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School of the Biological Sciences

 

 

Group Leader, Deparment of Physiology, Development, and Neuroscience, and Stem Cell Institute 

Srinjan Basu's research focuses on developing single-cell and single-molecule imaging approaches to improve our understanding of stem cell renewal and differentiation. Learn more. 

 

Research Areas


Stem cells 
Stem cell fate transitions
Cancer
Genome architecture
Chromatin
 

Techniques


Biophysics and computation
Single-cell Hi-C
Single-cell imaging
Single-molecule imaging
 
 
   

 

Research Theme


   Reproduction, Development and Lifelong Health

 

Publications

Journal articles

2022

  • Pal, D., Patel, M., Boulet, F., Sundarraj, J., Grant, O., Branco, M., Basu, S., Santos, S., Zabet, NR., Scaffidi, P. and Pradeepa, M., 2022. H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function
    Doi: 10.1101/2022.04.29.488986
  • Steindel, M., Orsine de Almeida, I., Strawbridge, S., Chernova, V., Holcman, D., Ponjavic, A. and Basu, S., 2022. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy. Methods Mol Biol, v. 2476
    Doi: http://doi.org/10.1007/978-1-0716-2221-6_16
  • Novo, CL., Wong, EV., Hockings, C., Poudel, C., Sheekey, E., Wiese, M., Okkenhaug, H., Boulton, SJ., Basu, S., Walker, S., Kaminski Schierle, GS., Narlikar, GJ. and Rugg-Gunn, PJ., 2022. Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells. Nat Commun, v. 13
    Doi: http://doi.org/10.1038/s41467-022-31198-3
  • 2020

  • Basu, S., Shukron, O., Ponjavic, A., Parruto, P., Boucher, W., Zhang, W., Reynolds, N., Lando, D., Shah, D., Sober, LH., Jartseva, A., Ragheb, R., Cramard, J., Floyd, R., Brown, G., Gor, K., Balmer, J., Drury, TA., Carr, AR., Needham, L-M., Aubert, A., Communie, G., Morey, L., Blanco, E., Barber, MA., Mohorianu, I., Bartke, T., Di Croce, L., Berger, I., Schaffitzel, C., Lee, SF., Stevens, TJ., Klenerman, D., Hendrich, BD., Holcman, D. and Laue, ED., 2020. Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics BioRxiv,
    Doi: 10.1101/2020.04.03.003178
  • Morf, J., Basu, S. and Amaral, PP., 2020. RNA, Genome Output and Input. Front Genet, v. 11
    Doi: http://doi.org/10.3389/fgene.2020.589413
  • Novo, CL., Wong, E., Hockings, C., Poudel, C., Sheekey, E., Walker, S., Schierle, GK., Narlikar, G. and Rugg-Gunn, P., 2020. Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells
    Doi: 10.1101/2020.06.08.139642
  • 2017

  • Stevens, TJ., Lando, D., Basu, S., Atkinson, LP., Cao, Y., Lee, SF., Leeb, M., Wohlfahrt, KJ., Boucher, W., O’Shaughnessy-Kirwan, A., Cramard, J., Faure, AJ., Ralser, M., Blanco, E., Morey, L., Sanso, M., Palayret, MGS., Lehner, B., Di Croce, L., Wutz, A., Hendrich, B., Klenerman, D. and Laue, ED., 2017. 3D structure of individual mammalian genomes studied by single cell Hi-C Nature,
    Doi: 10.1038/nature21429
  • Carr, AR., Ponjavic, A., Basu, S., McColl, J., Santos, AM., Davis, S., Laue, ED., Klenerman, D. and Lee, SF., 2017. Three-Dimensional Super-Resolution in Eukaryotic Cells Using the Double-Helix Point Spread Function Biophysical Journal, v. 112
    Doi: 10.1016/j.bpj.2017.02.023
  • 2016

  • Zhou, Y., Basu, S., Laue, E. and Seshia, AA., 2016. Single cell studies of mouse embryonic stem cell (mESC) differentiation by electrical impedance measurements in a microfluidic device. Biosens Bioelectron, v. 81
    Doi: 10.1016/j.bios.2016.02.069
  • Zhou, Y., Basu, S., Wohlfahrt, KJ., Lee, SF., Klenerman, D., Laue, ED. and Seshia, AA., 2016. A microfluidic platform for trapping, releasing and super-resolution imaging of single cells. Sens Actuators B Chem, v. 232
    Doi: 10.1016/j.snb.2016.03.131
  • Zhang, W., Aubert, A., Gomez de Segura, JM., Karuppasamy, M., Basu, S., Murthy, A., Diamante, A., Drury, TA., Balmer, J., Cramard, J., Watson, AA., Lando, D., Lee, SF., Palayret, M., Kloet, S., Smits, A., Deery, M., Vermeulen, M., Hendrich, B., Klenerman, D., Schaffitzel, C., Berger, I. and Laue, ED., 2016. The Nucleosome Remodeling and Deacetylase Complex NuRD Is Built from Preformed Catalytically Active Sub-modules Journal of Molecular Biology, v. 428
    Doi: 10.1016/j.jmb.2016.04.025
  • Needham, L-M., Basu, S., Taylor, E., Laue, ED., Klenerman, D., Lando, D. and Lee, SF., 2016. Improved Photo Physical Properties of mEos3 for Single Molecule Tracking BIOPHYSICAL JOURNAL, v. 110
    Doi: 10.1016/j.bpj.2015.11.2596
  • Basu, S., Tan, YL., Taylor, EJR., Laue, ED. and Lee, SF., 2016. Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localisation Microscopy. Methods Mol Biol, v. 1431
    Doi: 10.1007/978-1-4939-3631-1_17
  • Zhou, Y., Basu, S., Laue, ED. and Seshia, AA., 2016. Dynamic monitoring of single cell lysis in an impedance-based microfluidic device. Biomed Microdevices, v. 18
    Doi: 10.1007/s10544-016-0081-z
  • 2015

