RNA types and functions RNA transcription

RNA types, function and transcription: high-yield summary

1. DNA vs RNA

Feature

DNA

RNA

Sugar

Deoxyribose

Ribose, with a 2′-OH group

Bases

A, G, C, T

A, G, C, U

Usual structure

Double-stranded

Single-stranded

Main role

Stores genetic information

Gene expression, regulation and catalysis

RNA can fold through internal base pairing to form hairpins, stem-loops and complex three-dimensional structures.

Purines: adenine and guanine.
Pyrimidines: cytosine, thymine and uracil.


2. Major RNA types

RNA

High-yield function

mRNA

Carries the protein-coding sequence to ribosomes

rRNA

Forms the structural and catalytic core of ribosomes

tRNA

Delivers amino acids and matches them to mRNA codons

snRNA

Participates in pre-mRNA splicing as part of the spliceosome

snoRNA

Guides processing and chemical modification of rRNA

miRNA

Regulates gene expression by repressing translation and promoting degradation of target mRNAs

siRNA

Guides gene silencing, often by directing cleavage of a complementary mRNA

lncRNA

Regulates diverse cellular processes; can act as a molecular scaffold

Clinical link — inclisiran: An siRNA that reduces hepatic PCSK9 production, increasing LDL receptor availability and lowering LDL cholesterol. It treats elevated LDL; it is not a cure for familial hypercholesterolemia.


3. Transcription fundamentals

Transcription is the synthesis of RNA from a DNA template.

  • RNA polymerase reads the template DNA strand 3′ → 5′.

  • RNA is synthesized 5′ → 3′, as nucleotides are added to its 3′ end.

  • RNA is complementary to the template strand and has the same sequence as the coding strand, except that RNA contains U instead of T.

  • RNA polymerase can initiate RNA synthesis without a primer.

Example:

Strand

Sequence

Coding DNA

5′-ATGC-3′

Template DNA

3′-TACG-5′

RNA

5′-AUGC-3′

Stages

  1. Initiation: RNA polymerase and associated factors recognize the promoter. DNA opens locally, producing a transcription bubble.

  2. Elongation: Polymerase moves along the template and joins complementary ribonucleotides through phosphodiester bonds.

  3. Termination: Termination mechanisms cause the RNA transcript and polymerase to be released. These mechanisms differ among organisms and polymerases.

Upstream is toward the promoter; downstream is in the direction of transcription.


4. Eukaryotic RNA polymerases

Polymerase

Major products

RNA polymerase I

28S, 18S and 5.8S rRNAs

RNA polymerase II

mRNA, plus several noncoding RNAs, including most spliceosomal snRNAs and many miRNAs

RNA polymerase III

tRNA, 5S rRNA and some small RNAs

Exam distinction: Most rRNA is made by Pol I, but 5S rRNA is made by Pol III.

Inhibitors

  • Rifampicin: inhibits bacterial RNA polymerase; used in tuberculosis treatment.

  • α-Amanitin: strongly inhibits RNA polymerase II; severe mushroom poisoning can cause liver failure.


5. Eukaryotic gene structure and regulation

A gene contains the information needed to produce a functional RNA or protein. A typical protein-coding gene includes:

  • Promoter: DNA region where the transcription machinery assembles.

  • Exons: sequences retained in mature RNA. Exons can include untranslated regions, so they are not always entirely protein-coding.

  • Introns: sequences removed from pre-mRNA.

  • 5′ and 3′ untranslated regions (UTRs): transcribed but not translated; help regulate mRNA translation, stability and localization.

  • Regulatory elements: promoter-proximal elements and enhancers influence transcription.

The transcription start site is distinct from the translation start codon.

Promoters and transcription factors

  • The TATA box, when present, is typically around 25–30 base pairs upstream of the transcription start site.

  • TFIID, which contains the TATA-binding protein (TBP), helps position the Pol II transcription machinery.

  • CpG-island promoters are common in mammalian genes and may have several transcription start sites.

  • General transcription factors help recruit and position RNA polymerase II and initiate transcription.


6. Processing of eukaryotic pre-mRNA

The three major processing events are 5′ capping, splicing and 3′ cleavage/polyadenylation. Processing can occur while transcription is still underway.

A. 5′ capping

A 7-methylguanosine cap is added shortly after transcription begins through an unusual 5′–5′ linkage.

It helps:

  • Protect mRNA from degradation.

  • Support nuclear export.

  • Promote translation initiation.

B. RNA splicing

The spliceosome, made of small nuclear ribonucleoproteins (snRNPs) and other proteins, removes introns and joins exons.

Key signals in most introns:

  • 5′ splice site: usually begins with GU.

  • Branch point: contains an adenine.

  • 3′ splice site: usually ends with AG.

Splicing occurs through two transesterification reactions. The intron forms a lariat and is removed; the exons are joined.

Alternative splicing allows one pre-mRNA to produce different mature mRNAs and protein isoforms. In the lecture’s example, fibronectin is spliced differently in fibroblasts and hepatocytes.

C. 3′ cleavage and polyadenylation

  • The AAUAAA sequence is a common polyadenylation signal.

  • The pre-mRNA is cleaved downstream of this signal.

  • Poly(A) polymerase adds a poly(A) tail.

The tail contributes to mRNA stability, export and translation.


7. Clinical connections

Condition or treatment

Mechanism

β-Thalassemia

Mutations can reduce β-globin production by disrupting transcription, splicing or RNA processing. The IVS-I-110 variant creates an abnormal splice site.

Spinal muscular atrophy

Loss of functional SMN1 reduces SMN protein. SMN2 produces limited full-length protein because most of its transcripts skip exon 7.

mRNA vaccines

Delivered mRNA is translated by host ribosomes to produce an antigen, which stimulates an immune response.


Rapid review: what to memorize

  1. Template read 3′ → 5′; RNA made 5′ → 3′.

  2. RNA matches the coding DNA strand except U replaces T.

  3. Pol I: most rRNA; Pol II: mRNA; Pol III: tRNA and 5S rRNA.

  4. Pre-mRNA processing: 5′ cap, splicing, 3′ poly(A) tail.

  5. Typical splice signals: GU → branch-point A → AG.

  6. Exons are retained, but may contain untranslated sequences.

  7. Rifampicin → bacterial RNA polymerase; α-amanitin → Pol II.

Source: attached lecture, “RNA types and functions / RNA transcription,” especially slides 7–8, 12–20 and 23–47. The lecture lists Molecular Cell Biology, 8th edition, chapters 5, 8 and 9, as its resource.