CPSC 452 Exam 2

C value

Haploid DNA content

C value paradox

Lack of direct relationship between genome size and organismal complexity

Why can plants have larger genomes?

Genome duplication, expansion of family of transposons, polyploidy

Histone 

Relatively small proteins that have many basic residues such as that they associate with negatively charged DNA

Nucleosome

Consists of DNA wrapped two full turns (166 bp) around a globular octamer of histone proteins made up of two tetramers, each consisting of H2A, H2B, H3, and H4

Chromatin

Association of DNA with proteins- efficient packaging of DNA with different proteins into this

Heterochromatin 

Tightly packed, inaccessible to polymerase, usually repetitive, includes centromeres and telomeres 

Euchromatin

Gene rich, more transcription

Histones

Most abundant and important proteins that make up chromatin; relatively small proteins that contain many basic amino acid residues; highly positive net charge that allows them to bond strongly to negatively charged DNA; main function is formation of nucleosomes 

chiP-seq

Identify the regions of the genome that are interacting with a protein of interest

B chromosomes

Accessory or super numerary chromosomes, may be present in only some individuals from some populations in a species, irregular meiotic and mitotic behavior, long term survival depends on ability to survive efforts by host to eliminate or suppress them b/c they are often parasites

Genome variation within a species

Different snps, indels, condensed gene order but not spacing (ex the DNA in between genes)

Pan-genome

There is a core and there are accessory parts of a genome- ex in different strains, different accessory 

Meiosis

Reproductive cell, 4 daughter cells, synapsis of homologous chromosomes, sexual reproduction

Mitosis

Somatic cell, 2 daughter cells, no synapsis, growth and repair 

Meiosis Importance

Can purge deleterious mutations

Can break beneficial allelic combos 

Can be mutagenic through mismatch repair at sites of recombination

Excessive crossover rates might also promote genetic instability through a variety of structural rearrangements such as deletions, inversions, and translocations 

Chromosome knob

Darkly stained compared to surrounding chromatin 

Often contain repeated DNA sequences 

Defined in 1930s by McClintock 

Haldane mapping

Takes into account double crossovers

Interference

Crossovers discourage other crossovers from occurring nearby

Kosambi mapping

Takes into account double crossovers and interference

Crossover

Reciprocal exchange of genetic material 

Gene conversion

Nonreciprocal recombination

Doesn’t flip flop, only 1 gives

Bivalent

Association of 2 homologous chromosomes

Sister chromatid

Chromatids produced by a replication of a single chromosome

Chiasma 

Exchange configuration where 2 homologous non-sister chromatids visible in prophase 1 of meiosis; cytological manifestation of crossing over 

Telomere bouquet

Cytological structure forms during zygotene important for spindle formation 

Holliday Junction

A cross shaped configuration of 2 DNA molecules formed as an intermediate during recombination 

What are recombination hotspots?

Subtelomeric regions

Sources of genetic variation

Recombination, mutation

Mutagens

Irradiation, DNA intercalating agents, transposons

Somatic mutations

Affect cells in the body of an organism, not heritable 

Germ line mutations

Affect gametes, heritable and relevant to evolution

Transition

One purine (g and a) to another or one pyrimidine (c and t) to another 

Transversion

A purine to a pyrimidine or vice versa

Tautomerism

Molecule can exist in more than 1 chemical form 

Random ti/tv ration

0.5

Whole genome (depends on species) ti/tv ratio

1.5-2.0

Alignment errors

mean ti/tv ratio gets closer to randomness and ratio becomes lower 

Causes of low ti/tv

False positive variants

Alignment errors 

Sequencing bias 

Tandem duplications

Mutation in which new copies of the DNA are adjacent to the source DNA

Slipped-strand mispairing

Illegitimate base pairing in regions of repetitive DNA during replication coupled with inadequate DNA mismatch repair systems can produce deletions or insertions of repeat units 

Inversions

Either paracentric or pericentric

Paracentric

Do not span centromere

Pericentric 

Span centromere

Translocations

Sections of 2 chromosomes are exchanged 

RNA Polymerases (RNAPs)

Enzymes that synthesize the different types of RNA found in plant cells 

RNAPVI-III

Essential

RNAPIV

Synthesizes siRNAs

RNAPV

Transcribes noncoding RNAs involved in siRNA-mediated gene silencing

Transcriptional Machinery

Initiation, elongation, termination

Housekeeping genes

Always turned on in cells 

Differential gene expression

Gene expression varies depending on environmental cues or during development 

Methods to determine gene expression

qRT_PCR

In-situ hybridization 

Reporter proteins (fluorescent) 

