Photo of Rachel Simpson.

Rachel Simpson

Department

Microbiology and Immunology

Thesis Title

Functional characterization of MRB8180-containing complexes in trypanosome RNA editing

Residency

Internal Medicine, University of Rochester

Undergraduate Education

University of Rochester, Microbiology and Immunology

Thesis Advisor

Trypanosoma brucei mitochondria, a novel and essential process in a deadly human parasite. Specifically, I developed a new methodology to investigate the mechanisms of RNA editing termed TREAT (Trypanosome RNA Editing Alignment Tool) that employs a combination of high throughput sequencing and bioinformatics analyses. Through this work, I expanded our understanding of the complex mitochondrial transcriptome, elucidated the functions of essential editing factors whose roles had been largely unknown, and provided a powerful open source tool that is available to the larger parasitology research community. My work provides the first evidence that editing of a given mRNA can proceed through distinct pathways; i.e., the order in which a region is modified is a varied and regulated feature. In addition, my work demonstrated for the first time that non-linear, or seemingly “mis-edited”, modifications are essential to the editing process, generating the commonly observed junction regions that occur at the leading edge of editing.

Publications

  • High Throughput Sequencing Revolution Reveals Conserved Fundamentals of U-indel Editing. Zimmer, Sarah; Simpson, Rachel; Read, Laurie. WIREs RNA, Epub ahead of print, June 11, 2018. 
  • MRB7260 is essential for productive protein-RNA interactions within the RNA Editing Substrate Binding Complex during trypanosome RNA editing. McAdams, Natalie; Simpson, Rachel; Chen, Runpu; Sun, Yijun; Read, Laurie. RNA, Vol. 24, No. 4: 540-556. Epub January 12, 2018 
  • High-throughput sequencing of partially edited trypanosome mRNAs reveals barriers to editing progression and evidence for alternative editing. Simpson RM, Bruno AE, Bard JE, Buck MJ, Read LK. RNA. 2016 May; 22(5):677-95. doi: 10.1261/rna.055160.115. Epub 2016 Feb 23 
  • Trypanosome RNA Editing Mediator Complex proteins have distinct functions in gRNA utilization. Simpson, Rachel; Bruno, Andrew; Chen, Runpu ; Lott, Kaylen; Tylec, Brianna; Bard, Jonathan; Sun, Yijun; Buck, Michael; Read, Laurie. Nucleic Acids Research, Accepted May 8, 2017.

