Gen 4100 Exam 3 | Iowa State University

Euchromatin

• less condensed

• higher gene density

• easier to transcribe

  a. usually active transcriptionally

• generally found on chromosome arms

• lightly stained regions of chromosomes

Heterochromatin

• more condensed

• higher repeat content

• harder to transcribe

  a. usually inactive transcriptionally

• generally found near centromeres

• can be split into constitutive/facultative heterochromatin

• darker stained regions of chromosomes

• isn’t always tied to particular DNA sequences; it can spread

Constitutive Heterochromatin

• always condensed

• condensed in all cells (ex., Y chromosome)

Facultative Heterochromatin

• sometimes condensed

• condensed in only some cells and relaxed in other cells (ex., X chromosome)

ATAC-Seq

• used to detect open chromatin

• the assay for transposase-accessible chromatin with sequencing

Cytogenetics

• used to visualize chromosomes

• the branch of genetics that studies the structure of DNA within the nucleus

High-Resolution G-Banding

• the karyotype of a human male can be examined with high-resolution G-banding

• metaphase chromosomes stained with Giemsa have alternating bands of light and dark staining

• giemsa stain binds to AT-rich regions of chromosome

Fluorescent in Siti Hybridization (FISH)

• used to characterize genomes

• depends on hybridization between metaphase chromosomes and a labeled DNA sequence 

  a. chromosomes are spread on a glass slide and denatured to make them single-stranded

  b. a DNA sequence is labeled with a fluorescent tag to make it a probe

  c. the probe hybridizes into chromosomes at complementary regions

Histone Tails

• it can be modified through acetylation and methylation

• histone methylation: often pack chromosomes

• histone acetylation: unpack chromosomes

Four Types of Chromosomal Rearrangements

1. add or remove base pairs

2. deletions and duplications

3. relocate chromosomal regions without changing the number of base pairs

4. inversions and reciprocal translocations

Aberrant Crossing-Over

• it can cause deletion, duplication, and inversion

• crossing over between repeated sequences on homologous or nonhomologous chromosomes

Using Deletions to Locate Genes

• examine a phenotype of a heterozygote for recessive allele and deletion:

  a. if the phenotype is mutant, the mutant gene must lie inside the deleted region 

  b. if the phenotype is wild-type, the mutant gene must lie outside the deleted region

Consequences of Inversions

• depends on the relationship of the inversion with the centromere

• pericentric inversion: the centromere is within the inverted segment

• paracentric inversion: the centromere is not within the inverted segment

Two Classes of TEs

• class I: retrotransposons

  a. copy-and-paste mechanism of transposition through RNA intermediate 

• two types:

  a. LTR retrotransposons: long terminal repeat

  b. non-LTR retrotransposons 

• class II: DNA transposons

  a. cut-and-paste mechanism of direct transposition

• two subclasses:

  a. TIR transposons: terminal inverted repeat

  b. helitrons

Consequences of Transposable Elements on Genomes

1. TE insertion can result in altered gene expression

• TE can be inserted within the coding region of a gene or within the promoter and enhancer, which will affect its expression

2. gene relocation through TE transposition 

• due to the formation of composite TE

3. TEs can trigger spontaneous chromosomal rearrangements

• due to unequal crossing over between TEs