Kelly Trujillo


Kelly TrujilloPhone: 402-559-4493 (Office)
402-559-3441 (Lab)
402-559-6650 (Fax)

B.S. Biology, New Mexico Institute of Mining and Technology, 1995
Ph.D. Molecular Medicine, University of Texas Health Sciences center, 2002


Figure 1-The structure of chromatin. Modified from Iyer et al, BMC Biophusics 2011, 4:8The term “chromatin” refers to the complex of DNA and protein that exists in the nuclei of eukaryotic cells.  The protein component consists primarily of histones, which form an octamer that comprise the basic repeating unit of chromatin, the nucleosome.  Around each nucleosome are wrapped two superhelical turns (~147bp) of DNA, and arrays of nucleosomes form higher order structures that function to package and protect the genome in each and every cell.  Studies have indicated that not only does chromatin serve both packaging and protective roles, but it also helps to regulate access to the underlying genetic information for important biological functions including transcription, DNA repair, and DNA replication.  This access is controlled by the combined efforts of histone modifying enzymes and chromatin remodeling complexes.

Our lab studies issues pertinent to the regulation of DNA replication in a chromatin context.   DNA replication is initiated at discrete regions of the genome called replication origins.  In the budding yeast, Saccharomyces cerevisiae, origins are defined by partially conserved DNA sequences, which exist in nucleosome-free zones.  However, these sequences are flanked by well-positioned nucleosomes that help to create a chromatin environment suitable for origin firing upon S-phase.   Upon initiation of DNA replication, nucleosomes in front of the replication fork must be displaced in order for the replication machinery to pass.  Further, the re-establishment of chromatin structure on both daughter strands is necessary to promote fork progression and maintain genomic stability.  The dynamic displacement and subsequent re-establishment of chromatin structure is accomplished by the recycling of parental displaced histones together with the incorporation of newly synthesized histones and is regulated by a number of histone post-translational modifications (PTMs) that work in concert with histone chaperones and chromatin remodeling complexes. 

Not only must chromatin structure behind the replication fork be re-established, but the epigenetic information encoded by these nucleosomes in the form of histone PTMs, must also be maintained.  Failure to do so could alter transcriptional programs, destabilize zones of heterochromatin, or de-regulate specialized genomic features like centromeres and telomeres. 

Our research has revealed that mono-ubiquitylation of histone H2B (H2Bub1) near origins of replication in yeast is important for promoting DNA replication.  The mark is maintained on both daughter strands by the de novo recruitment of the E3 ubiquitin ligase enzyme, Bre1, to activated origins.  Failure to ubiquitylate H2B results in a defect in nucleosome assembly behind the fork, which in turn, slows fork progression and destabilizes the replication machinery.  Using a combination of genetic, biochemical, and molecular tools, my lab works to understand exactly how H2Bub1 assists in nucleosome assembly, and more importantly, how a breakdown in nucleosome assembly is communicated to the replication machinery to slow its progression. 
 Figure 2- H2Bub1 and Bre1 are present on chromatin near yeast replication origins throughout the cell cycle.  Upon initiation of DNA replication, nucleosomes are displaced in front of the replication machinery, and two nucleosomes are re-assembled in its wake.  H2Bub1 levels are maintained on newly assembled nucleosomes via the recruitment of additional Bre1 in a replication-dependent manner.  Nucleosome assembly is assisted by H2Bub1, which communicates with the replisome by an unknown mechanism to promote fork progression.

Student research opportunities in my lab:

Primary Research/Clinical Interests/Expertise:



Trujillo KM, Yuan SS, Lee EY, Sung P (1998) Nuclease activities in a complex of human recombination and DNA repair factors Rad50, Mre11, and p95. J. Biol. Chem. 273(34):21447-50.


Chen G, Yuan SS, Liu W, Xu Y, Trujillo K, Song B, Cong F, Goff SP, Wu Y, Arlinghaus R, Baltimore D, Gasser PJ, Park MS, Sung P, Lee EY (1999) Radiation-induced assembly of Rad51 and Rad52 recombination complex requires ATM and c-Abl. J. Biol. Chem. 274(18):12748-52.


