2026.03.01. Updated

All publications can also be found in Google Scholar. [Link]

Main Publications

1. [Must-Read] Light-induced targeting enables proteomics on endogenous condensates

   Choongman Lee, Andrea Quintana, Ida Suppanz, Alejandro Gomez-Auli, Gerhard Mittler, and Ibrahim I Cisse

   Cell, 2024 [Link]

   • Max-Planck-Gesellschaft News [Link]
   • Patent WO2024133013 - MEANS AND METHODS TO TARGET ENDOGENOUS CONDENSATES [Link]
   • The LiTEC (Light-induced Targeting of Endogenous Condensates) system establishes the first proof-of-concept for targeting and manipulating transcriptional condensates in living cells using optogenetics. By delivering BioID into these condensates as a cargo, it enables — for the first time — proteomic profiling of their native composition with minimal perturbation. LiTEC further highlights the potential for manipulating condensates in vivo, opening new avenues for dissecting their roles in gene regulation and cellular function.

2. [Must-Read] Direct observation of a condensate effect on super-enhancer-controlled gene bursting

   Manyu Du, Simon Hendrik Stitzinger, Jan-Hendrik Spille, Won-Ki Cho, Choongman Lee, Mohammed Hijaz, Andrea Quintana, and Ibrahim I Cisse

   Cell, 2024 [Link]

   • This study provides the first direct functional evidence for transcriptional condensates: the spatial and dynamic proximity of endogenous condensates to a super-enhancer–controlled gene locus regulates transcriptional bursting. Live-cell time-lapse imaging of Sox2 output and condensate dynamics shows that condensate contact enhances burst size and frequency, whereas disrupting condensate behavior abolishes this effect. These findings establish a causal role for transcriptional condensates in regulating gene expression.

3. A dual role for H2A.Z.1 in modulating the dynamics of RNA polymerase II initiation and elongation

   Constantine Mylonas, Choongman Lee, Alexander L Auld, Ibrahim I Cisse, and Laurie A Boyer

   Nature Structural & Molecular Biology, 2021 [Link]

4. A CRISPR/Cas9 platform for MS2-labelling of single mRNA in live stem cells

   Jan-Hendrik Spille, Micca Hecht, Valentin Grube, Won-ki Cho, Choongman Lee, and Ibrahim I Cisse

   Methods, 2019 [Link]

5. [Must-Read] Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

   Won-Ki Cho*, Jan-Hendrik Spille*, Micca Hecht, Choongman Lee, Charles Li, Valentin Grube, and Ibrahim I Cisse

   Science, 2018 [Link]

   • This work demonstrates that Mediator and RNA polymerase II form both transient and stable clusters in living mouse embryonic stem cells. These stable clusters, referred to as transcriptional condensates, exhibit liquid-like properties and assemble in a transcription-dependent manner, with Mediator acting as a scaffold for Pol II recruitment. These findings suggest that condensate formation plays a functional role in regulating gene expression.

6. Analysis of Tertiary Interactions between SART3 and U6 Small Nuclear RNA Using Modified Nanocapillaries

   Choongman Lee, Joon Kyu Park, Yeoan Youn, Joo Hyoung Kim, Kyo-Seok Lee, Nak-kyoon Kim, Eunji Kim, Eunice Eunkyeong Kim*, and Kyung-Hwa Yoo*

   Analytical Chemistry, 2017 [Link]

7. Selective detection of single-stranded DNA molecules using a glass nanocapillary functionalized with DNA

   Yeoan Youn, Choongman Lee, Joo Hyoung Kim, Young Wook Chang, Dug Young Kim, and Kyung-Hwa Yoo

   Analytical Chemistry, 2015 [Link]