Prof. Dr. Ibrahim Cissé
Director
Department of Biological Physics
Max Planck Institute, Freiburg, Germany
Super-resolution imaging of transcription
in live cells
We are always hiring
Outline
High School
(NIGER)
NCCU, B.S. in Physics
(North Carolina, USA)
PhD, Physics
(Univ. of Illinois, USA)
Post-Doc
(Ecole Normale Superieure – Paris, France)
Research Specialist, Biology
(HHMI Virginia, USA)
Professor (assistant to Associate with Tenure) in Physics
(MIT - Cambridge, USA)
Full Professor of Physics
(CalTech - Pasadena, USA)
Director
(Max Planck Gesellschaft - MPI-Freiburg, Germany)
Science is global!
Max Planck Gesellschaft (Max Plack Society)
Google AI says:
The Max Planck Society (Max-Planck-Gesellschaft) is an independent, non-profit German research organization that conducts basic research in natural sciences, life sciences , and the humanities through its 84 institutes and facilities. Founded in 1948 (and since 1911 Kaiser Wilhelm Society) it is Germany's most successful research institution with 31 Nobel laureates. The society is funded by federal and state governments, with its research focus on promoting excellence by attracting leading scientists who define their own subjects and have freedom in selecting staff.
�
Name Ibrahim Cissé
Nationality: USA & Niger
Institution: Max Planck Institute of Immunobiology & Epigenetics
Contact:+49 761 5108 422, cisse@ie-freiburg.mpg.de
Position: Director
Ph.D., Physics, University of Illinois at Urbana-Champaign, 2009
B.S., Physics, North Carolina Central University, 2004
Massachusetts Institute of Technology (MIT), Dept. of Physics
Associate Professor of Physics With Tenure, 2020-Present
Associate Professor of Physics, 2019-2020
Assistant Professor of Physics, MIT, 2014- 2019
Employment
California Institute of Technology (Caltech), Dept. of Physics/PMA
Full Professor of Physics, 2021
Max Planck Institute of Immunobiology & Epigenetics
Director, 2021- Present
Honors
MacArthur Fellow
Elected Fellow, American Physical Society (APS-Physics)
Next Einstein Fellow, African Institute of Mathematical Sciences, 2019
Elected Member of Europea Molecular Biolog Organisation (EMBO)
Science News (SN10), 10 Scientists To Watch List
In the spring of 1913, two German visitors, Max Planck and Walther Nernst, called upon Einstein in Zurich in the hope of persuading him to relocate to Berlin.[87] They offered him membership of the Prussian Academy of Sciences, the directorship of the planned Kaiser Wilhelm Institute for Physics and a chair at the Humboldt University of Berlin that would allow him to pursue his research supported by a professorial salary but with no teaching duties to burden him
-Wikipedia
NIH/NIGMS R01
(R01GM134734)
NIH New Innovator
(DP2CA195769)
Facilities @ MPI Freiburg
Imaging Facility
Proteomics Facility
FACS & Metabolomics Facility
Transgenic Mouse Facility
Animal (Mouse, FISH) Facility
Bioinformatics Facility
Deep Sequencing Facility
Fly Facility
Freiburg, Germany
Dept. of Biological Physics
Cissé Lab
MPI -Freiburg
icisse.org
We are always hiring
…
General interest
Cooperativity in weak & transient interactions
~kBT
“The whole is greater than the sum of its parts”
Complexity from macroscopic world to genome regulation
~Ffriction
School of fish
Ant colony
Body image wall321.com
Cisse et al. Science (2013)
1 meter
5 𝜇m
RNA Polymerase II
(Pol II)
2019 Breakthrough Prize
Xiaowei Zhuang
Single-Molecule Super-resolution (PALM/STORM,STED…)
The Nobel Prize in
Chemistry 2006
Roger D. Kornberg
Sub-diffractive Pol II clustering inside a cell nucleus
Transcription is when RNA Polymerase II (Pol II) decodes DNA into RNA
Fluorescence
“The History of Luminescence from Early Times until 1900” E. Newton Harvey (1957)
http://www.lfd.uci.edu/workshop/2006/
* I confess I do not like this term. I am almost inclined to coin a word, and call the appearance fluorescence, from fluor-spar, as the analogous term opalescence is derived from the name of a mineral.
