NUCLEAR ARCHITECTURE

FÁTIMA MANZANO NÚÑEZ

Sequencing projects

Elucidation of the cellular organization of genomes and its impact on genome regulation and activity

Next step

Questions

How is the genome organized in 3D space?

What are the fundamental principles of organization?

What are the molecular mechanisms that give rise to the organization patterns?

What are the physiological consequences of spatial genome organization?

Chromatin organization

Loops

LADs

Fig.1 T. Cremer and C. Cremer. Nature reviews . Vo. 2. 2001

LADslamina associated domains

Low gene expression levels

Nearly 40% of human genome consist on LADs

LADs

Only structuralproperties?

Lars Guelen et al. Nature. Vo. 453. 2008.

DamID technique

Dam (DNA adenine methyltansferase) + Protein

Methylated regions are amplified (PCR) and analyzed by high-throughput techniques

(microarrays or sequencing).

LADs

Study the association of chromatin to any protein

Alejandro Rodriguez et al. Biochemical Society Transactions . Vo. 41, p. 6, 2013.

Study LADs by DamIDLADs

Dam - Lamin B1

Interaction map

a)High levels of LADs alternate with low levels. Sharp transitions.

b) and c) LADs vary in size and are frequently 1 megabase (Mb) in size or larger

Fig. 1. Lars Guelen et al. Nature. Vo. 453. 2008.

Gene density and expression around LAD borders

LADs

Fig. 4. Lars Guelen et al. Nature. Vo. 453. 2008.

LoopsLoops

Structural elements with regulatory functions

Fig. 2. Tom Misteli. Cell. 128, 787–800, 2007

MHC II cluster

Fig.4. Emanuela V. Volpi1 et al. Journal of Cell Science 113, 1565-1576 . 2000.

Chromosome spatial organization

Internal vs.

peripherial Relative

positions

Translocations

Internal vs. peripheral

Change the position of genes during differentiation

Changes in transcriptional activity and gene density

Fig.2 Masahiko Kuroda et al. Journal of Cell Science. 117, 5897-5903, 2004.

Relative position

Fig. 3. Tom Misteli. Cell. 128, 787–800, 2007

Functional consequences of Global chromatin organization

Separate chromosomes into physical proximity

sharing transcription sites.

Separate chromosomes into physical interaction corregulating gene loci.

Trans-regulation.

Relative position important determinant of function

Translocations

Tissue-specific proximity of chromosomes correlates with tissue-specific translocation frequency

Fig. 3. Tom Misteli. Cell. 128, 787–800, 2007Fig.1. Luis A Parada et al. Genome Biology, Vo. 5, 7, R44. 2004

Tissue specific chromosomes organization

Conclusions Such areas that are nearly the lamina have low

gene density and transcription. Loops are structural elements with regulatory

functions. The organization of the genome is related with its

regulation. The organization of the genome depends of the

genes that are active or inactive, so also of the kind of cell and its differentiation level.

The organization can follow the internal vs. peripheral pattern or the relative position model.

Translocations have tissue-specific frequency.

Bibliography1. Alejandro Rodriguez et al. The links between chromatin spatial organization and biological

function. Biochemical Society Transactions . Vo. 41, p. 6, 2013.2. Emanuela V. Volpi1 et al. Large-scale chromatin organization of the major histocompatibility

complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. Journal of Cell Science 113, 1565-1576 . 2000.

3. Lars Guelen et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature. Vo. 453. 2008.

4. Luis A Parada et al. Tissue-specific spatial organization of genomes. Genome Biology, Vo. 5, 7, R44. 2004.

5. Masahiko Kuroda et al. Alteration of chromosome positioning during adipocyte differentiation. Journal of Cell Science. 117, 5897-5903, 2004.

6. Shlomit Farkash-Amar et al. Systematic Determination of Replication Activity Type Highlights Interconnections between Replication, Chromatin Structure and Nuclear Localization. Plos one. Vo. 7 , 11, 2012.

7. T. Cremer and C. Cremer. Chromosome territories nuclear architecture and gene regulation in mammalian cells. Nature reviews . Vo. 2. 2001.

8. Tom Misteli. Beyond the Sequence: Cellular Organization of Genome Function. Cell. 128, 787–800, 2007.