Journal: bioRxiv

Article Title: Mitochondrial RNA processing promotes translation by resolving structured precursor RNAs

doi: 10.64898/2026.07.30.741833

Figure Lengend Snippet: A) Schematic of human mitochondrial DNA expression. mt-mRNAs are colored by OXPHOS complex. mt-rRNAs are shown in orange and mt-tRNAs in dark grey. TSS, transcription start site. B) Representative Western blot analysis of OXPHOS subunits (left) and quantification of protein levels (right) from three replicate measurements of whole cell lysate from NT, FASTKD4 KO, and FASTKD4 KO rescue cells. Error bars represent standard deviation. Brown-Forsythe and Welch ANOVA test followed by Dunnett’s T3 multiple comparisons test, and significant p-values are indicated; *p-value < 0.05. kDa, kilodalton; EV, empty vector. C) Volcano plot depicting log2 fold change (FASTKD4 KO/NT control; x-axis) and -log10 adjusted p-value (y-axis) from RNA-seq. mt-mRNAs are highlighted. D) NT-normalized transcript abundance (relative to ACTB) for a subset of mt-mRNAs as quantified by RT-qPCR for three replicate measurements from NT, FASTKD4 KO, and FASTKD4-FLAG rescue cells. Error bars represent standard deviation. Brown-Forsythe and Welch ANOVA test followed by Dunnett’s T3 multiple comparisons test, and significant p-values are indicated; *p-value < 0.05 and **p-value < 0.01.

Article Snippet: Libraries were sequenced on an Illumina platform and processed using the Plasmidsaurus bioinformatic RNA-seq pipeline.

Techniques: Expressing, Western Blot, Standard Deviation, Plasmid Preparation, Control, RNA Sequencing, Quantitative RT-PCR

Journal: bioRxiv

Article Title: Mitochondrial RNA processing promotes translation by resolving structured precursor RNAs

doi: 10.64898/2026.07.30.741833

Figure Lengend Snippet: A) Western blot analysis confirming successful FASTKD4 KO in HEK293T cells for three independently generated clonal KO lines. NT, non-targeting control. B) CellTiter-Glo assay to quantify relative ATP production by NT and FASTKD4 KO cells when cultured in glucose media compared to media containing 2-DG or oligomycin. Error bars represent standard deviation. 2-DG, deoxyglucose. Two-way ANOVA followed by Sidak’s multiple comparison test, and significant p-values are indicated; ****p-value < 0.0001. C) Percentage live cells for NT and FASTKD4 KO cells cultured in either glucose media or media containing 10 mM 2-DG for 4 days, as determined by AnnexinV/PI staining and flow cytometry analysis. Two-way ANOVA followed by Sidak’s multiple comparison test; ns, not statistically significant. D) Representative Western blot analysis of OXPHOS subunits (left) and quantification of protein levels (right) from three replicate measurements of whole cell lysate from NT and FASTKD4 KO cells. Error bars represent standard deviation. Unpaired t-test with Welch’s correction, and significant p-values are indicated; *p-value < 0.05. E) Representative Western blot of OXPHOS protein stability (left) and quantification of protein levels (right) from two replicate measurements of whole cell lysate from NT and FASTKD4 KO cells after 0, 2, or 4 days of treatment with chloramphenicol (CAP). Error bars show standard deviation. Two-way ANOVA followed by Sidak’s multiple comparison test. Interaction not statistically significant unless otherwise indicated. F) Representative Western blot analysis of OXPHOS subunits (left) and quantification of protein levels (right) from three replicate measurements of whole cell lysate from NT and pooled FASTKD4 KO in HeLa. Error bars represent standard deviation. Statistical testing is the same as in D . G) Volcano plot depicting log2 fold change (FASTKD4-FLAG rescue/FASTKD4 KO; x-axis) and -log10 adjusted p-value (y-axis) from RNA-seq. mt-mRNAs are highlighted. H) NT-normalized transcript abundance (relative to ACTB) for a subset of mt-mRNAs as quantified by RT-qPCR for three replicate measurements from NT and pooled FASTKD4 KO HeLa cells. Error bars represent standard deviation. Statistical testing is the same as in D ; *p-value < 0.05, **p-value < 0.01.

Article Snippet: Libraries were sequenced on an Illumina platform and processed using the Plasmidsaurus bioinformatic RNA-seq pipeline.

Techniques: Western Blot, Generated, Control, Glo Assay, Cell Culture, Standard Deviation, Comparison, Staining, Flow Cytometry, RNA Sequencing, Quantitative RT-PCR

Journal: bioRxiv

Article Title: ATF4 and EcR interact to mediate both transcriptional activation and repression in the Drosophila fat body

doi: 10.64898/2026.03.10.710866

Figure Lengend Snippet: Counts per million (CPM) for the indicated transcripts from the RNAseq analysis in . ****=p<0.00001; ***=p<0.0001; **=p<0.001; *=p<0.05. Only significant comparisons are shown. Statistical tests are described in the methods.

Article Snippet: Duplicate RNA samples from independent crosses were submitted for each genotype to the Plasmidsaurus RNAseq analysis pipeline.

Techniques: RNA sequencing

Journal: bioRxiv

Article Title: ATF4 and EcR interact to mediate both transcriptional activation and repression in the Drosophila fat body

doi: 10.64898/2026.03.10.710866

Figure Lengend Snippet: A) Table summarizing the overall count of differentially regulated genes in RNAseq analyses performed in isolated fat bodies where the indicated RNAi lines are driven by Dcg-GAL4 . B) Venn-diagram showing the commonalities in the differentially downregulated (left) and upregulated genes (right) in A. C-E) Counts per million (CPM) for the indicated transcripts from the RNAseq analysis in A . C and D show data for known EcR targets, E shows data for known ATF4 targets. Also see Table S1 and S2 . ****=p<0.00001; ***=p<0.0001; **=p<0.001; *=p<0.05. Only significant comparisons are shown. Statistical tests are described in the methods.

Article Snippet: Duplicate RNA samples from independent crosses were submitted for each genotype to the Plasmidsaurus RNAseq analysis pipeline.

Techniques: RNA sequencing, Isolation