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 - 545893

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

Warnefors, M., Mössinger, K., Halbert, J., Studer, T., VandeBerg, J.L., Lindgren, I., Fallahshahroudi, A., Jensen, P., Kaessmann, H. (2017) Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation. Genome Res. 27: 1961-1973. URL

Marin, R., Cortez, D., Lamanna, F., Pradeepa, M.M., Leushkin, E., Julien, P., Liechti, A., Halbert, J., Brüning, T., Mössinger, K., Trefzer, T., Conrad, C., Kerver, H.N., Wade, J., Tschopp, P., Kaessmann, H. (2017) Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage. Genome Res. 27: 1974-1987. URL

Guschanski, K., Warnefors, M., and Kaessmann, H. (2017) The evolution of duplicate gene expression in mammalian organs. Genome Res. 27: 1461-1474. URL

Carelli, F.N., Hayakawa, T., Go, Y., Imai, H., Warnefors, M., and Kaessmann, H. (2016) The life history of retrocopies illuminates the evolution of new mammalian genes. Genome Res. 26: 301-314. 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

Julien, P., Brawand, D., Soumillon, M., Necsulea, A., Liechti, A., Schütz, F., Daish, T., Grützner, F., and Kaessmann, H. (2012) Mechanisms and evolutionary patterns of mammalian and avian dosage compensation PLoS Biol. 5: e1001328. 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

Henrichsen, C., Vinckenbosch, N., Zöllner, S., Chaignat, E., Pradervand, S., Frédéric Schütz, Ruedi, M., *Kaessmann, H. and *Reymond, A. (2009) Segmental copy number variation shapes tissue transcriptomes. Nat. Genet. 41: 424-429. URL

Rosso, L., Marques, A. C., Weier, M., Lambert, N., Lambot, M. A., Vanderhaeghen, P., and Kaessmann, H. (2008) Birth and rapid subcellular adaptation of a hominoid-specific CDC14 protein. PLoS Biol. 6:e140. URL

Potrzebowski, L., Vinckenbosch, N., Marques, A. C., Chalmel, F., Jegou, B., and Kaessmann, H. (2008) Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes. PLoS Biol. 6:e80. URL

Brawand, D., Wahli, W., and Kaessmann, H. (2008) Loss of egg yolk genes in mammals and the origin of lactation and placentation. PLoS Biol. 6: e63. URL

Vinckenbosch, N., Dupanloup, I., and Kaessmann, H. (2006) Evolutionary fate of retroposed gene copies in the human genome. Proc. Natl. Acad. Sci. U. S. A. 103: 3220-5. URL

Marques, A. C., Dupanloup, I., Vinckenbosch, N., Reymond, A., and Kaessmann, H. (2005) Emergence of young human genes after a burst of retroposition in primates. PLoS Biol. 3: e357. URL

Burki, F. and Kaessmann, H. (2004) Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux. Nat. Genet. 36: 1061-3. URL

Kaessmann, H., Wiebe, V., Weiss, G., Paabo, S. (2001) Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nat. Genet.27: 155-6. URL

Ingman, M., Kaessmann, H., Paabo, S., and Gyllensten, U. (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408: 708-13. URL  Cover, News & Views (Nature)

Kaessmann, H., Wiebe, V., and Paabo, S. (1999) Extensive nuclear DNA sequence diversity among chimpanzees. Science 286: 1159-62. URL

Kaessmann, H., Heissig, F., von Haeseler, A., and Paabo, S. (1999) DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nat. Genet. 22: 78-81. 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

* = equal contribution