Biology subjects

Che, R.

Publications and source records attributed to Che, R..

3 recordsLinked to original sources

bioRxiv2026

The overall and sequence-specific degradation of soil extracellular 16S rRNA genes across China: rates and influential factors

While extracellular DNA persistence substantially influences soil microbiome investigations, its degradation kinetics remain poorly quantified. Here, we developed a primer-labeled DNA approach coupled with microcosm incubation to determine the overall and sequence-specific degradation rates of extracellular DNA amplicon fragments across China. We observed substantial variations in the overall degradation rates of extracellular 16S rRNA gene amplicon fragments among the study sites, with degradation rate constants ranging from 0.05 to 0.16 day-1. The overall degradation rate constants showed significant correlations with soil moisture content, prokaryotic abundance, prokaryotic community profiles, and mean annual precipitation (MAP). The significant influences of moisture content on the overall degradation rates were further verified by a moisture gradient microcosm experiment. The sequence-specific degradation rate constant profiles were additionally correlated with pH, nitrogen content, and mean annual temperature (MAT). Furthermore, propidium monoazide (PMA)-based exclusion of extracellular DNA signals significantly altered soil prokaryotic abundance, richness, and prokaryotic community profiles, and the pool sizes of sequence-specific extracellular 16S rRNA gene amplicon fragments were significantly correlated with their respective degradation rates. This study developed a methodology for determining the overall and sequence-specific degradation rates of extracellular DNA amplicon fragments, highlighting the profound influences of extracellular DNA on soil microbial research and informing the optimization of environmental DNA technologies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/699460v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@b1b3e2org.highwire.dtl.DTLVardef@98f334org.highwire.dtl.DTLVardef@1870650org.highwire.dtl.DTLVardef@1af7105_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2025

Identification of Two Elusive Human Ribonuclease MRP-Specific Protein Components

All known protein components of one of the longest-studied human ribonucleoprotein ribozyme nuclear Ribonuclease MRP (RNase MRP), which processes pre-rRNA at ITS1 site 2, are shared with Ribonuclease P (RNase P), which cleaves pre-tRNA 5' leader sequences. Our genome-wide forward genetic screening identified two poorly characterized human genes, which we named RPP24 and RPP64. We show that these two genes are required for pre-rRNA ITS1 site 2 processing and their protein products efficiently associate with RNA MRP. Unlike all other human RNase MRP protein components, RPP24 and RPP64 are not required for RNase P activity and do not associate with RNase P-specific RNA H1. Despite extremely limited sequence homology, RPP24 and RPP64 exhibit predicted structural similarities to two RNase MRP-specific components in S. cerevisiae, with specific differences in RPP64 regions of substrate recognition. Collectively, our functional screening and validation revealed the first two protein components unique to human nuclear RNase MRP.

genetics↗

bioRxiv2024

Identification of Human Pathways Acting on Nuclear Non-Coding RNAs Using the Mirror Forward Genetic Approach

Despite critical roles in diseases, human pathways acting on strictly nuclear non-coding RNAs have been refractory to forward genetics. To enable their forward genetic discovery, we developed a single-cell approach that "Mirrors" activities of nuclear pathways with cytoplasmic fluorescence. Application of Mirror to two nuclear pathways targeting MALAT1s 3' end, the pathway of its maturation and the other, the degradation pathway blocked by the triple-helical Element for Nuclear Expression (ENE), identified nearly all components of three complexes: Ribonuclease P and the RNA Exosome, including nuclear DIS3, EXOSC10, and C1D, as well as the Nuclear Exosome Targeting (NEXT) complex. Additionally, Mirror identified DEAD-box helicase DDX59 associated with the genetic disorder Oral-Facial-Digital syndrome (OFD), yet lacking known substrates or roles in nuclear RNA degradation. Knockout of DDX59 exhibits stabilization of the full-length MALAT1 with a stability-compromised ENE and increases levels of 3'-extended forms of small nuclear RNAs. It also exhibits extensive retention of minor introns, including in OFD-associated genes, suggesting a mechanism for DDX59 association with OFD. Mirror efficiently identifies pathways acting on strictly nuclear non-coding RNAs, including essential and indirectly-acting components, and, as a result, uncovers unexpected links to human disease.

genetics↗