Biology subjects

Wolf, E. J.

Publications and source records attributed to Wolf, E. J..

5 recordsLinked to original sources

bioRxiv2025

Multifaceted mRNA analysis using programmed RNA cleavage byMucilaginibacter paludis Argonaute

Argonaute (Ago) endonucleases are ubiquitous across all domains of life and, like Cas nucleases, can be programmed by guide oligonucleotides to target and cleave specific nucleic acid sequences. However, unlike Cas enzymes, Agos are not restricted by sequence requirements such as protospacer adjacent motifs (PAMs) enhancing their utility as molecular tools. This study demonstrates diverse applications of the DNA-guided RNA-endonuclease Mucilaginibacter paludis Argonaute (Mpa Ago) for in vitro mRNA processing, e.g., 3 end polishing, and for mRNA analysis in combination with liquid chromatography tandem mass spectrometry (LC-MS/MS). Applications of the latter include the comprehensive assessment of 5 capping efficiency, 3 poly(A) tail length and composition, one-pot multiplexed cleavage for RNA sequencing, modification detection, and fingerprinting.

molecular biology↗

bioRxiv2021

ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motif within nuclear speckles

Quality control of mRNA represents an important regulatory mechanism for gene expression in eukaryotes. One component of this quality control is the nuclear retention and decay of misprocessed RNAs. Previously, we demonstrated that mature mRNAs containing a 5 splice site (5SS) motif, which is typically found in misprocessed RNAs such as intronic polyadenylated (IPA) transcripts, are nuclear retained and degraded. Here we demonstrate that these transcripts require the zinc finger protein ZFC3H1 for their decay and nuclear retention into nuclear speckles. Furthermore, we find that U1-70K, a component of the U1 snRNP spliceosomal complex, is also required for their nuclear retention and likely functions in the same pathway as ZFC3H1. Finally, we show that the disassembly of nuclear speckles impairs the nuclear retention of mRNAs with 5SS motifs. Together, our results suggest a model where mRNAs with 5SS motifs are recognized by U1 snRNP, which then acts with ZFC3H1 to both promote their decay and prevent nuclear export of these mRNAs by sequestering them in nuclear speckles. Our results highlight a splicing independent role of U1 snRNP and indicate that it works in conjunction with ZFC3H1 in preventing the nuclear export of misprocessed mRNAs.

molecular biology↗

bioRxiv2021

Structural Covariance Networks in Post-Traumatic Stress Disorder: A Multisite ENIGMA-PGC Study

IntroductionCortical thickness (CT) and surface area (SA) are established biomarkers of brain pathology in posttraumatic stress disorder (PTSD). Structural covariance networks (SCN) constructed from CT and SA may represent developmental associations, or unique interactions between brain regions, possibly influenced by a common causal antecedent. The ENIGMA-PGC PTSD Working Group aggregated PTSD and control subjects data from 29 cohorts in five countries (n=3439). MethodsUsing Destrieux Atlas, we built SCNs and compared centrality measures between PTSD subjects and controls. Centrality is a graph theory measure derived using SCN. ResultsNotable nodes with higher CT-based centrality in PTSD compared to controls were left fusiform gyrus, left superior temporal gyrus, and right inferior temporal gyrus. We found sex-based centrality differences in bilateral frontal lobe regions, left anterior cingulate, left superior occipital cortex and right ventromedial prefrontal cortex (vmPFC). Comorbid PTSD and MDD showed higher CT-based centrality in the right anterior cingulate gyrus, right parahippocampal gyrus and lower SA-based centrality in left insular gyrus. ConclusionUnlike previous studies with smaller sample sizes ([≤]318), our study found differences in centrality measures using a sample size of 3439 subjects. This is the first cross-sectional study to examine SCN interactions with age, sex, and comorbid MDD. Although limited to group level inferences, centrality measures offer insights into a nodes relationship to the entire functional connectome unlike approaches like seed-based connectivity or independent component analysis. Nodes having higher centrality have greater structural or functional connections, lending them invaluable for translational treatments like neuromodulation.

neuroscience↗

bioRxiv2019

TPR is required for the nuclear export of mRNAs and lncRNAs from intronless and intron-poor genes

While splicing has been shown to enhance nuclear export, it has remained unclear whether mRNAs generated from intronless genes use specific machinery to promote their export. Here we investigate the role of the major nuclear pore basket protein, TPR, in regulating mRNA and lncRNA nuclear export in human cells. By sequencing mRNA from the nucleus and cytosol of control and TPR-depleted cells, we provide evidence that TPR is required for the nuclear export of mRNAs and lncRNAs that are generated from intronless and intron-poor genes, and we validate this with reporter constructs. Moreover, in TPR-depleted cells reporter mRNAs generated from intronless genes accumulate in nuclear speckles and are bound to Nxf1. These observations suggest that TPR acts downstream of Nxf1 recruitment, and may allow mRNAs to leave nuclear speckles and properly dock with the nuclear pore. In summary, our study provides one of the first examples of a factor that is required for the nuclear export of intronless and intron-poor mRNAs and lncRNAs.

molecular biology↗

bioRxiv2018

Predicting cellular aging following exposure to adversity: Does accumulation, recency, or developmental timing of exposure matter?

Exposure to adversity has been linked to accelerated biological aging, which in turn has been shown to predict numerous health problems, including neuropsychiatric disease. In recent years, measures of DNA methylation-based epigenetic age - known as \"epigenetic clocks\" - have been used to estimate accelerated epigenetic aging. Yet, few studies have been conducted in children. Using data from the Avon Longitudinal Study of Parents and Children (n=973), we explored the prospective association between repeated measures of childhood exposure to seven types of adversity on epigenetic age assessed at age 7 using the Horvath and Hannum epigenetic clocks. With a Least Angle Regression variable selection procedure, we evaluated the effects of the developmental timing, accumulation, and recency of adversity exposure. We found that exposure to sexual or physical abuse, financial stress, or neighborhood disadvantage during sensitive periods in early and middle childhood best explained variability in the deviation of the Hannum epigenetic age from the chronological age. Secondary sex-stratified analyses identified particularly strong sensitive period effects, such that by age 7, girls who were exposed to abuse at age 3.5 were biologically older than their unexposed peers by almost 2 months. These effects were undetected in analyses comparing children \"exposed\" versus \"unexposed\" to adversity. Our results suggest that exposure to adversity may alter methylation processes in ways that perturb normal cellular aging and that these effects may be heightened during sensitive periods in development. Research is needed to demonstrate the effect of accelerated epigenetic aging on negative health outcomes following childhood adversity exposure.

genetics↗