Genome structure in eukaryotic cells Flashcards
What is the differences between Eukaryotic genomes and bacteria genomes
(could be essay)
- Size
- Linear/circular
- Number of chromosomes (karyotype) generally more than one chromosome
- Associated with proteins (histones)
- Gene-density (lower than bacteria cells)
- Gene size
- Structure of genes
- Presence/absence of introns/exons
- HGT/LGT (horizontal gene transfer)
- Origin(s) of replication multiple zones
Genome sizes and number of genes
- Genomes
- Size vs complexity
- Ploidy
- C-value paradox= no relationship between size of genome and complexity of organism
There may be a relationship between genome size and protein coding genes
Chromosome packing in eukaryotic cells
- DNA wrapped around histones(“beads on a string”) → chromatin (very dynamic structures) →regulation of gene activation
- chromosomes (centromeres, telomeres)
Chromatin Structure:
The basic unit of chromosome packing is the nucleosome, which consists of DNA wrapped around histone proteins. Nucleosomes resemble beads on a string and are the primary level of DNA organization in the cell.
Higher Order Structures:
Nucleosomes further fold and coil to form a 30-nanometer fiber. The 30-nanometer fiber represents a more condensed and compacted form of chromatin.
Chromosomes are organized into loop domains, where specific DNA regions are anchored to the nuclear matrix. This looping helps to bring distant regions of the chromosome into close proximity, facilitating interactions between regulatory elements.
Each chromosome occupies a distinct territory within the nucleus, preventing intermingling of genetic material between different chromosomes.
Heterochromatin and Euchromatin:
Heterochromatin is more condensed and contains genes that are often transcriptionally inactive.
Euchromatin is less condensed and contains genes that are actively transcribed.
autosomes
chromosomes that are not sex chromosomes
Human genome vs mouse genome
There are also large region of extended conserved segments
and syntenies (sequences)
first draft of human genome was published in 2001
Describe Synteny
the conservation of the order of genes or genetic markers on chromosomes between different species. When two or more species have a similar arrangement of genes in their genomes, they are said to exhibit synteny. Synteny is often used to describe the conservation of gene order during the course of evolution.
It indicates a common evolutionary history, where the relative arrangement of genes is maintained. Synteny is a valuable concept in comparative genomics, helping researchers understand genomic relationships, identify conserved regions (synteny blocks), and study genome evolution. It is especially useful for analyzing and comparing genomes, providing insights into the functional and structural aspects of genes across different species.
Pangenome
A pangenome is the complete set of genes present in a particular species, taking into account the genetic diversity among individual organisms within that species. It consists of two main components:
Core Genome:
The set of genes that are shared by all individuals within a species. These genes are considered essential for the basic functions and survival of the species.
Dispensable Genome:
The set of genes that varies among individuals within the species. These genes may be present in some individuals but absent in others, contributing to the overall genetic diversity of the species.
pangenome recognizes that a single reference genome may not fully represent the genetic diversity found this concept allows researchers to explore the variability in gene content and better understand the adaptability and evolutionary dynamics of the species.
Genome content
Genes
* protein-coding (alternate splicing, nesting)
* various RNA genes, e.g. long non-coding RNAs (e.g. rRNA, etc.), small non-coding RNAs (miRNA, snRNAs, snoRNAs, …), etc
Other sequences
* intergenic sequences (in between genes)
* low complexity repeats (centromeres, telomeres (hard to sequence)
* mobile elements (“selfish” DNA transposons)
* regulatory sequences
* DNA replication
* gene transcription
* splicing, gene rearrangement
miRNA
Biogenesis:
Transcribed from DNA to form pri-miRNAs.
Processed into pre-miRNAs and transported to the cytoplasm.
Maturation in the Cytoplasm:
Processed by Dicer to form mature miRNAs.
Mature miRNAs guide the RNA-induced silencing complex (RISC).
Target Recognition:
RISC complex binds to specific mRNAs based on sequence complementarity.
Post-Transcriptional Regulation:
Binding can lead to mRNA degradation or inhibition of translation.
Fine-tunes gene expression by regulating protein levels.
Role in Diseases:
Dysregulation of miRNAs implicated in various diseases.
Potential therapeutic targets for disease treatment.
In summary, miRNAs play a crucial role in regulating gene expression, contributing to the precision and flexibility of cellular processes.
Details about human nuclear genome
- Feb 2001: first draft
- but still a few gaps
- <2% protein coding
- ~21,000 protein-coding genes
- RNA genes (e.g. rRNA genes)
All the rest:
* DNA, pseudogenes, repeats, mobile elements.
* 95% intergenic sequences
* repetitive sequences (50%)
* low complexity repeats, centromeres, telomeres
* mobile elements
* transposable elements/retroviruses, e.g.
LINEs (Long interspersed nuclear elements) and SINEs (Short interspersed nuclear elements)
* regulatory sequences
Large genes with lots of introns
Huge genes normally contain lots of introns which means it is more susceptible to genetic diseases as there are loads of places it could go wrong.
Human mitochondrial genome
First draft in 1981
* 37 genes (28 on H strand, 9 in L strand)
* 22 tRNA genes, 2 rRNA genes (16S and 12S), 13 protein-coding genes (part of some proteins of the mitochondrial respiratory complex)
Minimum number of genes an organism needs to survive?
The minimal gene set for a simple, free-living organism like Mycoplasma genitalium was estimated to be around 300 to 400 genes.
