transcriptome

Transcriptome refers to the complete set of RNA transcripts produced by the genome under a given set of conditions, in a specific cell, tissue, or organism. It encompasses all RNA molecules transcribed from the genome, including messenger RNA (mRNA) that encodes proteins, as well as non-coding RNAs such as ribosomal RNA (rRNA), transfer RNA (tRNA), microRNAs, long noncoding RNAs (lncRNAs), and other small RNAs. In practice, many transcriptome analyses focus on the subset of polyadenylated RNA or on poly(A)+ transcripts, but the full transcriptome can include non-polyadenylated species as well.

The transcriptome is dynamic, varying with developmental stage, tissue type, environmental conditions, and disease state. It is determined by transcriptional regulation, splicing, and RNA processing, yielding multiple transcript isoforms from a single gene.

Advances in high-throughput sequencing, particularly RNA sequencing (RNA-Seq), have enabled comprehensive transcriptome profiling. Other methods include microarrays and targeted sequencing. RNA-Seq provides quantitative measurements of transcript abundance, detects novel transcripts and alternative splicing events, and can reveal post-transcriptional modifications indirectly.

Computational analysis involves quality control, alignment to a reference genome, assembly of transcripts (reference-guided or de novo), and quantification of expression. Differential expression analysis identifies transcripts whose abundance changes across conditions; isoform-level analysis examines alternative splicing patterns.

Applications include basic research into gene function, developmental biology, and cell differentiation; disease studies and biomarker discovery; drug response research; and comparative genomics to study evolutionary differences in transcriptomes.