Biology subjects

Goodrich, J.

Publications and source records attributed to Goodrich, J..

9 recordsLinked to original sources

bioRxiv2025

A Key Role for S-Nitrosylation in Immune Regulation and Development in the Liverwort Marchantia polymorpha

Nitric oxide (NO) is an important signaling molecule in flowering plant immunity. It rapidly accumulates in response to pathogen perception. In addition to its direct response to microbes, NO controls a range of defence responses primarily through S-nitrosylation. This process is a redox-dependent modification where a NO group attaches to the thiol of a cysteine residue, creating an S-nitrosothiol (SNO). To explore the role of S-nitrosylation more broadly, we characterised the single-copy S-nitrosoglutathione reductase 1 (MpGSNOR1) gene in the liverwort Marchantia polymorpha (Marchantia), a representative of a lineage widely diverged from flowering plants. We generated loss-of-function alleles using CRISPR/Cas9 genome editing. Disrupting MpGSNOR1 resulted in pronounced morphological alterations, highlighting the role of GSNOR1 in the structural development of Marchantia. Additionally, we show that MpGSNOR1 is essential for SNO homeostasis and immune function. Our results suggest that GSNOR was part of the tool kit of the ancestral land plant and functioned in immunity and development. HighlightFirst evidence from a Liverwort shows GSNOR controls immunity and development via S-nitrosylation, revealing these regulatory roles as ancient traits of land plants.

plant biology↗

bioRxiv2025

Synthesis and validation of a metal-organic framework able to quench DNA fluorescence

Access to practical research experience is typically limited for life science undergraduates at UK universities. This is confounded by a lack of time to pursue research given course commitments, and the competition for limited spaces on internships or other schemes. To overcome these issues, we hypothesised methods to increase students independent access to research, allowing them to design and undertake useful experiments from first principles. Here, we describe the methods allowing a group of undergraduates to successfully devise and completed a research project independent from their university and academic functions.

scientific communication and education↗

bioRxiv2024

Selection efficacy differs between lifestages in thehaploid-diploid Marchantia polymorpha subsp. ruderalis

Ploidy has profound effects on evolution. Perhaps the most compelling effect is related to dominance: In cells with more than one genome copy, the effects of non-dominant deleterious variants are masked to some extent, leading to a reduction in the efficacy of selection. This, in turn, leads to increased levels of nucleotide diversity, and it may also affect nucleotide substitution rates. To test this predicted association between ploidy and the efficacy of selection, we studied genome scale per-gene patterns of genetic diversity and divergence in the genome of the haploid-diploid bryophyte Marchantia. We treated lifestage gene expression bias as a continuous covariate and accounted for genomic autocorrelation patterns using smoothing splines in a general additive regression model (GAM) framework. Consistent with a lower efficacy of purifying selection, we found increased levels of sequence diversity, Wattersons{theta} , and net divergence at non-degenerate sites in genes with diploid-biased gene expression. These genes also showed reduced levels of codon usage bias. In addition, we found chromosome 5 to be an outlier with overall decreased levels of diversity, the site-frequency spectrum skewed towards common alleles, and increased linkage disequilibrium. In this study, we show the utility of generalized additive models in population genomics, and we present evidence for a ploidy associated difference in the efficacy of selection. We discuss parallels to the evolution of (diploid) sex chromosomes and why the patterns observed are unlikely to be mediated by masking.

evolutionary biology↗

bioRxiv2022

p53 binds more dynamically to response elements that are closer to the consensus sequence

The transcriptional activator p53 is a tumor suppressor protein that controls cellular pathways important for cell fate decisions, including cell cycle arrest, senescence, and apoptosis. It functions as a tetramer by binding to specific DNA sequences known as response elements (REs) to control transcription via interactions with co-regulatory complexes. Critical for understanding how p53 regulates gene expression is unraveling the fundamental mechanisms by which it binds to REs. Toward this goal we have used an in vitro single molecule fluorescence approach to quantify the dynamic binding of tetrameric p53 to five native REs in real time under equilibrium conditions. We found little evidence of dimer/DNA complexes as intermediates to the formation or dissociation of p53 tetramer/DNA complexes; however, tetramer/DNA complexes can exchange dimers at some REs. Determining rate constants for association and dissociation revealed two kinetically distinguishable populations of tetrameric p53/RE complexes. For the less stable population, the rate constants for dissociation were larger at REs closest to consensus, showing the more favorable binding sequences form the least kinetically stable complexes. Together our real time measurements provide insight into mechanisms with which tetrameric p53 forms complexes on different native REs.

biochemistry↗

bioRxiv2022

A transcription factor module regulating stomatal formation is co-opted for the development of setae in the astomatous liverwort Marchantia polymorpha

The evolution of special types of cells requires the acquisition of new gene regulatory networks controlled by transcription factors (TFs). In stomatous plants, a TF module formed by subfamilies Ia and IIIb basic helix-loop-helix TFs (Ia-IIIb bHLH) regulates stomatal formation; however, how this module evolved during land plant diversification remains unclear. Here, we show that, in the astomatous liverwort Marchantia polymorpha, a Ia-IIIb bHLH module regulates the development of a unique sporophyte tissue, the seta, which is found in mosses and liverworts. The sole Ia bHLH gene, MpSETA, and a IIIb bHLH gene, MpICE2, regulate the cell division and/or differentiation of seta lineage cells. MpSETA can partially replace the stomatal function of Ia bHLH TFs in Arabidopsis thaliana, suggesting that a common regulatory mechanism underlies the setal and stomatal formation. Our findings reveal the co-option of a Ia-IIIb bHLH TF module for regulating cell fate determination and/or cell division of distinct types of cells during land plant evolution.

