corso di Genomica a.a. 2010-2011lezione 23-24

• laurea magistrale Biotecnologia Industriale

Martedì 21 dicembre 2010

aula 6Aorario : 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 omeoticiVertebrate 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.

AbstractThe 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 RAR-responsive elementsReferences1. 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 proteinsCell. 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 Polycomb-dependent regulatory region with similarities to Drosophila PREs, indicating conservation in the mechanisms that target PcG function in mammals and flies.

genomica e riprogrammazionele 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 crescereanche 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 celluleCell Res. 2008 Dec;18(12):1177-89. Yamanaka factors critically regulate the developmental signaling network in mouse embryonic stem cells. Liu X, Huang J, Chen T, Wang Y, Xin S, Li J, Pei G, Kang J. Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. Abstract Yamanaka factors (Oct3/4, Sox2, Klf4, c-Myc) are highly expressed in embryonic stem (ES) cells, and their over-expression can induce pluripotency in both mouse and human somatic cells, indicating that these factors regulate the developmental signaling network necessary for ES cell pluripotency. However, systemic analysis of the signaling pathways regulated by Yamanaka factors has not yet been fully described. In this study, we identified the target promoters of endogenous Yamanaka factors on a whole genome scale using ChIP (chromatin immunoprecipitation)-on-chip in E14.1 mouse ES cells, and we found that these four factors co-occupied 58 promoters. Interestingly, when Oct4 and Sox2 were analyzed as core factors, Klf4 functioned to enhance the core factors for development regulation, whereas c-Myc seemed to play a distinct role in regulating metabolism. The pathway analysis revealed that Yamanaka factors collectively regulate a developmental signaling network composed of 16 developmental signaling pathways, nine of which represent earlier unknown pathways in ES cells, including apoptosis and cell-cycle pathways. We further analyzed data from a recent study examining Yamanaka factors in mouse ES cells. Interestingly, this analysis also revealed 16 developmental signaling pathways, of which 14 pathways overlap with the ones revealed by this study, despite that the target genes and the signaling pathways regulated by each individual Yamanaka factor differ significantly between these two datasets. We suggest that Ya manaka factors critically regulate a developmental signaling network composed of approximately a dozen crucial developmental signaling pathways to maintain the pluripotency of ES cells and probably also to induce pluripotent stem cells.

engineered embrionic stem cells ES

the magic Brewby Janet Rossant,University of Torontojanet.rossant@sickkids.ca news and views, Nature vol 448, 19 July 2007, pp 260-262 QuickTime™ e un

decompressore TIFF (LZW)sono necessari per visualizzare quest'immagine.

Yamanaka factorsNature. 2007 Jul 19;448(7151):318-24. Epub 2007 Jun 6. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedlinger K, Bernstein BE, Jaenisch R. Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA. Comment in: * Nature. 2007 Jul 19;448(7151):260-2. Abstract Nuclear transplantation can reprogramme a somatic genome back into an embryonic epigenetic state, and the reprogrammed nucleus can create a cloned animal or produce pluripotent embryonic stem cells. One potential use of the nuclear cloning approach is the derivation of 'customized' embryonic stem (ES) cells for patient-specific cell treatment, but technical and ethical considerations impede the therapeutic application of this technology. Reprogramming of fibroblasts to a pluripotent state can be induced in vitro through ectopic expression of the four transcription factors Oct4 (also called Oct3/4 or Pou5f1), Sox2, c-Myc and Klf4. Here we show that DNA methylation, gene expression and chromatin state of such induced reprogrammed stem cells are similar to those of ES cells. Notably, the cells-derived from mouse fibroblasts-can form viable chimaeras, can contribute to the germ line and can generate live late-term embryos when injected into tetraploid blastocysts. Our results show that the biological potency and epigenetic state of in-vitro-reprogrammed induced pluripotent stem cells are indistinguishable from those of ES cells.