A sequence of four nucleotides arranged in a certain pattern, encoding information, constitutes an organism’s genetic material or DNA (deoxyribonucleic acid). The linear arrangement of DNA components and their partition into chromosomes is referred to as a genomic organisation. “Genome organisation” can also refer to the arrangement of DNA sequences inside the nucleus and the three-dimensional structure of chromosomes.
Eukaryotic genomes are linear and follow the Watson-Crick Double Helix structural model. They are contained within chromosomes, bundles of DNA and proteins (Histone) known as nucleosomes. The protein-coding genes in eukaryotic genomes are organised in exons and introns, which represent the coding sequence and intervening sequence, respectively, indicating the functionality of the RNA section of the genome.
Also, read: Double Helix Structure of DNA
Table of Contents
- Eukaryotic Genome Configuration
- Eukaryotic Genome Organisation
- Gene Expression in Eukaryotes
- Frequently Asked Questions (FAQs)
Eukaryotic Genome Configuration
The eukaryotic genome configuration consists of protein-coding regions, gene regulatory regions, gene-related sequences, and intergenic DNA or extra genic DNA, which comprises low copy number and moderate or high copy number repetitive sequences. The configuration is shown in the flowchart below.
Eukaryotic Genome Organisation
Basic facts on eukaryotic nuclear genomes are as follows:
- Eukaryotic genomes include two characteristics that pose a significant information processing problem.
- The standard multicellular eukaryotic cell has a substantially larger genome than a prokaryotic cell.
- Many genes can only be expressed in certain types of cells due to cell specialisation.
- A huge amount of DNA that does not direct the synthesis of RNA or protein is included in the reported 35,000 genes in the human genome.
- The eukaryotic DNA is intricately organised. The DNA-protein complex known as chromatin is not only linked to proteins but is also structured at a higher structural level than the DNA-protein complex in prokaryotes.
- Eukaryotic cells have a significantly higher concentration of DNA in their nuclei than prokaryotic cells.
Structure of the Chromatin
Chromatin is the intricate structure of DNA and protein that comprises chromosomes and consists of linear unbroken double-stranded DNA. There are two types of chromatin:
- Euchromatin
- Heterochromatin
Euchromatin: It is a lightly packed chromatin that is enriched in genes, and is often under active transcription (but not always). Euchromatin contrasts sharply with heterochromatin, which is densely packed and much less available for transcription. The euchromatic region constitutes 92% of the human genome.
Heterochromatin: It is a densely compacted form of DNA or compressed DNA, which comes in multiple variants. These variants fall somewhere between facultative heterochromatin and constitutive heterochromatin. Both are involved in how genes are expressed.
The primary proteins that comprise chromatin are called histones and DNA is wrapped around these histone proteins. There are five main histone classes connected to the eukaryotic genome: H1, H2A, H2B, H3 & H4. These basic proteins are positively charged at normal pH levels, making it easier for negatively charged DNA to bind to them.
Packing of DNA
Level 1: Histone Proteins
- Histone proteins are present at the primary level
- The negatively charged DNA forms an intense bond with the positively charged amino acids.
- Every eukaryote contains the five main types of histones.
- The nucleosome resembles beads on a string in unfolded chromatin.
- The beaded thread appears to remain largely unaltered during the cell cycle.
- Histones pass the DNA temporarily during DNA replication. They remain with the DNA throughout transcription.
- Nucleosomes enable RNA-synthesising polymerases to migrate along the DNA by altering their size and position.
Level 2: The beaded thread coils into the 30-nm chromatin fibre as chromosomes undergo mitosis.
Level 3: This fibre develops looped domains that are joined to a nonhistone protein scaffold.
Level 4: The metaphase chromosome is produced by the coiling and folding of the looping domains.
Interphase chromatin is usually less compressed than mitosis chromatin with the 30-nm fibres and looped domains remaining unaffected. The chromatin of each chromosome takes up a limited area within the interphase nucleus. Chromosomes in interphase have heterochromatin, highly condensed, and euchromatin, less condensed.
DNA-Level Eukaryotic Genome Organisation
The majority of DNA in eukaryotes (97% in humans) can not code for protein or RNA.
- Regulatory sequences are found in non-coding areas.