Mickelsen S, Snyder C, Trujillo K, Bogue M, Roth DB, Meek K (1999) Modulation of terminal deoxynucleotidyltranferase activity by the DNA-dependent protein kinase. J. Immunol. 163(2):834-43.


Chen L, Trujillo K, Sung P, Tomkinson AE (2000) Interactions of the DNA ligase IV-XRCC4 complex with DNA ends and the DNA-dependent protein kinase. J. Biol. Chem. 275(34):26196-205.


Sung P, Trujillo KM, Van Komen S (2000) Recombination factors of Saccharomyces cerevisiae. Mut. Res. 451(1-2):257-75.


Sigurdsson S, Trujillo K, Song B, Stratton S, Sung P (2001) Basis for avid homologous DNA strand exchange by human Rad51 and RPA. J. Biol. Chem. 276(12):8798-806.


Trujillo KM and Sung P (2001) DNA Structure-specific nuclease activities in the Saccharomyces cerevisiae Rad50-Mre11 complex. J. Biol. Chem. 276(38):35458-64.


Anderson DE, Trujillo KM, Sung P, Erickson HP (2001) Structure of the Rad50-Mre11 DNA repair complex from Saccharomyces cerevisiae by electron microscopy. J. Biol. Chem. 276(40):37027-33.


Chen L*, Trujillo K*, Ramos W, Sung P, Tomkinson AE (2001) Promotion of Dnl4-catalyzed DNA end-joining by the Rad50/Mre11/Xrs2 and Hdf1/Hdf2 complexes. Molecular Cell 8(5):1105-15.


Mallory JC, Bashkirov VI, Trujillo KM, Solinger JA, Dominska M, Sung P, Heyer WD, Petes TD (2003) Amino acid changes in Xrs2p, Dun1p, and Rfa2p that remove the preferred targets of the ATM family of protein kinases do not affect DNA repair or telomere length in Saccharomyces cerevisiae. DNA Repair 2(9):1041-64.


Trujillo KM*, Roh DH*, Chen L, Van Komen S, Tomkinson A, Sung P (2003) Yeast Xrs2 binds DNA and helps target Rad50 and Mre11 to DNA ends. J. Biol. Chem. 278(49):48957-64.


De Jager M, Trujillo KM, Sung P, Hopfner KP, Carney JP, Tainer JA, Connelly JC, Leach DR, Kanaar R, Wyman C (2004) Differential arrangements of conserved building blocks among homologs of the Rad50/Mre11 DNA repair protein complex. J. Mol. Biol. 339(4):937-49.


Chen L*, Trujillo KM*, Van Komen S, Roh DH, Krejci L, Lewis K, Resnick M, Sung P, Tomkinson AE (2005) Effect of amino acid substitutions in the Rad50 ATP binding domain on DNA double-strand break repair in yeast. J. Biol. Chem. 280(4):2620-27.


Trujillo KM, Bunch JT, Baumann P (2005) Extended DNA binding site in Pot1 broadens sequence specificity to allow recognition of heterogeneous fission yeast telomeres. J. Biol. Chem. 280(10):9119-28.


Trujillo KM and Osley MA (2008) INO80 meets a fork in the road. Nature Struct. and Mol. Biol. 15(4):332-334.


Tsukuda T, Trujillo KM, Martini E, Osley MA (2009) Analysis of chromatin   remodeling during formation of a DNA double-strand break at the yeast mating type locus. Methods 48(1):40-5.


Trujillo KM, Tyler RK, Ye C, Berger SL, Osley MA (2010) A genetic and molecular toolbox for analyzing histone ubiquitylation and sumoylation in yeast. Methods, 54(3):296-303.


Trujillo KM and Osley MA (2012) A Role for H2B Ubiquitylation in DNA Replication. Molecular Cell,

*These authors contributed equally


    Current Grants:

    National Institutes of Health/National Cancer Institute

    K22 CA163485