FLAM-seq analysis pipeline

FLAM-seq analysis pipeline profiles full-length mRNA molecules, including coding regions and poly(A) tails, to measure poly(A) tail length and non-A nucleotide composition and to relate tail features to 3' UTR length, alternative polyadenylation, and promoter usage.

Key Features:

• Full-length mRNA sequencing: Produces sequences of entire mRNA molecules encompassing coding regions and poly(A) tails.
• cDNA library preparation: Uses a complementary DNA (cDNA) library preparation method to capture full-length transcripts.
• Single-molecule sequencing integration: Integrates single-molecule sequencing technology for readout of full-length cDNAs.
• Poly(A) tail length measurement: Measures poly(A) tail length at single-transcript resolution.
• Non-A nucleotide detection: Detects non-adenine nucleotides within poly(A) tails, with reported prevalence of cytosines.
• High-throughput profiling: Recovers full-length mRNA sequences from thousands of genes within a single sample.
• Transcript feature associations: Identifies relationships between poly(A) tail length and transcript features such as 3' UTR length, alternative polyadenylation, and promoter usage.

Scientific Applications:

• Human cell lines: Applied to human cell lines to profile poly(A) tail length and composition across transcripts.
• Brain organoids: Used in brain organoids to investigate transcript-specific tail features in complex tissue models.
• Caenorhabditis elegans: Applied to the model organism Caenorhabditis elegans for organismal-scale analysis of mRNA tails.
• 3' UTR and tail length studies: Reveals correlations between 3' UTR length and poly(A) tail length.
• Alternative polyadenylation and promoter analysis: Identifies links between alternative polyadenylation sites and alternative promoters associated with different poly(A) tail lengths.
• Poly(A) tail composition analysis: Uncovers substantial presence of non-adenine nucleotides, particularly cytosines, within poly(A) tails.

Methodology:

No computational steps are explicitly stated in the provided description; the method description specifies cDNA library preparation and single-molecule sequencing integration but not specific computational procedures.