Journal: bioRxiv

Article Title: Fasting disrupts the InsP₆–HDAC3 axis to drive ER stress–mediated clearance of DNA-damaged cells and enforce tissue quality control

doi: 10.64898/2026.05.24.727426

Figure Lengend Snippet: (A) Workflow for proteomic analysis of FACS-purified IECs from Ileum. Schematic created in BioRender (CHATTERJEE, S., 2026; https://BioRender.com/mtrovit ). (B) Volcano plot showing differentially expressed proteins in starved versus untreated mouse crypts. (C) Pathway enrichment analysis of upregulated proteins. (D) Heatmap of selected proteins associated with ER stress (red), integrated cellular stress (blue), and starvation responses (green, positive control), highlighting CDK5RAP3. (E) Network visualization of enriched biological processes and pathways related to cellular stress responses, including ER stress, unfolded protein response, and proteotoxic stress. (F) Immunoblot analysis of CDK5RAP3, CHOP, IRE1, and calreticulin in untreated, starved, and refeed conditions. The tests were conducted under two different exposures, 3 sec blue and 45 sec pink, and were validated using antibodies from Proteintech yellow and Bethyl green. (G) Volcano plot of bulk RNA sequencing from purified crypts of untreated and starved mice, highlighting CDK5RAP3 among differentially expressed transcripts during fasting. (H) Heat map of CUT&RUN analysis of H3K27ac signal in untreated and starved samples (highlighted blue). (I) Overlap of RNA-seq, and CUT&RUN datasets. (J) Genome browser tracks showing H3K27ac enrichment at the CDK5RAP3 transcription start sites (highlighted blue). (K) Immunoprecipitation of pan-acetylated proteins from 400 μg protein lysate followed by immunoblotting for CDK5RAP3 from untreated and starved samples. Data represent n = 3 independent biological replicates unless otherwise indicated; mean ± SD where applicable.

Article Snippet: Eluted DNA from CUT&RUN was used for library construction with the CUTANATM CUT&RUN Library Prep Kit (EpiCypher, Cat. #14-1001 and #14-1002), according to the manufacturer’s instructions.

Techniques: Purification, Positive Control, Western Blot, RNA Sequencing, Immunoprecipitation

Journal: bioRxiv

Article Title: Fasting disrupts the InsP₆–HDAC3 axis to drive ER stress–mediated clearance of DNA-damaged cells and enforce tissue quality control

doi: 10.64898/2026.05.24.727426

Figure Lengend Snippet: (A) Experimental conditions including untreated (UT), heat shock (HS), cold shock (CS), osmotic stress (OS), oxidative stress (OXS), UV-induced DNA damage (UV), amino acid deprivation (A.A), and growth factor deprivation (GFD) followed by western blot. Created in BioRender. CHATTERJEE, S. (2026) https://BioRender.com/mtrovit . (B) Immunoblot analysis of pan-histone acetylation (PanAc) and total H3 in HEK, HCT116, and MEF cells under the indicated conditions. (C) Quantification of PanAc normalized to H3 in HEK, HCT116, and MEF cells (n = 3; mean ± SD). (D) Heat map of CUT&RUN analysis showing H3K27ac signal distribution in UT and GFD conditions in HCT116 cells. (n = 2). (E) Genome browser tracks showing H3K27ac enrichment at the CDK5RAP3 locus in untreated and GFD HCT116 cells. (n = 2). (F) Heatmap and volcano plot of gene expression changes under GFD in HCT116 cells highlighting CDK5RAP3. (G) Overlap of CDK5RAP3-associated datasets from HCT116 and mouse samples. (H) Immunoprecipitation of acetylated proteins (from 400 μg lysate) followed by immunoblotting for CDK5RAP3 from HDAC1 and HDAC3 knockout HCT116 cells under UT and GFD conditions. (n=3). (I) Immunoblot analysis of CDK5RAP3, H3K27ac, H4K16ac, and histone controls following treatment with histone acetyltransferase inhibitors under GFD conditions. MG149 (35µM) Tip60 inhibitor, A485 (10µM) P300 inhibitor treated in GFD for 12 hours.(n=3) (J) Immunoblot analysis of CDK5RAP3, RPL26 UFMylation, CHOP, and IRE1 in UT and GFD HCT116 cells.(n=3) (K) Schematic of HDAC3 PROTAC-mediated degradation. Created in BioRender (CHATTERJEE, S., 2026; https://BioRender.com ). Western blot analysis in HCT116 cells assessed the time-dependent degradation of HDAC3 after PROTAC treatment and the effect of compound washout. (L) Immunoblot and quantification of IPMK and IPPK protein levels in HCT116 cells (n = 3 to 13; mean ± SD). (M) ChIP–qPCR analysis of CDK5RAP3 under UT, GFD, and GFD+CP-InsP₆ treated HCT116 cells (n = 3; mean ± SD). (N) Immunoprecipitation of CDK5RAP3 from 400 μg of protein lysate from HCT116 cells followed by immunoblotting for acetylation under indicated conditions. (n = 3) All dots in bar plots represent individual biological replicates.

Article Snippet: Eluted DNA from CUT&RUN was used for library construction with the CUTANATM CUT&RUN Library Prep Kit (EpiCypher, Cat. #14-1001 and #14-1002), according to the manufacturer’s instructions.

