4. Module 4

Module 4: Removal of introns from pre-mRNA by splicing

Author:Meg Laakso (Eastern University)
Last Update:Feb 25, 2020
Version:0.0.1

4.1. Investigation 1: Examining RNA-Seq data

Learning Objectives

  • Predict the location of the transcription start site and the number of exons and introns in a gene using RNA Seq evidence tracks.

We will continue to focus on isoform A of transformer (referred to as tra-RA). Here we will focus on data from experiments that assess the RNA population in cells. This data can be used to help us identify exons and introns for the gene under study.

All RNAs in the cell are collectively known as the “transcriptome,” as almost all RNA is produced by transcription from a DNA template. (In some cases, RNA is made from an RNA template.) The transcriptome includes messenger RNAs, ribosomal RNAs, transfer RNAs, and other RNAs that have specialized functions in the cell.

RNA can be harvested from cells or a whole organism like Drosophila and converted to DNA, then sequenced to produce RNA-Seq (RNA Sequencing) data. First, extracted mRNA that has been fully spliced is copied back to DNA with the enzyme called reverse transcriptase. Short fragments of the copied or complementary DNA are sequenced, and then these segments are mapped back to the genome. By analyzing the mapping data, it is possible to know which and how many messenger RNAs have been synthesized.

This is a powerful technique that allows us to see when and where different genes are expressed. This kind of information can help researchers and clinicians know which genes are expressed in different types of cancer, for example. Here and in the next modules we are going to use RNA-Seq data to explore how the transformer (tra) gene is expressed in male vs. female Drosophila.

RNA-Seq data can indicate where transcription occurs, to the exact nucleotide. The number of RNA-Seq fragments that map to a given site also tells us how many copies of the RNA are present in the sample. Remember from Module 3 that the initial RNA transcripts are quickly processed to remove the introns. Hence in total RNA from a cell, sequences from exons will be much more abundant than sequences from introns. We will use RNA-Seq data to help us find the exon-intron boundaries for tra-RA, the isoform of the tra gene that is expressed in female fruit flies.

  1. Open a web browser on your computer. Internet Explorer, Mozilla Firefox, Safari, or Chrome will work for this investigation. Go to the GEP Mirror of the UCSC Genome Browser at http://gander.wustl.edu. Follow the instructions given in Module 1 to navigate to the contig1 project in the D. melanogaster July 2014 (Gene) assembly.

Note

Reminder: Configure the Genome Browser Gateway page as follows:

  1. Select D. melanogaster under “REPRESENTED SPECIES”
  2. Select July 2014 (Gene) under “D. melanogaster Assembly”
  3. Enter contig1 in the “Position/Search Term” text box
  4. Then click on the GO button and the screen below will appear (Figure 4.1)
Genome browser view of contig1

Figure 4.1. A screen shot of the “contig1” project.

As you will remember, this section of DNA is 11,000 base pairs long and is part of the left arm of chromosome 3, which is about 28,100,000 bp long. If your Browser window is showing other evidence tracks, reset by clicking on default tracks.

  1. Let’s start by setting the evidence tracks we want to see. Click on the hide all button. Then open only the tracks that will provide data for this investigation. Note that you will not be able to see the DNA sequence until you “zoom in” at step 4.
  2. Change the display mode for the “RNA-Seq Coverage” track to full, then click refresh.

You will see blue and red histograms representing RNA-Seq data generated using RNA samples from adult females and adult males, respectively. This allows us to infer the pattern of RNA synthesis, and to look for similarities and differences between the sexes. Both similarities and differences are apparent!

  1. Zoom in to view only the tra gene by entering contig1:9,800-10,900 in the “enter position or search terms” text box (Figure 4.2).
RNA-Seq read coverage for the tra gene

Figure 4.2. Histograms representing RNA-Seq data in transformer (tra).

  1. We are now looking at the region of chromosome 3 where the tra gene is located. Compare the blue and red histograms for Adult Females and Adult Males. Note that there are numbers on the y-axis that show how many RNA reads (sequences from transcripts) map to that position.

Question 1

List two ways in which the histograms are similar.

Question 2

List one way that the histograms differ (other than color).

