L14 and 15 Genomics and Genome projects

When did HGP officially begin NIH and DOE in the US

1990

• aimed to map and sequence the entire human genome

when did the first complete sequence of a bacterial genome (H.influenza) found

1995

• setting a precedent for more complex organisms

when was information freely available and placed in the public domain within 24 hours-bermuda principles

1996

when was the working draft of 90% of the genome made with 99% accuracy

2000

when was the HGP declated complete in April 99% of the human genome with an accuracy of 99.9%

2003

why do we sequence the genome

• blueprint of life

• 3 billion base pairs

• coding and non-coding sequence

• regulatory sequences

• high order structure

• chromosome maintenance

• comparative searches

what are model organisms

• small genome ‘value for money’

• easy organisms to manipulate

• provide information on fundamental biological processes

• technology development

• useful for comparative genomics

describe the outcomes of 2011 bacterial infection in Europe

• revealed an unidentified new strain of E.coli

• insight into the antibiotic resistance characteristics

• insight to why bacteria was so virulent and also why it seemed to be targeting adults

describe the outcomes of the black death

modern day ancestors have no unique sequence differences suggesting the apparent increased virulence during 1347-1351 likely had other contributary factors

describe the outcomes of genotype sequencing of the plague of justinian

• revealed the 541-543 historical event was yersinia pestis

• revealed the strain vanished and 1347-1351 was a completely new strain

describe the outcome of the HGP in comprehensive genome mapping

provided a detailed map of the human genome, identifying approximately 20,000 to 25,000

describe the outcome of the HGP in technological advancements

• spurred the development of high-throughput sequencing technologies, bioinformatics tools and data storage solutions

• reduced the cost and time required for DNA sequencing dramatically

describe the outcome of the HGP in scientific discoveries

identified genetic variants associated with various diseases, enhancing our understanding of the genetic basis of health and disease

describe the outcome of the HGP through collaborative efforts

fostered international collaboration among scientists, leading to the establishment of global databases and resources like the Ensemble genome browser

what are the major issues identifying genes within genomes-limitations of the HGP

• how big is a valid open reading frame

• identification of RNA splice sites

what is the short open reading frame (ORF)

• encoding 3 amino acids

• several such reads throughout the genome

what is the searching start codons for each gene in different reading frames

ATG

• reads as a triplet

what is the start codon for short open reading frames (ORFs)

ATG

what is the stop codon for short open reading frames (ORFs)

TAA

describe incomplete coverage as a limitation to pre-mRNA splicing

• some highly repetitive and structurally complex regions of the genome, such as centromeres and telomeres

• major gaps in 2003 sequencing data

• recent advancement in sequencing technology filled most gaps

describe genetic variation as a limitation to pre-mRNA splicing

different individuals

• doesn’t capture the full extent of human genetic diversity

describe functional understanding as a limitation to pre-mRNA splicing

many identified genes have unknown functions, and the regulatory mechanisms governing gene expression are complex and not fully understood

describe the problems in gene identification by genome analyses in Saccharomyces cerevisiae

• 0.001 the size of the human genome

• genes are tightly packed

• little repetitive DNA

• RNA alterative splicing occurs to complicate gene identification

• simple genetics are performed

describe the advantages in gene identification by genome analyses in Saccharomyces cerevisiae

• nearly 30 years after obtaining the S.cerevisiae genome sequence 10% of the 6600 open reading frames are classified as ‘Dubious’

• further 10% are classified as ‘uncharacterised’

• 26% have not been linked with any biological process

what are the advancements of HGP

• foundation for precision medicine -cancer treatment, pharmacogenomics

• gene therapy

• genetic screening

• several open databases being accessible

• comparative genomics-widely popular

describe findings of human genome sequencing of rare childhood conditions in addenbrookes hospital <3

• 1 in 4 intensive care patients had a genetic disorder

• 66% cases the mutation occurred spontaneously

• childs symptoms/appearance was only rarely a good predictor of a genetic conditon

• diagnosis in 2-3 weeks avoiding further invasive tests and sometimes led to treatment change

• in 2019, any baby/child admitted to intensive care in England with an unexplained condition became eligible, together with parents, for whole genome sequencing

• starting in 2023 all seriously ill children in england with an unexplained disorder will be eligible for genome analysis

what are the computational analyses of sequence

• prediction of function-roles for model organisms

• prediction of protein localisation

• prediction of protein domains/modification

• identification of regulatory sequences

• characterisation of protein families

describe the functional characterisation of mutant proteins

analysis of predicted catalytic mutant Msh2 proteins from human colon cancer was confirmed by expressing the proteins in yeast

defects in critical protein-protein interactions

reduced steady state levels of Msh2

mutations affected the activity of the mismatch repair complex

describe genetic variation

• any two unrelated humans have 3 million differences in DNA sequence

• 10,000 of these differences cause changes in proteins

describe the bottleneck in personalised medicine

• interpreting genetic variation and its role in disease is challenging

• crucial for developing personalised drug treatments

describe mutation effects

many single amino acid changes in proteins causing human diseases are believed to be due to protein instability

describe potential treatments

• simple diet supplements might restore protein function for specific mutations

• e.g. vitamin B6-dependent enzyme issues linked to neuronal disorders

• studies using yeast to express human genes reveal unpredicted defects, aiding in understanding genetic variation

how do we identify conserved domains

BLAST

describe the homeodomain

• DNA binding domain involved in the transcriptional regulation of eukaryotic development

• may bind to DNA as monomers or as homo/heterodimers in a sequence-specific manner

how do we search for potential serine/threonine/tyrosine phosphorylation sites

NetPhos programme

how do we search for potential serine/threonine/tyrosine phosphorylation sites

• investigate protein phosphorylation in vivo and if so whether the identified threonine residue is important

• test genetically and biochemically the potential role of the programme predicted kinase

• does the phosphorylation change in a cell cycle dependent manner?

• mutate the threonine residue to a glutamic acid, aspartic acid or alanine residue to investigate the role of phosphorylation

how do we identify regulation sequences

identify all promoters containing a transcription factor binding site

kinases have well characterised homology with…domains

catalytic

genome analysis allows inference of…

the function of uncharacterised kinases by family studies

genome analysis allows identification of…

conserved and organism specific families of protein kinases

several years ago, how many yeast ORFs had no experimentally determined function

~3700

by computational analysis, how many yeast ORFs had some similarity or motif suggesting possible functions

~2200

how many ORFs did we not understand whatsoever and why is this

~1500

• outstripped our ability to do the required experiments

what are the major issues of medical genomics

• analysis of gene function

• genetic variation

• ethics

• genetic counselling

• developing treatments and approaches utilising this information