CBG.

02: Genomes ON THE IMMORALITY OF TELEVISION SETS:
“FUNCTION” IN THE HUMAN GENOME
ACCORDING TO THE EVOLUTION-FREE GOSPEL OF
ENCODE PROJECT WRITE EULOGY FOR JUNK ENCODE (Dan Graur)
DNA
- less than 10% of the genome is evolutionarily
conserved through purifying selection
- human DNA has 3 billion bases - according to ENCODE, a biological function can be
- instead of the expected 100,000 genes, the initial maintained indefinitely without selection, which implies that at
analysis found about 35,000 and that number has since been
least 80-10=70% of the genome is perfectly invulnerable to
whittled down to about 21,000
deleterious mutations, either because no mutation can ever
- 80% of the human genome serves some purpose,
occur in these “functional” regions or because no mutation in
biochemically speaking: these regions can be deleterious
- specify landing spots for proteins that influence - problems in ENCODE logic:
gene activity o seldom used “causal role” definition of
- strands of RNA with myriad roles biological function and then applying it inconsistently to
- places where chemical modifications serve to
different biochemical properties
silence stretches of our chromosomes
o logical fallacy “affirming the consequent”
- a gene’s regulation is far more complex than
o failing to appreciate the crucial difference
previously thought, being influenced by multiple stretches of between “junk DNA” and “garbage DNA”
regulatory DNA located both near and far from the gene o using analytical methods that yield biased
itself and by strands of RNA not translated into proteins errors and inflate estimates of functionality
(=noncoding RNA) o favouring statistical sensitivity over specificity
- 11,224 DNA stretches are classified as pseudogenes, o emphasizing statistical significance rather than
“dead” genes now known to be active in some cell types or
the magnitude of the effect
individuals
- in biology, there are 2 main concepts of function:
- there are many “genes” out there in which DNA o “selected effect”: function of a trait is the
codes for RNA, not a protein, as the end product effect for which it was selected, or by which it
- various cell genes home in on different cell is maintained
compartments, as if they have fixed addresses where they o “causal role”: historical and non-evolutionary:
operate: some go to the nucleus, some to the nucleolus and for a trait Q to have a “causal role” function, G,
some to the cytoplasm
it is necessary and sufficient that Q performs G


GINGERAS: the fundamental unit of the genome and the
(ex:) TATAAA – maintained by natural selection to bind a
basic unit of heredity should be the transcript – the piece of transcription factor; a mutated sequence, resembling this one,
RNA decoded from DNA- and not the gene also binds the transcription factor, but does not result in
transcription (no adaptive or maladaptive consequence); hence,
- 5% of the human genome is conserved across the second sequence has no selected effect function, but its
mammals
causal role function is to bind a transcription factor
- DNA’s bases function in gene regulation through

their interactions with transcription factors and other
- from an evolutionary viewpoint, a function can be
proteins; assigned to a DNA sequence if and only if it is possible to
- 8% of the genome falls within a transcription factor destroy it; unless a genomic functionality is actively protected by
binding site, a percentage that is expected to double once selection, it will accumulate deleterious mutations and will cease
more transcription factors have been tested to be functional
- the fact that sometimes it is difficult to identify
selection should never be used as a justification to ignore
selection altogether in assigning functionality to parts of the
human genome
- the surest indicator of the existence of a genomic
function is that losing it has some phenotypic consequence for
the organism
- functional regions of the genome should evolve more
slowly and be more conserved among species than non-
functional ones
- Ward and Kellis confirmed that approx.. 5% of the
genome is interspecifically conserved and an additional 4% of
the human genome in under selection
- According to ENCODE:
o 74.7% of the genome is transcribed
o 56.1% is associated with modified histones

