Gene regulation in health and disease: Interrogating your immune system for prognostics and diagnostics
All cells in our body share the same DNA. Differential interpretation of this DNA by gene regulatory programs is fundamental for cellular specialization, health, and disease. All signals that impact gene expression must ultimately be integrated at the transcription start site (TSS), the place where RNA polymerase starts transcribing and thus bringing your genome to life. Capturing all momentarily active or “nascent” transcription start sites therefore not only provides a snapshot of the current state of a cell, but also reveals the underlying regulatory network(s).
Our lab specializes in capturing these momentarily active or nascent transcription start sites from fresh, frozen, or banked tissues or other samples (“nascent transcriptomics”) – indeed, anything where RNA can be isolated from. We’re fascinated by how gene regulatory programs differentially decode our DNA in distinct settings, and how these programs not only allow making a complex multicellular organism such as yourself but can also trigger different responses to medical treatment or environmental challenge such as viral infection. The goal of our research is to diagnose and better understand the molecular basis underlying differential outcomes: “Why do some of us get sick or respond a treatment why others don’t?” – to eventually further personalized treatment approaches for humans and animals.
Latest publications
- Dynamic activity in cis-regulatory elements of leukocytes identifies transcription factor activation and stratifies COVID-19 severity in ICU patients. Lam MTY, Duttke SH et al. Cell Reports Medicine. 2023, PMID: 36758547
- Glucocorticoid Receptor-Regulated Enhancers Play a Central Role in the Gene Regulatory Networks Underlying Drug Addiction. Duttke SH et al., Frontiers in Neuroscience. 2022, PMID: 35651629
- Decoding Transcription Regulatory Mechanisms Associated with Coccidioides immitis Phase Transition Using Total RNA. Duttke SH et al. mSystems. 2022, PMID: 35076277
The spatial grammar of our genome: Decoding gene regulation from the perspective of the transcription start site
Many biological phenomena including health and disease can be traced to the proper or improper expression of a gene or genomic loci. Hence, knowledge of the molecular mechanisms that regulate genome expression is critical to understand a wide range of biological and biomedical topics. Exploiting natural genetic and organismic variation, genomics, and bioinformatics we thrive to greater our understanding of the fundamental molecular mechanisms that regulate the expression of genomes, especially from the perspective of the transcription start site (TSS). Capturing the transcription start site also provides a spatial anchor which revealed that many transcription factors (TFs), including canonical activators like NRF1, NFY, Sp1, activate or repress transcription initiation depending on their precise position relative to the TSS. As such, this spatial grammar of transcription factor function can collectively guide the site and frequency of transcription initiation. More broadly, this spatial grammar could explain how similar assortments of transcription factor binding sites (DNA motifs) can generate distinct gene regulatory outcomes depending on their spatial configuration, and underscore a critical role for transcription start site data in decoding the regulatory information of our genome.
Latest publications
- DNMT3A haploinsufficiency causes dichotomous DNA methylation defects at enhancers in mature human immune cells. Lim JY, Duttke SH, et al. Journal of Experimental Medicine. 2021, PMID: 33970190
- Identification and dynamic quantification of regulatory elements using total RNA. Duttke SH, et al. Genome Research. 2019, PMID: 31649059
- Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Link VM, Duttke SH, et al. Cell. 2018, PMID: 2977994
Human dispersed transcription initiation:
Based on their pattern of transcription initiation, regulatory elements such as promoters and enhancers are commonly grouped into ‘focused’ or ‘dispersed’. Focused initiation starts from a single or a few closely spaced sites while dispersed regulatory elements start from multiple dispersed sites. The mechanisms underlying these two modes of transcription are distinct. Focused initiation is largely dependent on core promoter elements such as the TATA box or DPE, is predominant in yeast, flies, and commonly featured in your textbook. It is well understood, in part, as in vitro transcription systems facilitated the characterization and purification of the underlying key factors and sequence elements. By contrast, dispersed promoters largely lack core promoter elements and do not faithfully transcribe in vitro. Thus, in 2023, we still do not know how dispersed initiation, and thus expression of over 75% of human genes and enhancers is regulated. We thrive to develop new experimental approaches to define the DNA motifs, transcription factors and mechanisms underlying the abundant yet little studied mode of dispersed initiation. Ultimately, it is our goal to establish a paradigm for this abundant, important, but little understood mode of human gene regulation.
