HUGE Lecture 2 08/27/26

Intron definition

section of genome spliced out during RNA processing (mRNA generation)

Exon definition

section of genome coding for a protein

UTR definition

untranslated region- regulatory sequence included in mRNA transcript

How many protein coding genes in the human genome

20,000 ~1-2% of the genome

What length of introns do highly expressed genes typically have and why

shorter introns because long introns cost a lot of time and energy in transcription

Why do some genes have high intronic content

genes with a lot of intronic content can be highly regulated

How are protein-coding genes easy to identify in a genome sequence

presence of an open reading frame- start to stop codon

What happens to protein sequences during evolution

often conserved during evolution and reading frames are very similar in size across closely related species

Transcript variant definition

different species of RNA that represent the same sequence with differently spliced exons

Isoform definition

one of several different versions of a molecule produced from the same gene

Two reasons why determining the exact number of protein-coding genes was difficult

• initially predicted based on open reading frames but number was found to be inflated when genome sequences of other mammals were completed, and gene counterparts could not be found

• neighboring genes were found to represent components of the same gene

Readthrough transcription (conjoined genes) definition

genes that make both mRNA and non-coding RNA that are difficult to identify and systematically classify

Genes within genes for antisense strands

small protein genes can be located on the antisense strand within a larger gene

Genes within genes for sense strands

small RNA genes can be located on the sense strand of a larger gene

Antisense strand definition

the DNA strand that acts as a template during transcription

Sense strand definition

the DNA strand that has the same nucleotide sequence as the messenger RNA (mRNA), except it has thymine (T) instead of uracil (U) running from 5’ to 3’

Gene density across the genome

• varies from chr to chr

• heterochromatin almost devoid of genes

• high density in subtelomeric space

What is much of the genome composed of

a lot of repetitive DNA

Satellite DNA definition

High copy number tandemly repeated DNA (heterochromatin)

What does satellite DNA contribute to

formation of crucial chromosome structures, heterochromatin establishment, genome stability, and development

What is satellite DNA used in

DNA forensics (DNA fingerprinting)

Trnasposon repeats (transposable elements) definition

DNA that can change its position within a genome

What is the benefit of transposons

Transposons increase genetic diversity and can also regulate gene expression

What is the negative of transposons

May induce human genetic disease (insertional mutagenesis)

LINE definition

long interspersed nuclear element- code reverse transcriptase and endonuclease for self mobility

SINE acronym meaning

short interspersed nuclear element- rely on LINEs for reserve transcriptase and endonuclease

How do LINEs work

• transposon sequence is transcribed

• RNA intermediate is formed

• RNA intermediate is reverse transcribed

• DNA intermediate is formed

• DNA intermediate is integrated into target DNA

How do SINEs work

• transposon DNA is excised

• DNA intermediate is formed

• DNA intermediate is integrated into target DNA

Retrovirus-like elements definition

persist within the human genome as remnants of ancient retroviral infections- code for reverse transcriptase and integrase

Whole genome duplication history

last occurred hundreds of millions of year ago, many duplicated genes not retained throughout evolutionary history

Tandem duplication definition

unequal crossing over between homologous chromosomes or sister chromatids

Duplicative transposition by recombination

unstable regions of euchromatin recombine with other chromosomes (different chr combine)

RNA-directed duplicative transposition

RNAs are reversed transcribed into cDNA and integrated into a new chromosomal location

Non-allelic homologous recombination

genetic recombination that happens between two DNA sequences that look very similar, but are not matching alleles or exact partners- can lead to tandem duplication

Pseudogenes definition

nonfunctional segments of DNA that resemble functional genes but have been mutated into an inactive form over the course of evolution

Non-processed pseudogenes definition

whole gene duplicates in which one gene copy has become inactive due to mutation

Processed pseudogenes definition

copies of mRNAs that are reverse transcribed into cDNA and integrated into the genome; lack a promoter, and have usually accumulated mutations

Unitary pseudogene definition

formerly functional gene is no longer required (not evolutionarily advantageous) and is inactivated by mutation (no functional counterpart in the same genome)

What percentage of pseudogenes are non-processed, processed, and unitary

Non-processed- 25%

Processed- 75%

Unitary- few reported

What can duplicated genes not inactivated to pseudogenes be bad

they can be toxic and potentially disease causing

What is the largest gene superfamily in the human genome

olfactory receptor genes

What can happen if a new gene is

inactivating mutations may silence one copy

What can happen if a new gene is advantageous

natural selection may favor retention of the new, modified sequence

How can pseudogenes lead to disease

Non-allelic homologous recombination

How can pseudogenes complicate genetic testing

if a gene of interest has a pseudogene we could be amplifying the pseudogene simultaneously and variance seen could be from pseudogene

List of small DNA seq variation

SNV (SNP), insertion, deletion, and indel

SNV(SNP) acronym

single nucleotide variant

Indel variant definition

combination of insertion and deletion

List of structural DNA sequence variants

CNV, inversions, and translocations

CNV definition

copy number variant (deletion/duplication)

Inversions definition

two double-stranded breaks allows for sequence inversion

Translocations definition

DNA exchange between two different chromosomes (no change in DNA content)

De novo variant definition

noninherited genetic variants

How many de novo variants is each child born with on average

70

Segmental duplication definition

blocks of DNA that typically share 90% sequence identity (~5% of the euchromatin)

Segmental duplication evolutionary origin

segmental duplications have undergone little sequence divergence, are present only within higher primates, and thus suggest a very recent evolutionary origin

Why are segmental duplications important in human genetics

many deletion/duplication disorders result from recombination when chromosomes are misaligned because of them (non-allelic homologous recombination)

What type of genetic variant varies greatly across individuals

CNVS (copy number variants)

Are segmental duplications fixed (constant) in humans

yes

How can CNVs be adaptive

the amount of gene product is proportional to the number of gene copies, if more of a specific protein is advantageous in a specific environment, then more CNVs are also advantageous

Example of CNVs being adaptive

salivary amylase gene copy number is higher in populations that consume a high-starch diet

DNA fingerprinting definition

Technique used to determine the probable identity of a person based on unique nucleotide sequences

What does DNA fingerprinting actually do

Assesses repetitive regions of genomic DNA (mini/microsatellite DNA) - unique signature

DNA fingerprinting technique

1. Isolate DNA from blood sample

2. Digest DNA with restriction enzymes(s)

3. Separate DNA fragments using gel electrophoresis

4. Transfer DNA fragments to a nitrocellulose membrane

5. Incubate membrane with radioactively labeled DNA probes (target satellite DNA)

6. Expose to film to visualize labeled DNA fragments

How many short tandem repeat (STR) markers does CODIS USA utilize and what is the match probability

14 markers with a <1 in a trillion match probability