Andrew D. Holmes's research while affiliated with University of California, Santa Cruz and other places

... In tRFtarget 2.0, we endeavored to resolve this problem by incorporating the original name of tRFs and their corresponding nucleotide sequences for reference. Moreover, we integrated standardized IDs, which were generated using tDRnamer ( 45 ), a consistent and uniform tRF naming system published in 2023, for each tRF sequence indexed in tRFtarget. The tRF IDs assigned by tDRnamer encompass comprehensive information to index the unique sequence, including the name of source tRNA, the tRF position within the source tRNA, the total number of matching source tRNAs, as well as potential variations (Figure 2 ). ...

... The copyright holder for this preprint this version posted November 11, 2023. ; https://doi.org/10.1101/2023.11.11.566681 doi: bioRxiv preprint Human references described here were used as in 24 sequences and references were prepared as described 43 . ncRNA from Ensembl and lncRNA from Gencode were concatenated. ...

... ucsc. edu/ tDRna mer/) for uniform naming of the referenced tDRs [18]. ...

... Eight human tRNA-iMet-CAT genes are identical in sequence (iMet-CAT-1-1 to iMet-CAT-1-8) and are all predicted to be active, based on the sequence features of the genes and their flanking DNA [54]. As these genes have identical binding sites for TFIIIC (within their transcribed regions), they might be expected to recruit p300 with similar efficiencies, leading to similar strengths of H3K27ac. ...

... Gene expression profiles of AOA in soil resemble pure culture reference strains To evaluate competition between different AOA phylotypes, in situ gene expression profiles of the six major AOA lineages in our soils were compared to three AOA strains, for which RNA seqbased gene expression patterns in nutrient-replete, exponentially growing cultures were available [48,51,52], similar to the approach described previously for N. viennensis [48]. The log 2transformed rpoB-normalized RPKM values of key metabolism genes showed highly similar expression patterns in soils and pure culture strains (Fig. 5 and Supplementary Table S15). ...

... As expected, targeted sequencing around the D47 site did not generate RT mutations in tRNA analyzed from WT or DUS3L KO cells, however we found ~30% T-to-C mutation specifically at position 47 when RNA from WT cells was treated with NaBH 4 before RT ( Supplementary Fig. 12). In contrast, NaBH 4 -treated RNA from DUS3L KO cells lacked any mutation at U47 indicating that the NaBH 4 -induced mutational signature was specific to D. Encouraged by this result, we generated high-throughput sequencing libraries from total tRNA isolated from WT HEK293T or DUS3L KO cells by adapting the ARM-seq/DM-seq methods 36,37 and analyzed NaBH 4 -dependent mutational events across all identified tRNA species using VarScan variant detection software 38 Next, we analyzed individual mutational events at predicted D positions (using the Sprinzl tRNA position numbering system 39 ) in NaBH 4 -treated WT RNA and the untreated control for all tRNA isodecoder families in our data. We collapsed isodecoder-specific data according to tRNA anticodon sequence and found 66 potential D modification sites that showed 3-fold or higher mutation rate in the NaBH 4 -treated sample as compared to the control, with the majority exhibiting 10-100-fold difference in mutation rate (Fig. 5c). ...

... For all analyses, the genome assembly and annotation for the Haloferax volcanii DS2 strain, downloaded from the NCBI database, and also matching the haloVolc1 version on the UCSC Microbial Genome Browser [72] (http:// micro bes. ucsc. ...