Human genome

Genome

complete set of DNA sequence (nuclear and mitochondrial)

Mitochondrial Genome (mtDNA)

37 genes total (2 rRNA/ 22 tRNAs/ 13 oxidative phosphorylation), mutation rate 10x nuclear, compact (no junk), maternally inherited, Multigenetic transcripts, small (16.6kb), no histones, highly redundant, mitochondrial disease result mutation in mtDNA or nuclear

Human (nuclear) genome project

Sanger sequencing, 2001, computer prediction verified with cDNA sequencing, is reference, telomere to telomere sequencing filling gaps

Human pangenome approach

represent genomic diversity better than single reference

Information content of human genome

greater due to transcriptional regulatory complexity (alternative splicing/start sites), 25 000 genes but >100000 proteins (1 protein = 1+ protein)

Human genome complexity

multiple transcriptional start site in single gene (nested), alternative splicing, complex transcriptional regulatory region in non coding, post translational modification create more proteins

Human genome content

1-2% encoded proteins, 98% introns/regulatory/repetitive/intergenic

Gene families

multiple copies of closely related gene from single ancestral gene (paralogues), often in cluster on chromosome, arise through duplication events

Mechanism of gene duplication

Local/duplicated nearby - unequal crossing over, new genomic location - DNA rearrangement/retrocopying, large scale/chromsomal

Unequal crossing over

repetitive sequence misalign during meiosis, local duplication in one and deletion in other chromosome, ca be part/entire or multiple gene

Chromosomal rearrangements and duplications

chromosome breakage/recombination move/duplicate DNA segment to different location

Mobile elements

Class 1 -Retrotransposons/Class 2 DNA transposons, can disrupt gene depending where inserted

Retrotransposons

copy and paste, via RNA intermediate, encode reverse transcriptase, LTR or non LTR, about 40% of human genome, duplication by copying mRNA back into genome -pseudogene (lack promoter/introns)

DNA transposons

cute and paster, via DNA intermediate, transposase to excise and reinsert. flanked terminal inverted repeats, few percent of human genome - mostly evolutionary remnants (no longer active)

Barbara McClintock

discovered transposable element, developed technique to visualize corn chromosomes

Whole genome duplication (WGD)

duplication of entire chromosome complement, produce extra copy of every gene, 2 rounds in vertebrate evolution, 3 round in Teleost fish evolution

What happens after duplication

Redundancy, Subfunctionlization/specialize, Neofunctionalization, Gene loss/pseudogenization

gene duplication effect on genes

produce copy number variation

gene redundancy

duplicated gene retain overlapping function, loss of one buffered by other, loss of both reveal underlying fuction

Gene loss/pseudogenization

one copy of redundant gene accumulates mutation, in absence of selection, cause pseudogene

Neofunctionlization

mutation alter activity/expression, novel function, if new function important selection against mutation the eliminate

Subfunctionalization

mutation alter activity/expression, specialized function, can alter coding sequence or transcriptional regulatory(ex: active different tissue), if new function important selection against mutation the eliminate

Hox genes

family of homeobox transcription factor, differentially expressed along rostrocaudal (head-tail) axis, cluster amount vary

Hox cluster in human

amount vary between species, humans had 2 rounds genome duplication to get 4, unequal combination cause variation in cluster → specialization/degradation

Hox gene redundancy

hox loss of function lethal in drosophila bc only 1 copy (no redundancy), duplication can create partial functional redundancy (paralogues buffer effect)

Hyaluronidase

enzyme, degrade hyaluronan, humans have 2 cluster of 3 paralogue → specialized, different AA sequence mean different enzymatic activity (pH) and tissue expression, loss of function(lysosomal storage disorder/accumulation) has subtle effect bc partial functional redundancy

Pseudogene

look like gene but do not produce functional proteins, from degraded redundant/retro transposed that accumulate mutation in absence of selection, Nonprocessed vs processed

Nonprocessed pseudogenes

vestigial gene, inactivated by mutation in critical coding/regulatory sequences

Processed pseudogenes

from reverse transcription/genomic reinsertion of processed mRNA, lack promoter/introns

Non coding RNAs

do not produce proteins,ex: long non coding RNA and microRNA

Long non coding RNA (lncRNA)

adopt complex secondary/tertiary folding structures, ex: XIST

XIST (x-inactivation specific transcript)

lncRNA, transcribed from inactive X chromosome, act with other ncRNA/protein from X inactivation centre (XIC), essential for X inacivation

MicroRNAs

regulate expression by binding mRNA produced, negative regulator of gene expression (silence)- translation repression/mRNA degradation, 22nt long, bind partially complementary sites (3’UTR usually)

Human Genome diversity

more diversity in African than any other population, bias in studies bc most sequence genome European

What is a gene? (what to consider)

regulatory element within other genes (distant/shared), gene within intron of other, polycistronic (cotranscribed), what are physical boundaries