Genome

A genome is the whole DNA sequence of an orgasm. It includes both coding and non-coding sequences.

Genes are the coding sequences. In humans only 1.5% of the genome contain genes.

DNA changes

DNA is not constant and can change within the cell.

Bacteria can undergo DNA transformation.

Eukaryotes can undergo transfection, which is the introduction of DNA without a virus.

Transduction is introduction of foreign DNA via a viral vector.

Gene Transfection [youtube.com]

Bacterial transformation [youtube.com].

Chromatin

Our 3 billion base pair long strand of DNA is packaged into a cell's nucleus. There is structure required to fit such a long string into the nucleus.

Histones are proteins that are positively charged. They bind tightly to DNA's negative phosphate groups. A nucleosome is 8 histones with DNA.

The nuclesomes form the beads in the 'beads on a string' view. In this form DNA is open for transcription. This form is known as euchromatin.

Only eukaryotes have nucleosomes.

When H1 histone is added, it becomes 30nm fibre, made up of many nucleosomes. This is not open for transcription.

The 30nm fibre forms loops of 300nm in length.

The 300nm loops are compressed and folded into 250nm wide fibre.

Tight coiling of the 250nm fibre forms chromatid of a chromosome.

Chromatin is the complex of the histone proteins and DNA.

chromatin roles

Tightly packing DNA into the cell's nucleus

Protecting DNA from damage

Regulates gene expression

Strengthen DNA for mitosis

Histone modification

Also known as chromatin remodelling.

Histones help with the chromatin structure. When reading DNA, DNA must be unpacked and opened up. To make it accessible histone proteins could be modified (e.g. add acetyl, methyl or phosphate groups) temporarily. This allows polymerase and other enzymes access to the DNA.

DNA Packaging: Nucleosomes and Chromatin [nature.com]

Chromatin [nature.com]

Genome size and organism complexity

Length of genome doesn't correlate to organism complexity. Human genome is about 3B, while lungfish is about 130B base pairs.

Gene count doesn't correlate either. Humans have around 20K while rice has 50K.

The discrepancy can be explained by alternative splicing. The same gene can lead to different protein isoforms (splice variants), which increase the number of different biologically functioning proteins in the organism.

Post translation modification can also create different functional proteins.

Regulatory sequences that originate from non-coding DNA, such as promoters, enhancers, silencers affect transcription.

Gene number and complexity [evolverzone.com]

Transcription regulation and animal diversity [ndsu.edu]

Variation among species [wikipedia.org]

Prokaryote vs Eukaryote gene expression (or protein synthesis)

Prokaryotes are simpler.

RNA processing

RNA modification happens post transcription in eukaryotic cells only. Prokaryotes have no nucleus so ribosomes can move closer to where transcription occurs.

In eukaryotes only, the primary transcript is made and then the following processes occur:

  • 5' capping or mRNA capping at the 5' end of the transcript.
  • 3' polyadenylation or the addition of a poly A tail to the 3' end of transcript.
  • Alternative splicing, done by the spliceosome, removes introns and potentially some exons from the transcript.

Protein Synthesis: Prokaryotes vs. Eukaryotes [youtube.com]

Differences in translation between prokaryotes and eukaryotes [youtube.com]

Modern View

Much of the genome lies close to a regulatory event: 95% of the genome lies within 8kb of a DNA-protein interaction.

The number of bases in gene regulation is higher than bases in exons.

The ratio of non-coding to coding DNA correlates to organism complexity.

Alternative splicing means different transcription start sites, and a gene can span multiple loci.

The presence of non-coding anti-sense (reverse direction) transcripts in the euchromatin.

Histone modification change the structure of chromatin (due to charge), also other non-histone proteins can complex with histones and then change the chromatin. Open by acetylation, closed by methylation.

CpG island, is a region of DNA where there are more CG pairs than usual. If the CpGs are methylated then the promoters will be silenced.

Retrotransposons (DNA -> RNA -> DNA)

Evolutionary Elements

Compared with other mammals, 5% of the human genome is evolutionary constrained. This means changes to these portions of the genome would be deleterious (or harmful).

Negative selection

Negative selection, or stabilising selection is conservation of functional elements that are common between different species.

Positive selection, or adaptive selection, is conservation of functional elements within a species. These elements are the differences between species.

Neutral selection is no restriction on non-functional sequences.

Challenges

Sequencing

Sequencing the data cheaply and accurately with sufficient coverage.

Data Handling

Data storage and analysis

Security

Anonymised, ethics.

ENCODE

Encyclopedia of DNA elements

RefSeq

A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

RefSeq [http://www.ncbi.nlm.nih.gov].

Browsers

UCSC Genome Browser.

ensembl.

References

ENCODE [wikipedia.org].

SAG Lecture notes 1.