor keeps promoters open to allow promoter-proximal pausing. in prep.

Williams BC, Filter JJ, Blake-Hodek KA, Wadzinski BE, Fuda NJ, Shalloway D, Goldberg ML. (2014) Greatwall-phosphorylated Endosulfine is Both an Inhibitor and a Substrate of PP2A-B55 Heterotrimers. eLIFE; 3:e01695.

Fuda NJ and Lis JT. (2013) A new player and pathway in Pol II pausing. EMBO J.; 32(13):1796-1798.

Kwak H, Fuda NJ, Core LJ, Lis JT. (2013) Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing. Science; 339:950-953.

Fuda NJ, Buckley MS, Wei W, Core LJ, Waters CT, Reinberg D, Lis JT. (2012) Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain required for efficient transcription of heat shock genes. Mol Cell Biol.; 32(17):3428-37.

Salamanca HH, Fuda NJ, Shi H, Lis JT. (2011) An RNA Aptamer Perturbs Heat Shock Transcription Factor (HSF1) Activity in Drosophila melanogaster. Nucleic Acids Res.; 39(15):6729-6740.

Bartkowiak B, Liu P, Phatnani HP, Fuda NJ, Cooper JJ, Price DH, Adelman K, Lis JT, Greenleaf AL. (2010) CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. Genes Dev.; 24(20):2303-2316.

Fuda NJ, Ardehali MB, Lis JT. (2009) Defining Regulatory Mechanisms in RNA Polymerase II Transcription In Vivo. Nature; 461(7261):186-192.

Ardehali MB, Yao J, Adelman K, Fuda NJ, Petesch SJ, Webb WW, Lis JT. (2009) Spt6 enhances the elongation rate of RNA polymerase II in vivo. EMBO J.; 28(8):1067-1077.

Ni Z, Saunders A, Fuda NJ, Yao J, Suarez JR, Webb WW, Lis JT. (2008) P-TEFb is critical for the maturation of RNA polymerase II into productive elongation in vivo. Mol Cell Biol.; 28(3):1161-1170.

Sullivan DT, MacIntyre R, Fuda N, Fiori J, Barrilla J, Ramizel L. (2003) Analysis of glycolytic enzyme co-localization in Drosophila flight muscle. J. Exp. Biol.; 206 (12):2031-2038.


August 2013 - GAGA FACTOR REGULATION OF PROMOTER-PROXIMAL PAUSING IN DROSOPHILA Nicholas J. Fuda and John T. Lis. Cold Spring Harbor Laboratory Conference - Mechanism of Eukaryotic Transcription.

August 2009 - REGULATION OF PROMOTER-PROXIMAL PAUSING ON DROSOPHILA HSP70. Nicholas J. Fuda and John T. Lis. Cold Spring Harbor Laboratory Conference - Mechanism of Eukaryotic Transcription.

June 2008 - REGULATION OF PROMOTER-PROXIMAL PAUSING ON DROSOPHILA HSP70. Nicholas J. Fuda and John T. Lis. FASEB Conference - Transcriptional Regulation during Cell Growth, Differentiation and Development.


Cornell University, Ithaca, NY
Ph.D. in Molecular Biology

Syracuse University, Syracuse, NY
B.S. in Biology