Genome Biology - Oral Exam Flashcards

What is a sequence motif?

A short, recurring pattern in DNA, RNA, or protein that typically has a specific biological function. For example, promoters, enhancers, or repressors.

What is a cis-regulatory element (CRE)?

A functional non-coding DNA sequence found on the same chromosome as its target gene. For example, TATA box, GC box.

What is a cis-regulatory module (CRM)?

A short region containing clusters of multiple CREs that control gene expression.

Structure of a sequence motif

A sequence motif is a short sequence of nucleotides or amino acids. A motif is typically represented by a consensus sequence, which shows the preferred nucleotide at each position.

• Some positions contain a specific nucleotide, such as A, T, C or G.

• Other positions can contain alternative nucleotides, indicating that some variation is allowed.

• The sequence is written in the 5′ to 3′ direction.

Structure of a CRE

A CRE is a short, non-coding DNA sequence. It contains a specific DNA motif that acts as a binding site for an individual transcription factor. CREs are located on the same chromosome as the genes they regulate and can influence transcription by increasing or decreasing gene expression. Examples include core promoter elements, proximal control elements, enhancers, silencers and insulators.

Structure of a CRM

CRMs are touching clusters of CREs, typically 100 bp to 1 kb in length.

Each CRE contains a short DNA motif that acts as a binding site for a transcription factor. These motifs have a specific order which allows multipe TFs and co-regulatory proteins to work together, allowing CRMs to combine different signals and regulate gene expression.

Functions of a motif

• Acts as a binding site for proteins to attach to the DNA.

• Provides a recognition site: Motifs allow specific transcription factors to recognise and bind to particular regions of DNA.

• Helps regulate gene expression: When a TF binds to a motif within a cis-regulatory element (CRE), it can influence the level of transcription of a target gene.

• Contributes to transcriptional specificity: Different motifs are recognised by different TFs, helping determine which genes are expressed and when.

• Contributes to combinatorial regulation: Multiple motifs within a cis-regulatory module (CRM) allow different TFs to bind and work together to integrate regulatory signals.

• The TATA box is a core promoter motif recognised by the TATA-binding protein (TBP), which is part of TFIID. This helps initiate assembly of the RNA polymerase II pre-initiation complex.

Functions of a CRE

CREs are molecular switches that regulate the amount of transcript produced from a gene, and when and where transcription is activated in the tissues of an organism.

Different types of CREs have different functions. Promoters initiate transciption, enhancers enhance gene expression, silencers repress gene expression.

Functions of a CRM

Their function is to integrate signals from multiple TFs.

They allow coordinated regulation of gene expression, meaning that a single gene can be controlled by multiple CRMs, or a single CRM can regulate multiple different genes.

They can be far away from the gene in regions labelled ehancers, silencers, or insulators, or sometimes within genes inside introns or UTRs.

Differences between motifs, CREs, and CRMs

A motif is the short DNA sequence pattern itself. A CRE is the non-coding DNA region containing a binding site for a transcription factor. Multiple TF-binding motifs can occur together within a larger region to form a cis-regulatory module (CRM).

What is a core promoter?

the core promoter is a short region of DNA surrounding the transcription start site (TSS) that helps position RNA polymerase II so that transcription can begin.

It is an important regulatory region of a eukaryotic gene because it provides the binding sites needed for the general transcription factors (GTFs) to assemble the pre-initiation complex (PIC).

The core promoter typically extends from approximately −40 bp upstream to +40 bp downstream of the TSS.

• The TSS is designated +1 and marks where transcription begins.

• The core promoter contains several short DNA sequence motifs.

• It can extend downstream of the TSS into the first exon, which may contain part of the 5′ untranslated region (5′ UTR).

TATA Box

Position:

- Located approximately 25–30 base pairs upstream of the TSS.

Role:

• Has the consensus sequence 5′-TATA(A/T)A(A/T)-3′.

• Recognised by the TATA-binding protein (TBP), which is a component of TFIID.

• TFIID binding to the TATA box initiates the sequential assembly of the pre-initiation complex.

• Helps position RNA polymerase II for transcription initiation.

TFIIB-Recognition Element (BRE)

Position:

• Located immediately upstream of the TATA box.

• Your notes also identify a downstream BRE-like element (BREd), located just downstream of the TATA box.

Role:

• Typically a short, GC-rich motif of approximately 7 base pairs.

• Has the consensus sequence 5′-(G/C)(G/C)(G/A)CGCC-3′.

• Recognised by the general transcription factor TFIIB.

• Helps orient the direction of transcription.

• Further stabilises the binding of TFIID and RNA polymerase II to the promoter, supporting PIC assembly.

Initiator Element (Inr)

Position:

- Located directly at the TSS (+1).

Role:

• Has the consensus sequence 5′-YYAN(T/A)YY-3′.

  • Y = pyrimidine.

  • N = any nucleotide.

  • The adenine (A) often corresponds to the TSS.

• Recognised by TFIID.

• Helps accurately determine where transcription begins.

• Functions in both TATA-containing and TATA-less promoters.

• Can cooperate with or substitute for the TATA box to help position RNA polymerase II.

Downstream Promoter Element (DPE)

Position:

• Located downstream of the TSS, at approximately +28 to +34 base pairs.

• Found within the transcribed region.

Role:

• Has the consensus sequence 5′-(A/G)G(A/T)(C/T)(G/A/C)(C/T)G-3′.

• Recognised by TFIID.

• Works together with the Inr in some TATA-less promoters to help orient RNA polymerase II towards the TSS without an upstream TATA box.

• The DPE is found exclusively in promoters that lack a TATA box.

Motif Ten Element (MTE)

Position:

• Located downstream of the TSS, at approximately +18 to +27 base pairs.

• Can overlap with the DPE.

Role:

• Has a poorly defined consensus sequence.

• Recognised and bound by TFIID.

• Often works together with the Inr in TATA-less promoters.

• Facilitates strong transcription in conjunction with the DPE.

Core promoter organisation

• The core promoter is a short region of DNA surrounding the transcription start site, typically extending from approximately −40 to +40 base pairs relative to the TSS. It often extends into the first exon, which contains the 5′ UTR.

• It is organised into several sequence motifs. The TATA box is located approximately 25–30 base pairs upstream of the TSS, with the BRE immediately upstream of it. The Initiator element, or Inr, is located directly at the TSS. Downstream of the TSS are the MTE, at +18 to +27, and the DPE, at +28 to +34, which can overlap.

• These motifs are recognised by general transcription factors, which assemble with RNA polymerase II to form the pre-initiation complex. Not all promoters contain every motif, and different combinations influence how efficiently and accurately transcription is initiated.