Microarrays 

RNAseq 

Basal elements

Necessary for RNA polymerase binding

Generally within 50 bps of transcription initiation site '

Not all types of promoters are always present 

Example: TATA box 

Cis-acting elements

Not conserved

On the same DNA molecule 

Activation, repression of modulation of modulation of gene expression

Usually 1-2 kb upstream of transcription start site, but can be in introns, exons, or downstream of where termination occurs 

Short (<10bp) 

Vary in base composition 

Cis-regulatory module

Cluster of cis-elements

Can be classified as enhancers or silencers 

Proximal promoter elements

Regulatory elements found in the vicinity of the transcriptional start site

Insulator

Cis regulatory module that blocks signals from enhancers and silencers 

Trans-acting factors 

Interact directly with basal transcriptional machinery or indirectly through mediator 

Influences rate at which transcription occurs 

Trans-acting factors that bind cis-elements that are usually transcription factors and are specific transcription factors

Gene regulatory network

Collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins 

Epigenetics

Leads to exact same DNA sequence and different phenotype 

Gene expression

Can be influenced by changes in the genome that do not involve mutations in the DNA sequence 

Epigenetic modifications

Species, tissue, organelle, and age-specific

DNA methylation

Methylation of cytosine bases in nuclear dna by enzymes called dna methyltransferases

What base does dna methylation occur in plants? 

Cytosine 

Methylation located in promoter

Decreased transcription

Methylation located in gene

High expression

Bisulfide sequencing

Treatment of dna with sodium bisulfite converts cytosines but not methylated cytosines into uracil - then the two sequences are compared to see where tjhe methylation is 

Posttranscriptional histone modifications

Methylation, acetylation, phosphorylation

Methylation occurs?

Predominately on lysine residues of histones H3 and H4 by histone methyltransferases

Acetylation

Transfer of acetyl group from acetyl coenzyme a to different lysine

Flowering Locus C

represses initiation of flowering; repression removed during winter with prolonged cold period (through vernalization), polycomb repressive complex 2 represses flc gene by tri-methylation of lysine 27 of histone H3. FLC off=flowering can commence with environmental signals (photocopied) 

Epigenetic code

Phenomenon of interacting histone modifications. Indicated that specific combinations of modification may be linked to defined functional effects

Epigenetic states

Certain combinations of modifications are prevalant 

ChiP-seq

Identify regions of the genome that are interacting with a protein of interest

Identifying genome wide binding sites of protein of interest

Specific transcription factor

ATAC seq

Determine chromatin accessibility across the genome 

Sequences regions of open chromatin and helps uncover how chromatin packaging and other factors affect gene expression

Which regions of the genome are involved in gene regulation

What sequencing does not require prior knowledge of regulatory elements? 

ATAC seq

qRT-PCR

Few genes under different conditions

1 specific gene/a few

rna to dna, then uses pcr

RNA seq 

Global understanding how gene expression changes in response to a stimulus 

Difference between rna seq and qrt-pcr

The number of genes involved

Paramutation 

epigenetic phenomenon where one allele can heritably silence another, leading to a change in gene expression that is passed down through generations without altering the underlying DNA sequence

Why does paramutation matter?

Heritable, explanation for non-mendelian inheritance, gene regulation (trans-homolog interactions), epigenetic memory

Paramutation can occur

Between either genetically identical or genetically distinct alleles

Paramutable alleles

Susceptible to these conversion-type behaviors

Paramutagenic alleles

Instigate or facilitate changes

Neutral allele

Neither paramutagenic or paramutable

Paramutations common in maize

r1, b1, pl1, p1- all encode transcriptional activators of flavonoid pigment biosynthesis 

RNA directed transcriptional silencing 

siRNA target sequences correlated with dna methylation/histone modification

Involvement of RNA-directed dna methylation (RdDM)

Histone methylation/acetylation

dna methylation patterns 

What role do tandem repeats have in paramutation? 

Repeated sequences give distinct chromatin structures

Folds around histone

RNA from tandem repeats creates a larger pool of which span the full repeat sequence as opposed to rna from single copy sequences

more rna transcribed 

Why is it important to study paramutations? 

Inbreeding depression/hybrid vigor 

Inheritance of complex human diseases

Stability of transgenes during genetic modification

Climate change-adaptive mechanisms 

How widespread is paramutation?

We don’t really know!

What do transposable elements in spotted kernels mean?

When it happens in development leads to the spotting pattern

How does genetic variation arise?

Mutations

Recombination