Learning Outcomes - Week 4 - The Genome in 3 Dimensions Flashcards
Learning Objectives: We can find the human genome in: the _________ (_____________ cells), the ___________ (__________ cells), ____________
The nucleus (Interphase)
The cytoplasm (mitotic)
Mitochondria
Learning objectives: molecular biology techniques (name all 5)
- ChIP (specific protein-DNA interactions)
- ChIP-sep (global protein-DNA interactions)
- 3C (DNA-DNA ‘interactions’)
- ATAC-seq (open/closed chromatin)
- FISH (location of a specific DNA sequence on chromosomes)
Learning objective: define chromatin
the material of which the chromosomes of organisms other than bacteria (i.e. eukaryotes) are composed, consisting of protein, RNA, and DNA
Learning objective: define heterochromatin
Heterochromatin is a constituent of eukaryotic genomes with functions spanning from gene expression silencing to constraining DNA replication and repair. Inside the nucleus, heterochromatin segregates spatially from euchromatin and is localized preferentially toward the nuclear periphery and surrounding the nucleolus
Learning objective: define euchromatin
Euchromatin is the part of the chromatin involved in the active transcription of DNA into mRNA. As euchromatin is more open in order to allow the recruitment of RNA polymerase complexes and gene regulatory proteins, so transcription can be initiated.
Learning objective: define interphase
the resting phase between successive mitotic divisions of a cell, or between the first and second divisions of meiosis
During interphase, the cell grows and makes a copy of its DNA. During the mitotic (M) phase, the cell separates its DNA into two sets and divides its cytoplasm, forming two new cells.
Learning objective: define mitosis
Mitosis is a process of cell duplication, in which one cell divides into two genetically identical daughter cells. In the various stages of mitosis, the cell’s chromosomes are copied and then distributed equally between the two new nuclei of the daughter cells
Learning objective: define sister-chromatid
A chromatid is one of the two identical halves of a chromosome that has been replicated in preparation for cell division. The two “sister” chromatids are joined at a constricted region of the chromosome called the centromere
Learning objective: define promoter
A promoter, as related to genomics, is a region of DNA upstream of a gene where relevant proteins (such as RNA polymerase and transcription factors) bind to initiate transcription of that gene. The resulting transcription produces an RNA molecule (such as mRNA)
Learning objective: define enhancer
Regulate transcription in a spatial- or temporal-specific manner and function independently of both distance from and orientation to the promoter. Enhancers are also usually modular.
Learning objective: define silencer
Sequence-specific elements that confer a negative (silencing or repressing) effect on the transcript of a target gene
Learning objective: define insulator
Also known as boundary elements. Block genes from being affected by the transcriptional activity of neighbouring genes
Learning objective: define core promoter
The region at the start of a gene that serves as a docking site for the basic transcriptional machinery
Learning objective: define proximal promoter elements
The region immediately upstream (up to a few hundred base pairs) typically containing multiple binding sites for activators
Learning objective: define chromosome territories
chromosome territories are regions of the nucleus preferentially occupied by particular chromosomes.
Learning objective: define centromere
the region of a chromosome to which the microtubules of the spindle attach, via the kinetochore, during cell division.
Learning objective: define telomere
Telomeres, the specific DNA–protein structures found at both ends of each chromosome, protect genome from nucleolytic degradation, unnecessary recombination, repair, and interchromosomal fusion. Telomeres therefore play a vital role in preserving the information in our genome.
Learning objective: define mitochondrial DNA
The mitochondria DNA is circular and devoid of histone proteins, unlike the DNA present in the nucleus which is linear and is wound around a histone protein core. The mitochondrial DNA is a double-stranded molecule. Was this answer helpful?
Learning objective: explain the concept of transcriptional regulation in 3D and spatially in the nucleus
The transcription factors bind to certain sequences of DNA in the nucleus and cause transcription of cell division-related genes. The products of these genes are various types of proteins that make the cell divide (drive cell growth and/or push the cell forward in the cell cycle).
Learning objective: explain the concept of changes in chromatin during the cell cycle
Learning objective: explain the concept of molecular biology techniques
The main techniques used in molecular biology are cloning, PCR (Polymerase Chain Reaction), nucleic acid electrophoresis, DNA microarray analysis, in situ hybridization (HIS), sequencing (Sanger or Next Generation Sequencing (NGS)
Learning objective: explain the concept of inheritance of mitochondrial disorders
Learning objective: Explain the molecular technique of ChIP (sequence protein-DNA interactions)
Chromatin ImmunoPrecipitation (ChIP)
kIdentify the location in the genome (DNA) to which your protein of interest binds (DNA-protein interaction). You use an antibody to your protein of interest.
Learning objective: Explain the molecular technique of ChIP-sep (global protein-DNA interactions)
What is ChIP-Seq? By combining chromatin immunoprecipitation (ChIP) assays with sequencing, ChIP sequencing (ChIP-Seq) is a powerful method for identifying genome-wide DNA binding sites for transcription factors and other proteins.
Learning objective: Explain the molecular technique of 3C (DNA-DNA ‘interaction’)
3C methods measure the proximity of DNA elements through restriction enzyme digestion and ligation; sequencing of the resultant chimeric fragments produces a population-based interaction frequency as the output
Learning objective: Explain the molecular technique of ATAC-seq (open/closed chromatin)
Learning objective: Explain the molecular technique of FISH (location of a specific DNA sequence on chromosome)
FISH = Fluorescence In Situ Hybridization
FISH identifues the location of DNA sequences in the genome
b, d
(Example of a question that is very detailed and will not be asked)
Describe the different steps of ATAC-seq, used to map open chromatin
