corso di Genomica a.a. 2010-2011
lezione 23-24
• laurea magistrale Biotecnologia
Industriale
Martedì 21 dicembre 2010
aula 6A
orario : Martedì ore 14.00 - 16.00
Giovedì ore 13.00 - 15.00
D. Frezza
dinamica del genoma
il genoma è lo stesso i tessuti differenziano,
la regolazione, è la stessa dei procarioti e poi non è più
cambiata?
il genoma eucariote a parte la diploidia cosa ha di
diverso?
è solo più grande o è anche più complesso?
la parte di genoma non trascritto e non tradotto come
funziona e a cosa serve?
modificazioni epigenetiche
con epigenetica si tende a includere molte cose
escluderei i cambiamenti conformazionali ed i legami con
proteine come fattori di trascrizione e altri tipi di proteine
non istoniche
è ancora molto oscuro il funzionamento del genoma non
codificante a parte le regioni limitrofe con strutture
regolative note
le strutture regolative più ampie sono le Locus Control
Region vicine ai cluster es. Globine, Ig
i cluster dei geni omeotici
Vertebrate Hox gene regulation: clustering and/or colinearity?
Denis DubouleE-mail The Corresponding Author Department of Zoology and Animal
Biology, University of Geneva, Sciences III, Quai Ernest Ansermet 30, 1211 Geneva 4,
SwitzerlandAvailable online 19 April 2002.
Abstract
The relationship between the clustered organization of vertebrate Hox genes and their
coordinate transcription in space and time is still lacking a convincing mechanistic
explanation. Recent work on the regulatory interactions within Hox complexes
suggests some reasons why these genes have remained clustered. Although these
results do not address the puzzling issue of colinearity directly, they nevertheless add
novel important input to the debate.
Abbreviations: ES embryonic stem; RAR retinoic acid receptor; RAREs RARresponsive elements
References
1. R Krumlauf , Hox genes in vertebrate development. Cell 78 (1994), pp. 191–200.
2. E Lewis , A gene complex controlling segmentation in Drosophila. Nature 276
(1978), pp.
policomb proteins
Cell. 2010 Jan 8;140(1):99-110.
A region of the human HOXD cluster that confers polycomb-group responsiveness.
Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE.
Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
Abstract
Polycomb group (PcG) proteins are essential for accurate axial body patterning
during embryonic development. PcG-mediated repression is conserved in
metazoans and is targeted in Drosophila by Polycomb response elements (PREs).
However, targeting sequences in humans have not been described. While
analyzing chromatin architecture in the context of human embryonic stem cell
(hESC) differentiation, we discovered a 1.8kb region between HOXD11 and
HOXD12 (D11.12) that is associated with PcG proteins, becomes nuclease
hypersensitive, and then shows alteration in nuclease sensitivity as hESCs
differentiate. The D11.12 element repressed luciferase expression from a reporter
construct and full repression required a highly conserved region and YY1 binding
sites. Furthermore, repression was dependent on the PcG proteins BMI1 and EED
and a YY1-interacting partner, RYBP. We conclude that D11.12 is a Polycombdependent regulatory region with similarities to Drosophila PREs, indicating
conservation in the mechanisms that target PcG function in mammals and flies.
genomica e riprogrammazione
le cellule embrionali staminali
tessuto adulto può sdifferenziare oppure restano un po’ di
cellule non completamente differenziate per poter rigenerare
il tessuto cicatriziale è connettivale e ricomincia a crescere
anche nel miocardio dove non si formano neoplasie
geni Octr3 e 4, Sox2, Klf4, c-Myc necessari e sufficienti per
dare staminalità e totipotenza a cellule differenziate
in embriologia si parlava di fattori diffusibili, per lo più fattori
di trascrizione, ma il genoma è sempre lo stesso e si può
riattivare e riprogrammare
avanti e indietro
staminalità delle cellule
Cell Res. 2008 Dec;18(12):117 7-89.
