Spradlin, S. | Search bioRxiv

bioRxiv2025

Structural and functional clues challenge the hypothesis that the yjdF riboswitch is natively regulated through broad recognition of azaaromatic compounds

While most riboswitches are highly selective for their cognate ligand, the yjdF riboswitch is distinct in its ability to bind a broad set of aromatic compounds. This observation has led to the hypothesis that this RNA is regulated by toxic azaaromatic compounds, triggering a detoxification mechanism by activating translation of the YjdF protein in response to ligand binding. To understand how these compounds turn on gene expression by the yjdF riboswitch, we determined the crystal structure of the Bacillus subtilis yjdF riboswitch in complex with activating (chelerythrine) and non-activating (lumichrome) ligands. These structures reveal that the RNA binds these compounds in a near-identical fashion, adopting the same local and global conformation. However, the unexpected extension of the regulatory helix through formation of several base pairs from highly conserved nucleotides suggests that this element plays an important role in ligand-dependent gene expression. Using a reporter assay in B. subtilis, we found that chelerythrine-dependent activation is insensitive to mutation of these conserved nucleotides that are essential for activation of the riboswitch. These data suggest that the yjdF riboswitch is responsive to a yet unknown cellular metabolite and remains an orphan riboswitch. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC="FIGDIR/small/660367v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@11c4765org.highwire.dtl.DTLVardef@19374faorg.highwire.dtl.DTLVardef@1e4fb22org.highwire.dtl.DTLVardef@23816f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2020

Genome-wide binding analysis of 195 DNA Binding Proteins reveals "reservoir" promoters and human specific SVA-repeat family regulation

A key aspect in defining cell state is the complex choreography of DNA binding events in a given cell type, which in turn establishes a cell-specific gene-expression program. In the past two decades since the sequencing of the human genome there has been a deluge of genome-wide experiments which have measured gene-expression and DNA binding events across numerous cell-types and tissues. Here we re-analyze ENCODE data in a highly reproducible manner by utilizing standardized analysis pipelines, containerization, and literate programming with Rmarkdown. Our approach validated many findings from previous independent studies, underscoring the importance of ENCODEs goals in providing these reproducible data resources. This approach also revealed several new findings: (i) 1,362 promoters, termed reservoirs, have up to 111 different DNA binding-proteins localized on one promoter yet do not have any expression of steady-state RNA (ii) The human specific SVA repeat element may have been co-opted for enhancer regulation. Collectively, this study performed by the students of a CU Boulder computational biology class (BCHM 5631 - Spring 2020) demonstrates the value of reproducible findings and how resources like ENCODE that prioritize data standards can foster new findings with existing data in a didactic environment.

genomics↗