1. The Significant Rise of Neuronal
Epigenetics: A Focus on Adult
Neurogenesis
Daniel Tagg - 89555
Final Year Project – Presentation 22 June 2015
2. Epigenetic and Adult Neurogenesis: a
combined history
(Holliday, 2006)
Pre
1900's
M
endel's w
ork on
Heritability
1939W
addington
coins term
'epigenetics'
1969Griffith
discovers DNA
m
ethylation
1974Arber links DNA
m
ethylation
to
gene
regulation
!980Chrom
atin
structure
predicted
!990sonwards
Explosion
in
epigeneticresearch
1998
Erikssonsdiscovery of
adult neurogenesis in
hum
ans provides
conclusive
proof of the
concept &
signals
the
end
of the
previous dogm
a
1979Kapm
an
lim
itsthe
extentofadult
neurogenesisto
the
olfactorybulb
&
dentate
gyrusofrodents
1962Altm
an
providesfirst
experim
entalproofof
adultneurogenesis
1928Cajalproposesthat
neurogenesisislim
ited
to
earlydevelopm
ent
3. • Working definition of epigenetics:
– “Heritable changes in patterns of gene expression that are not encoded in the primary
DNA sequence itself”
• DNA methylation
– Occurs predominantly on cytosine residues , ‘CpG islands’
– Involved in Genomic ‘imprinting’ , X chromosome inactivation
– DNA methyltransferases catalyses this methylation
– Active DNA demethylation in mammals ?
• Chromatin modifications
– 0ver 60 known residue modifications, some repressive, some activating, some both?
– Histone acetyltransferases, methylation…….
– ATP dependent remodelling complexes
• Non coding RNA (ncRNA)
– ‘fine tune’ gene expression networks
– The greatest subset of epigenetic factors.
– Numerous types of ncRNA including; micro (miRNA), short interfering (siRNA)……
Epigenetic regulatory mechanisms
(Kouzarides, 2007)
5. • Within the two defined regions, adult neural stem cells (NSCs) are
present.
• Adult neurogenesis mimics embryological neurogenesis.
• It therefore goes through the following stages:
– Stem cell maintenance and proliferation
– Fate specification
– Migration
– Survival
– Neuronal maturation and integration
• Each one of these stages involve a variety of molecular mediators released
from the ‘neurogenic niche.’
• These signals can be broadly divided into two groups:
– Intrinsic – produced by NSCs and progenitors, (mostly transcription factors)
– Extrinsic – produced by surrounding glia and endothelial cells. Such ‘niche’ signals
include neurotransmitters, growth factors, hormones, and injurious stimuli.
Adult neurogenesis:
Regulated at every step
(Alvarez-Buylla, 2004)
6. • The majority of the evidence gathered for this project was derived through subject
specific searches on PubMed & Web of knowledge/science.
• The following search term was used:
– (neuronal OR neural OR nerve OR neurone OR neurones) AND (epigenetics OR epigenetic OR DNA
AND methylation).
• The number of results for each search were then limited at 5 year intervals and
recorded for the date range of 1940 to 2015 (2011).
• From knowledge of previous bibliographic studies the increase in publications was
predicted to exhibit an exponential relationship of the following standard form:
– Where P = the number of publications, P0 = the starting amount, r is the denoted growth constant, t
represents time, and e is a mathematic constant.
• Thereafter, statistical analysis (SPSS) was performed in order to ascertain the
validity of this model.
Data collection & analysis
10. • Epigenetic regulatory mechanisms are dynamic, and therefore heritability
is an unknown quantity in this regard.
• Adult neurogenesis essentially mirrors the latter stages of embryological
neurogenesis and is controlled by its neurogenic niche.
• Environmental stimuli including neuronal activity can lead to the
transduction of phenotypic changes though specific epigenetic
mechanisms.
• Importantly, epigenetic regulatory mechanisms are involved in every
stage of adult neurogenesis.
• It is useful to view epigenetic modifications as fine tuning mechanisms of
gene transcription.
• Of the epigenetic modifiers ncRNAs are perhaps the most interesting.
Neuronal epigenetics: general and
emerging concepts
11. Future Research Directions &
Questions ?
• To what extent are epigenetic modifications heritable - which specific
modifications & at which gene loci?
• What molecular mediators lead to the occurrence of adult neurogenesis
outside the two consensus regions?
• To what extent do ncRNAs determine the specificity of epigenetic
factors?
• What determines which gene loci are dynamically regulated and what are
the temporal and spatial elements to this?
• What factors are preventing the translation of neuronal epigenetic
research into treatments?
12. (Key references – in order of appearance)
•Holliday, R. 2006. Epigenetics: a historical overview. Epigenetics, 1, 76-80.