To recap: The blue histogram represents the sequenced messenger RNA from female fruit flies, and represents the form of the tra gene referred to as isoform A (tra-RA). The red histogram represents the RNA-Seq data from male fruit flies. The mRNA in males is different from that in females, and this second isoform of the tra gene is called isoform B (tra-RB).

Question 3

Recall that our other evidence (see Module 3) indicates that tra-RA extends from 9,851 to 10,846. How many gaps do you see in the histograms in this interval?

Each gap corresponds to an intron — there is very little RNA-Seq signal for that part of the gene because the intronic RNA was spliced out before the mRNA was collected and sequenced.

Question 4

How many exons do you see?

Remember that the exon is the “expressed” part of the gene and there will be either a sharp, or broad, peak in the RNA-Seq histogram.

Question 5

Do females or males make more transformer mRNA or do they express it at about the same level?

  1. Now that you’ve examined the evidence yourself, let’s go back and review.

    Gaps (introns)

    Figure 4.3 is a screen shot of the genome browser with gaps circled. Note that there are 2 gaps in females, and 2 gaps in males. The first gap in females looks a little strange because it doesn’t have clean boundaries, suggesting a mixed population of processed transcripts.

    Exons

    Brackets have been drawn underneath the RNA-Seq data for Adult Female flies, corresponding to the three exons that are expressed.

    Isoforms

    Note that isoform A and isoform B of the tra gene are the result of alternative splicing. For other genes, isoforms may have different transcription start sites. Isoforms of a gene always have different mRNA sequences, but they may have the same protein sequence. To learn more about isoforms and genes, watch the Genes and Isoforms video.

Interpret RNA-Seq read coverage in the two samples

Figure 4.3. In this screen shot of the tra gene, introns have been circled and exons have brackets underneath them.

Question 6

Using the information you’ve gathered so far, make a diagram of the tra-RA (female specific) isoform with 3 exons and 2 introns. Represent exons as rectangular boxes and introns as lines connecting the boxes. Number each exon and intron (start from left with “exon 1”).

Question 7

Where is the promoter in relation to the exons and introns? Mark the putative Transcription Start Site in your diagram with a bent arrow pointing in the direction of transcription.

4.2. Investigation 2: Identifying splice sites

Learning Objectives

  • Identify splice donor and acceptor sites using the genome browser.

We will again focus on tra-RA to identify splice sites, that is, the exact nucleotides where splicing occurs to remove introns from the pre-mRNA.

4.2.1. Background

Two software programs, called TopHat and Bowtie, use the RNA-Seq data to graphically represent the exon junctions. The resulting graphic on the genome browser coincidentally looks something like a little bowtie (two small boxes connected by a thin line) (Figure 4.4). The boxes represent the sequenced mRNA (the exons), and the line represents a gap (the intron). The exon junction can be inferred when the first part of a sequenced fragment from the RNA population matches (for example) DNA positions 50-100 and the second part of the same fragment matches DNA positions 200-250; the RNA from positions 101-199 must have been taken out of the middle!

Short sequences are present at the beginning and end of each intron that allow the spliceosome — the molecular machinery that cuts out introns — to precisely remove the intron, leaving only the exon sequences in the mature mRNA. The first two nucleotides of the intron are the splice donor site and almost always the nucleotides “GT”. The last two nucleotides of the intron are the splice acceptor site and almost always the nucleotides “AG”. (Recall your observations in Module 3.) For more information on RNA-Seq and the search for splice junctions, watch the RNA-Seq and TopHat video

Illustration of an intron-exon junction

Figure 4.4. A diagram of intron-exon junctions.

4.2.2. Use the Genome Browser to identify splice sites

  1. Using the same Genome Browser page, reset the Browser by clicking on hide all. Then open the tracks that will provide the information we want for Investigation 2. (See the beginning of Investigation 1 for a reminder on how to get to the Genome Browser page.)
  2. Change the display mode for the “Base Position” track to dense, and then click refresh. (Note that you will not be able to see the DNA sequence until you “zoom in”.)
  3. Change the display mode for the “RNA-Seq Coverage” track to full, and then click refresh.
  4. You will again see blue and red histograms representing the RNA-Seq data (indicating the amount of mRNA synthesized) in females and males, respectively. We will focus on the blue histogram (Adult Females) again. As we did in Module 3, let’s customize the RNA-Seq track by setting the “Data view scaling” field to use vertical viewing range setting and the “max” field under “Vertical Viewing range” to 37. Remember that you gain access to these settings by clicking on the RNA-Seq Coverage link under the RNA-Seq Tracks green bar.
  5. Change the display mode for the “Exon Junctions” track to full, and then click refresh. The rectangular boxes joined by a thin black line will help you identify the exon-intron boundaries.