Yamanaka factors critically regu late the developmental signali ng network in mouse embryonic stem
cell s. Liu X, Huang J, Chen T, Wang Y, Xin S, Li J, Pei G, Kang J.
Laboratory of Molecular Cell Biology, Institute of Biochemi stry and Cell Biology, Shanghai
Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
Abstract
Yamanaka factors (Oct3/4, Sox2, Klf 4, c-Myc) are highly expressed in embryonic stem (ES) cell s,
and their over-expression can induce pluripotency in both mouse and human somatic cell s,
indicating that these factors regu late the developmental signali ng network necessary for ES cell
pluripotency. However, systemi c analy sis of the signali ng pathways regu lated by Yamanaka factors
has not yet been fully described. In this study, we identifi ed the target promoters of endogenous
Yamanaka factors on a whole genome scale using ChIP (chromatin imm unoprecipitation)-on-chip
in E14.1 mouse ES cell s, and we found that these four factors co-occupied 58 promoters.
Interestingly , when Oct4 and Sox2 were analy zed as core factors, Klf4 functioned to enhance the
core factors for development regulation, whereas c-Myc seemed to play a distinct role in regu lating
metaboli sm. The pathway analy sis revealed that Yamanaka factors coll ectively regu late a
developmental signali ng network composed of 16 developmental signali ng pathways, nine of which
represent earli er unknown pathways in ES cell s, including apoptosis and cell -cycle pathways. We
further analy zed data from a recent study exami ning Yamanaka factors in mouse ES cell s.
Interestingly , this analy sis also revealed 16 developmental signali ng pathways, of which 14
pathways overlap with the ones revealed by this study, despite that the target genes and the
signali ng pathways regulated by each individual Yamanaka factor differ signifi cantly between these
two datasets. We sugges t that Yamanaka factors critically regu late a developmental signali ng
network composed of approxim ately a dozen crucial developmental signali ng pathways to maintain
the pluripotency of ES cell s and probably also to induce pluripotent stem cell s.
engineered embrionic stem cells ES
the magic Brew
by Janet Rossant,
University of Toronto
[email protected]
news and views,
Nature vol 448,
19 July 2007, pp 260-262
Quic kTime™ e un
dec ompres sore TIFF (LZW)
s ono nec es sari per visualiz zare ques t'immagine.
Yamanaka factors
Nature. 2007 Jul 19;448(7151):318 -24. Epub 2007 Jun 6.
In vitro reprogrammi ng of fi broblasts into a pluripotent ES-cell -li ke state.
Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedli nger K, Bernstein BE, Jaenisch
R. Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology,
Cambridge, Massachusetts 02142, USA.
Comm ent in: * Nature. 2007 Jul 19;448(7151):2 60-2.
Abstract
Nuclear transplantation can reprogramm e a somatic genome back into an embryonic epigenetic
state, and the reprogramm ed nucleus can create a cloned anim al or produce pluripotent embryonic
stem cell s. One potential use of the nuclear cloning approach is the derivation of 'customi zed'
embryonic stem (ES) cell s for patient-specifi c cell treatment, but technical and ethical
considerations im pede the therapeutic appli cation of this technology. Reprogrammi ng o f fi broblasts
to a pluripotent state can be induced in vitro through ectopic expression of the four transcription
factors Oct4 (also call ed Oct3/4 or Pou5f1), Sox2, c-Myc and Klf 4. Here we show that DNA
methylation, gene expression and chromatin state of such induced reprogramm ed stem cell s are
simil ar to those of ES cell s. Notably , the cell s-derived from mouse fi broblasts-can form viable
chim aeras, can contribute to the germ li ne and can generate li ve late-term embryos when injected
into t etraploid blastocysts. Our resu lts show that the biological potency and epigenetic state of invitro-reprogramm ed induced pluripotent stem cell s are indistinguishable from those of ES cell s.