Wenyi Feng, PhD

RESEARCH ABSTRACT

How do defects in DNA replication lead to genomic instability? This question bears on our understanding of a wide spectrum of human diseases, including chromosome fragility, cancer, neurodegeneration, and even autoimmune disorders. Eukaryotic chromosomal DNA replication is a process that is at once robust and vulnerable. It is accurate and able to withstand environmental stress, such as DNA damage and replication impediments, through a highly evolved checkpoint mechanism. Yet the very act of replication, if executed in an untimely or uncoordinated fashion, can give rise to genomic instability.

My laboratory is interested in understanding the mechanisms of genomic instability induced by DNA replication stress.  Previous work including ours had established that replication stress induces extensive single-stranded DNA formation at replication forks, which ultimately results in double stranded DNA breaks (DSBs).  We further demonstrated that DSBs occur more frequently at the genes that are subject to transcription induction by the drug used to elicit replication stress-for instance-hydroxyurea, an inhibitor of the ribonucleotide reductase.  This suggests that replication-transcription collision underlies DSB formation.  We are currently more rigorously testing the hypothesis by using a variety of replication stress-inducing drugs to induce, and systematically map, DSBs in the model organism, Saccharomyces cerevisiase.  Our hypothesis would predict that the genomic locations that are most susceptible to DSBs are correlated with heightened gene expression due to drug induction.  We are performing deep-sequencing experiments to simultaneously query the genome for DSB formation by Break-seq and gene expression by RNA-seq.  We are also performing experiments to address if the relative speeds of the replication and transcription machineries during collisions play a role in DSB formation.

Equipped with the powerful tool of Break-seq we are also mapping replication stress-induced DSBs in mammalian cells, known as chromosome fragile sites (CFSs), which play an important role in genomic rearrangements and the genesis of a wide range of human diseases including cancer.  We have systematically identifying DSBs in cells derived from patients with the Fragile X Syndrome (FXS), the most common inherited mental retardation.  We have observed that in the FXS model, replication stress-induced CFSs are preferentially localized to the R-loop forming sequences (RLFSs), which are cis-elements with high probability of forming DNA:RNA hybrids during transcription.  This led to the discovery that the protein that is deficient in the FXS, FMRP, has a novel function in genome maintenance by preventing R-loop formation during replication-transcription conflict, thus shedding light on the underlying etiological basis for FXS.  Our current endeavors take us beyond this disease model to examine different cancer genomes to discover new "at-risk" gene such as novel tumor suppressors.

Select Publications:

Feng W. and Chakraborty A. (2017) Fragility Extraordinaire: Unsolved mysteries of chromosome fragile sites. Advs Exp Med Biol. 1042:489-526. doi: 10.1007/978-981-10-6955-0_21.

Feng W. (2016) Mec1/ATR, the Program Manager of Nucleic Acids Inc. Genes (Basel). 8(1). pii: E10. doi: 10.3390/genes8010010. Review.

Peng J, Feng W. (2016) Incision of damaged DNA in the presence of an impaired Smc5/6 complex imperils genome stability. Nucleic Acids Res. pii: gkw720. [Epub ahead of print]

Hang LE, Peng J, Tan W, Szakal B, Menolfi D, Sheng Z, Lobachev K, Branzei D, Feng W, Zhao X. (2015) Rtt107 is a multi-functional scaffold supporting replication progression with partner SUMO and ubiquitin ligases. Mol Cell. 60:268-79.

Hoffman EA, McCulley A, Haarer B, Arnak R, Feng W. (2015) Break-seq reveals hydroxyurea-induced chromosome fragility as a result of unscheduled conflict between DNA replication and transcription. Genome Res. 25:401-12.

Peng J, M. K. Raghuraman, Feng W. (2014) Analysis of ssDNA gaps and DSBs in genetically unstable yeast cultures. Methods Mol Biol. 1170:501-15.

Peng J, M. K. Raghuraman, Feng W. (2014) Analysis of replication timing using synchronized budding yeast cultures. Methods Mol Biol. 1170:477-99.

McCulley A, Haarer B, Viggiano S, Karchin J, Feng W. (2014) Chemical suppression of defects in mitotic spindle assembly, redox control, and sterol biosynthesis by hydroxyurea. G3. 4(1):39-48.

Feng W*, Di Rienzi S, Raghuraman M K, Brewer B J. (2011) Replication stress-induced chromosome breakage is correlated with replication fork progression and is preceded by single-stranded DNA formation. G3. 1(5):327-35. *Corresponding author.

Feng W, Bachant J, Collingwood D, Raghuraman M K, Brewer B J. (2009) Centromere replication timing determines different forms of genomic instabilit in Saccharomyces cerevisiae checkpoint mutants during replication stress. Genetics. 183(4):1249-60.

Feng W, Collingwood D, Boeck M E, Fox L, Alvino G, Fangman W L, Raghuraman M K, Brewer B J. (2006) Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication. Nature Cell Biol. 8(2):148-55.

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