Supporting Data for "ZC3H8 regulates rDNA transcription by suppression of R loop formation"

Project Overview:

This project investigates the role of ZC3H8, a nucleolar protein, in safeguarding genomic integrity during ribosome biogenesis. The nucleolus, as the site of ribosomal RNA (rRNA) synthesis, is one of the most transcriptionally active regions in the cell and is particularly vulnerable to genomic instability. Ribosomal DNA (rDNA), which resides in the nucleolus, is prone to the formation of R loops—three-stranded nucleic acid structures that can interfere with transcription, thereby threatening genome stability.

The study demonstrates that ZC3H8 may play a critical role in suppressing R loop formation at rDNA loci. Mechanistically, ZC3H8 functions in concert with DHX9, an RNA helicase known to resolve R loops. ZC3H8 binds preferentially to single-stranded RNA, and this interaction is proposed to stabilize the RNA strand during DHX9-mediated unwinding of R loops. This cooperative mechanism supports efficient rRNA synthesis while preserving the structural and functional integrity of the rDNA.

Dataset Contents:

The dataset includes raw and processed experimental data organized by thesis chapters and figures. Data formats include high-resolution immunofluorescence images, Western blot scans, quantification files, RNA-seq datasets, and schematic illustrations. All files are arranged to mirror the thesis structure, ensuring clear correspondence between data and manuscript figures.

Key Directories and File Types:

Chapter 1 – Introduction (Figures 1.1–1.2):

Adobe Illustrator (.ai) schematics illustrating rDNA structure and nucleolar functions.

Chapter 3 – Experimental Results (Figures 3.1–3.13):

Raw Data:

• Immunofluorescence images (.tif, .rar)
• Western blot scans (Image Lab format)
• RNA-seq analysis files (.csv, .xlsx, .txt)
• EMSA gel images
• Quantification data (.pzfx, .pzf) from GraphPad Prism
• Protein structure prediction outputs (AlphaFold, PyMOL)

Organised Data:

• Finalized figure panels (.tif)
• Schematics (.ai) and processed visualizations used directly in the thesis manuscript.

Software and Equipment Used:

• Image Analysis: Fiji (ImageJ v1.53f51)
• Quantitative Analysis: GraphPad Prism (v7.0 or higher)
• Microscopy: Zeiss LSM 780 confocal microscope

Intended Use:

The dataset supports reproducibility and transparency of the thesis findings. It is intended for researchers interested in rDNA transcription, nucleolar biology, RNA processing, and protein–nucleic acid interactions. The detailed file organization facilitates targeted reuse of specific data elements (e.g., IF quantifications, RNA-seq processing).