Scripture

Scripture reconstructs transcriptomes from paired-end Illumina RNA-Seq cDNA sequencing to enable unbiased assembly and annotation of coding and noncoding genes in mammalian cells.

Key Features:

• Ab Initio Reconstruction: Reconstructs transcriptomes using only RNA-Seq reads and the reference genome without relying on existing annotations.
• Full-Length Gene Structure Determination: Assembles full-length gene structures for most known expressed genes, demonstrated in mouse embryonic stem cells, neuronal precursor cells, and lung fibroblasts.
• Identification of Transcript Variability: Detects novel 5' start sites, 3' ends, and internal coding exons indicating transcript variation in protein-coding genes.
• Noncoding RNA Analysis: Determines gene structures of large intergenic noncoding RNAs (lincRNAs) and antisense loci, reconstructing over a thousand lincRNAs in the reported datasets.

Scientific Applications:

• Transcriptome Exploration: Provides an unbiased view of known and novel transcripts to characterize gene expression dynamics across samples.
• Functional Genomics: Enables identification of novel transcript variants and noncoding RNAs for downstream experimental and functional studies.
• Comparative Transcriptomics: Allows comparison of transcriptomic landscapes across cell types or conditions to identify condition-specific expression patterns.

Methodology:

Align RNA-Seq reads to the reference genome to assemble transcripts; determine exon–intron structures, transcript start sites, and transcript ends without prior annotation; and perform iterative validation and refinement of reconstructed transcript models.