Transcription and RNA Processing

Core Concept

Transcription is the synthesis of an RNA copy of a gene's DNA sequence, carried out by RNA polymerase. It is the first step of the central dogma — DNA → RNA → protein — converting stored genetic information into a form the cell can use to build proteins. In eukaryotes, the initial transcript is then processed (capped, tailed, and spliced) into mature mRNA.

Key Concepts

The central dogma

The flow of genetic information is DNA → RNA → protein. DNA is the permanent store; transcription makes an RNA working copy of a gene; translation (next note) reads that RNA to assemble a protein. (Some viruses reverse the flow — reverse transcription — but the DNA → RNA → protein direction is the general rule of life.)

RNA polymerase and the promoter

RNA polymerase unwinds a short stretch of DNA and links ribonucleotides into RNA, moving 5′→3′ along the template. It does not need a primer. Transcription begins at a promoter — a specific DNA sequence upstream of the gene that RNA polymerase (with the help of transcription factors) recognizes and binds. The promoter determines where transcription starts and which strand is read.

Template strand vs. coding strand

Of the two DNA strands, only one — the template (noncoding) strand — is copied into RNA, using complementary base pairing (with uracil (U) replacing thymine). The other strand, the coding strand, has the same sequence as the RNA (with T instead of U) and is not used as a template. Which strand serves as template differs from gene to gene.

Elongation and termination

During elongation, RNA polymerase adds RNA nucleotides complementary to the template (A pairs with U, C with G), growing the transcript 5′→3′. Termination occurs when the polymerase reaches a terminator sequence and releases the transcript. In prokaryotes this mRNA can be translated immediately; in eukaryotes it must first be processed.

Eukaryotic RNA processing

Eukaryotic pre-mRNA undergoes three major modifications before leaving the nucleus: (1) a 5′ cap (a modified guanine nucleotide) is added to the 5′ end, protecting the RNA and helping the ribosome bind; (2) a poly-A tail (a string of adenines) is added to the 3′ end, protecting against degradation and aiding export; and (3) splicing removes introns (noncoding sequences) and joins exons (coding sequences) together, catalyzed by the spliceosome (a complex of RNA and protein).

Alternative splicing

Because a single pre-mRNA can be spliced in more than one way — different combinations of exons joined, or some exons skipped — one gene can produce multiple different proteins. This alternative splicing helps explain how ~20,000 human genes can encode far more protein products, contributing to tissue-specific and developmental diversity.

How It Works

Transcription factors guide RNA polymerase to the promoter, where the polymerase unwinds the DNA and selects the template strand. The polymerase moves along the template 3′→5′ (synthesizing RNA 5′→3′), adding U for each A, G for each C, and so on, until it reaches a terminator and falls off. In eukaryotes, the pre-mRNA then gets its 5′ cap and poly-A tail, and the spliceosome cuts out introns and ligates exons. The mature mRNA — capped, tailed, spliced — is exported to the cytoplasm for translation.

How it works

Transcription factors guide RNA polymerase to the promoter, where the polymerase unwinds the DNA and selects the template strand. The polymerase moves along the template 3′→5′ (synthesizing RNA 5′→3′), adding U for each A, G for each C, and so on, until it reaches a terminator and falls off. In eukaryotes, the pre-mRNA then gets its 5′ cap and poly-A tail, and the spliceosome cuts out introns and ligates exons. The mature mRNA — capped, tailed, spliced — is exported to the cytoplasm for translation.

Common confusions

• "Both DNA strands are transcribed." Wrong — only the template strand is copied into RNA.
• "The template strand has the same sequence as the mRNA." Wrong — the coding strand matches the mRNA (with T→U); the template is complementary.
• "RNA polymerase needs a primer." Wrong — that's DNA polymerase; RNA polymerase can start from scratch at the promoter.
• "Thymine pairs with uracil." Wrong — in RNA, A pairs with U; T is simply not used in RNA.
• "Introns are junk that does nothing." Oversimplified — some introns are regulatory or code for other RNAs; and their removal/splicing is essential for making correct mRNA.

Quick review

• DNA → RNA → protein (central dogma).
• RNA polymerase binds the promoter and reads the template strand.
• RNA is made 5′→3′; A pairs with U.
• Coding strand = mRNA sequence; template strand = its complement.
• Processing: 5′ cap, poly-A tail, intron removal/exon joining.
• Spliceosome does the splicing; alternative splicing creates protein diversity.