Natural biological memory systems

Summary
Nature use different specific mechanisms to write, store, and read memory.Here I plan to make an inventory of these mechanisms, to finally highlight the common motifs and architecture that could successfully be used to build a reliable genetic memory device.

Background
By memory, we intend a mechanism allowing information storage and retrieval.

In general terms, memory in biological systems can be described as the capacity of the system to maintain a state induced by a particular event, even when this causative event has disappeared.

Depending the timeframe during which the state is maintained, we can talk about short- or long-term memory. At least for long-term memory, memory set up implies switching from one stable state to another. Thus, althought the existence of many different types of switches, most of the memory systems can occupy two (bistables) or more (multistables) stable states without intermediary state.

this part to be continued...

=Basic classification of memory mechanisms=

Genetic
Refers to the information stored in the DNA sequence itself.


 * mutation
 * insertion
 * case of integrases
 * orientation
 * case of invertases
 * recombination
 * Double strand breaks (DSBs) repair
 * Gene conversion(meiosis)
 * crossing-over (meiosis)

Epigenetic
Refers to information stored by others means than DNA sequence itself. An epigenetic change in gene expression can be described as "... a change in the state of expression of a gene that does not involve a mutation,but that is nevertheless inherited in the absecnce of signal (or event) that initiated this change" (Ptashne, 2007).

  Different kinds of network motifs can be used to retain the state induced by a stimulus. Positive or auto-positive feedback between signalling proteins is one recurrent motif encountered in natural memory systems.Once activated, the system autostimulates and then maintain the induced state. Systems comprising two genes repressing the expression of each other are also widely encountered.
 * '''DNA methylation
 * '''Histones post-translational modifications?
 * proteine structure (prions proteins) url
 * Feedback loops

However, the network wiring motif by itself is not sufficient to make an efficient switch. Various parameters like cooperativity make that a given biological system can exhibits multistability.

Examples

 * Brain memory
 * cell Fate decisions
 * X-chromosome inactivation wiki
 * Short-term memory in yeast cerevisiae PMID 17997309
 * Signaling network motifs involved in the formation of biological memory PMID 17374382

=References:=

A non exhaustive inventory of nature's strategies to write and maintain memory


 * Memory module in Xenopus oocyte maturation (Ferrell's lab) PMID 14647386
 * Phage lambda
 * Memory in microbes:
 * bacterial chemotaxis
 * PMID: 2829179
 * PMID: 2010059


 * PMID: 18324309
 * multistep epigenetic switch: PMID: 17220888
 * immunological memory
 * cell differentiation
 * brain memory circuits

Note: would be nice to add a topic on bistability and multistability URL URL URL

Back to Jerome's notebook 

Back to Endy genetic memory notebook 


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