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School of the Biological Sciences

 

Jussi Taipale

 

Group Leader, Department of Biochemistry

Jussi Taipale aims to understand two systems-level questions that are presently poorly understood: the mechanisms that control growth of tissues and organisms, and the rules that specify how DNA sequence determines when and where genes are expressed. Learn more.

 

Research Areas

Transcriptional control of growth
Cancer genomics
 
 
 
 

Techniques

High-throughput biology
HT-SELEX
 
 
 
 
    

 

Research Theme

 

Publications

Journal articles

2021

  • Sahu, B., Pihlajamaa, P., Zhang, K., Palin, K., Ahonen, S., Cervera, A., Ristimäki, A., Aaltonen, LA., Hautaniemi, S. and Taipale, J., 2021. Human cell transformation by combined lineage conversion and oncogene expression. Oncogene, v. 40
    Doi: http://doi.org/10.1038/s41388-021-01940-0
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  • Lidschreiber, K., Jung, LA., von der Emde, H., Dave, K., Taipale, J., Cramer, P. and Lidschreiber, M., 2021. Transcriptionally active enhancers in human cancer cells. Mol Syst Biol, v. 17
    Doi: http://doi.org/10.15252/msb.20209873
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  • Yan, J., Qiu, Y., Ribeiro Dos Santos, AM., Yin, Y., Li, YE., Vinckier, N., Nariai, N., Benaglio, P., Raman, A., Li, X., Fan, S., Chiou, J., Chen, F., Frazer, KA., Gaulton, KJ., Sander, M., Taipale, J. and Ren, B., 2021. Systematic analysis of binding of transcription factors to noncoding variants. Nature, v. 591
    Doi: http://doi.org/10.1038/s41586-021-03211-0
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  • Reint, G., Li, Z., Labun, K., Keskitalo, S., Soppa, I., Mamia, K., Tolo, E., Szymanska, M., Meza-Zepeda, LA., Lorenz, S., Cieslar-Pobuda, A., Hu, X., Bordin, DL., Staerk, J., Valen, E., Schmierer, B., Varjosalo, M., Taipale, J. and Haapaniemi, E., 2021. Rapid genome editing by CRISPR-Cas9-POLD3 fusion. Elife, v. 10
    Doi: http://doi.org/10.7554/eLife.75415
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  • Kuisma, H., Bramante, S., Rajamäki, K., Sipilä, LJ., Kaasinen, E., Kaukomaa, J., Palin, K., Mäkinen, N., Sjöberg, J., Sarvilinna, N., Taipale, J., Kauppi, L., Tumiati, M., Hassinen, A., Pitkäniemi, J., Jalkanen, J., Heikkinen, S., Pasanen, A., Heikinheimo, O., Bützow, R., Välimäki, N. and Aaltonen, LA., 2021. Parity associates with chromosomal damage in uterine leiomyomas. Nat Commun, v. 12
    Doi: http://doi.org/10.1038/s41467-021-25806-x
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  • Berta, DG., Kuisma, H., Välimäki, N., Räisänen, M., Jäntti, M., Pasanen, A., Karhu, A., Kaukomaa, J., Taira, A., Cajuso, T., Nieminen, S., Penttinen, R-M., Ahonen, S., Lehtonen, R., Mehine, M., Vahteristo, P., Jalkanen, J., Sahu, B., Ravantti, J., Mäkinen, N., Rajamäki, K., Palin, K., Taipale, J., Heikinheimo, O., Bützow, R., Kaasinen, E. and Aaltonen, LA., 2021. Deficient H2A.Z deposition is associated with genesis of uterine leiomyoma. Nature, v. 596
    Doi: http://doi.org/10.1038/s41586-021-03747-1
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    2020

  • Yi, W., Li, J., Zhu, X., Wang, X., Fan, L., Sun, W., Liao, L., Zhang, J., Li, X., Ye, J., Chen, F., Taipale, J., Chan, KM., Zhang, L. and Yan, J., 2020. CRISPR-assisted detection of RNA-protein interactions in living cells. Nat Methods, v. 17
    Doi: http://doi.org/10.1038/s41592-020-0866-0
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  • Jolma, A., Zhang, J., Mondragón, E., Morgunova, E., Kivioja, T., Laverty, KU., Yin, Y., Zhu, F., Bourenkov, G., Morris, Q., Hughes, TR., Maher, LJ. and Taipale, J., 2020. Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences. Genome Res, v. 30
    Doi: http://doi.org/10.1101/gr.258848.119
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  • Dodonova, SO., Zhu, F., Dienemann, C., Taipale, J. and Cramer, P., 2020. Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Nature, v. 580
    Doi: http://doi.org/10.1038/s41586-020-2195-y
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    2019

