Biology subjects

Forrest, D.

Publications and source records attributed to Forrest, D..

5 recordsLinked to original sources

bioRxiv2026

Widespread coupling of promoters and terminators of transcription in bacteria

Transcription underpins the expression of genetic information and is viewed as a series of independent initiation and termination events. In bacteria, promoters and terminators of transcription are therefore considered distinct regulatory elements. Here, we challenge this view. Genome-scale analyses reveal that promoters and terminators are extensively coupled. Thus, initiation and termination sites, for adjacent transcription units, frequently overlap. This conserved organisation arises because the DNA sequences, which direct termination, also contribute to promoter function. This couples neighbouring transcription units and generates regulatory interference between RNA polymerases. These findings define a universal mechanism for coordinating transcription across bacterial genomes.

microbiology↗

bioRxiv2024

H-NS is a bacterial transposon capture protein

The histone-like nucleoid structuring (H-NS) protein is a DNA binding factor, found in {gamma}-proteobacteria, with functional equivalents in diverse microbes. Universally, such proteins are understood to silence transcription of horizontally acquired genes. Here, we identify transposon capture as a major overlooked function of H-NS. Using genome scale approaches, we show that H-NS bound chromosomal regions are transposition "hotspots". Since H-NS often interacts with pathogenicity islands, such targeting creates clinically relevant phenotypic diversity. For example, in Acinetobacter baumannii, we identify altered motility, biofilm formation, and interactions with the human immune system. Transposon capture is mediated by the DNA bridging activity of H-NS and, if absent, more ubiquitous transposition results. Consequently, transcribed and essential genes are disrupted. Hence, H-NS directs transposition to favour evolutionary outcomes useful for the host cell.

microbiology↗

bioRxiv2023

The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli

Nucleoid associated proteins (NAPs) maintain the architecture of bacterial chromosomes and regulate gene expression. Thus, their role as transcription factors may involve three-dimensional chromosome re-organisation. While this model is supported by in vitro studies, direct in vivo evidence is lacking. Here, we use RT-qPCR and 3C-qPCR to study the transcriptional and architectural profiles of the H-NS-regulated, osmoresponsive proVWX operon of Escherichia coli at different osmolarities and provide in vivo evidence for transcription regulation by NAP-mediated chromosome re-modelling in bacteria. We show that activation of proVWX in response to a hyperosmotic shock involves the destabilization of H-NS-mediated bridges anchored between the proVWX downstream and upstream regulatory elements (DRE and URE), and between the DRE and ygaY that lies immediately downstream of proVWX. The re-establishment of these bridges upon adaptation to hyperosmolarity represses the operon. H-NS and H-NS-like proteins are wide-spread amongst bacteria, suggesting that chromosome re-modelling may be a typical feature of transcriptional control in bacteria.

molecular biology↗

bioRxiv2020

Widespread divergent transcription from prokaryotic promoters

Promoters are DNA sequences that stimulate the initiation of transcription. In all prokaryotes, promoters are believed to drive transcription in a single direction. Here we show that prokaryotic promoters are frequently bidirectional and drive divergent transcription. Mechanistically, this occurs because key promoter elements have inherent symmetry and often coincide on opposite DNA strands. Reciprocal stimulation between divergent transcription start sites also contributes. Horizontally acquired DNA is enriched for bidirectional promoters suggesting that they represent an early step in prokaryotic promoter evolution.

molecular biology↗

bioRxiv2019

Cortical RORβ is required for layer 4 transcriptional identity and barrel integrity.

Retinoic Acid-Related Orphan Receptor Beta (ROR{beta}) is a transcription factor (TF) and marker of layer 4 (L4) neurons, which are distinctive both in transcriptional identity and the ability to form aggregates such as barrels in rodent somatosensory cortex. However, the relationship between transcriptional identity and L4 cytoarchitecture is largely unknown. We find ROR{beta} is required in the cortex for L4 aggregation into barrels and thalamocortical afferent (TCA) segregation. Interestingly, barrel organization also degrades with age. Loss of ROR{beta} delays excitatory input and disrupts gene expression and chromatin accessibility, with downregulation of L4 and upregulation of L5 genes, suggesting a shift in cellular identity. Expression and binding site accessibility change for many other TFs, including closure of neurodevelopmental TF binding sites and increased expression and binding capacity of activity-regulated TFs. Lastly, a putative target of ROR{beta}, Thsd7a, is downregulated without ROR{beta}, and Thsd7a knockout alone disrupts TCA organization in adult barrels.

neuroscience↗