IEA - Expressão gênica: é complexo mesmo ou só estão faltando partes?

Gene Expression: is it really complex or is it

just missing parts ?

USP – University of Sao Paulo

LabPIB – Laboratório de Processamento de Informação Biológica http://labpib.fmrp.usp.br

Prof. Dr. Vênciorvencio@usp.br

Who are we ?

Who are we ?

Complex Systems

Complex Systems

Complex Systems

2 + 2 > 4

2 + 2 > 4

2 + 2 = 5

1) Do we know all parts to sum them up ?

2) What are the interactions among parts ?

Joyce & Palsson, Nat Rev Mol Cell Biol (2006)

Biological Motivation

2012 update on Joyce & Palsson, Nat Rev Mol Cell Biol (2006)

RNA-protein interaction

RNA-RNA interaction

structuromics

ncRNA

Biological Motivation

RNA-protein interaction

RNA-RNA interaction

ncRNA

Biological Motivation

2012 update on Joyce & Palsson, Nat Rev Mol Cell Biol (2006)

structuromics

RNA-protein interaction

RNA-RNA interaction

ncRNA

Biological Motivation … today

2012 update on Joyce & Palsson, Nat Rev Mol Cell Biol (2006)

structuromics

Bonneau et al., Cell (2007)

from wikipedia's “halobacterium” entry

~ 5 μm

from webmineral.com Mineralogy Database's “halite” entry

~ 1 cm

Bonneau et al., Cell (2007)

Bonneau et al., Cell (2007)

Bonneau et al., Cell (2007)

2 + 2 = 5

1) Do we know all parts to sum them up ?

2) What are the interactions among parts ?

Bonneau et al., Cell (2007)

2 + 2 = 5

1) Do we know all parts to sum them up ?

2) What are the interactions among parts ?

No, ncRNAs are still missing

Some are known,

but protein-RNA are missing

ncRNA discovery by high-throughput sequencing RNA-seq

Wang et al., Nat Rev Gen (2009)

ncRNA discovery by high-throughput sequencing RNA-seq

Felipe ten Caten, Diego Martinez, Lívia Zaramela - PhD Candidates

ncRNA discovery by high-throughput sequencing RNA-seq

Felipe ten Caten, Diego Martinez, Lívia Zaramela - PhD Candidates

ncRNA discovery by high-throughput sequencing RNA-seq

There is a transcript

but there is no protein

Protein-RNA interaction discovery by RIP-Seq

Lívia Zaramela - PhD Candidate

Very similar to known

Chip-seq but for RNA

interactions

from wikipedia's “ChIP-sequencing” entry

Protein-RNA interaction discovery by RIP-Seq

Marcos Abraão - PhD Candidate

Support Vectors

So... back to the original question

is it really complex or is it just missing parts?

So... back to the original question

is it really complex or is it just missing parts?

Probably both.

http://www.systemsbiology.org.au/

USP – University of Sao Paulo

LabPIB – Laboratório de Processamento de Informação Biológica http://labpib.fmrp.usp.br

Prof. Dr. Vênciorvencio@usp.br

Thank you for your attention!

USP – University of Sao Paulo

LabPIB – Laboratório de Processamento de Informação Biológica http://labpib.fmrp.usp.br

Prof. Dr. Vênciorvencio@usp.br

“ Simplicity is a great virtue but it requires hard work to

achieve it and education to appreciate it. And to make

matters worse: complexity sells better ”

-- E. Dijkstra.