RNA Systems Biology Laboratory

The RNA Systems Biology Laboratory asks how cells regulate the birth, life and death of RNA molecules using Next Generation Sequencing (NGS).

We are experiencing a major re-think in cell biology. Up until very recently, the major focus in gene-regulation was on DNA and DNA-binding proteins. However, it turns out that RNA is not just a passive intermediary between DNA and proteins; RNA also has structural and regulatory functions in addition to its coding functions. Therefore, the RNA Systems Biology Laboratory is interested in how both coding and non-coding RNA is expressed and regulated in cells, and how the fine-tuning of this expression, which differentiates health from disease, is maintained.

NGS provides a holistic, systems level view of the RNA expression profile in cells, and since disease often leaves signature fingerprints of deregulation on such profiles, NGS can be a powerful diagnostic for various disease states including for cancer. The RNA Biology laboratory uses custom RNA-seq technologies in a diverse set of model organism and cultured-cells to study RNA dynamics. Specifically, we are interested in the post-transcriptional regulation of RNA that determines when, where and how often, mRNA is translated to make proteins. Because we seek to understand how every RNA in our system is regulated, our experiments often have 100s of millions of data-points and thus require the input of computational biologists.

Most Recent Publications

Dynamics of ribosome scanning and recycling revealed by translation complex profiling.

Archer SK, Shirokikh NE, Beilharz TH, Preiss T.

Regulation of messenger RNA translation is central to eukaryotic gene expression control. Regulatory inputs are specified by them RNA untranslated regions (UTRs) and often target translation initiation. Initiation involves binding of the 40S ribosomal small subunit (SSU) and associated eukaryotic initiation factors (eIFs)near the mRNA 5' cap; the SSU then scans in the 3' direction until it detects the start codon and is joined by the 60S ribosomal large subunit (LSU) to form the 80S ribosome. Scanning and other dynamic aspects of the initiation model have remained as conjectures because methods to trap early intermediates were lacking. Here we uncover the dynamics of the complete translation cycle in live yeast cells using translation complex profile sequencing (TCP-seq), a method developed from the ribosome profiling approach. We document scanning by observing SSU footprints along 5' UTRs. Scanning SSU have 5'-extended footprints (up to~75 nucleotides), indicative of additional interactions with mRNA emerging from the exit channel, promoting forward movement. We visualized changes in initiation complex conformation as SSU footprints coalesced into three major sizes at start codons (19, 29 and 37 nucleotides). These share the same 5' start site but differ at the 3' end, reflecting successive changes at the entry channel from an open to a closed state following start codon recognition. We also observe SSU 'lingering' at stop codons after LSU departure. Our results underpin mechanistic models of translation initiation and termination, built on decades of biochemical and structural investigation, with direct genome-wide in vivo evidence. Our approach captures ribosomal complexes at all phases of translation and will aid in studying translation dynamics in diverse cellular contexts. Dysregulation of translation is common in disease and, for example, SSU scanning is a target of anti-cancer drug development. TCP-seq will prove useful in discerning differences in mRNA-specific initiation in pathologies and their response to treatment.

Nature. 2016
Understanding the regulation of coding and noncoding transcription in cell populations.

Beilharz TH.

Whole transcriptome analyses have unveiled the uncomfortable truth that we know less about how transcription is regulated then we thought. In addition to its role in classic promoter-driven transcription of coding RNA, it is now clear that RNA Pol II also drives abundant expression of noncoding RNA. For the majority of this the functional significance remains unclear. Moreover, its regulation and impact are hard to predict because it often proceeds in unexpected ways from cryptic promoters, including by driving convergent antisense transcription from within 3' UTRs. This review suggests that its time to rethink how we envisage gene expression by inclusion of the regulatory architecture of the full genetic locus, and expanding our thinking to encompass the fact that we generally study cells within heterogeneous populations.

Curr Genet. 2016
More publications