the Stephen Floor lab

Understanding how the information contained in RNA sequences
controls gene expression in development and cancer

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About the lab


What We Do

Our cells are like machines. Genes in our DNA are the instructions to produce each part (proteins, RNA, and other molecules). Each part must be accurately produced in the right amount for cells to work properly. Mistakes in these processes cause many diseases, including cancer.

Messenger RNA sequences instruct the cell what protein part to make, and influence how much is made. Other RNA molecules also affect how cells work. Our lab studies how these processes work normally and how they are altered in human diseases.

Left: phase separation like oil and water of RNA binding proteins and RNA into round foci under cellular stress.

A Scientific Description

We study the many ways RNA influences human gene expression. How do mRNA sequences specify protein production levels? How do changes to the biophysics of RNA in cells influence gene expression, and what role(s) do RNA chaperones play? How are these processes changed in human diseases, and can the changes be corrected?

The Floor lab uses genome editing, functional genomics, biochemistry, and cell biology to explore these and other questions. Learn more about our projects or recent work.

We are members of the Department of Cell and Tissue Biology & Helen Diller Family Comprehensive Cancer Center, and Biophysics, Biomedical Sciences, & Tetrad Graduate Programs.

Thanks to the UCSF PBBR, the California Tobacco Releated Disease Research Program, and the NIH New Innovator program for supporting our work!

Projects


RNA chaperones

Remodeling of RNA by DEAD-box RNA chaperones
DEAD-box proteins use the energy of ATP hydrolysis to remodel RNA structures and RNA-protein complexes. We study how DEAD-box proteins influence gene expression through mechanical work.

Transcript isoform translation

Translational output of the human transcriptome
Most human genes give rise to multiple mRNAs through alternative mRNA processing. Each mRNA may include different coding sequences, regulatory sequences, or both. We measure how well different mRNAs are translated and use this information to control transgene expression.

RNA in disease

RNA in developmental disorders and cancer
DEAD-box proteins and other aspects of RNA biology are altered in numerous human diseases. We are studying how alteration of the DEAD-box protein DDX3 drives formation of the brain tumor medulloblastoma, and other RNA-related processes in disease.

RNA granules

Cell biophysics & phase separation of RNA
RNA molecules exist in a crowded cytoplasm. RNA and RNA-binding proteins partition into phase-separated RNA granules under some conditions. We investigate the role of RNA chaperones like DEAD-box proteins in this balance.

The lab

This is us

Lab members


...

Lorenzo Calviello, PhD

Postdoc

B.S.,M.S. Molecular Biosciences: University of Pisa
Ph.D.: MDC/BIMSB (Uwe Ohler lab)

...

Ann Deng

Technician

B.A. Molecular and Cell Biology, B.A. Music:
UC Berkeley

...

Stephen N. Floor, PhD

Principal Investigator (CV)

stephen.floor@ucsf.edu

B.S. Physics, Computer Science: Univ. of Kansas
Ph.D.: UCSF Biophysics (John Gross lab)
Postdoc: Berkeley (Doudna lab)

...

Ziad Jowhar

Graduate Student (BMS/MSTP)

B.S. Biology and Neuroscience: Emory University

...

José Liboy Lugo

Graduate Student (Tetrad)

B.S. Industrial Biotechnology:
University of Puerto Rico, Mayaguez

UCSF Discovery Fellow

...

Yizhu Lin, PhD

Postdoc

B.S. Biology, University of Science and Technology of China
Ph.D.: Carnegie Mellon University Biological Sciences (Joel McManus lab)

...

Srivats Venkataramanan, PhD

Postdoc

B. Tech & M. Tech: Indian Inst. of Tech. Madras, Biotechnology
PhD: UCLA Molecular, Cell, and Dev. Biology
(Tracy Johnson lab)

NIGMS F32 Fellow

...

Kevin Wilkins

Graduate Student (BMS)

BS: Notre Dame,
Biologial Science and Medieval Studies

TRDRP Predoctoral Scholar

...