- They are usually introns.
- The genome contains several copies of repetitive DNA.
In mammals, tandemly repetitive DNA, also known as satellite DNA, makes up 10-15% of the genome. These are denser than the surrounding areas, and differential ultracentrifugation results in the formation of a distinct band around them. The overall length of DNA at each location distinguishes between three different types of satellite DNA.
Some genetic abnormalities are brought on by unusually long sections of tandemly repeated nucleotide triplets within the afflicted gene.
- Numerous CGG repeats in the fragile X gene are the primary cause of fragile X syndrome.
- Repetition of CAG, which is translated into proteins with a lengthy string of glutamines, causes Huntington’s disease.
- The number of repeats is connected with the severity of the disease and the age at which these disorders first appear.
Most mammalian genomes include interspersed repetitive DNA to a degree of 25–40%.
appear throughout the genome at various locations. They are similar but typically not identical to one another.
Eukaryotic Gene Families
Multigene families are collections of identical or extremely similar genes, whereas the majority of genes are only found in a single copy per haploid pair of chromosomes. These probably originated from a single ancestor gene. Multigene family members might be grouped or scattered throughout the genome.
Multigene families containing identical genes are arranged in tandem clusters. Generally, it includes the genes for histone proteins or RNA products. The transcription unit that encodes the three largest rRNA molecules is replicated tandemly a large number of times. Ribosomal subunits are created when three rRNA molecules from this transcript are cleaved and combined with proteins and other types of rRNA.
Nonidentical genes represent the two interrelated families of globin genes, α (alpha) and ß (beta), of haemoglobin, located on different chromosomes. Each globin subunit expresses its various forms at various stages of development.
Sequences from both families express themselves at various developmental stages, including embryonic, foetal, and/or adult. The transmission of oxygen from the mother to the developing foetus is ensured by the increased oxygen affinity of embryonic and foetal haemoglobin compared to adults.
The variations in genes result from mutations that build up in the gene copies over several generations. These alterations could potentially result in the formation of pseudogenes, DNA segments with sequences resembling those of true genes but incapable of producing functional proteins.
Also, read: Important Notes for NEET Biology – Chromosome Structure
Gene Expression in Eukaryotes
Many different mechanisms, such as gene loss, gene amplification, and gene rearrangement, influence the gene expression in eukaryotes. Differentially transcribed genes have varied uses for their RNA transcripts. Gene expression is regulated by multiple gene families, which also control its frequency and diversity.
The extent of knowledge about gene expression in eukaryotes that exists now is primarily due to biochemical techniques, not conventional genetics. The regulatory areas of eukaryotic genes and the cellular substances that affect gene expression will be discovered using the new techniques that enable the study and manipulation of purified genes with established functions.
The most significant and commonly used control point for gene expression is transcription initiation.
Non-coding DNA fragments are called control elements to operate as transcriptional regulators by binding to transcription factors. Transcriptional factors are required before eukaryotic RNA polymerase can begin transcription. One transcription factor identifies the TATA box.
Enhancers, distal regulatory elements, can be several nucleotides away from the promoter, downstream from the gene or even inside an intron. DNA bending makes it possible for transcription factors, activators, and enhancers associated with them to make contact with the promoter’s protein initiation complex.
Eukaryotic genes also include repressor proteins known as silencers that bind to DNA regulatory regions. Repression might largely function at the chromatin modification level.
Each protein typically has two domains: one that binds to DNA and the other that binds to other transcription factors.
The genes that code for the enzymes in a metabolic pathway may be dispersed across various chromosomes. The connection of each gene in a dispersed group with a particular control element or set of control elements is essential for coordinated gene expression. They bind to the same set of transcription factors, promoting concurrent gene transcription.
Functional proteins are frequently produced by processing eukaryotic polypeptides. Regulation may take place during cleavage, chemical alterations, and transportation to the appropriate position. For instance, the mutation in the genes for a chloride ion channel protein preventing it from reaching the plasma membrane induces cystic fibrosis.
The defective protein is immediately broken down. The life span of regular proteins is limited by the cell through selective degradation.
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Related Links:
- Difference between Prokaryotic and Eukaryotic Cells
- Human Genome Project
- Molecular Basis of Inheritance
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