Bioinformatics and Functional Genomics Student ID: 21485094

Lecturer: Dr. Obed Brew Beatriz Manso

ANALYSING DNA REPEATS

To organize coding sequence and to replicate the genome and transmit them accurately to progeny

cells, repeated signals in DNA are required. Such signals in DNA facilitate the expression of unique

coding sequences.

There are 5 types of Repetitive DNA are described in eukaryotics cells:

• Interspersed repeats

• Processed pseudogenes

• Simple sequence repeats

• Segmental duplications

• Blocks of tandem repeats

These repetitive DNA types can be divided into two classes:

• Tandem repetitive sequences (known as satellite DNA)

• Interspersed repeats.

A satellite DNA sequence is one that contains short head-to-tail tandem repeats that include specific

motifs in the pattern.

Macrosatellites, minisatellites, and microsatellites account for one third of DNA repeats

Bioinformatics and Functional Genomics Student ID: 21485094

Lecturer: Dr. Obed Brew Beatriz Manso

Part 1 - Tandem repeats: TTAGGG in subtelomeric region

1. Go to NCBI (https://ncbi.nlm.nih.gov/) ➔ search for Reference Sequence: NT_024477.14 ➔

copy the FASTA file for the sequence

2. Go to NCBI BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) ➔ BLAST ➔ Select BLASTN

(Nucleotide BLAST) ➔ type/paste your sequence TTAGGGTTAGGGTTAGGG into the query box.

3. Select Align two or more sequences ➔ paste NT_024477.14 FASTA file

4. Search against the human genome database

a. What tandem repeats matched to the sequence?

TTAGGGTTAGGGTTAGGG

b. How many Tandem Repeat matches did you find in this sequence?

844, because I used the updated version NT_024477.15

c. What is NT_024477.14, and on which chromosome is this reference sequence?

It’s the NCBI Reference Sequence and its on chromosome 12

d. What are the possible effects of these repeats in this reference sequence?

Tandem repeat describes a pattern that helps determine an individual's inherited traits.

Tandem repeats can be very useful in determining parentage. Short tandem repeats are used for

certain genealogical DNA tests. DNA is examined from microsatellites within the chromosomal

DNA. Parentage can be determined through the similarity in these regions.

Part 2 - Repetitive α-satellite DNA

Repeat steps 1 – 4 in Part 1 with reference sequence IDs X07685 (query) and AC125634 (subject)

1. How many repetitive α-satellite DNA did you find?

144

Bioinformatics and Functional Genomics Student ID: 21485094

Lecturer: Dr. Obed Brew Beatriz Manso

2. Download the DotPlot result and explain the findings

The dotpot shows regions of similarity based on the BLAST results. The query sequence is

represented on the X-axis and the numbers represent the bases/residues of the query and the

subject is is represented on the Y-axis and again the numbers represent the bases/residues of the

subject.

The lines in this plot represent the alignment. The number of lines shown in the plot is the same as

the number of alignments found by BLAST.

Part 3: Interspersed repeats

1. Go to UCSC Genome Browser ➔ Table Browser

2. In the Find position, select Human Assembly Human Dec 2013 GRCh38 ➔ Type chr11:5,240,001-

5,253,000 into the Position/Search area ➔ then click Go

3. At the results page ➔ scroll down to the bottom, ➔ select Track Search ➔ Type Repeat in the

search dialogue box ➔ search through the list and select RepeatMasker to full

4. Click get output to see repetitive DNA elements such as SINE, LINE, LTR, and DNA transposon.

Part 4: RepeatMasker

(http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker

1. Go to NCBI, search and copy the FASTA file for reference sequence U01317.1

2. Go to RepeatMasker and paste the FASTA file for U01317.1 into the Sequence query inbox ➔

select rmblast ➔ human for DNA source

3. Click Submit Sequence

Bioinformatics and Functional Genomics Student ID: 21485094

Lecturer: Dr. Obed Brew Beatriz Manso

1. What gene is represented by U01317.1?

Human beta globin region on chromosome 11

2. What is the total number of repeats found in this gene?

27392bp

3. What types of repeats, and how many per each repeat are found in this gene?

SINEs – 24, LINEs -21, LTR elements – 6, DNA elements-2