Techniques: Western Blot, Gene Expression, Immunoprecipitation, Knock-Out, ChIP-qPCR

Journal: Nature Communications

Article Title: Small RNA genomics of Aedes aegypti mosquitoes discovers infectious viruses that trigger an RNA interference response

doi: 10.1038/s41467-026-71964-1

Figure Lengend Snippet: a Overview of the Mosquito Small RNA Genomics (MSRG) pipeline applied to a survey of whole mosquitoes from Americas, Asia, Africa and laboratory strains. b Implementation of the VirusDetect program with updated GBVRL and custom databases for comprehensive mosquito virus detection. c Summary tabulation of the samples and RNA libraries analyzed in this study.

Article Snippet: Small RNA libraries were made using NEBNext Small RNA Library Prep Set (NEB #E7330) with up to 5 μg of RNA input.

Techniques: Virus

Journal: Nature Communications

Article Title: Small RNA genomics of Aedes aegypti mosquitoes discovers infectious viruses that trigger an RNA interference response

doi: 10.1038/s41467-026-71964-1

Figure Lengend Snippet: a Bubble plot of vsmRNAs from Africa Ae. aegypti colony strains. Number of reads per million is reflected by bubble diameter, and color represents strand bias of reads, red is plus strand biased, blue is minus strand biased. Dashed pink line boxes mark the PCLV and FORMV noted in panels ( c ) and ( d ), respectively. b Map of Africa locations where the Ae. aegypti colonies or samples originated. Map data ©2025 Google. c Coverage plots of PCLV small RNAs from a selection of African Ae. aegypti showing high M-fragment piRNAs rivaling the S-fragment piRNAs. d The FORMV vsmRNA coverage from African Ae. aegypti colonies from the McBride lab and an independent Kedougou, Senegal sample from Olmo et al. . The black arrow points to male-specific viral piRNA species. e Three examples of FORMV long RNAs sequenced from matched samples in ( d ).

Article Snippet: Small RNA libraries were made using NEBNext Small RNA Library Prep Set (NEB #E7330) with up to 5 μg of RNA input.

Techniques: Selection

Journal: Nature Communications

Article Title: Small RNA genomics of Aedes aegypti mosquitoes discovers infectious viruses that trigger an RNA interference response

doi: 10.1038/s41467-026-71964-1

Figure Lengend Snippet: a Bubble plot of vsmRNAs from lab strains. Reads per million represented by bubble diameter, strand bias represented by color, red is plus strand biased, blue is minus strand biased. See Supplementary Data for sample details. Lab initials: BZL=Benzon Research, MY = M. Younger, DB = D. Brackney, JM = J. Marques, ZT = Z. Tu, GH = G. Hughes, TC = T. Colpitts, BH = B. Hay, GP = G. Pijlman labs. b Coverage plots of long RNAs compared to small RNAs for viruses from the BZL strain of Ae. aegypti females and dormant eggs. c Coverage plots of TMBTLV small RNAs from GP lab strains also infected with Zika virus (ZIKV). d Scatterplot comparing matched small and long RNA libraries from Ae. aegypti . Sequencing RPM are plotted on a logarithmic scale. Sample dots are colored by sex, and clustered samples are in labeled ovals. e Coverage plots of two Florida exhibiting abundant long RNA signal for the Toti-like virus but negligible vsmRNAs in the upper plots that contrast both long and small RNAs against an R1-Ele4 TE. f Coverage plots of long RNAs versus small RNAs for the Formosus virus and R1-Ele4 TE from both males and females of the ENT African colony.

Article Snippet: Small RNA libraries were made using NEBNext Small RNA Library Prep Set (NEB #E7330) with up to 5 μg of RNA input.

Techniques: Infection, Virus, Sequencing, Labeling

Journal: Nature Communications

Article Title: Small RNA genomics of Aedes aegypti mosquitoes discovers infectious viruses that trigger an RNA interference response

doi: 10.1038/s41467-026-71964-1

Figure Lengend Snippet: a Our methodology to molecularly validate the small RNA detection of ISVs are true viruses that can be isolated and verified for triggering the RNAi response in mosquito cells. b RT-PCR detection of TMBTLV RNAs S1 and S2 during multiple rounds of blind passaging, starting with BZL mosquito homogenate as the initial virus infection source placed onto C6/36-NL and Aag2 mosquito cells. The ladder is the 1KbPlus DNA ladder, and uncropped gels are in the source data files. c Virus infection kinetics measured in C6/36-NL and Aag2 cells over 12 days using droplet digital PCR (ddPCR). Flasks with 1 million cells were infected on Day 0 with 20 K viral copies per infection. Virus stocks are from filtered media from subsequent passage from the experiment in (a). Error bars correspond to the 95% confidence interval from Poisson Distribution in the ddPCR analysis algorithm centered around the mean from each reading that contained >15 K droplets replicates. Additional virus infection kinetics measurements are shown in Supplementary Fig. . T-flask illustration from NIAID NIH BioArt Source (bioart.niaid.nih.gov/bioart/303).

Article Snippet: Small RNA libraries were made using NEBNext Small RNA Library Prep Set (NEB #E7330) with up to 5 μg of RNA input.

Techniques: RNA Detection, Isolation, Reverse Transcription Polymerase Chain Reaction, Passaging, Virus, Infection, Digital PCR