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Daniela Strenkert

Assistant Professor

Department of Plant Biology

Research: Multi-omics resolution of photosynthetic performance

Our lab is using systems biology approaches to get a quantitative understanding of gene regulation in photosynthetic organisms. We study changes in chromatin structure, transcript, protein and metabolite composition holistically, to fully capture the conserved regulatory programs managing different environmental inputs. For this purpose, we are utilizing simple, eukaryotic, single-celled algae to answer fundamental questions about the acclimation of photosynthetic organisms to the various challenges they face in their habitats. In the process, we are using mutants (via CRISPR mediated gene editing or from public depositories) and highly-controlled photo-bioreactor systems to ensure that we discover the individual contributions of key regulators to specific challenges.

Our ultimate goal is to unravel how different environmental cues are sensed, processed and memorized to define how photosynthetic organisms successfully adapt to the challenges they face in their daily life. Ideally these studies will pave the way to identify novel genetic or chemical strategies to improve the capacity of a phototrophic organism to respond to environmental stress more efficiently. In addition to research applications, this will be useful for industrial processes, for example in the production of biofuels or therapeutic proteins/compounds in algae, or in agriculture, to increase resilience towards adverse environmental conditions. Currently we focus our efforts on three synergistic areas of research.

A day in the life of a green algae

In the photosynthetic model alga Chlamydomonas reinhardtii we want to fully capture the adjustments made to DNA structure, transcription, protein and metabolite pools over the course of a regular day, with 12 hours of darkness at lower night-time temperatures, to define the regulatory programs throughout the day. Previously, we combined a high-resolution transcriptomic dataset with a proteomic approach, describing staged events in the progression of the Chlamydomonas cell cycle, for example the sequential production of the different thylakoid membrane complexes following dawn, or distinct phases in the expression of proteins involved in photoprotection or central carbon metabolism. We want to integrate this data with additional layers of information, especially at the regulatory level: (I) DNA structure changes, especially at the level of histone modifications which control transcript expression and memory, (II) individual transcription factor binding patterns and (III) translational control and protein modification. As in our previous work we use genome-wide approaches yielding absolute quantitative measurements, when possible on the single cell level.

While the progression of an algal cell through its life cycle is a powerful model for a systems biology approach, we work to expand this approach to conditions that are relevant in the face of global warming and climate change, such as temperature, nutrient and light perturbations and heavy metal toxicity. Or in other words: how does a pretty “bad” day in an alga’s life look like and what strategies did evolve in a eukaryotic green algae like Chlamydomonas that enable its survival during environmental stress?

Transcriptome data from hundreds of different samples under various conditions is publicly available, we complement these existing resources to gain a systems-level understanding of algae biology. This research will fill critical gaps of understanding of the acclimation responses and form the foundational principles for predictive biology in algae, with the long term goal to enable design or modification of biological systems.

An ENCODE like atlas of histone modifications in the green lineage (GreENCODE)

Regulatory processes at all levels control the successful acclimation of an organism to environmental stimuli. Epigenetic regulation is a key process where different states of transcriptional activity of a gene are realized without the altering of the underlying DNA sequence and in absence of a specific regulatory protein. This is achieved either by modification of the DNA itself, especially using methylation of the DNA base cytosine, or by post-translational modification of the structural proteins packing the DNA, the so-called histones. While DNA methylation, especially in promoter areas, generally results in gene silencing, post-translational modifications of histones, such as methylation and acetylation of various amino acids, play crucial roles in both promoting and silencing gene activity. While the histone residues harboring post-translational modifications are generally conserved between taxa, their individual contribution towards gene regulation has evolved independently in different organisms. We are assembling a comprehensive atlas of histone modifications in algae in order to decipher the green algae’s histone code. We are using Chromatin-Immunoprecipitation (ChIP) and other techniques followed by deep sequencing to describe the modification patterns genome-wide. Integrating these layers into datasets describing transcript abundance allows us to identify how these marks affect transcription. A fundamental understanding of algal chromatin biology is crucial in order to be able to manipulate the biological system in the future.

A graph measuring Gene wide distribution pattern of H3K4me3 and H3K4me1
Gene wide distribution pattern of H3K4me3 and H3K4me1.
The distribution of H3K4me3 and H3K4me1 along all Chlamydomonas genes in three time points during the cell cycle was visualized using heat maps. For each gene, the histone modification intensity is displayed along –2 kb to 2 kb regions around the TSSs. Genes shown in both heat maps are sorted based on H3K4me3 enrichment. Blue color indicates enrichment over genomic DNA, red color indicates depletion as compared to genomic DNA.

Regulatory RNAs, proteins and processes 

Regulators are key components for successful acclimation programs. They come in many different forms and are involved in sensing, translocation, protein stability/modification, transcriptional/translational control and signal transduction to crucially manage environmental inputs. Even other processes like energy distribution, spatial or membrane organization are critically involved at many steps of regulatory processes. While many of these components have been identified in the past, others have been neglected and the role of many of these components is understudied with respect to their biological role during acclimation. We want to integrate all regulatory processes involved in acclimation to environmental challenges into a larger framework, allowing to fully capture regulation to various stimuli.

One understudied aspect of these are (long) non-coding RNAs, which play crucial roles in the fate of protein-coding transcripts, either by promoting or blocking translation, improving RNA stability or inducing RNA degradation, and can affect epigenetic regulation via chromatin modifying enzymes.

A illustration showing long non-coding R N As
Functions of long non-coding RNAs (lncRNAs) can impact genetic output at almost every stage of a gene´s life cycle: lncRNAs (depicted in green) are involved in a variety of cellular processes including chromatin remodeling (polycomb mediated gene silencing), transcriptional control (RNA-DNA hybrids, formation at promoters), post-transcriptional processing (alternative splicing).

Identification of (long) non-coding RNAs is greatly facilitated by characteristic chromatin domains. Using different layers of genome-wide data we were able to assemble a curated catalogue of Chlamydomonas‘ (long) non-coding RNAs. Our lab’s research focus will be on identifying the role of these RNAs in response to light during the diurnal cycle. We use fluorescence in situ hybridization (FISH) to determine their spatial distribution within the cell and Cas9/CRISPR to investigate the function of selected RNAs and their specific contribution to stress acclimation. Shedding light on the involvement (long) non-coding RNAs and chromatin modifying enzymes in regulating gene expression will allow to further understand and manipulate this biological system in the future.