Laurence D. Hurst
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View article: Bacterial gene 5′ ends have unusual mutation rates that can mislead tests of selection
Bacterial gene 5′ ends have unusual mutation rates that can mislead tests of selection Open
Despite early assumptions of neutrality, numerous mechanisms are now thought to cause selection on synonymous mutations, commonly supported by a low evolutionary rate at synonymous sites ( K s ). This has been best evidenced in the first ~…
View article: ERV3-MLT1 provides cis-regulatory elements for human placental functioning and are commonly dysregulated in human-specific preeclampsia
ERV3-MLT1 provides cis-regulatory elements for human placental functioning and are commonly dysregulated in human-specific preeclampsia Open
Background Owing to their transcription factor binding sites, endogenous retroviruses (ERVs) can act as cis-regulatory-elements (CREs). By invading genomes in waves, ERVs offer a substrate for lineage-specific adaptations but also, when dy…
View article: Co-option of an endogenous retrovirus (LTR7-HERVH) in early human embryogenesis: becoming useful and going unnoticed
Co-option of an endogenous retrovirus (LTR7-HERVH) in early human embryogenesis: becoming useful and going unnoticed Open
While it is straightforward to understand why most mutations affecting functional sequence are harmful, how genomic changes result in new beneficial traits is harder to understand. Domestication of transposable elements (TEs) is an importa…
View article: Cell Compartment is a Predictor of Protein Rate of Evolution, but not in the Manner Expected: Evidence Against the Extended Complexity Hypothesis
Cell Compartment is a Predictor of Protein Rate of Evolution, but not in the Manner Expected: Evidence Against the Extended Complexity Hypothesis Open
What accounts for the variation between proteins in their rate of evolution per synonymous substitution (i.e. dN/dS, alias ω)? Previous analyses suggested that cell location is predictive, with intracellular proteins evolving slower than m…
View article: Why AGG is associated with high transgene output: passenger effects and their implications for transgene design
Why AGG is associated with high transgene output: passenger effects and their implications for transgene design Open
In bacteria, high A and low G content of the 5′ end of the coding sequence (CDS) promotes low RNA stability, facilitating ribosomal initiation and subsequently a high protein to transcript ratio. Additionally, 5′ NGG codons are suppressive…
View article: RID is required for both repeat-induced point mutation and nucleation of a novel transitional heterochromatic state for euchromatic repeats
RID is required for both repeat-induced point mutation and nucleation of a novel transitional heterochromatic state for euchromatic repeats Open
To maintain genome integrity, repeat sequences are subject to heterochromatin inactivation and, in Neurospora, repeat-induced point mutation (RIP). The initiating factors behind both are poorly understood. We resolve the paradoxical observ…
View article: Epistasis, core-genome disharmony, and adaptation in recombining bacteria
Epistasis, core-genome disharmony, and adaptation in recombining bacteria Open
Recombination of short DNA fragments via horizontal gene transfer (HGT) can introduce beneficial alleles, create genomic disharmony through negative epistasis, and create adaptive gene combinations through positive epistasis. For non-core …
View article: Genes for highly abundant proteins in Escherichia coli avoid 5’ codons that promote ribosomal initiation
Genes for highly abundant proteins in Escherichia coli avoid 5’ codons that promote ribosomal initiation Open
In many species highly expressed genes (HEGs) over-employ the synonymous codons that match the more abundant iso-acceptor tRNAs. Bacterial transgene codon randomization experiments report, however, that enrichment with such “translationall…
View article: Staring at the onco-exaptation: the two-faced medley of an ancient retrovirus, HERVH
Staring at the onco-exaptation: the two-faced medley of an ancient retrovirus, HERVH Open
Cell senescence suppresses tumors by arresting cells at risk of becoming malignant. However, this process in turn can affect the microenvironment, leading to acquisition of a senescence-associated secretory phenotype (SASP) that renders se…
View article: Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation.
Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation. Open
Scripts and datasets for the paper: Genes for highly abundant proteins in Escherichia coli avoid 5’ codons that promote ribosomal initiation.
View article: Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation.
Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation. Open
Scripts and datasets for the paper: Genes for highly abundant proteins in Escherichia coli avoid 5’ codons that promote ribosomal initiation.
View article: Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation.
Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation. Open
Scripts and datasets for the paper: Genes for highly abundant proteins in Escherichia coli avoid 5’ codons that promote ribosomal initiation.
View article: A new human embryonic cell type associated with activity of young transposable elements allows definition of the inner cell mass
A new human embryonic cell type associated with activity of young transposable elements allows definition of the inner cell mass Open
There remains much that we do not understand about the earliest stages of human development. On a gross level, there is evidence for apoptosis, but the nature of the affected cell types is unknown. Perhaps most importantly, the inner cell …
View article: In bacteria 5' CDS ends are commonly enriched for codons that cause stronger ribosomal initiation, but genes for highly abundant proteins avoid them.
