Ruprecht-Karls-Universität Heidelberg

Henrik Kaessmann
ZMBH Research Group Leader

Im Neuenheimer Feld 282
69120 Heidelberg, Germany
Tel. +49 (0) 6221 - 545854
Fax +49 (0) 6221 - 545507

Welcome to the Kaessmann lab



Functional evolution of mammalian genomes

Mammals are characterized by specific phenotypic traits that include lactation, hair, and relatively large brains with unique structures. Individual mammalian lineages have, in turn, evolved characteristic traits that distinguish them from others. These include obvious anatomical differences but also differences related to reproduction, life span, cognitive abilities, behavior, and disease susceptibility. The molecular changes (i.e., changes in protein/RNA sequences or expression levels) underlying these phenotypic shifts and the associated selective pressures have only recently begun to be investigated based on an increasing number of available mammalian genomes. Our group performs integrated bioinformatics analyses pertaining to the functional evolution of mammalian genes (and associated phenotypic changes) on the basis of publicly available genomic data as well as data generated by the wet lab unit of the group. We have been interested in a range of topics related to the functional evolution of genomes from primates and other mammals. In the framework of our current projects, we are producing large amounts of transcriptome and genome (e.g., epigenome) data for a unique collection of tissues from representative mammals and outgroup species (e.g., birds) using next generation sequencing technologies. Topics of current projects that are based on these data include the origins and/or functional evolution of protein-coding genes, alternative splicing, long noncoding RNAs, microRNAs, and sex chromosomes.


Selected publications

Original papers

Sarropoulos, I., Sepp, M., Frömel, R., Leiss, K., Trost, N., Leushkin, E., Okonechnikov, K., Joshi, P., Giere, P., Kutscher, L.M., Cardoso-Moreira, M., Pfister, S.M., and Kaessmann, H. (2021) Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells. Science. doi: 10.1126/science.abg4696. URL

Mazin, P.V., Khaitovich, P., Cardoso-Moreira, M., and Kaessmann, H. (2021) Alternative splicing during mammalian organ development. Nat. Genet. 53:924-935. URL

Wang, Z.Y., Leushkin, E., Liechti, A., Ovchinnikova, S., Mößinger, K., Brüning, T., Rummel, C., Grützner, F., Cardoso-Moreira, M., Janich, P., Gatfield, D., Diagouraga, B., de Massy, B., Gill, M.E., Peters, A.H.F.M., Anders, S., and Kaessmann, H. (2020) Transcriptome and translatome co-evolution in mammals. Nature 588: 642-647. URL

Cardoso-Moreira M., Halbert, J., Valloton, D., Velten, B., Chen, C., Shao, Y., Liechti, A., Ascenção, K., Rummel, C., Ovchinnikova, S., Mazin, P.V., Xenarios, I., Harshman, K., Mort, M., Cooper, D.N., Sandi, C., Soares, M.J., Ferreira, P.G., Afonso, S., Carneiro, M., Turner, J.M., VandeBerg, J.L., Fallahshahroudi, A., Jensen, P., Behr, R., Lisgo, S., Lindsay, S., Khaitovich, P., Huber, W., Baker, J., Anders, S., Zhang, Y.E., and Kaessmann H. (2019) Gene expression across mammalian organ development. Nature 571: 505-509. URL

Sarropoulos, I., Marin, R., Cardoso-Moreira, M., and Kaessmann, H. (2019) Developmental dynamics of lncRNAs across mammalian organs and species. Nature 571: 510-514. URL

Cortez, D., Marin, R., Toledo-Flores, D., Froidevaux, L., Liechti, A., Waters, P.D., Grützner, F., and Kaessmann, H. (2014) Origins and functional evolution of Y chromosomes across mammals. Nature 508: 488-493. URL

Necsulea, A., Soumillon, M., Warnefors, M., Liechti, A., Daish, T., Zeller, U., Baker, J.C., Grützner, F., and Kaessmann, H. (2014) The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505: 635-640. URL

Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., Albert, F.W., Zeller, U., Khaitovich, P., Grützner, F., Bergmann, S., Nielsen, R., Pääbo, S., and Kaessmann, H. (2011) The evolution of gene expression levels in mammalian organs. Nature 478: 343-348. URL


Necsulea, A. and Kaessmann, H. (2014) Evolutionary dynamics of coding and noncoding transcriptomes. Nat. Rev. Genet. 5: 734-48. URL

Kaessmann, H. (2010) Origins, evolution and phenotypic impact of new genes. Genome Res. 20: 1313-1326. URL

Kaessmann, H., Vinckenbosch, N., and Long, M. (2009) RNA-based gene duplication: mechanistic and evolutionary insights. Nat. Rev. Genet. 10: 19-31. URL