Chapter 11: Chromosome Structure and DNA sequence organization

Eukaryotic chromosomes

-Only visible during mitosis

-10-100 million base pairs in length

-Several 100-1000 genes interspersed throughout

-Origin of Replication are about 100,000 bp apart

-Centromere is the recognition site for kinetochore microtubules

-Telomeres have repetitive sequences at both ends

-Other repetitive sequences near centromere and interspersed throughout

Human nucleus

-5-10 um, 46 chromosomes

-contain enough DNA to extend to more than 2 meters

Linear DNA

interacts with proteins, which affect the degree of chromatin compaction

Histones

basic, positively charged proteins that play a critical structural role in chromatin

-have a globular domain and a charged, flexible histone tail

Non-histones

less positively charged proteins, dont make DNA so compact but keeps DNA together

-bind the linker region and also aid in chromatin compaction, they also may effect gene expression

Linear double stranded DNA

-wraps around an octamer (8 histones) of 2 copies each of 4 histones to form nucleosome

-H2A, H2B, H3 and H4 are the core histones

Core histones

H2A, H2B, H3 and H4

Nucleosomes

-repeating structural unit of chromatin and condense its structure by 7-fold

-147 base pairs of DNA winds around the histone octamer and resembles beads on a string

H1

the linker histone that binds to spacer DNA between nucleosomes, but not as tightly as the core histones

30-nm solenoid

-nucleosomes closely associate with each other form this and is compacted 50 fold

-histone protein H1 plays a key role in this packaging

-This structure is characteristic of the uncoiled chromatin fiber in interphase

-Going into metaphase, the 30-nm structures are folded into a series of lop domains that are 300 nm structures

Euchromatin

-not tightly coiled

-less condensed regions of chromosomes that are transcriptionally active

Heterochromatin

-condensed

-tightly compacted regions of chromosomes that are, in general, transcriptionally inactive

-Unique to eukaryotes

-replicates later during S phase than euchromatin

-Important in maintaining the structural integrity of chromosomes

-Ex: inactive X chromosome is condensed into heterochromatic Barr body

-Translocation of genes into heterochromatic regions can alter gene expression- if too tightly wound, unable to be expressed

Chromatin remodeling

-when chromatin can be induced to change its structure

-histone tails are targets for a variety of chemical modification that regulate chromatin folding and gene expression

-Acetylation, methylation and phosphorylation of amino acids in histone tails

-makes chromatin unwind for DNA replication or for it to become tightly wound, makes it active or inactive

-Open: transcription happens

-Close: transcription doesn’t happen

Repetitive DNA

-59%

-regulatory DNA

-dont know its function

Unique noncoding DNA

-15%

-makes muscle cells, dont produce stomach enzymes

Introns and other parts of genes

-24%

-form preRNA

Regions of genes that encode proteins

2%

Middle repetitive sequences

-include tandem repeats and interspersed retrotransposons

Tandem repeats include:

-Multiple copy genes

-Variable number of tandem repeats (VNTRs)

-Short tandem repeats (STRs)

Multiple copy genes

-E.g., rDNA- clustered on the short arm of acrocentric chromosomes (13, 14, 21, 22)

Variable number of tandem repeats (VNTRs)

-15-100 bp repeated sequences within and between genes that extend for 1-20 kb in length

-Clusters of VNTRs throughout the genome are called minisatellites

Short tandem repeats (STRs)

-Di-, Tri-, tetrea-, penta repeats (2-6 bp long)

-Clusters of STRs throughout the genome are called microsatellites

-Most common is (CA)n, where n is 5 to 50 repeats

Retrotransposon

-Copy and paste

-replicates and inserts DNA somewhere else

DNA transposon

-cut and paste

-gene changes site or location

Interspersed retrotransposons

-Transposable sequences are interspersed and can relocate within the genome

-Short interspersed elements (SINEs) make up 13% of genome

• <500 bp long present in 50,000+ times in human genome, best characterized is the ALU family, which are 200-300 bp long and make up 5+% of the human genome

-Long interspersed elements (LINEs) make up 21% of genome; ~6 kb long and present ~850,000 times in human genome

Single nucleotide polymorphisms (SNPs)

-the most common type of genetic variation

-Occur once in every 500-1000 bp; 10 million SNPs in the human genome

-Most are between genes and have been used to identify genes in the human genome

-are also used for personalized genomic medicine