  • Palayret, M., Armes, H., Basu, S., Watson, AT., Herbert, A., Lando, D., Etheridge, TJ., Endesfelder, U., Heilemann, M., Laue, E., Carr, AM., Klenerman, D. and Lee, SF., 2015. Virtual-'light-sheet' single-molecule localisation microscopy enables quantitative optical sectioning for super-resolution imaging. PLoS One, v. 10
    Doi: 10.1371/journal.pone.0125438
  • Lu, F-K., Basu, S., Igras, V., Hoang, MP., Ji, M., Fu, D., Holtom, GR., Neel, VA., Freudiger, CW., Fisher, DE. and Xie, XS., 2015. Label-free DNA imaging in vivo with stimulated Raman scattering microscopy. Proc Natl Acad Sci U S A, v. 112
    Doi: 10.1073/pnas.1515121112
  • 2015. Correction for Lu et al., Label-free DNA imaging in vivo with stimulated Raman scattering microscopy. Proc Natl Acad Sci U S A, v. 112
    Doi: http://doi.org/10.1073/pnas.1519382112
  • 2013

  • Gebhardt, JCM., Suter, DM., Roy, R., Zhao, ZW., Chapman, AR., Basu, S., Maniatis, T. and Xie, XS., 2013. Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat Methods, v. 10
    Doi: http://doi.org/10.1038/nmeth.2411
  • Gebhardt, JCM., Suter, DM., Roy, R., Zhao, ZW., Chapman, AR., Basu, S., Maniatis, T. and Xie, XS., 2013. Single-molecule imaging of transcription factor binding to DNA in live mammalian cells Nature Methods, v. 10
    Doi: http://doi.org/10.1038/nmeth.2411
  • 2012

  • Zhang, X., Roeffaers, MBJ., Basu, S., Daniele, JR., Fu, D., Freudiger, CW., Holtom, GR. and Xie, XS., 2012. Label-free live-cell imaging of nucleic acids using stimulated Raman scattering microscopy. Chemphyschem, v. 13
    Doi: http://doi.org/10.1002/cphc.201100890
  • 2008

  • Nolan, ME., Aranda, V., Lee, S., Lakshmi, B., Basu, S., Allred, DC. and Muthuswamy, SK., 2008. The polarity protein Par6 induces cell proliferation and is overexpressed in breast cancer. Cancer Res, v. 68
    Doi: http://doi.org/10.1158/0008-5472.CAN-07-6567
  • Laue, ED., Lando, D., Basu, S., Stevens, T., Riddell, A., Wohlfahrt, K., Cao, Y., Boucher, W., Leeb, M., Atkinson, L., Lee, S., Hendrich, B. and Klenerman, D., Combining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell Nature Protocols,
  • Laue, ED., Lando, D., Stevens, T. and Basu, S., Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols Nucleus,
  • Laue, ED., Basu, S., Needham, LM., Lando, D., Taylor, EJR., Wohlfahrt, K., Shah, D., Boucher, W., Tan, YL., Bates, LE., Tkachenko, O., Cramard, J., Lagerholm, BC., Eggeling, C., Hendrich, B., Klenerman, D. and Lee, SF., FRET-enhanced photostability allows improved single-molecule tracking of proteins and protein complexes in live mammalian cells Nature Communications,
  • Wiese, M., Bannister, A., Basu, S., Boucher, W., Wohlfahrt, K., Christophorou, M., Nielsen, M., Klenerman, D., Laue, E. and Kouzarides, T., Citrullination of HP1γ 1 chromodomain affects association to chromatin Epigenetics and Chromatin,
  • Wurmser, A. and Basu, S., Enhancer-Promoter Communication: It’s Not Just About Contact Frontiers in Molecular Biosciences, v. 9
    Doi: http://doi.org/10.3389/fmolb.2022.867303
  • Pal, D., Patel, M., Boulet, F., Sundarraj, J., Grant, OA., Branco, MR., Basu, S., Santos, SDM., Zabet, NR., Scaffidi, P. and Pradeepa, MM., H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function Nature Structural and Molecular Biology,
    Doi: 10.1038/s41594-023-01016-5
  • Datasets
  • Zhou, Y., Basu, S., Wohlfahrt, KJ., Lee, SF., Klenerman, D., Laue, ED. and Seshia, AA., Research data supporting "A microfluidic platform for trapping, releasing and super-resolution imaging of single cells"
    Doi: 10.17863/CAM.589
  • Zhou, Y., Basu, S., Laue, ED. and Seshia, AA., Research data supporting "Dynamic monitoring of single cell lysis in an impedance-based microfluidic device"
    Doi: 10.17863/CAM.588
  • Zhou, Y., Basu, S., Laue, E. and Seshia, AA., Research data supporting "Single cell studies of mouse embryonic stem cell (mESC) differentiation by electrical impedance measurements in a microfluidic device"
    Doi: 10.17863/CAM.587
  • Other publications

    2022

  • Sielaff, H., Basu, S. and Zhao, ZW., 2022. Editorial: Imaging Approaches to Unravel Chromatin Organization and Nuclear Dynamics. Front Mol Biosci, v. 9
    Doi: http://doi.org/10.3389/fmolb.2022.929370