The Myth The Myth of Junk of Junk DNADNA

Dr. Raymond G. BohlinFellow, Discovery InstituteProbe Ministries

Non-Protein Coding DNA 2001 – 65,000 mRNAs, but only 4% from

exons 2002 – ENCODE found 11,655 non-

protein-coding RNAs 2005 – most of mammalian DNA is

transcribed 2008 – both strands used in

transcription and frequently from overlapping segments

Evolutionary predictions If a sequence is non-functional, then

over time the sequence should degrade

If a sequence is functional, then the sequence should be conserved by natural selection.

Non-Protein-coding DNA 2005 – non-coding regions in humans

and mice, hundreds of nucleotides long are identical.

Such ultra conserved regions (UCR) regulate developmentally important functions

This is not expected by evolution!

Introns Introns are not just inert spacers

between exons 2005 – intronic sequence is highly

conserved between humans, mice, rats, dogs and chickens – likely functional

Mammalian thyroid receptor gene produces two variant proteins with opposite effects – splicing is regulated by an intron.

Co-expressed loci are clustered together along in the Co-expressed loci are clustered together along in the nucleus, sometimes to “create” genesnucleus, sometimes to “create” genes

Chromosome 2 loop

Chromosome 21 loop

Chromosome 5 loop

Nuclear compartmentwith concentrated

transcription factors

Pseudogenes A pseudogene is a gene that closely

resembles a functional gene but appears to be a useless leftover

Pseudogenes as defined above would be predicted by evolution but difficult under ID

The human genome may have as many as 2000 pseudogenes

pseudogenes Some pseudogenes appear to suppress

expression of the functional gene. The pseudogene can be transcribed and

this transcript binds to the mRNA sequence of the functional gene, thus blocking translation. “RNA interference”

Transcribed pseudogenes serve as “perfect decoys” for RNA degrading enzymes, thus enhancing expression.

Repetitive Sequences About half of the mammalian genome

consists of various types of repetitive sequences.

Long Interspersed Nuclear Elements – LINEs

Short Interspersed Nuclear Elements – SINEs

Endogenous Retroviruses - ERVs

Overview of LINEsLINEs and SINEs have different structural arrangements. The major LINE in the human

genome is the L1. This sequence: Is found throughout Mammalia but is largely taxon-specific Is variously truncated at the 5’ end: ranges from 6-8kb to a few hundred bps in length Has a biased chromosomal distribution: AT-rich chromosome bands and the X-chromosome

(A-rich ‘tail’)

Species-specificregulatory region

ORF1ORF2: Reverse transcriptase

and endonuclease

G-densePu:Py

element

3’ UTR

(A-rich ‘tail’)

Chimp- vs. Human-Specific L1s*C

him

p

Hum

an

271 L1Hs(Ta) elements 252 L1 nonTa elements 490 L1Pa2 elements

0 L1Hs(Ta) elements 210 L1 nonTa elements 476 L1Pa2 elements

5-6 Million Years Ago

*Mills, R.E. et al. 2006. Recently mobilized transposons in the human and chimpanzee genomes. Am. J. Hum. Genet. 78: 671-679.

Remember the layout of a mammalian gene? Many human gene folders are bordered by species-specific repertoires of L1s.

“Gene” 1

“Gene” 2

“Gene” 3 “Gene” 5

“Gene” 4

RNA outputs

L1s L1s

Almost forty percent Almost forty percent of human nuclear of human nuclear matrix attachment matrix attachment elements are L1 elements are L1 sequencessequences.

Overview of SINEs

The major SINE in the human genome is Alu. Unlike LINE-1, Alu (and other SINEs) do not encode enzymes for their mobilization. This sequence:

Is primate-specific—subfamilies are distributed in a taxonomically hierarchical manner (same with LINE-1)

Is ~300 bps in length; consists largely of two dimers (with sequence differences)

Has a biased genomic distribution: GC-rich chromosome bands

(A-rich ‘tail’)

Monomer A

CentralA-stretch

31 bpinsert

Monomer B

Chimp- vs. Human-Specific SINEs*C

him

p

Hum

an864 SVA (SINE) elements 396 SVA (SINE) elements

5-6 Million Years Ago

263 AluS elements 1,709 AluYa5 elements 1,290 AluYb8 elements

484 AluY elements

356 AluYc1 elements 261 AluYg6 elements

50 AluS elements 10 AluYa5 elements 9 AluYb8 elements

360 AluY elements

979 AluYc1 elements 1 AluYg6 elements

1167 other Alu elements 233 other Alu elements

*Mills, R.E. et al. 2006. Recently mobilized transposons in the human and chimpanzee genomes. Am. J. Hum. Genet. 78: 671-679.

Any seemingly random aspect of chromosome sequence arrangement is not. A case in point involves endogenous retroviruses (ERVs):

A. Human ERVs contribute 51,197 promoter elements that initiate transcription at various stages (Conley et al., Bioinformatics 24: 1563-1567, 2008).B. Mouse ERVs are highly expressed at the 2-cell embryo stage (and are the earliest to be transcribed in the zygote) and are essential for ontogenesis (Kigami et al., Biology of Reproduction 68: 651-654, 2003).

ERVs In humans ERVs help regulate blood cell

production and metabolizing fat ERVs also regulate gene expression in

the gastrointestinal tract, mammary glands, and testes.

The ERV derived protein syncitin is required for the fusion of fetal and maternal cells in the placenta.

Although less than 2% of genomic DNA in many Although less than 2% of genomic DNA in many vertebrates (e.g., mammals) can be placed in the vertebrates (e.g., mammals) can be placed in the traditional “gene” category, nearly all sequences are traditional “gene” category, nearly all sequences are transcribed in a cell- and tissue-specific manner.transcribed in a cell- and tissue-specific manner.

DNA as Computer Information carried by DNA is

bidirectional, multi-layered, and interleaved.

Repetitive elements format and punctuate the information at different scales

Cells can write codes onto non-coding DNA so phenotype is not always equal to genotype

“metaprogramming” – Cornell Conf.