Project description:The viral miRNA miR-K6-5p encoded by the DNA tumor virus Kaposi’s sarcoma-associated herpesvirus exhibits offset, sequence similarity with the tumor suppressive cellular miR-15/16 family, as well as sharing a short seed match to the cellular miR-214 (nts 2-7). We investigated how gene regulation by the viral miR-K6-5p is related to regulation by these cellular miRNAs by performing transcriptome analysis. mRNA-Seq was done in HEK 293T NoDice cells (Bogerd et al., RNA 2014) lacking Dicer which severely impaired the maturation of miRNAs thereby eliminating confounding effects of endogenously expressed miR-15/16 family. We transfected mature miRNA mimics of miR-16, miR-K6-5p wild-type, a variant of miR-K6-5p with a U at nt 1 instead of a C to control of RISC loading (miR-K6 5’U), miR-214, or a control mimic into NoDice cells, and harvested total RNA 2 days post-transfection.

2019-11-01 | GSE128576 | GEO

Betaproteobacteria bacterium strain:JGI CrystG Aug02-3-K6

Project description:Betaproteobacteria bacterium strain:JGI CrystG Aug02-3-K6 Genome sequencing

| PRJNA403024 | ENA

K6-Linked Ubiquitylation Signals Reactive Aldehyde-Induced RNA-Protein Crosslink Resolution

Project description:Reactive aldehydes induce the formation of RNA-protein crosslinks (RPCs), RPCs in the mRNA stall the ribosome and inhibit translation, RPCs are K6-linked ubiqutylated by RBR-type E3 ligase RNF14, RPCs are resolved in a UBXN1-VCP/p97-dependent manner

2023-11-03 | GSE240625 | GEO

Aspergillus nidulans strain:FGSC A4 K6 | isolate:ATCC 38163

Project description:Aspergillus nidulans FGSC A4 K6 Resequencing genome sequencing

| PRJNA332770 | ENA

Oxalobacteraceae bacterium JGI 0001002-K6

Project description:Oxalobacteraceae bacterium JGI 0001002-K6

| PRJNA176064 | ENA

Atypical K6-linked ubiquitylation marks toxic RNA-protein crosslinks induced by formaldehyde

Project description:Reactive aldehydes are produced during cellular metabolism and can accumulate in specific tissues particularly when aldehyde clearance mechanisms are impaired. Reactive aldehydes induce DNA-DNA and DNA-protein crosslinks (DPCs) that are repaired by different DNA repair pathways. Cellular toxicity of endogenous formaldehyde has been attributed to the damage of the genomic DNA and consequent inhibition of transcription. However, whether damage to other cellular macromolecules and interference with additional metabolic processes contributes to formaldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces toxic RNA-protein crosslinks (RPCs) in mRNA that inhibit translation and induce a specific RPC stress response pathway that is characterized by linkage-specific ubiquitylation. RPCs in the mRNA are recognized by stalling ribosomes and marked by K6-linked ubiquitylation that promotes their clearance by the ubiquitin-dependent unfoldase VCP.

2023-09-01 | GSE225044 | GEO

Genome-wide single nucleotide polymorphism array and whole-genome sequencing reveal the inbreeding progression of Banna minipig inbred line [Seq]

Project description:We sequenced and analyzed the genome of a highly inbred miniature Chinese pig strain, the Banna Minipig Inbred Line (BMI). we conducted whole genome screening using next generation sequencing (NGS) technology and performed SNP calling using Sus Scrofa genome assembly Sscrofa11.1.

2020-12-31 | GSE157688 | GEO

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