Our graphical output viewer will look like the screen shot below (Figure 4.5).

View of the *tra* RNA-Seq data

Figure 4.5. View of the tra RNA-Seq data with the splice donor site in intron 1 circled.

  1. Zoom in to the area that is circled — click and drag the cursor just above the numbers, or use zoom buttons.
  2. Set the screen so that you can see about 15–20 nucleotides, as shown in the example below (Figure 4.6).
TopHat junctions near the splice donor site of exon 1

Figure 4.6. TopHat data (in black) for adult males and adult females indicating an exon junction.

The blue histogram stops at the end of exon 1. The last three nucleotides of exon 1 are “G-A-G”.

Question 8

What is the coordinate of the last nucleotide in exon 1?

Question 9

What are the first two nucleotides of intron 1?

This is called the 5’ splice site or “splice donor site.”

  1. Zoom out so that you can see all of the tra gene. Let’s use TopHat to help us find the 3’ end of the intron. Examine the Exon Junctions track. The first intron-exon junction predicted by TopHat (black) seems to align with the red histogram data from males; the second junction aligns better with the blue histogram data from females (Figure 4.7).
Compare TopHat and RNA-Seq data for adult males and females

Figure 4.7. TopHat and RNA-Seq data for males and females.

  1. Let’s examine the 3’ end of intron 1 more closely. Change the “enter position or search terms” field to contig1:10,140 and then click go. Zoom out 10x and then 3x (Figure 4.8).
Genome Browser view of the beginning of exon 2 of tra-RA

Figure 4.8. Graphical viewer centered on the junction between intron 1 and exon 2 of the tra-RA (female specific) isoform.

Question 10

What are the last two nucleotides of the female tra-RA intron 1?

This is called the 3’ splice site or “splice acceptor site”.

Question 11

What is the coordinate of the first nucleotide in the female tra-RA exon 2?

4.3. Investigation 3: Identify the splice sites for intron 2

We can use the same approach to map the exon-intron boundaries of the second intron.

Review steps #2–5 in Investigation 2. Then repeat the process to answer the following questions about the 5’ splice donor and 3’ splice acceptor sites for the tra-RA (female specific) intron 2.

1. Zoom into the sequence surrounding the 5’ splice donor for the tra-RA (female specific) intron 2.

Summary Question 1

What are the last three nucleotides of the female tra-RA exon 2?

Summary Question 2

What is the coordinate of the last nucleotide in the female tra-RA exon 2?

Summary Question 3

What are the first two nucleotides of the female tra-RA intron 2?

  1. Zoom out as needed so that you can see all of intron 2. Use the TopHat evidence track to find the 3’ end of intron 2.
  2. Click and drag so that the end of intron 2 is centered in the viewer. Then zoom in so that you can see the nucleotide sequence.

Summary Question 4

What are the last two nucleotides of the female tra-RA intron 2?

Summary Question 5

What is the coordinate of the first nucleotide in the female tra-RA exon 3?

Summary Question 6

Using the information you’ve gathered so far, make a graphical picture of the tra-RA (female specific) isoform with 3 exons and 2 introns. Number each exon and intron at the corresponding DNA coordinates. Add the coordinates for first and last nucleotide of the exons that you have found so far. Add the sequences of the splice donor and splice acceptor sites at the appropriate locations.

Summary Question 7

Where do you think the promoter is located in relation to your gene model? What evidence do you have to support your idea, using the evidence tracks we have displayed (Base Position, RNA-Seq Coverage, Exon Junctions)?

Bonus Question 1

Support your hypothesis by gathering additional data. Recall our explorations in Module 2 and 3. You might want to open the tracks “D. mel. cDNAs,” and “TSS Annotations,” both in full. What type of evidence is shown by each of these tracks (refer to Module 2)? Finally, to see tra-RA as currently annotated in FlyBase, open the “tra Isoform” track on full, or to see both isoforms open the “FlyBase Genes” track in pack. Do these results support your model? Do any ambiguities remain?