and because the IN HUMANS FOR RECENTLY ACQUIRED molecular process generating extra DNA outpaces those getting REGULATORTY FUNCTIONS rid of it. that are recognised by a group of transcription factors called coding genes GATA2. ENCODE: THE ROUGH GUIDE TO THE HUMAN similar selective pressures act in humans and across GENOME mammals . regions that do not overlap with active ENCODE seemingly endless stream of “genome-wide association elements and inactive chromatin states show lower studies” (GWAS). there is interest. They also showed that . suggesting that some loss of constraint 60 percent more likely to lie within functional. mammalian conserved regions lacking ENCODE . . mobile elements correspond to both? Yes. biochemically active. geneticists have run a .“We’re now working with lots of different disease o the belief that “future potential” constitutes “a biologists looking at their data sets. ZHOU. Some of the rest make intuitive genome size sense. especially in promoters and enhancers. but are typically devoid of function: “Literally. The something to do with function team found five SNPs that increase the risk of Crohn’s. evolve . The ENCODE team have mapped all of these to activity show reduced human constraint relative to active their data. conserved across mammals. Imagine a massive table. a substantial factor of human constraint lies outside mammalian-conserved regions . “In some function” sense. Others are head-scratchers. They found that just 12 percent of the SNPs lie regions. mRNA splice sites and regulatory elements. and is subject to additional elements evolve neutrally or confer a lineage- purifying selection specific fitness advantage . selection GWAS studies are working from disease in. within protein-coding areas.2% is found in open-chromatin areas regions. transcription is fundamentally a stochastic process understanding how they affect our risk of disease. less than 2% of the histone modifications may have . “It was . 2004)) ENCODE study.” Where they against excess genome is extremely efficient due to the meet. BRENNER: differentiated between “junk DNA” and “garbage DNA”. ENCODE is working form the genome out. 2003.” says Birney. between replication time and. these also show higher primate divergence relative compared to random SNPs. “That wasn’t something that the Crohn’s disease . nematode Caenorhabditis elegans has 20.517 protein. I was in the room [when they got the result] and I . Across . the nunfunctional DNA .” says Birney. Take Crohn’s disease. This suggests o 8.” says Birney. and . mammalian conservation suggests that aprox. in the majority of known bacterial species. the team have identified 400 enormous effective population sizes. Lots. human constraint correlates with mammalian conservation. Are there hotspots? Are there SNPs that . lack coding went: Yes!” potential due to the presence of disruptive mutations.” In other words. Down the left side are all very rapidly and are mostly subject to no functional constraint). and provides many fresh leads for .6% consists of methylated CpG dinucleotides different genes. So far. “Suddenly we’ve o a lack of knowledge of he original and correct made an unbiased association between a disease and a piece sense of the term of basic biology. . and many of them are new. but more than 80% is transcribed. They have thrown up a long list of SNPs – variants provide a more accurate neutral reference than repeats that at specific DNA letters—that correlate with the risk of can have exapted functions different conditions. o 15. suggesting that they may of disease. it’s a new lead to follow up o the belief that evolution can always can rid of on. or associated with chromatin states suggestive of regulatory functions ENCODE HYPE . indifferent DNA refers to DNA sites that are functional.5% binds transcription factors that many of these variants are controlling the activity of o 4. Of these. transcribed. introns (some human introns harbour regulatory the top are all the possible cell types and transcription sequences TISHKOFF. classes of sequences that are known to be abundantly one of those too good to be true moments. pseudogenes (up to 1/10 transcribed. attempting to understand the genetic basis constraint than ancestral repeats. as well as being useless. a substantially larger portion is but show no evidence of selection against point mutations. generation time are correlated with 50 and 100 were predictable. For the last decade. and the fact that such hotspots that are worth looking into. 2006 as well as sequences that produce factors (proteins that control how genes are activated) in the small RNA molecules (HIROSE. . although only 5% of the human genome is . however. bound by A SLIGHTLY DIFFERENT RESPONSE TO TODAY’S a regulator. hence. 5% of “PURPOSE IS THE ONLY THING EVOLUTION CANNOT PROVIDE” the human genome is conserved due to noncoding and regulatory roles. misconceptions in common objections to “junk DNA” biologists had on their radar. the excess DNA in our genome is junk and it is there EVIDENCE OF ABUNDANT PURIFYING SELECTION because it is harmless. the diseases that people have done GWAS studies for. non-coding predates human-macaque divergence . a type of bowel disorder. the disease-associated ones are to active regions. suggesting recent loss in function and activity. is deleterious. while . raising the question of whether the deletion of these sites.

in MMU3 desert. protein-coding constraint occurs primarily in conserved regions. this suggests that mutations outside conserved elements play important roles in both human evolution and disease MEGABASE DELETIONS OF GENE DESERTS . some large-scale deletions of the non-coding DNA . the functional importance of the roughly 98% of the . genome-wide association studies suggest that 85% of disease-associated variants are noncoding. the heterozygous mice appeared phenotypically normal . phenotypic parameters measures in the homozygous deletion mice. the deletions weren’t lethal in embryons because of approx. the method by which nucleosomes solve these opposed needs is not well understood. a collection of repar enzymes corrects mammalian genomes not corresponding to protein coding chemical changes inflicted on the strands by environmental sequences remains largely undetermined insults . nearly RESULT IN VIABLE MICE all of our cells) contain a copy of this genome. nucleosomes protect the delicate strands (=gene deserts) can be well tolerated by any organism from physical damage . even though the strength of human constraint is higher in conserved elements . beta-galactosidase expression harm. polymerases must be allowed access to the DNA. encoded in 3 billion bp of DNA . both to transcribe mRNA for building new proteins and to replicate the DNA when the cell divides. a fraction similar to the proportion of human constraint that we estimate lies outside protein-coding regions. whereas regulatory constraint is primarily lineage-specific.243 human-mouse conserved non-coding elements . molecular level impact: only 2 out of the 108 . nucleosome must be stable. as proposed during mammalian radiation . . compared with controls: o post-natal survival rates for 25 weeks o measurable growth retardation o clinical chemistry tests (general and specific plasma parameters) o morphological abnormalities o abnormal growth o tissue degeneration o organ mass was similar in both groups of deletion mice and their wild-type littermates . on the other hand. the boundaries for the deletions permitted proximate regulatory elements nearby the flanking genes to remain intact . but may involve a partial unfolding of the DNA from around the . quantitative assays revealed detectable alterations in levels requiring it to perform 2 opposite functions simultaneously: of expression: Prkacb reduced in the heart and Rpp30 on one hand. the job of the nucleosome is paradoxical. almost half of human constraint lies outside NUCLEOSOME mammalian-conserved regions. reduced in the brain sheltering structures that compact the DNA and keep it from . deletion of a gene desert mapping to mouse chromosome 3 and in chromosome 19 (with no evidence of transcription) à contain 1. rate 1:2:1 (wild-type : heterozygous : mutant homozygous) . the homozygous deletion mice for both deletions were viable . this is usually related to the removal of genes with redundancy elsewhere in the genome . each of our cells (or more correctly. forming tight. nucleosome must be labile enough promoter to allow the information in the DNA to be used. although gene inactivation can sometimes fail to result in detectable phenotype.

