Difference Between Chromosome Walking and Jumping

Key Difference – Chromosome Walking vs Jumping
 

Chromosome walking and chromosome jumping are two technical tools used in molecular biology for locating genes on the chromosomes and physical mapping of the genomes. Chromosome walking is a technique used to clone a target gene in a genomic library by repeated isolation and cloning of adjacent clones of the genomic library. Chromosomal jumping is a special version of chromosomal walking which overcomes the breakpoints of chromosomal walking. Chromosomal walking can only sequence and map small lengths of chromosomes while chromosomal jumping enables sequencing of large parts of chromosomes. This is the key difference between Chromosomal walking and chromosomal jumping.

CONTENTS
1. Overview and Key Difference
2. What is Chromosome Walking
3. What is Chromosome Jumping
4. Side by Side Comparison – Chromosome Walking vs Jumping
5. Summary

What is Chromosome Walking?

Chromosome walking is a tool which explores the unknown sequence regions of chromosomes by using overlapping restriction fragments. In chromosome walking, a part of a known gene is used as a probe and continued with characterizing the full length of the chromosome to be mapped or sequenced. This goes from the marker to the target length. In chromosome walking, the ends of each overlapping fragments are used for hybridization to identify the next sequence.

The probes are prepared from the end pieces of cloned DNA and they are subcloned. Then they are used to find the next overlapping fragment. All these overlapping sequences are used to construct the genetic map of the chromosome and locate the target genes. It is a method of analyzing long stretches of DNA by small overlapping fragments from the recontructed genomic library.

Chromosome Walking Technique – Steps

1. Isolation of a DNA fragment which contains the known gene or marker near target gene

2. Preparation of the restriction map of the selected fragment and subcloning the end region of the fragment to use as a probe
3. Hybridization of the probe with the next overlapping fragment
4. Preparation of the restriction map of the fragment 1 and subcloning of the end region of the fragment 1 to use as a probe for the identification of the next overlapping fragment.
5. Hybridization of the probe with the next overlapping fragment 2

6. Preparation of the restriction map of fragment 2 and subcloning of the end region of the fragment 2 to serve as a probe for the identification of the next overlapping fragment

Above steps should be continued till the target gene or up to 3’ end of the total length of the sequence.

Chromosome walking is an important aspect of cytogenetic in finding SNPs of many organisms and analyzing the genetically transmitted diseases and finding mutations of relevant genes.

What is Chromosome Jumping?

Chromosomal jumping is a technique used in molecular biology for physical mapping of genomes of the organisms. This technique was introduced to overcome a barrier of the chromosomal walking which arose upon finding the repetitive DNA regions during the cloning process. Therefore, chromosome jumping technique can be considered as a special version of chromosomal walking.  It is a rapid method compared to chromosomal walking and enables bypassing of the repetitive DNA sequences which are not prone to be cloned during chromosomal walking. Chromosomal jumping narrows the gap between the target gene and the available known markers for genome mapping.

Chromosome jumping tool starts with the cutting of a specific DNA with special restriction endonucleases and ligation of the fragments into circularized loops. Then a primer designed from a known sequence is used to sequence the circularized loops. This primer enables jumping and sequencing in an alternative manner. Hence, it can bypass the repetitive DNA sequences and rapidly walk through the chromosome for the search of the target gene.

The discovery of the gene encodes for cystic fibrosis disease was done using the chromosomal jumping tool. Combined together, chromosomal jumping and walking can enhance the genome mapping process.

What is the difference between Chromosome Walking and Jumping?

Chromosome Walking vs Jumping
Chromosome is a tool used in molecular biology for genome mapping and locating specific genes.	Chromosome jumping is a tool used for physical mapping of genomes and rapid finding of target genes in the chromosomes.
Comparative Lengths of Sequencing
Only small fragments can be cloned by chromosomal walking.	Larger lengths of the chromosomes can be mapped by the chromosomal jumping.
Cloning Repetitive DNA in Chromosomes
Chromosome walking technique has a difficulty in walking through the repeating DNA sequences found in chromosomes.	It enables bypassing the repetitive DNA sequences. Therefore there is no difficulty when finds them during the sequencing.
Factors Affecting the Processes
The success of the process depends on the size of the genome and the distance that must be “walked” from a known genomic position toward the desired gene.	The success does not depend on the size of the genome of the distance from marker to target.
Effects of Uncloned DNA
Chromosomal walking can be stopped by uncloned DNA fragments.	The lowest note piccolos can play is D4.
Need for a Known Sequence
The process starts with a known gene near the target.	The process requires a known fragment for primer designing.

Summary – Chromosome Walking vs Jumping

Chromosomal walking is frequently applied when it is known that a particular gene is located near a previously cloned gene in a chromosome and it is possible to identify it with repeated isolation of adjacent genomic clones from the genomic library. However, when repetitive DNA regions are found during the chromosomal walking technique, the process cannot be continued. Hence, the technique breaks from that point. Chromosomal jumping is a molecular biological tool which overcomes this limitation for mapping genomes. It bypasses these repetitive DNA regions which are difficult to clone and helps in physical mapping of genomes. This is the main difference between chromosome walking and jumping.

References:
1. Nakaseko, Yukinobu, Yasuhisa Adachi, Shin-ichi Funahashi, Osami Niwa, and Mitsuhiro Yanagida. “Chromosome walking shows a highly homologous repetitive sequence present in all the centromere regions of fission yeast.” The EMBO Journal. U.S. National Library of Medicine, May 1986. Web. 22 Mar. 2017
2. Taheri, Ali. “Chromosome walking and jumping.” Advancements in Genetic Engineering. OMICS International, 30 Oct. 2013. Web. 22 Mar. 2017