4.4. Homework: Determining splice sites for the spd-2 gene

  1. Open a web browser on your laptop. Internet Explorer, Mozilla Firefox, Safari, or Chrome will work for this investigation. Go to the GEP Mirror of the UCSC Genome Browser at http://gander.wustl.edu. Follow the instructions given in Module 1 to navigate to the contig1 project in the D. melanogaster July 2014 (Gene) assembly.

Note

Reminder: Configure the Genome Browser Gateway page as follows:

  1. Select D. melanogaster under “REPRESENTED SPECIES”
  2. Select July 2014 (Gene) under “D. melanogaster Assembly”
  3. Enter contig1 into the “Position/Search Term” text box
  4. Click on the GO button

As you will remember, this section of DNA is 11,000 base pairs long (Figure 4.9) and is part of the left arm of chromosome 3, which is about 28,100,000 bp long. If your Browser window is showing other evidence tracks, reset by clicking on default tracks.

Genome Browser view of contig1

Figure 4.9. A screen shot of the “contig1” project.

  1. Let’s start by setting the evidence tracks we want to see. Click on the hide all button, then open only the tracks that will provide data for this investigation:
    • Base Position: dense
      • Note that you will not be able to see the DNA sequence until you zoom in. If the Base Position is changed to full, you can see the amino acid tracks also.
    • RNA-Seq Coverage: full
      • You will see blue and red histograms representing RNA-Seq data generated using RNA samples from adult females and adult males, respectively.
    • Exon Junctions: full
      • The exon junctions will help you to find the splice donor and splice acceptor sites.
    • D. mel. cDNAs: full
      • This track was used extensively in previous modules, and is useful for confirming the sequence of the mature mRNA. Remember that a cDNA is a DNA copy of an mRNA.

3. Zoom in to view only the spd-2 gene by entering contig1:5,750-9,800 in the “enter position or search terms” text box.

We are now looking at the region of chromosome 3 where the spd-2 gene is located.

Summary Question 1

How many exons does spd-2 have?

Summary Question 2

How many introns does spd-2 have?

4.4.1. Part 1: Identifying splice sites for Intron 1

You remember from class that short sequences are present at the beginning and end of each intron that allow the spliceosome to precisely remove each intron, leaving only the exon sequences in the mature mRNA. The first two nucleotides of the intron are “GT” and the last two nucleotides are “AG” (Figure 4.10).

Diagram of an intron

Figure 4.10. A bowtie diagram

  1. Zoom in to the end of exon 1. Set the screen so that you can see about 15–20 nucleotides.

Summary Question 3

What are the last three nucleotides of exon 1? What is the coordinate of the last nucleotide in exon 1?

Summary Question 4

What are the first two nucleotides of intron 1?

  1. Zoom out so that you can see all of intron 1, and use TopHat to help find the end of the intron. Examine the Exon Junctions track. Then zoom in so that you can see the nucleotide sequence.

Summary Question 5

What are the last two nucleotides of intron 1?

Summary Question 6

What is the coordinate of the first nucleotide in exon 2?

4.4.2. Part 2: Identifying splice sites for Intron 2

Let’s use the same approach to map the exon-intron boundaries for intron 2. Review the steps you used in Part 1, then repeat the process to answer the following questions about the 5’ splice donor and 3’ splice acceptor sites for intron 2.

  1. Zoom in to the sequence surrounding the 5’ splice donor for intron 2.

Summary Question 7

What are the last three nucleotides of exon 2?

Summary Question 8

What is the coordinate of the last nucleotide in exon 2?

Summary Question 9

What are the first two nucleotides of intron 2?

  1. Zoom out as needed so that you can see all of intron 2. Use TopHat to find the end of intron 2.
  2. Click and drag so that the end of intron 2 is centered in the viewer. Then zoom in so that you can see the nucleotide sequence.

Summary Question 10

What are the last two nucleotides of intron 2?

Summary Question 11

What is the coordinate of the first nucleotide in exon 3?

Summary Question 12

Using the information you’ve gathered so far, make a graphical picture of the spd-2 gene with 3 exons and 2 introns. Number each exon and intron. Add the coordinates for first and last nucleotide of the exons that you have found so far. Add the sequences of the splice donor and splice acceptor sites at the appropriate locations. Finally, add a bent arrow for the transcription start site.