"dispersive reflection”
George G. Stokes Philosophical Transaction (The Royal Society, 1852)
>500nm
488nm
510nm
Ernst Abbe engraved memorial, Univ of Jena
http://www.feynmanlectures.caltech.edu/I_30.html
Jellyfish (Aequorea Victoria) Image Credit: montereybayaquarium.org
A genetically encoded fluorescent molecule:
The Green Fluorescent Protein (GFP)
200 nm
2D-fitting
200 nm
Localization
200 nm
200 nm
200 nm
200 nm
200 nm
200 nm
200 nm
200 nm
200 nm
Conventional diffraction limited image
General principle
of single-molecule based super-resolution
200 nm
200 nm
200 nm
200 nm
200 nm
200 nm
200 nm
200 nm
200 nm
200 nm
200 nm
200 nm
2D single-molecule-based super-resolution
time-correlated Super-Resolution (tcPALM)
Cisse et al. Science (2013) 341
“PALM/STORM works with only static or fixed sub-structures”
“PALM/STORM works with only static or fixed sub-structures”
highly dynamic and living
Example tcPALM trace
RNA Pol II forms transient, sub-diffractive clusters in live mammalian cells
Pol II clusters in live cancerous (human) cells
Cisse et al. Science (2013)
Pol II clusters in differentiated (mice) live cells
Cho et al. eLife (2016)
Cho et al. Scientific Reports (2016)
Pol II/Mediator clusters in live stem cells
Cho et al. Science (2018)
Sabari…Young et al. Science (2018)
Guo…Young et al. Nature (2019)
Du et al. Cell (2024)
Lee et al. Cell (2024)
Mechanism of first order phase transition
Narayanan et al. eLife (2019)
Pol II clusters dynamics correlate directly with mRNA output
RNA (gene)
A cluster of Pol II on the RNA gene!
Pol II clusters
Cho et al. eLife (2016) e13617
Collaboration with L. Lavis (Janelia)
T. Lionnet, B. English (Singer Lab, Janelia),
The classical view of transcription initiation:
A single Pol II activates genes
Pol II
DNA
transient Pol II clusters help productive transcription initiation
Pol II (N~80, t~8s)
mRNA (N~4)
DNA
Cho et al. eLife (2016) e13617
endogenous beta-actin gene
NIH/NIGMS R01
(R01GM134734)
NIH New Innovator
(DP2CA195769)
Facilities @ MPI Freiburg
Imaging Facility
Proteomics Facility
FACS & Metabolomics Facility
Transgenic Mouse Facility
Animal (Mouse, FISH) Facility
Bioinformatics Facility
Deep Sequencing Facility
Fly Facility
Freiburg, Germany
Dept. of Biological Physics
Cissé Lab
MPI -Freiburg
icisse.org
Today, highlight recent works by
Dr Manyu Du
Dr. Choongman Lee
Dr. Haneul Yoo
We are always hiring
Dr Manyu Du 🡪 Assistant Prof. Penn State (2025)
Dr Choongman Lee 🡪 on the market !!
NIH/NIGMS R01
(R01GM134734)
NIH New Innovator
(DP2CA195769)
Facilities @ MPI Freiburg
Imaging Facility
Proteomics Facility
FACS & Metabolomics Facility
Transgenic Mouse Facility
Animal (Mouse, FISH) Facility
Bioinformatics Facility
Deep Sequencing Facility
Fly Facility
Freiburg, Germany
Dept. of Biological Physics
Cissé Lab
MPI -Freiburg
icisse.org
We are always hiring