Gene Expression: Transcription

Introduction

DNA sequences known as genes encode proteins or functional RNAs. However, even protein-coding genes do not directly drive protein synthesis but act through the process of gene expression. Gene expression includes two main processes:

1. Transcription: RNA synthesis occurs on the DNA template.

2. Translation: protein synthesis takes place on the RNA template.

In eukaryotic cells, RNA molecules undergo several processing steps before translation can occur.

Question on the topic

The nucleotide sequence of a DNA strand serving as a template for transcription is given below. 5'-AACCTGACAGA-3'

What is the nucleotide sequence of the RNA produced on this template?

Note that nucleic acid sequences should be written in the 5'-3' direction.

Answer

UCUGUCAGGUU

RNA polymerase

The main enzyme involved in transcription is RNA polymerase which catalyses the synthesis of RNA using the DNA template. Similar to DNA polymerase, RNA polymerase elongates RNA in the 5'-to-3' direction. However, unlike DNA polymerase, RNA polymerase does not require a primer to initiate polynucleotide synthesis.

In bacteria, a single RNA polymerase enzyme is responsible for transcription. Eukaryotes typically possess three RNA polymerases, each responsible for transcribing different types of genes. However, all eukaryotic protein-coding genes are transcribed by RNA polymerase II.

Eukaryotic RNA polymerase II Image source: Litvinanna - Own work using https://www.rcsb.org/structure/1WCM, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=77523301

The RNA produced on a protein-coding gene is referred to as messenger RNA (mRNA). Transcription of other genes results in non-coding RNAs, which include ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), microRNAs (miRNAs) and several other RNA types.

Initiation of Transcription

To start transcription, RNA polymerase must bind to a specific DNA sequence known as a promoter, which marks the start site for RNA synthesis. Most, though not all, promoters are located upstream from (before) the transcription start site.

Image source: Connie Rye, Robert Wise, Vladimir Jurukovski, Jean DeSaix, Jung Choi, Yael Avissar - Biology, Oct 21, 2016, https://openstax.org/books/biology/pages/15-2-prokaryotic-transcription

Transcription initiation in bacteria usually requires just the RNA polymerase and one additional protein called σ factor. Promoters, though variable, typically contain similar sequences located at positions -10 and -35 upstream from the transcription start site. The initiation of transcription requires the unwinding of a short region of DNA which is stabilised by σ factor. This open DNA region is termed a transcription bubble. Once the transcription bubble is formed, RNA polymerase initiates RNA synthesis. Just one of the DNA strands called the template strand is used for transcription.

In eukaryotes, the binding of the promoter by RNA polymerase requires the assistance of multiple additional proteins known as transcription factors. A typical promoter recognised by RNA polymerase II contains a conserved nucleotide sequence rich in adenines and thymines.

RNA polymerase II and transcription factors required to bind the promoter Image source: ByCNX OpenStax - http://cnx.org/contents/[email protected]:rZudN6XP@2/Introduction, CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=49929297

Elongation

The RNA polymerase moves downstream from the transcription start site adding nucleotides to the growing RNA molecule. The elongated RNA grows in the 3' direction.

RNA elongation Image source: Rosti1985 - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=89613003

Multiple RNA polymerase enzymes can transcribe the same gene at the same time to increase RNA production.

Multiple RNA polymerase enzymes transcribe three closely located genes. "Begin" indicates the 5' end of the coding strand of DNA, where new RNA synthesis begins; "end" indicates the 3' end, where the transcripts are almost complete. RNA polymerase molecules are seen on DNA as dots. Image source: CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=1830046

Transcription Termination

Termination in bacteria occurs when RNA polymerase encounters a termination signal. In most cases, termination involves the formation of a "hairpin" structure which results in polymerase detaching from the transcript.

Transcription termination in bacteria Image source: Untitled image. "Stages of transcription". Accessed February 29, 2024. https://www.khanacademy.org/science/biology/gene-expression-central-dogma/transcription-of-dna-into-rna/a/stages-of-transcription

In eukaryotes, the process of transcription termination is more sophisticated and is not yet fully understood. The enzyme RNA polymerase encounters a specific sequence called polyadenylation signal which marks the end of the transcript and recruits an additional enzyme that cleaves the newly synthesised RNA. Despite the cleavage of the RNA, RNA polymerase may continue transcription until it is eventually pushed away from the DNA by enzymes responsible for degrading the non-functional RNA.

Summary

The video below summarises the transcription and provides some additional details: