csRNA-seq

csRNA-seq identifies transcription start sites (TSSs) of stable and unstable RNAs at single-nucleotide resolution from total RNA to map transcription initiation and regulatory elements across eukaryotes.

Key Features:

• Single-Nucleotide Resolution: Detects TSSs with single-nucleotide precision.
• Sensitivity to Transcriptional Changes: Highly sensitive to acute changes in transcription, identifying more regulated transcripts than traditional RNA sequencing methods.
• Detection of Unstable Transcripts: Captures unstable transcripts including enhancer RNAs, primary microRNAs (pri-miRNAs), antisense transcripts, and promoter upstream transcripts.
• Broad Eukaryotic Applicability: Applicable across eukaryotes, including multicellular animals, plants, and fungi.
• Integration with Epigenomic Data: Facilitates integration with epigenomic data and reveals histone modification patterns such as histone H3 trimethylation (H3K4me3) enrichment at TSSs of stable transcripts and H3K27ac marking nucleosomes downstream of active TSSs.
• Capture of 5' Cap-Protected RNAs: Sequences the 5' ends of cap-protected RNAs from total RNA to capture both stable and unstable transcripts for TSS mapping.
• Dynamic Quantification: Enables identification and dynamic quantification of regulatory elements from total RNA.

Scientific Applications:

• Regulatory Element Identification: Enables identification and dynamic quantification of regulatory elements within total RNA to study transcriptional regulation.
• Evolutionary Insights: Provides comparative insights into conserved mechanisms of transcription initiation spanning 1.6 billion years of eukaryotic evolutionary history.
• Histone Modification Roles: Aids elucidation of the roles of posttranslational histone modifications in transcription regulation, indicating ancient and fundamental functions.

Methodology:

Sequences the 5' ends of cap-protected RNAs from total RNA to capture stable and unstable transcripts and identify TSSs at single-nucleotide resolution.