Download The whole issue of chromatin dynamics and Gene positioning

Barkha Bhatnagar
3rd November, 2008
Structure of chromosome
Interphase Nucleus
Chromatin Dynamics
Gene poor chromosomes
Gene rich chromosomes
Schneider et al, 2007
Spector et al, 2003
Example of the model
Branco et al, 2006
Chromatin Dynamics
Interchromosomal interaction
Schneider et al, 2007
Branco et al, 2006
Present model – Interchromosomal network model
Branco et al, 2006
Chromosome territories and nuclear bodies
Schneider et al, 2007
Chromosome territories and nuclear bodies
Kumaran et al, 2008
Main Objective
The dynamic interactions between chromatin and nuclear
bodies or their constituents and the impact of these interactions
on nuclear structure and functions.
Outline
1. Genes on the move (Gene Positioning)
• Nuclear Periphery
• Loop out Chromosomal Territories - Intrachromosomal interaction
• Interchromosomal interaction
2. Estradiol-induced interchromosomal interaction
3. Actin/motor-mediated interchromosomal interactions
4. Gene interactions at nuclear speckles
1. Nuclear Periphery
Nuclear Pore Complex
Active genes are associated with nuclear periphery – eg. - S. cerevisiae,
D. melanogaster, and mammalian cells (β-globin locus during erythroid maturation)
Interaction of β-globin locus and Pol II in erythroid maturation
Changing nuclear landscape with erythroid differentiation
Ragoczy et al, 2006
2. Loop out chromosome territories – short distance
Example – mouse erythroid progenator cells
Schneider et al, 2007
Fraser et al., 2007
2. Loop out chromosome territories – long range (V/J interaction of Ig)
2. Loop out chromosome territories – long range (T cell receptors - β and αδ)
3. Interchromosomal interaction – loci present on different chromosomes
Interaction of Th2 cytokine locus and the promotor of IFN-γ gene
LCR – locus control region
Schneider et al, 2007
3. Interchromosomal interaction – long distance (enhancer)
• Olfactory genes – long distance chromatin interaction
• 1,300 genes comprise of receptor family and only one olfactory receptor
is expressed in a particular neuron and expression is mono-allelic
• Choice of specific olfactory receptor gene to be expressed in a given
neuron is mediated by interaction between the gene and the enhancer
element, called H element
Enhancer – short region of DNA that can bound
with proteins to enhance transcription
Cis and trans interactions of the H enhancer and olfactory-receptor genes
Fraser et al., 2007
Fraser et al., 2007
3. Interchromosomal interaction – genome inprinting
Genome imprinting – genetic phenomenon by which certain genes are
expressed in a parent-of-origin-specific manner
CTCF – Insulator are cis acting DNA elements that prevent the enhancer
and promotor interaction when present between them
CTCF – chromatin insulator protein, possibly present during interphase
ICR region – imprinting control region
E – enhancer, Igf2 – insulin like growth factor 2, H19 – gene for non-coding RNA
Outline
1. Genes on the move (Gene Positioning)
• Nuclear Periphery
• Loop out Chromosomal Territories - Intrachromosomal interaction
• Interchromosomal interaction
2. Estradiol-induced interchromosomal interaction
3. Actin/motor-mediated interchromosomal interactions
4. Gene interactions at nuclear speckles
Article
RETRACTED: Nuclear Receptor-Enhanced Transcription Requires Motor- and
LSD1-Dependent Gene Networking in Interchromatin Granules
Esperanza Nunez1, 2, 7, Young-Soo Kwon4, 7, Kasey R. Hutt1, 5, Qidong Hu1, Maria Dafne
Cardamone1, 6, Kenneth A. Ohgi1, Ivan Garcia-Bassets1, David W. Rose3, Christopher K. Glass4, Michael
G. Rosenfeld1, , and Xiang-Dong Fu3, ,
SUMMARY
This article has been retracted at the request of the authors. Please see Elsevier Policy on Article Withdrawal
(http://www.elsevier.com/locate/withdrawalpolicy).Reason: Shortly after publication of this paper, concerns were
brought to the authors' attention regarding similarities in the plots quantifying the interchromosomal distances
derived from FISH images. The authors undertook extensive investigation and confirmed a series of data
duplications and transversions in the original dataset. Although they continue to believe the central conclusions
of the paper based on confirmation and further studies by other scientists in their laboratories, given the extent
of errors in the published plots, the authors feel compelled to retract the paper. They apologize to the scientific
community for any confusion these errors may have caused and wish to sincerely thank the colleagues who
communicated this problem to them in recent weeks.
• Estradiol – estrogen (sex hormone), receptor ER-α
• Purpose of experiment – to determine whether ligands for nuclear
receptors induce interchromosomal interactions critical for specific
programs of gene expression
TFF1 gene regulated by ER-α
TFF1 – Trefoil factor 1, associated with breast cancer, located on chr 21
GREB1 – Gene regulated in breast cancer 1 protein, located on chr 2
SPECKLES – Interchromatin granule cluster, contain splicing factor
• E2, steroid hormone in
MCF7 and HMECs cell lines
• 2 - 60 minute – interaction
between TFF1 and GREB1
• 50% monoallelic and 50%
diallelic
• Non-homologous
• Specific interchromosomal interactions in response to nuclear hormone
signaling
Question - How rapidly such signals are transduced resulting in the
coordinate movement and association of these genes
- How intranuclear signaling cascade is controlling the
movement and subsequent interaction of TFF1 and GREB1
• Hypothesize – Involvement of actin / motor elements
• Use actin inhibitors, siRNA technique to block functioning of actin/myosin
– which abolished E2 induced interchromosomal interactions
Confirms – role for actin/myocin in ER-α-dependent interchromosomal
interaction and gene movement
Where are interacting genes localized ?
Gene interaction at nuclear speckles
Speckles – rich in pre-RNA splicing factors, many other proteins involved
in gene regulations
Immuno-DNA FISH analysis by using 20 different probes to ER-α
targeted genes and also marker for speckle protein (anti-SC35)
- ER-α target genes colocalized with speckles upon E2 induction
Conclusion 1- The whole issue of chromatin dynamics and Gene positioning - is a deep
understanding of chromatin interaction through its element in the particular
nuclear structure and its effect in determining the epigenetics of the Gene
expression .
2-Nuclear Organization and Function are co-ordinated and intimately linked to
each other- Long distance Interchromatin interaction and intrachromatin
interaction are the result of a co-ordinated movement through motor protein to
bring two long distance genes in the certain nuclear domain ( like ie speckle) to
enhance their gene expression .
3-Nuclear bodies like speckle are active center for transient chromosomal
interaction- Nuclear bodies provide a clear platform (a particular Nuclear domain)
where the chromosomal interaction can perform its co-ordinated event like mRNA
transcription and RNA processing much faster by using concentrated resources .
4- Nuclear periphery and nuclear domain interact with extra loop of chromatin ,
out of its chromosomal territory to bring out certain gene expression, to share the
transcriptional machinery, to perform recombination to re-arrange the genes.
Thanks for your attention
http://en.wikipedia.org/wiki/Fluorescent_in_situ_hybridization