Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

An analysis of palindromic content in the genicand intergenic regions of bacterial genomes

Oliver Bonham-Carter, Lotfollah Najjar, Ishwor Thapa andDhundy Bastola

10 February 2012

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

Two Objectives:

Objective 1: To determine the distribution of palindromesthroughout bacterial DNA.

Objective 2: To determine the relation of the distribution tothe genome structure.

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

DNA Palindromes are Complementary Words

→ →5′ − cccATcc− 3′

3′ − gggTAgg− 5′

← ←

A =⇒ T, T =⇒ A and C =⇒ G, G =⇒ C

The palindrome AT is the only common word; it is read thesame way from the 5-prime end of both strands.

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

What are Short DNA Palindromes?

4 to 10 bases long and are reverse compliments of themselves.

For word-length, Lp, the total possible is 4Lp2 (number of total

possible in an exhaustive list).

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

What are Restriction Enzymes?

Restriction Enzymes (REs) are proteins that cut at specific,short palindromic sites, along DNA.

Palindromes are naturally found in DNA (bacterial genomes).

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

Methylation: Host’s DNA

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

The Palindromes of New Cells Are Methylated

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

Restriction Enzymes are Part of an Immune Response

A Bacterial Defense System

Palindromes occur naturally in the genomes of invadingpathogens (i.e. virus, phages, etc).

In foreign genomes, they have not been methylated.

In times of a threat, the bacterial host releases restrictionenzymes which target and cleave the invading DNA at specificpalindromic words, killing the attacker.

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

Defense: Attacker’s DNA

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

Motivation: Palindromes Have Biological Significance

Avoidance of Palindromic Content in Bacterial Genomes

1 M. S. Gelfand and E. V. Koonin, 1997

Short palindromes in bacterial genomes occur inbelow-expected counts.Suggested that un-methylated (unprotected) palindromicregions of DNA could be accidentally targeted and destroyedby host’s own immune responses.

2 Eduardo P.C. Rocha, Antoine Danchin, and Alain Viari, 2001

Avoidance is necessary since these palindromes are usuallyfound in invading pathogens (immune response)

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

Where is Palindromic Avoidance Happening?

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

Alternative Hypothesis:

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

Finding Palindromic Avoidance in the Genome Group:

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

Results of the Mann-Whitney Test

Ha: The palindromic content in the intergenic region isstochastically greater than that of the genic region.

The “only” indicates that this number of palindromes is significantonly at the α = 0.01 level.

Our hypothesis is more consistent for shorter palindromes (yellowcells) but less so for larger ones (orange cells). Shorter palindromesare more abundant in the intergenic region.

Palindromic distribution is independent of GC-content of thegenomes.

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

What We Learned and Future Work:

1 Short palindromes do not have a uniform distribution and areunder represented in genic regions of bacterial genomes.

2 Palindromes add instability to the genome which genic regionsseem unable to tolerate.

3 This palindromic distribution across the bacterial genome isthe result of some biological mechanism.

4 This mechanism behind the phenomenon will require biologicalvalidation (studies of DNA folding and structure, etc).

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned

References

M. S. Gelfand and E. V. Koonin, Avoidance of palindromicwords in bacterial and archaeal genomes: a close connectionwith restriction enzymes, Nucleic Acids Res. 1997 June 15;25(12): 2430-2439.

Eduardo P.C. Rocha, Antoine Danchin, and Alain Viari,Evolutionary Role of Restriction/Modification Systems asRevealed by Comparative Genome Analysis, Genome Res.2001. 11: 946-958

Palindromes Outline Methylation Immune Response Motivation Alternative Hypothesis What We Learned