Retrotransposons are “copy-and-paste” insertional mutagens that substantially contribute to mammalian genome content. Retrotransposons often carry long terminal repeats (LTRs) for retrovirus-like reverse transcription and integration into the genome. Long non-coding RNAs (lncRNAs) are a heterogeneous group of genome-encoded RNAs, many of which have been shown to have important biological functions. With our collaborators from the Laboratory of epigenetic regulations, group of Petr Svoboda we generated a catalogue of lncRNAs expressed during oocyte-to-embryo transition from microarray and next generation sequencing datasets. Remarkably, many of the identified lncRNAs are novel and have unique expression patterns.

in collaboration with Petr Svoboda from Institute of Molecular Genetics of the ASCR

Long non-coding RNA exchange during the oocyte-to-embryo transition in mice.
Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes.
The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3’ processing.
Genetic variation in human DNA replication timing.
A retrotransposon-driven Dicer isoform directs endogenous siRNA production in mouse oocytes.

Human immunodeficiency virus (HIV-1) has the capacity to establish latent infections, which is a major barrier to the development of a cure for AIDS. To ensure productive infection, HIV-1 has to integrate into cellular DNA. The integration is not random, HIV-1 targets preferentially the outer shell of the CD4+ T cell nucleus and it has been shown that nuclear 3D structure plays a role in dictating HIV-1 integration patterns. In collaboration with group of Marina Lusic, we are now focused to better understand what  defines genomic regions that are recurrently targeted by HIV-1 and how cromatin features and their 3D nuclear organisation influences HIV-1 integration pattern selection.

in collaboration with Marina Lusic from Universitätsklinikums Heidelberg