000 bp restriction fragments. it indicates for each chromosome the whereabouts of genes or other “heritable markers”. single nucleotide polymorphism (SNP) are sites in a which may be circular DNA mole. Bp genomic region of 2 different people. some regions of the genome resist cloning in YACs and others are prone to rearrangements (PRIMER ON MOLECULAR GENETICS) . as the information in the of “foreign” DNA can be inserted into them. reaching out to neighbouring nucleosomes and reinserted into a yeast cell. or clone.168) and Y . the histone proteins are perfectly designed for their jobs. but they shed light on chromosome structure and fragments.mosomes constructed from yeast or bacterial genomic DNA. sequences that mark the ends encircled by 2 loops of DNA. for instance. of the same fragment of human particular genes more accessible to polymerases. one loop at a time.ment length. that interact strongly with the negatively-charged phosphate groups of the DNA. The result is a colony of yeast cells. however.” The classic example is the cloning vector. to 250 million bp then. on the other hand. largest known human gene is dystrophin 2. repeat sequences are thought to have no direct different genomic sequences. scientists believe that human genome has at least 10 mil SNPs . with their subtly . and it even shares in genetic terms. the nucleus contains cell division. . . the average gene is 3. as if it were part of the yeast’s normal complement regulatory enzymes that chemically modifies these tails to of chromosomes.4 mil. chromosome 1 has the most genes (3. the cell makes containing a copy.some is then nucleosome. and sequences required for chromosome are not completely globular like most other proteins à they separa- have long tails. which reproduces the YAC during binding them tightly together. The characteristic all these vectors share is that fragments . sequences that initiate replication. nucleosomes also modify the activity of the the host reproduces itself. with distances measured in centimorgans (=measure of recombination frequency) à the closer 2 genes are on a single chromosome the less likely they are to get split up during genetic recombination à when they are close enough that the chances of being separated are only 1/100 they are said to be separated by a distance of 1 centimorgan .cules derived from bacteria genome where individuals differ in their DNA sequence. each chromosome is a physically separated specific recognition sites. which then produce different patterns when dynamics sorted according to size . which comprises nearly a quarter of their .a third necessary tool is some means of DNA chromosome has the fewest (344) “amplification. when digested with a particular restriction enzyme. the surface of the octamer is decorated with positively charged AA. whereby the DNA is read inserted DNA is replicated along with the rest of the vector as . the tails extend outward from the compact of human DNA. usually 4 or 6 nucleotides long molecule of DNA that ranges in length from about 50 million . is constructed by assembling the essential genes that they store: each nucleosome is composed of 8 functional parts of a nat. HUMAN GENOME PROJECT (TO KNOW OURSELEVES) genetic linkage map: based on careful analyses of human inheritance patterns. in this way. the human genome is not so very different from physical maps: distances between features are measured not that of chimpanzees or mice. or YAC. but in “real” physical units (base pairs) many common elements with the genome of lowly fruit fly . often by a single base . of the chromosomes. A yeast artificial chromo. can yield dissimilar sets of functions. restriction enzyme: cleave dsDNA molecules at . each weaken their interactions. DNA from the same . This engineered chromo.ural yeast chromosome—DNA “histone” proteins bundled tightly together at the centre.some.nucleosome. this serves to glue the DNA strand to the protein core. or from bacteriophages (viruslike parasites of bacteria). identical segments of human DNA yield identical sets of . allowing DNA their particular information to be copied and used to build new proteins . so much so that histones are nearly identical in all non-bacterial organisms.tion during cell division—then splicing in a frag. even slight modifications can be lethal. or artificial chro. the histone proteins.