•Kouzarides, T. 2007. Chromatin modifications and their function. Cell, 128,
693-705.
•Gould, E. 2007. How widespread is adult neurogenesis in mammals? Nat Rev
Neurosci, 8, 481-8.
•Alvarez-Buylla, A. & Lim, D. A. 2004. For the long run: maintaining germinal
niches in the adult brain. Neuron, 41, 683-6.
•Sun, J., Ming, G. L. & Song, H. 2011. Epigenetic regulation of neurogenesis in
the adult mammalian brain. Eur J Neurosci, 33, 1087-93.
References
Editor's Notes
The aim of my report was discover current knowledge and concepts within the field of epigenetic regulatory mechanisms as applied to adult neurogenesis. In doing so this identifies the questions that still need to be answered and highlights the potential subfields for development, all of which will culminate in treatments for neurological disease.
Quick fly through:
“Genetics and epigenetics unsurprisingly have a common origin with Gregor Mendel, however it was not until 1939 that Conrad Waddington coined………. ”
“the development of the field of Adult neurogenesis has not been without controversy……”
Link:
“Similarly to the field of adult neurogenesis there have been controversies within the conceptual development of the term epigenetics”
“The original definition of epigenetics coined by Conrad Wellington has undergone some significant changes and whilst the working definition of epigenetics is …… I think that it is inadequate…….”
“For those of who are unfamiliar with the structure before you, this is a schematic diagram of the adult rat brain…… and as mentioned previously the views on adult neurogenesis have shifted significantly over the last century. This has meant that the two areas where adult neurogenesis almost certainly occurs is the SGZ and SVZ.”
NSC maintenance and subsequent differentiation, migration and integration are controlled by a variety of so called intrinsic or genetic (Cheng et al., 2005) and extrinsic or environmental cues (Hagg, 2005). Such regulation occurs within specific spatially defined local environments called neurogenic ‘niches’ (Alvarez-Buylla and Lim, 2004). Important stem cell intrinsic regulators include Hedgehog (SHH) signalling which is thought to be involved in the establishment as well as the maintenance of NSCs within both the SVZ and the SGZ (Han et al., 2008 ; Balordi and Fishell, 2007). SHH is but one of many intrinsic factors (Table 3 below) that are involved in the maintenance and subsequent differentiation of NSCs, with other factors such as leukaemia inhibitory factor (LIF) similarly playing a role within the maintenance of the NSC (Bauer and Patterson, 2006). Additionally extrinsic or environmental signals also play an important and overlapping role with intrinsic factors (Pignatelli and Belluzzi, 2010). These extrinsic factors can be grouped into the categories of neurotransmitters, growth factors, hormones and environmental stimuli such as injury (Pignatelli and Belluzzi, 2010).
Link: “Interacting with both the stem cell intrinsic and extrinsic factors are the epigenetic modulators of the above stages of adult neurogenesis, and in order to track the interest within this field I decided to study the change in the fields bilbliome over the last 60 years”
Be Brief
The hypothesised exponential model of growth showed a strong correlation to the observed increase in the extent of the neuronal epigenetic bibliome (p<0.01). A similar relationship was observed for the increase in publications within the larger domain of epigenetics as a whole (data not shown).
What does this signify?
This exponential trend shows a field in its infancy.
Exponential increase in understanding?
It remains to be seen if the exponential increase in the number of publications is being translated into a similar increase in the translation of treatments to the clinic.
Link to next slide:
An area that shows great promise in itself and with regards to translation to the clinic is adult neurogenesis related, epigenetic regulatory mechanisms. The case for this is clear when the potential regenerative potential for adult neurogenesis is considered in the light of epigenetic mechanisms which may regulate this process.
The Polycomb group (PcG) complex of proteins are involved in histone methylation, with B lymphoma Mo-MLV insertion region 1 homolog (mouse) (Bmi1) involved in the catalysis of H3K27 methylation (Alkema et al., 1997). Bmi1 has been shown to moderate the maintenance of NSCs via the cell cycle inhibitor p16, with levels of SVZ derived NSCs decreased in Bmi1 knockout mice (Molofsky et al., 2003). Furthermore the PcG complex has also been linked to repression of the Sox-2 promoter, and as Sox-2 is a fundamental maintainer of ‘stemness’ this is another example of an epigenetic modification in NSC maintenance (Mohn et al., 2008). These processes are also regulated by the antagonistic actions of the trithorax group (TrxG) complex proteins, which play a role in the differentiation of NSCs (Ringrose and Paro, 2007).
