Yartseva V, Takacs CM, Vejnar CE, Lee MT‡, Gira
Yartseva V, Takacs CM, Vejnar CE, Lee MT‡, Giraldez AG‡. 2017. RESA identifies mRNA regulatory sequences with high resolution. Nature Methods 14, 201-207.
Contact
Office: (412) 624-9186
Lab: (412) 624-9191
A518 Langley Hall
4249 Fifth Avenue
Pittsburgh, PA 15260
Potential Ph.D. students interested in gene regulation, development, evo-devo and/or computational genomics are encouraged to apply here!
For most animals and plants, the genetic instructions that guide early embryogenesis are inherited as RNA. During a short window of development, these RNA coordinate all cellular activity, including the processes that induce the first rounds of transcription from the embryonic genome. Eventually those maternally inherited RNA are destroyed, as newly transcribed embryonic RNA assume control of the embryo. This period of development is called the maternal-to-zygotic transition.
Maternally inherited RNA encode the instructions to reprogram an egg into pluripotent embryonic cells, the precursors to all cell types in the adult organism. Thus, we study eggs and their RNA to better understand the mechanisms underlying cellular identity and pluripotency, and how they have evolved. Our tool kit includes genetics and embryology in zebrafish and Xenopus, and high-throughput experimental and computational genomics across animals.
- Taylor Ayers, Technician
- Matthew Hurton, Graduate Student
- Wesley Phelps, Graduate Student
- Jayesh Kumar Sundaram, Graduate Student
- Lauren Wolf, Technician
Reischauer S, Stone O, Villasenor A, Chi N, Jin
Reischauer S, Stone O, Villasenor A, Chi N, Jin SW, Martin M, Lee MT, Fukuda N, Marass M, Fiddes I,
Kuo T, Chung WS, Salek S, Lerrigo R, Alsio J, Luo S, Tworus D, Augustine SA, Mucenieks S, Nystedt B, Giraldez AJ, Schroth GP, Andersson O, Stainier DY. 2016. Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification. Nature 535(7611), 294-8.
Francis C, Natarajan S, Lee MT, Khaladkar M, Bu
Francis C, Natarajan S, Lee MT, Khaladkar M, Buckley PT, Sul JY, Eberwine J, Kim J. 2014. Divergence of RNA localization between rat and mouse neurons reveals the potential for rapid brain evolution. BMC Genomics 15(1), 883.
Lee MT#, Bonneau AR#, Giraldez AJ‡. Zygotic gen
Lee MT#, Bonneau AR#, Giraldez AJ‡. Zygotic genome activation during the maternal-to-zygotic transition. 2014. Annu Rev Cell Dev Biol 30(1), 18.1-18.33.
Bazzini AA, Johnstone TG, Christiano R, Mackowi
Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. 2014. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J 33(9), 981-993.
Khaladkar M, Buckley PT, Lee MT, Francis C, Egh
Khaladkar M, Buckley PT, Lee MT, Francis C, Eghbal MM, Chuong T, Suresh S, Kuhn B, Eberwine J, Kim J. 2013. Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons. PLoS One 8(10), e76194.
Lee MT#, Bonneau AR#, Takacs CM, Bazzini AB, Di
Lee MT#, Bonneau AR#, Takacs CM, Bazzini AB, DiVito KR, Fleming ES, Giraldez AJ. 2013. Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. Nature 503(7476), 360-364.
Eberwine J, Lovatt D, Buckley P, Dueck H, Franc
Eberwine J, Lovatt D, Buckley P, Dueck H, Francis C, Kim, TK, Lee J, Lee M, Miyashiro K, Morris J, Peritz T, Schochet T, Spaethling J, Sul JY, Kim J. 2012. Quantitative biology of single neurons. J R Soc Interface 9(77), 3165-3183.
Bazzini AA#, Lee MT#, Giraldez AJ. 2012. Riboso
Bazzini AA#, Lee MT#, Giraldez AJ. 2012. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336(6078), 233-237.
Kim TK, Sul JY, Peternko NB, Lee JH, Lee M, Pat
Kim TK, Sul JY, Peternko NB, Lee JH, Lee M, Patel VV, Kim J, Eberwine JH. 2011. Transcriptome transfer provides a model for understanding the phenotype of cardiomyocytes. Proc Natl Acad Sci USA 108(29), 11918-11923.
Buckley PT#, Lee MT#, Sul JY, Miyashiro KY, Bel
Buckley PT#, Lee MT#, Sul JY, Miyashiro KY, Bell TJ, Fisher SA, Kim J, Eberwine J. 2011. Cytoplasmic intron retention provides multiple mechanisms for localizing dendritic mRNAs. Neuron 69(5), 877-884.
Dr. Lee received his Ph.D. in Genomics and Computational Biology in 2009, with Dr. Junhyong Kim at the University of Pennsylvania; was a postdoctoral fellow with Dr. Antonio Giraldez at Yale University; and joined the Department in 2016.
Basil O'Connor Scholar, March of Dimes (2017-2019)