Chapter 21, Problem 1NST

In a sequence encompassing 99.4 percent of the euchromatic regions of human chromosome 1, Gregory et al. [(2006) Nature 441:315–321] identified 3141 genes.

1. (a) How does one identify a gene within a raw sequence of bases in DNA?
2. (b) What features of a genome are used to verify likely gene assignments?
3. (c) Given that chromosome 1 contains approximately 8 percent of the human genome, and assuming that there are approximately 20,000 genes, would you consider chromosome 1 to be “gene rich”?

Summary Introduction

To determine: The ways by which an individual can identify a gene within a raw sequence of bases in DNA.

Introduction: The bioinformatics includes the use of computer hardware and software, mathematics applications to organize, share and analyze data that is related to gene structure, gene sequence and expression; and protein structure and function.

Explanation of Solution

To annotate a gene, an individual identifies gene-regulatory sequences such as promoters, enhancers, and silencers that are found upstream of genes. A person can also identify downstream elements such as termination sequences and in-frame triplet nucleotides that are part of the coding region of the gene. Moreover, 5’ and 3’ splice sites are also used. These splice sites distinguish exons from introns. The polyadenylation sites can also be used in annotation.

Thus, a person can identify a gene from the raw sequence of bases by identifying gene-regulatory sequences and the downstream elements.

Summary Introduction

To determine: The characteristics of a genome which are used to verify similar gene assignment.

Introduction: Gene is a unit of DNA that is present on a chromosome. It controls the development of one or more traits. The gene is the basic unit through which genetic information is passed from parent to offspring.

Explanation of Solution

The similarity to other annotated sequences provides an approach to a sequence’s functions, and it confirms a particular genetic assignment. Direct sequencing of cDNAs from various tissues and developmental stages aids in verification.

Thus, direct sequencing of cDNAs of a genome is used to verify similar gene assignment.

Summary Introduction

To determine: Whether the chromosome 1 will be considered as “gene rich” provided that it contains approximately 8 % of the human genome and 20,000 genes.

Introduction: The human genome is referred to as the genome of Homo sapiens. The human genome consists of 23 pairs of the chromosome with a total of about 3 billion DNA base pairs.

Explanation of Solution

The 3141 genes identified on chromosome 1which constitute 15.7 % of the total number of genes in the human genome (estimated to be 20,000). As per the given information, chromosome 1 contains 8 % of the human genome and nearly 16 % of the genes; one can say that chromosome 1 is “gene rich”.