Other epigenetic mechanisms also have a role within the proliferation of NSCs. These include the transcriptional co-activator Querkopf (Qkf) which has been shown to exhibit HAT activity (Champagne et al., 1999). Interestingly, Qkf knockout mice have been shown to have reduced proliferation of NSCs within the SVZ (Merson et al., 2006).
The opposing action of the trithorax (TrxG) complex proteins on the actions of PcG leads to transcriptionally active chromatin domains through the maintenance of H3K4 methylation (Ringrose and Paro, 2007). A TrxG member named mixed-lineage leukaemia 1 (MLL1) has been shown to be important in the differentiation of adult NSCs, with its action potentially mediated through the recruitment of an unknown H3K27 demethylase, which is thought to act at certain gene loci such as Mash1, Olig2 and DLX2 (Lim et al., 2009 ; Ma et al., 2010). As a proof of concept, the H3K27 demethylase known as Jmjd3 has been shown to play a role in NSC differentiation (Jepsen et al., 2007).
The miRNA miR-124 is the most highly expressed miRNA within the adult brain (Lagos-Quintana et al., 2002) and its expression is regulated in the process of differentiation from NPCs to mature neurons (Deo et al., 2006). miR-124 specifically targets SOX 9 with downstream signalling leading to the differentiation of NSCs in the SVZ (Cheng et al., 2009).
Histone modifications such as histone deacetylation (HDAC) play a vital role in adult NSC development especially during maturation. The use of GLAST-CreERT2 mice has elucidated the temporally dynamic functions of HDAC2 in adult NSCs, with HDAC2 knockouts resulting in the abnormal maturation and subsequent death of adult neurons within both the SGZ and the SVZ (Jawerka et al., 2010).
DNA methylation is another important epigenetic mechanism whose effects are thought in part to be mediated by methyl-CpG-binding proteins (ref). The significance of this process is highlighted through methyl-CpG-binding protein 1 (Mbd1) mice who exhibit defective adult neurogenesis (Zhao et al., 2003). In this case the action of Mbd1 this is thought to be mediated through the regulated expression of fibroblast growth factor 2 (Fgf2) (Li et al., 2008).
Another ncRNA implicated in the control of differentiation of adult NSCs is the Mbd1 controlled miR-184, which acts as a post transcriptional repressor of Numb-like and therefore a repressor of NSC differentiation (Liu et al., 2010). The methyl-cytosine-binding protein 2 (MeCP2) has been posited to have a role within adult NSCs, with its actions brought about through miR-137 (Zhou et al., 2006 ; Szulwach et al., 2010). miR-137 further represses the translation of a H3K27 methyltransferase called Ezh2 and therefore levels of H3K27 methylation are reduced within cells of the adult SGZ (Szulwach et al., 2010). This is a brilliant example of the interaction between multiple epigenetic mechanisms, and it especially shows how ncRNA can be a core transcriptional orchestrator.
Histone modifications such as histone deacetylation (HDAC) play a vital role in adult NSC development especially during maturation. The use of GLAST-CreERT2 mice has elucidated the temporally dynamic functions of HDAC2 in adult NSCs, with HDAC2 knockouts resulting in the abnormal maturation and subsequent death of adult neurons within both the SGZ and the SVZ (Jawerka et al., 2010).
Epigenetic mechanisms hold a prominent position with regards to transducing environmental effects into changes in gene expression. Neuronal activity within the DG results in either DNA demethylation mediated release of the MeCP2-mSin3A complex bound to brain derived neurotrophic factor (BDNF) promoter IV, (Martinowich et al., 2003) or the calcium influx mediated phosphorylation of MeCP2 and its subsequent release from the same promoter, or both (Zhou et al., 2006). Thus the association of these epigenetic modifications with the neurogenic transcription factor BDNF are thought to be linked to the maturation of adult NSCs. Another epigenetic factor linked to the maturation of NSCs is the protein Gadd25b (Ma et al., 2009). The actions of Gadd25b occur in collaboration with unknown DNA excision-repair mechanisms which have been associated with active DNA demethylation (Ma et al., 2009).
In mice models subjected to electroconvulsive stimulation, the knockout of Gadd45b results in both the decreased dendritic growth of new-born DG cells and stasis of neural progenitors (Ma et al., 2010).
Link:
“The role of epigenetic factors in the integration of developing neurons into the mature neuronal environment has not been extensively researched at present, and further research needs to occur regarding the epigenetic moderation of each stage of adult neurogenesis. However enough research has been collated so that concepts have been formed and subsequently challenged in accordance with the scientific method”
1st point …. and therefore its current definition is ambiguous.
5th point …. multiple epigenetic factors interact and are involved in ‘cross talk’ at different gene loci.
