Research Groups > Epigenetics Computational Regulatory Genomics

“Our research investigates how regulatory information is encoded in DNA, how it is interpreted and how it is communicated across cells in multicellular organisms”

The development of complex organisms critically depends upon regulation of gene activity across dozens, hundreds or millions of cells in time and space. This regulation ensures the fidelity of development of complex structures and the overall function of the organism. Its disruption therefore often leads to disease.
We study gene regulation at the genomewide level using computational genomics and epigenomics. Our major research interests focus on:
  • Structure and function of gene promoters
  • Function and genomic distribution of gene regulatory elements
  • Function of transcription factors
  • Regulation of the production of transcription factors i.e. transcriptional regulatory networks (TRNs)
  • Association of different modes of regulation with epigenetic marks and their inheritance
Our recent work centres on the functional classification of core promoters, the development of methods to correctly assign regulatory elements to the genes they regulate, and the role of the epigenome in guiding development.

 




Promotor type and responsiveness to enhancers. Ldb1 complex binding around promotor genes involved in erythroid differentiation.

  Computational Regulatory Genomics
Group head

Boris Lenhard (Dr)

Group members

Amit Adlakha

Chain-Florey Fellow
Email

Piotr Balwierz (Dr)

Anja Baresic (Dr)

Slavica Dimitrieva (Dr)

Vanja Haberle (Miss)

PhD Student

Nathan Harmston (Dr)

Elizabeth Ing-Simmons (Ms)

Malcolm Perry (Mr)

Ge Tan (Mr)

Visiting worker

Sam Tung (Mr)

Admin contact

Christine Greig (Ms)

Telephone 34318
Email
Contact details
Selected publications
Zuin, J., Franke, V., van Ijcken, W. F., van der Sloot, A., Krantz, I. D., van der Reijden, M. I., Nakato, R., Lenhard, B., Wendt, K. S., 2014. A Cohesin-Independent role for NIPBL at promoters provides insights in CdLS. PLoS Genetics 10 (2). | Full text

Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., Ntini, E., Arner, E., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Lilje, B., Rapin, N., Bagger, F. O. O., Jørgensen, M., Andersen, P. R. R., Bertin, N., Rackham, O., Burroughs, A. M., Baillie, J. K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C. J., Meehan, T. F., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C. O., Heutink, P., Hume, D. A., Jensen, T. H. H., Suzuki, H., Hayashizaki, Y., Müller, F., FANTOM Consortium, Forrest, A. R., Carninci, P., Rehli, M., Sandelin, A., Kawaji, H., Baillie, J. K., de Hoon, M. J., Haberle, V., Lassmann, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jørgensen, M., Dimont, E., Arner, E., Schmid, C., Schaefer, U., Medvedeva, Y. A., Plessy, C., Vitezic, M., Severin, J., Semple, C. A., Ishizu, Y., Young, R. S., Francescatto, M., Alam, I., Albanese, D., Altschuler, G. M., Arakawa, T., Archer, J. A., Arner, P., Babina, M., Rennie, S., Balwierz, P. J., Beckhouse, A. G., Pradhan-Bhatt, S., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, A. M., Califano, A., Cannistraci, C. V., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H. C., Dalla, E., Davis, C. A., Detmar, M., Diehl, A. D., Dohi, T., Drabløs, F., Edge, A. S., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G. J., Favorov, A. V., Fisher, M. E., Frith, M. C., Fujita, R., Fukuda, S., Furlanello, C., Furuno, M., Furusawa, J.-i., Geijtenbeek, T. B., Gibson, A. P., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Hitchens, K. J., Ho Sui, S. J., Hofmann, O. M., Hoof, I., Hori, F., Huminiecki, L., Iida, K., Ikawa, T., Jankovic, B. R., Jia, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori-Katayama, M., Kasianov, A. S., Kasukawa, T., Katayama, S., Kato, S., Kawaguchi, S., Kawamoto, H., Kawamura, Y. I., Kawashima, T., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L. M., Kitamura, T., Klinken, S. P., Knox, A. J., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kwon, A. T., Laros, J. F., Lee, W., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Mackay-sim, A., Manabe, R.-i., Mar, J. C., Marchand, B., Mathelier, A., Mejhert, N., Meynert, A., Mizuno, Y., de Lima Morais, D. A., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Motohashi, H., Mummery, C. L., Murata, M., Nagao-Sato, S., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nakazato, K., van Nimwegen, E., Ninomiya, N., Nishiyori, H., Noma, S., Nozaki, T., Ogishima, S., Ohkura, N., Ohmiya, H., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D. A., Pain, A., Passier, R., Patrikakis, M., Persson, H., Piazza, S., Prendergast, J. G., Rackham, O. J., Ramilowski, J. A., Rashid, M., Ravasi, T., Rizzu, P., Roncador, M., Roy, S., Rye, M. B., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schneider, C., Schultes, E. A., Schulze-Tanzil, G. G., Schwegmann, A., Sengstag, T., Sheng, G., Shimoji, H., Shimoni, Y., Shin, J. W., Simon, C., Sugiyama, D., Sugiyama, T., Suzuki, M., Suzuki, N., Swoboda, R. K., 't Hoen, P. A., Tagami, M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tatum, Z., Thompson, M., Toyoda, H., Toyoda, T., Valen, E., van de Wetering, M., van den Berg, L. M., Verardo, R., Vijayan, D., Vorontsov, I. E., Wasserman, W. W., Watanabe, S., Wells, C. A., Winteringham, L. N., Wolvetang, E., Wood, E. J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Zabierowski, S. E., Zhang, P. G., Zhao, X., Zucchelli, S., Summers, K. M., Suzuki, H., Daub, C. O., Kawai, J., Heutink, P., Hide, W., Freeman, T. C., Lenhard, B., Bajic, V. B., Taylor, M. S., Makeev, V. J., Hume, D. A., Hayashizaki, Y., 2014. An atlas of active enhancers across human cell types and tissues. Nature 507 (7493), 455-461. Abstract

Haberle, V., Li, N., Hadzhiev, Y., Plessy, C., Previti, C., Nepal, C., Gehrig, J., Dong, X., Akalin, A., Suzuki, A. M. M., van Ijcken, W. F., Armant, O., Ferg, M., Strähle, U., Carninci, P., Müller, F., Lenhard, B., 2014. Two independent transcription initiation codes overlap on vertebrate core promoters. NatureAbstract

Harmston, N., Baresic, A., Lenhard, B., 2013. The mystery of extreme non-coding conservation. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 368 (1632).

Thongjuea, S., Stadhouders, R., Grosveld, F. G., Soler, E., Lenhard, B., (2013). r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. Nucleic acids researchAbstract

Lenhard, B., Sandelin, A., Carninci, P., (2012). Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nature reviews Genetics 13 (4), 233-245. Abstract

Ragvin, A., Moro, E., Fredman, D., Navratilova, P., Drivenes, Ã., Engström, P. G., Alonso, M. E., Mustienes, E., Skarmeta, J. L., Tavares, M. J., Casares, F., Manzanares, M., van Heyningen, V., Molven, A., Njølstad, P. R., Argenton, F., Lenhard, B., Becker, T. S. (2010). Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3. PNAS 107, 775–780. Abstract

Soler, E., Andrieu-Soler, C., de Boer, E., Bryne, J. C., Thongjuea, S., Stadhouders, R., Palstra, R.-J., Stevens, M., Kockx, C., van IJcken, W., Hou, J., Steinhoff, C., Rijkers, E., Lenhard, B., Grosveld, F. (2010). The genome-wide dynamics of the binding of ldb1 complexes during erythroid differentiation. Genes & Development 24, 277–289. Abstract

Akalin, A., Fredman, D., Arner, E., Dong, X., Bryne, J., Suzuki, H., Daub, C., Hayashizaki, Y., Lenhard, B. (2009). Transcriptional features of genomic regulatory blocks. Genome Biology 10, R38+. Abstract

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