Professional/Educational Meetings/Abstracts

  • RNA Editing Mediator Complex proteins have distinct functions in gRNA utilization and reveal the essentiality of non-contiguous editing modifications. *Simpson, Rachel; Bruno, Andrew; Bard, Jonathan; Chen, Runpu; Sun, Yijun; Buck, Michael; and Read, Laurie. Northeast Regional APSA Meeting, Rochester, NY. October, 2017. *Presenter
  • RNA Editing Mediator Complex proteins have distinct functions in gRNA utilization and reveal the essentiality of non-contiguous editing modifications. *Simpson, Rachel; Bruno, Andrew; Bard, Jonathan; Chen, Runpu; Sun, Yijun; Buck, Michael; and Read, Laurie.  29th Annual Buffalo Conference on Microbial Pathogenesis.  May, 2017. *Oral presenter
  • RNA Editing Mediator Complex proteins have distinct functions in gRNA utilization and reveal the essentiality of non-contiguous editing modifications. *Simpson, Rachel; Bruno, Andrew; Bard, Jonathan; Chen, Runpu; Sun, Yijun; Buck, Michael; and Read, Laurie.  7th Kinetoplastid Molecular Cell Biology Meeting.  April, 2017.  *Presenter
  • High throughput sequencing of partially edited RNAs provides insight into the roles of the TbRGG2 Supcomplex Proteins in Trypanosome RNA editing.  *Simpson, Rachel; Bruno, Andrew; Bard, Jonathan; Chen, Runpu; Sun, Yijun; Buck, Michael; and Read, Laurie.  Northeast Regional APSA Meeting. October, 2016.  *Presenter
  • High throughput sequencing of partially edited RNAs provides insight into the roles of the TbRGG2 Supcomplex Proteins in Trypanosome RNA editing.  *Simpson, Rachel; Bruno, Andrew; Bard, Jonathan; Chen, Runpu; Sun, Yijun; Buck, Michael; and Read, Laurie.  The Rustbelt RNA Meeting. October, 2016. *Presenter
  • High throughput sequencing of partially edited RNAs provides insight into the roles of the TbRGG2 Supcomplex Proteins in Trypanosome RNA editing.  *Simpson, Rachel; Bruno, Andrew; Bard, Jonathan; Chen, Runpu; Sun, Yijun; Buck, Michael; and Read, Laurie.17th Annual Molecular Parasitology Meeting, September 2016. *Presenter
  • High Throughput Sequencing of Partially Edited RNAs Provides Insight into the Roles of the TbRGG2 Subcomplex proteins in Trypanosome RNA Editing. *Simpson, Rachel; Bruno, Andrew; Bard, Jonathan; Buck, Michael and Read, Laurie K.  28th Annual Buffalo Conference on Microbial Pathogenesis, May 2016. *Presenter
  • High Throughput Sequencing of Partially Edited RNAs Provides Insight into Trypanosome RNA Editing Progression and the Role of the TbRGG2 Subcomplex. *Simpson, Rachel; Bruno, Andrew; Bard, Jonathan; Buck, Michael and Read, Laurie K. 2nd Annual Genetics, Genomics and Bioinformatics Research Day, January 2016. *Oral Presenter
  • High Throughput Sequencing of Partially Edited RNAs Provides Insight into Trypanosome RNA Editing Progression and the Role of the TbRGG2 Subcomplex. *Simpson, Rachel; Bruno, Andrew; Bard, Jonathan; Buck, Michael and Read, Laurie K. The Rustbelt RNA Meeting, October 2015. *Presenter
  • Functions of MRB1 complex proteins in kinetoplastid RNA editing illuminated by deep sequencing of partially edited RNA populations.  *Simpson, Rachel; Bruno, Andrew; Sun, Yijun; and Read, Laurie K. Sixth Kinetoplastid Molecular Cell Biology Meeting, April 2015. *Presenter
  • Trypanosome RNA Editing Alignment Tool:  Using deep sequencing to understand the roles of accessory factors in kinetoplastid RNA editing. *Simpson, Rachel; Bruno, Andrew; and Read, Laurie K.  1st Annual Genetics, Genomics and Bioinformatics Research Day, January 2015. *Presenter
  • Trypanosome RNA Editing Alignment Tool:  Using deep sequencing to understand the roles of accessory factors in kinetoplastid RNA editing. *Simpson, Rachel; Bruno, Andrew; and Read, Laurie K. The Rustbelt RNA Meeting, October 2014. *Presenter
  • Trypanosome RNA Editing Alignment Tool:  Using deep sequencing to understand the roles of accessory factors in kinetoplastid RNA editing. *Simpson, Rachel; Bruno, Andrew; and Read, Laurie K. The Tri-Institutional MSTP Conference, October 2014. *Presenter
  • MRB8180 is indispensible for editing of pan-edited RNAs in Trypanosoma brucei. *Simpson, Rachel; Ammerman, Michelle L.; Sakyiama, Joseph; and Read, Laurie K. The Many Lives of RNA Research Symposium, October 2013. *Presenter
  • MRB8180 is indispensible for editing of pan-edited RNAs in Trypanosoma brucei. *Simpson, Rachel; Ammerman, Michelle L.; Sakyiama, Joseph; and Read, Laurie K. MD-PhD Research Day, October 2013. *Presenter
  • Dual core processing: MRB1 is an essential trypanosome RNA editing complex.  Ammerman, Michelle; *Simpson, Rachel; Hashimi, Hassan; Kafkova, Lucie; Faktorova, Drahomira; Lukes, Julius; Read, Laurie.  25th Annual Buffalo Conference on Microbial Pathogenesis, 2013. *presenter
  • Dual core processing: MRB1 is an essential trypanosome RNA editing complex.  *Ammerman, Michelle; *Simpson, Rachel; Hashimi, Hassan; Kafkova, Lucie; Faktorova, Drahomira; Lukes, Julius; Read, Laurie.  Fifth Kinetoplastid Molecular Cell Biology Meeting, April 2013. *co-presenters
  • The antimicrobial activity of medicinal plants used by traditional healers of Northern Peru to treat infectious disease.  3rd Annual Global Health Day.  The Office of Global Health Initiatives, The Gender Institute.  Buffalo, NY, March, 2013.
  • The antimicrobial activity of medicinal plants used by traditional healers of Northern Peru to treat infectious disease.  Medical Student Research Forum, 2012.
  • Building a teen-friendly primary care practice: Assessing staff attitudes toward teen sexuality and contraception.  Maldonado LM, Lesnewski R, Simpson R. 9th International Conference on Urban Health, New York, NY, October, 2010.
  • Building a teen-friendly primary care practice: Assessing staff attitudes toward teen sexuality and contraception.  Maldonado LM, Lesnewski R, Simpson R. 138th APHA Annual Meeting, Denver, CO, November, 2010.
  • Building a Teen-friendly Practice: Assessing Staff Attitudes Toward Teen Sexuality And Contraception. Maldonado LM, Lesnewski R, Simpson R. STFM 2010 Conference on Practice Improvement: Assembling the Patient-centered Team, San Antonio, TX, December 2010.

Awards/Honors

  • 2016 Best Talk Awards--2nd Place (2nd Annual Genetics, Genomics and Bioinformatics Research Day)
  • Outstanding Poster Award (Rustbelt RNA Meeting 2015)
  • UB Medical Student Summer Research Fellowship (2011)
  • Bausch and Lomb Award Winner (University of Rochester, 2005-2009)
  • Rush Rhees Scholar (University of Rochester, 2005-2009)
  • Charles S. Daily Scholarship (2005-2009)

Medical School Activities

  • Independent Student Assessment Committee Chair (2018-2019)
  • Micro Club
  • Medical School Curriculum Committee (Class of 2014 Representative, 2010-2012)
  • Physicians for Human Rights (founding member, 2011-2012)
  • International Health Interest Group (Co-President, 2011-2012)
  • Lighthouse Medical Clinic (volunteer, 2012-present)

Extracurricular Interests

Meditation, Dance, Music, Cycling