Yeo Lab

Degrees

Ph.D., Bioinformatics, UCSD, 2008
B.S., Biochemistry, University of New Mexico, 2001

Summary

Kasey Hutt received his B.S. in Biochemistry from the University of New Mexico in 2001, and his Ph.D. in Bioinformatics from the University of California, San Diego in 2008, from Dr. Michael G. Rosenfeld’s lab. His thesis work primarily focused on two projects: design and analysis of a more sensitive ChIP-on-chip technology, termed DNA Selection and Ligation (DSL), and the analysis of next generation sequencing data derived from ChIP experiments (ChIP-seq). The DSL technique was used in conjunction with ChIP (ChIP-DSL) to identify previously unknown, lower affinity binding sites for the estrogen receptor protein. This technique was also amenable to the 3C assay (used to describe interacting regions of the genome), and facilitated the discovery of intra- and interchromosomal interactions. Dr. Hutt’s ChIP-seq data analysis was used to efficiently reveal large groups of correlating histone marks, as well as a set of novel binding events of the Neuronal Restrictive Silencing Factor (NRSF) to regions not containing the NRSF binding site. Currently, Dr. Hutt is developing new methods for analyzing sequencing data from the similar CLIP assay, which identifies RNA bound to proteins.

Publications

Transcriptome–pathology correlation identifies interplay between TDP‑43 and the expression of its kinase CK1E in sporadic ALS. Krach F, Batra R, Wheeler EC, Vu AQ, Wang R, Hutt K, Rabin SJ, Baughn MW, Libby RT, Diaz‑Garcia S, Stauffer J, Pirie E, Saberi S, Rodriguez M, Madrigal AA, Kohl Z, Winner B, Yeo GW, Ravits J. Acta Neuropathologica, 2018.

Nxf1 natural variant E610G is a semi-dominant suppressor of IAP-induced RNA processing defects. Concepcion D, Ross KD, Hutt KR, Yeo GW, Hamilton BA. PLoS genetics, 2015

Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration. Lagier-Tourenne C, Baughn M, Rigo F, Sun S, Liu P, Li HR, Jiang J, Watt AT, Chun S, Katz M, Qiu J, Sun Y, Ling SC, Zhu Q, Polymenidou M, Drenner K, Artates JW, McAlonis-Downes M, Markmiller S, Hutt KR, Pizzo DP, Cady J, Harms MB, Baloh RH, Vandenberg SR, Yeo GW, Fu XD, Bennett CF, Cleveland DW, Ravits J. PNAS, 2013

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs. Lagier-Tourenne C , Polymenidou M * , Hutt KR , Vu AQ, Baughn M, Huelga SC, Clutario KM, Ling SC, Liang TY, Mazur C, Wancewicz E, Kim AS, Watt A, Freier S, Hicks GG, Donohue JP, Shiue L, Bennett CF, Ravits J, Cleveland DW & Yeo GW. Nature Neuroscience, 2012.

LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. Wilbert MW, Huelga SC, Kapeli K, Stark TJ, Liang TY, Chen SX, Yan BY, Nathanson JL, Hutt KR, Lovci MT, Kazan H, Vu AQ, Massirer KB, Morris Q, Hoon S, Yeo GW. Molecular Cell, 2012. [Mol Cell]

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. Polymenidou M , Lagier-Tourenne C , Hutt KR * , Huelga SC, Moran J, Liang TY, Ling SC, Sun E, Wancewicz E, Mazur C, Kordasiewicz H, Sedaghat Y, Donohue JP, Shiue L, Bennett CF, Yeo GW , Cleveland DW ( * authors contributed equally, ** co-corresponding). Nature Neuroscience, 2011. [PMID: 21358643]

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang YL, Pasquinelli AE, Yeo GW. Nature Structural and Molecular Biology, 2010. [PMID: 20062054]

Hu, Q., Y.S. Kwon, E. Nunez, M.D. Cardamone, K.R. Hutt, K.A. Ohgi, I. Garcia-Bassets, D.W. Rose, C.K. Glass, M.G. Rosenfeld, and X.D. Fu, Enhancing nuclear receptor-induced transcription requires nuclear motor and LSD1-dependent gene networking in interchromatin granules. Proc Natl Acad Sci U S A, 2008. 105(49): p. 19199-204. [PMID: 19052240]

Lunyak, V.V., G.G. Prefontaine, E. Nunez, T. Cramer, B.G. Ju, K.A. Ohgi, K. Hutt, R. Roy, A. Garcia-Diaz, X. Zhu, Y. Yung, L. Montoliu, C.K. Glass, and M.G. Rosenfeld, Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science, 2007. 317(5835): p. 248-51. [PMID: 17626886]

Garcia-Bassets, I., Y.S. Kwon, F. Telese, G.G. Prefontaine, K.R. Hutt, C.S. Cheng, B.G. Ju, K.A. Ohgi, J. Wang, L. Escoubet-Lozach, D.W. Rose, C.K. Glass, X.D. Fu, and M.G. Rosenfeld, Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell, 2007. 128(3): p. 505-18. [PMID: 17289570]

Kwon, Y.S., I. Garcia-Bassets, K.R. Hutt, C.S. Cheng, M. Jin, D. Liu, C. Benner, D. Wang, Z. Ye, M. Bibikova, J.B. Fan, L. Duan, C.K. Glass, M.G. Rosenfeld, and X.D. Fu, Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc Natl Acad Sci U S A, 2007. 104(12): p. 4852-7 [PMID: 17360330]

Formally acknowledged in B.R. Stallard, J.G. Taylor, Quantifying multivariate classification performance - the problem of overfitting, Proceedings of SPIE, 1999, 3753, p 48.