Albert Xu

Graduate Student (BMS/MSTP)

BS: UC Berkeley, Molecular and Cell Biology

Lab alumni:


Lesly Montano Zolano, 2020, Biotech Partners Intern. Next: returned to Berkeley High School
Peter Bowman-Davis, 2019-2020, Visiting High School Student. Next: returned to Justin-Siena High School
Luisa Arake de Tacca, 2019, Joint Graduate Student with Jamie Cate. Next: Scientist at Acrigen Biosciences
Emily Ehsan, 2019, Visiting Undergrad. Next: returned to Cornell for her sophomore year
Bao Thai, 2017-2019, Technician. Next: MD/PhD program at Arizona
Malvika Tejura, 2017-2019, Technician. Next: Research Assistant at Ultima Genomics
Katie Blackwell, 2018, SRTP summer student. Next: returned to UT Dallas for her junior year
Skylar Johnson, 2018, Biotech Partners Intern. Next: returned to community college

Recent publications


DDX3X and DDX3Y are redundant in protein synthesis

Venkataramanan S, Calviello L, Wilkins K, and Floor SN. (2020)

DDX3 depletion represses translation of mRNAs with complex 5′ UTRs

Calviello L, Venkataramanan S, et al., Landthaler M, and Floor SN. (2020)

Pathogenic DDX3X mutations impair RNA metabolism and neurogenesis during fetal cortical development.

Lennox AL, Hoye ML, et al., Floor SN, Silver DL, and Sherr EH. (2020)

For a complete list of publications please click here or grab an RSS feed

Contact us


We're always excited to talk with people interested in the lab! Applicants, journalists, educators - get in touch!

Postdoc applicants email Stephen with your CV and why you'd like to work in the lab.
For info about what it's like to be a postdoc at UCSF and associated policies, click here.

Rotation students: multiple projects available! Email Stephen to discuss.

Prospective graduate students please apply through one of the UCSF BMS or iPQB graduate programs or another UCSF graduate program.

The Floor lab welcomes people of any race, religion, national origin, gender, political affiliation, sexual orientation, and eligible age or disability.

513 Parnassus Ave
HSW 740
San Francisco, CA 94143

News


November 2020: Ziad joined as a BMS/MSTP graduate student!

September 2020: Two new preprints posted in the same week!

September 2020: Congratulations to José for being selected as a UCSF Discovery Fellow!

May 2020: Welcome to Peter Bowman-Davis and Lesly Montano Zolano who will join us for the summer!

May 2020: Albert Xu joined as a BMS/MSTP graduate student!

May 2020: Congratulations to José for passing his qualifying exam!

March 2020: Our paper with the Silver and Sherr labs is published!

August 2019: Welcome to Ann Deng, a new technician, and José Liboy who has joined the lab!

June 2019: Kevin is awarded a predoctoral fellowship from the TRDRP!

June 2019: Welcome to Emily Ehsan and Albert Xu who are joining us for the summer!

May 2019: Our preprint identifying the set of mRNAs that require DDX3 for translation is out!

May 2019: Congrats to Kevin, PhD candidate, for passing his qualifying exam!

December 2018: Welcome to Yizhu Lin, our new postdoc joining from Joel McManus's lab!

October 2018: The lab is funded by the NIH New Innovator program!

July 2018: Welcome to Lorenzo Calviello, our new postdoc joining us from Uwe Ohler's lab!

July 2018: Welcome to Luisa Tacca, a visiting graduate student from Jamie Cate's lab at UC Berkeley!

June 2018: Welcome to Kevin Wilkins, our first graduate student, and Katie Blackwell for the summer from SRTP!

March 2018: Welcome to Srivats Venkataramanan, our first postdoc from Tracy Johnson's lab!

February 2018: The lab is funded by the TRDRP for medulloblastoma research!

December 2017: The lab is funded by the UCSF PBBR!

July 2017: Bao and Malvika join in starting the lab!