Genome Organization and Regulation Vocabulary

Flashcards about Genome organization and regulation

Chromosomes

The genomes of eukaryotes are divided up into these structures that are accurately duplicated and passed on from one generation to the next.

Transposable elements

Mobile genetic elements that amplify via an RNA intermediate (Retro-transposons) or copy and move via DNA (DNA transposons).

Telomeres and Centromeres

Structural components of chromosomes that stabilize linear DNA, ensure replication of chromosome ends, and allow for chromosome segregation.

Tandem Repeats/Simple Repeats

Short nucleotide sequences that are repeated for long stretches of DNA, found in subtelomeric repeats and microsatellites.

Segmental duplication

Large blocks of DNA that are present at 2 or 3 locations.

Proteins for DNA packaging

Specialized proteins that bind to and fold DNA, generating a series of coils and loops for higher levels of organization.

Chromatin

Complex of proteins with the nuclear DNA of eukaryotic cells.

Nucleosomes

Basic unit of eukaryotic chromosome structure, visualized as beads on a string by electron microscope.

Histones

Small, highly conserved, arginine and lysine-rich proteins that form the core of nucleosomes.

Linker Histone H1

Histone that seals off two full turns of DNA around the histone octamer.

Solenoid Model

Model where bent linker DNA sequentially connects each nucleosome core, creating a structure where nucleosomes follow each other along the same helical path.

Zigzag Model

Model where straight linker DNA connects two opposing nucleosome cores, creating opposing rows of nucleosomes that form a “two-start” helix.

Heterochromatin

Highly compacted, transcriptionally inactive chromatin.

Euchromatin

Transcriptionally active, less condensed and accessible chromatin.

Constitutive heterochromatin

Heterochromatin found in all cell types, typically surrounds centromeres and telomeres, and includes repetitious sequences like satellite DNA.

Facultative heterochromatin

Heterochromatin found in some cells but euchromatic in others; an example is the mammalian Barr body.

Barr Body

Structure found in the cells of female mammals that represents the transcriptionally inactivated X chromosome.

Chromosome Territories

Specific regions in a nucleus where chromosomes are arranged; these territories are maintained throughout evolution.

Histone Chaperones

Proteins that transport newly synthesized histones, present histones to histone-modifying enzymes, store free histones, deposit histones onto DNA, and remove histones from the nucleosome.

Epigenetic Marks

Epigenetic features that maintain phenotypes in different cells.

Epigenomics

The overall chromatin state of the cell.

Epigenetic Writers

Enzymes such as histone acetyltransferases (HATs) and histone methyltransferases (HMTs) that lay down epigenetic marks on amino acid residues on histone tails.

Epigenetic Erasers

Enzymes such as histone deacetylases (HDACs) and lysine demethylases (KDMs) that catalyse the removal of epigenetic marks.

Post translational modifications of histones

Adding marks or tags onto histone tails through acetylation, methylation, phosphorylation, ADP-ribosylation, ubiquitination, and citrullination.

Histone Readers

Proteins that recognize and bind histone codes/modifications.

Bromodomains

Evolutionarily conserved acetylation recognition modules that adopt a distinct structural fold known as the BRD fold.