plant biology↗

bioRxiv2022

A genome-wide mutational constraint map quantified from variation in 76,156 human genomes

The depletion of disruptive variation caused by purifying natural selection (constraint) has been widely used to investigate protein-coding genes underlying human disorders, but attempts to assess constraint for non-protein-coding regions have proven more difficult. Here we aggregate, process, and release a dataset of 76,156 human genomes from the Genome Aggregation Database (gnomAD), the largest public open-access human genome reference dataset, and use this dataset to build a mutational constraint map for the whole genome. We present a refined mutational model that incorporates local sequence context and regional genomic features to detect depletions of variation across the genome. As expected, proteincoding sequences overall are under stronger constraint than non-coding regions. Within the non-coding genome, constrained regions are enriched for known regulatory elements and variants implicated in complex human diseases and traits, facilitating the triangulation of biological annotation, disease association, and natural selection to non-coding DNA analysis. More constrained regulatory elements tend to regulate more constrained protein-coding genes, while non-coding constraint captures additional functional information underrecognized by gene constraint metrics. We demonstrate that this genome-wide constraint map provides an effective approach for characterizing the non-coding genome and improving the identification and interpretation of functional human genetic variation.

genetics↗

bioRxiv2021

The herpes simplex virus 1 protein ICP4 acts as both an activator and repressor of host genome transcription during infection

Infection by Herpes simplex virus 1 (HSV-1) impacts nearly all steps of gene expression in the host cell. The regulatory mechanisms by which this occurs, and the interplay between host and viral factors, have yet to be fully elucidated. Here we investigated how the occupancy of RNA polymerase II (Pol II) on the host genome changes during HSV-1 infection and is impacted by the viral immediate early protein ICP4. Pol II ChIP-seq experiments revealed a reduction of Pol II occupancy across the bodies of hundreds of host genes that was dependent upon ICP4. Concomitantly, Pol II levels increased across the bodies of several hundred genes, the majority of which also depended on ICP4 for activation. Our data suggest ICP4 regulates repression of Pol II at host genes by inhibiting recruitment of Pol II, while it regulates activation by promoting release of Pol II from promoter proximal pausing into productive elongation. Consistent with this, relative levels of the pausing factors NELF-A and Spt5 were reduced on an HSV-1 activated gene in an ICP4 dependent manner. Exogenous expression of ICP4 revealed that ICP4 can activate, but not repress, transcription of some genes in the absence of infection in a manner that correlates with the chromatin state of the gene. Together our data support the model that ICP4 decreases promoter proximal pausing on host genes activated by infection, and ICP4 is necessary, but not sufficient, to repress transcription from host genes during viral infection.

genomics↗

bioRxiv2019

Release of human TFIIB from actively transcribing complexes is triggered upon synthesis of 7 nt and 9 nt RNAs

RNA polymerase II (Pol II) and its general transcription factors assemble on the promoters of mRNA genes to form large macromolecular complexes that initiate transcription in a regulated manner. During early transcription these complexes undergo dynamic rearrangement and disassembly as Pol II moves away from the start site of transcription and transitions into elongation. One step in disassembly is the release of the general transcription factor TFIIB, although the mechanism of release and its relationship to the activity of transcribing Pol II is not understood. We developed a single molecule fluorescence transcription system to investigate TFIIB release in vitro. Leveraging our ability to distinguish active from inactive complexes, we found that nearly all transcriptionally active complexes release TFIIB during early transcription. Release is not dependent on the contacts TFIIB makes with its recognition element in promoter DNA. We identified two different points in early transcription at which release is triggered, reflecting heterogeneity across the population of actively transcribing complexes. TFIIB releases after both trigger points with similar kinetics, suggesting the rate of release is independent of the molecular transformations that prompt release. Together our data support the model that TFIIB release is important to maintain the transcriptional activity of Pol II as initiating complexes transition into elongation complexes.

biochemistry↗

bioRxiv2019

Single molecule studies reveal that p53 tetramers dynamically bind response elements containing one or two half sites

The tumor suppressor protein p53 is at the nexus of cell fate decisions, including apoptosis, senescence, and cell cycle arrest. p53 is a tetrameric transcription factor that binds to DNA response elements to regulate transcription of its target genes, a process activated by cellular stress. p53 response elements consist of two decameric half-sites, and most data suggest one p53 dimer in the tetramer binds to each half-site. Despite a broad literature describing p53 binding to DNA, unanswered questions remain, due in part to the need for more quantitative and structural studies with the full length protein. Here we describe a single molecule fluorescence system to visualize full length p53 tetramers binding to DNA in real time. The data reveal a dynamic interaction with many p53 binding and dissociation events occurring on single DNA molecules over minutes. We found that p53 tetramers bound to response elements containing only a single half site. The kinetic stability of tetramer/DNA complexes depended on the number of half sites and the helical phasing between them, with the most stable complexes forming on DNA containing two adjacent half sites. The forward rate of binding was not strongly impacted when one half site was mutated. These studies provide real time kinetic measurements of full length p53 tetramers binding to single molecules of DNA, and reveal new insight into the mechanisms by which this nucleoprotein complex forms.

biochemistry↗