  • Sahu, B., Pihlajamaa, P., Zhang, K., Palin, K., Ahonen, S., Cervera, A., Ristimäki, A., Aaltonen, L., Hautaniemi, S. and Taipale, J., 2019. Cellular transformation by combined lineage conversion and oncogene expression
    Doi: 10.1101/525600
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  • Haapaniemi, E., Botla, S., Persson, J., Schmierer, B. and Taipale, J., 2019. Reply to "CRISPR screens are feasible in TP53 wild-type cells". Mol Syst Biol, v. 15
    Doi: http://doi.org/10.15252/msb.20199059
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    2018

  • Lambert, SA., Jolma, A., Campitelli, LF., Das, PK., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, TR. and Weirauch, MT., 2018. The Human Transcription Factors. Cell, v. 172
    Doi: http://doi.org/10.1016/j.cell.2018.01.029
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  • Taipale, AJ., Yin, Y., Das, PK., Jolma, A., Zhu, F., Popov, A., Xu, Y. and Nilsson, L., 2018. Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima eLife,
    Doi: http://doi.org/10.7554/eLife.32963
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  • Kondelin, J., Salokas, K., Saarinen, L., Ovaska, K., Rauanheimo, H., Plaketti, R-M., Hamberg, J., Liu, X., Yadav, L., Gylfe, AE., Cajuso, T., Hänninen, UA., Palin, K., Ristolainen, H., Katainen, R., Kaasinen, E., Tanskanen, T., Aavikko, M., Taipale, M., Taipale, J., Renkonen-Sinisalo, L., Lepistö, A., Koskensalo, S., Böhm, J., Mecklin, J-P., Ongen, H., Dermitzakis, ET., Kilpivaara, O., Vahteristo, P., Turunen, M., Hautaniemi, S., Tuupanen, S., Karhu, A., Välimäki, N., Varjosalo, M., Pitkänen, E. and Aaltonen, LA., 2018. Comprehensive evaluation of coding region point mutations in microsatellite-unstable colorectal cancer. EMBO Mol Med, v. 10
    Doi: http://doi.org/10.15252/emmm.201708552
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  • Palin, K., Pitkänen, E., Turunen, M., Sahu, B., Pihlajamaa, P., Kivioja, T., Kaasinen, E., Välimäki, N., Hänninen, UA., Cajuso, T., Aavikko, M., Tuupanen, S., Kilpivaara, O., van den Berg, L., Kondelin, J., Tanskanen, T., Katainen, R., Grau, M., Rauanheimo, H., Plaketti, R-M., Taira, A., Sulo, P., Hartonen, T., Dave, K., Schmierer, B., Botla, S., Sokolova, M., Vähärautio, A., Gladysz, K., Ongen, H., Dermitzakis, E., Bramsen, JB., Ørntoft, TF., Andersen, CL., Ristimäki, A., Lepistö, A., Renkonen-Sinisalo, L., Mecklin, J-P., Taipale, J. and Aaltonen, LA., 2018. Contribution of allelic imbalance to colorectal cancer. Nat Commun, v. 9
    Doi: http://doi.org/10.1038/s41467-018-06132-1
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  • Taipale, J., 2018. Informational limits of biological organisms. EMBO J, v. 37
    Doi: http://doi.org/10.15252/embj.201696114
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    2017

  • Dave, K., Sur, I., Yan, J., Zhang, J., Kaasinen, E., Zhong, F., Blaas, L., Li, X., Kharazi, S., Gustafsson, C., De Paepe, A., Månsson, R. and Taipale, J., 2017. Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth. Elife, v. 6
    Doi: http://doi.org/10.7554/eLife.23382
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  • Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, PK., Kivioja, T., Dave, K., Zhong, F., Nitta, KR., Taipale, M., Popov, A., Ginno, PA., Domcke, S., Yan, J., Schübeler, D., Vinson, C. and Taipale, J., 2017. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science, v. 356
    Doi: http://doi.org/10.1126/science.aaj2239
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  • Schmierer, B., Botla, SK., Zhang, J., Turunen, M., Kivioja, T. and Taipale, J., 2017. CRISPR/Cas9 screening using unique molecular identifiers. Mol Syst Biol, v. 13
    Doi: http://doi.org/10.15252/msb.20177834
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  • Zhu, F., Farnung, L., Kaasinen, E., Sahu, B., Yin, Y., Wei, B., Dodonova, SO., Nitta, KR., Morgunova, E., Taipale, M., Cramer, P. and Taipale, J., The interaction landscape between transcription factors and the nucleosome Nature, v. 562
    Doi: http://doi.org/10.1038/s41586-018-0549-5
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