In bacteria 5' CDS ends are commonly enriched for codons that cause stronger ribosomal initiation, but genes for highly abundant proteins avoid them. Open
Scripts and datasets for the paper: In bacteria 5’ CDS ends are commonly enriched for codons that cause stronger ribosomal initiation, but genes for highly abundant proteins avoid them.
View article: Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters
Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters Open
Background There is widespread interest in the three-dimensional chromatin conformation of the genome and its impact on gene expression. However, these studies frequently do not consider parent-of-origin differences, such as genomic imprin…
View article: A Novel Gene Controls a New Structure: PiggyBac Transposable Element-Derived 1, Unique to Mammals, Controls Mammal-Specific Neuronal Paraspeckles
A Novel Gene Controls a New Structure: PiggyBac Transposable Element-Derived 1, Unique to Mammals, Controls Mammal-Specific Neuronal Paraspeckles Open
Although new genes can arrive from modes other than duplication, few examples are well characterized. Given high expression in some human brain subregions and a putative link to psychological disorders [e.g., schizophrenia (SCZ)], suggesti…
View article: Stop Codon Usage as a Window into Genome Evolution: Mutation, Selection, Biased Gene Conversion and the TAG Paradox
Stop Codon Usage as a Window into Genome Evolution: Mutation, Selection, Biased Gene Conversion and the TAG Paradox Open
Protein coding genes terminate with one of three stop codons (TAA, TGA, or TAG) that, like synonymous codons, are not employed equally. With TGA and TAG having identical nucleotide content, analysis of their differential usage provides an …
View article: Selfish centromeres and the wastefulness of human reproduction
Selfish centromeres and the wastefulness of human reproduction Open
Many human embryos die in utero owing to an excess or deficit of chromosomes, a phenomenon known as aneuploidy; this is largely a consequence of nondisjunction during maternal meiosis I. Asymmetries of this division render it vulnerable to…
View article: Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection
Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection Open
The assumption that conservation of sequence implies the action of purifying selection is central to diverse methodologies to infer functional importance. GC-biased gene conversion (gBGC), a meiotic mismatch repair bias strongly favouring …
View article: Sequence conservation need not imply purifying selection: evidence from mammalian stop codon usage
Sequence conservation need not imply purifying selection: evidence from mammalian stop codon usage Open
The assumption that conservation of sequence implies the action of purifying selection is central to diverse methodologies to infer functional importance. In mammals, however, GC-biased gene conversion (gBGC), a meiotic mismatch repair bia…
View article: Transgene-design: a web application for the design of mammalian transgenes
Transgene-design: a web application for the design of mammalian transgenes Open
Summary Transgene-design is a web application to help design transgenes for use in mammalian studies. It is predicated on the recent discovery that human intronless transgenes and native retrogenes can be expressed very effectively if the …
View article: In rice splice variants that restore the reading frame after frameshifting indel introduction are common, often induced by the indels and sometimes lead to organism-level rescue
In rice splice variants that restore the reading frame after frameshifting indel introduction are common, often induced by the indels and sometimes lead to organism-level rescue Open
The introduction of frameshifting non-3n indels enables the identification of gene-trait associations. However, it has been hypothesised that recovery of the original reading frame owing to usage of non-canonical splice forms could cause r…
View article: Evidence from Drosophila Supports Higher Duplicability of Faster Evolving Genes.
Evidence from Drosophila Supports Higher Duplicability of Faster Evolving Genes. Open
The faster rate of evolution of duplicated genes relative to singletons has been well documented in multiple lineages. This observation has generally been attributed to a presumed release from constraint following creation of a redundant, …
View article: Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage
Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage Open
In bacteria stop codons are recognized by one of two class I release factors (RF1) recognizing TAG, RF2 recognizing TGA, and TAA being recognized by both. Variation across bacteria in the relative abundance of RF1 and RF2 is thus hypothesi…
View article: Causes and Consequences of Purifying Selection on SARS-CoV-2
Causes and Consequences of Purifying Selection on SARS-CoV-2 Open
Owing to a lag between a deleterious mutation’s appearance and its selective removal, gold-standard methods for mutation rate estimation assume no meaningful loss of mutations between parents and offspring. Indeed, from analysis of closely…
View article: Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption
Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption Open
Transcripts containing premature termination codons (PTCs) can be subject to nonsense-associated alternative splicing (NAS). Two models have been evoked to explain this, scanning and splice motif disruption. The latter postulates that exon…