User:AAR3643/Epigenetic regulation of neurogenesis

Sandbox belonging to Andre Ribeiro, Amulya Cherian, and Andrew Spires.

Trevor's comments in magenta

Edit Key:

All edits and additions are bolded and italicized.

Responses to professor comments are underlined.

Please get rid of the outline, but please also keep the edit key.

Article Draft

Article body

Embryonic neurogenesis

Histone modifications (cleanup edit)

Neural stem cells develop the cortex in a precise "inside out" manner with carefully controlled timing mechanisms*1*. Early born neurons form deep layers in the cortex while newer born neurons form the upper layers. This timing program is seen in vitro as well as in vivo. Mutant analysis has shown that histone methylation modulates the production of deep layer and upper layer neurons through epigenetic regulation. Specifically, deletion of a portion of the PRC2 complex, Ezh2, encoding histone methyltransferase, led to a twofold reduction of POU3F2/BRN2-expressing and SATB2 expressing upper layer neurons without affecting the number of neurons in layers V and VI *2* *3*. Similarly, increased histone acetylation through the use of histone deacetylase (HDAC) inhibitor valproic acid, an epilepsy therapeutic, in mouse embryonic stem cell-derived neural progenitors not only induced neuronal differentiation, but also selectively enriched the upper layer neuronal population. Therefore, it has been proposed that HDAC inhibition promotes the progression of neuronal differentiation, leading to a fate-switch from deep-layer producing progenitors into upper-layer progenitors. However, the reasons behind this selective differentiation and timing control as a result of HDAC inhibition are not yet fully understood.

What's the mechanism for your proposed edit? What happens to development when there are fewer of these types of neurons?

The majority of the paragraph above titled "Histone modifications (cleanup edit)" was unedited content from the original article currently published on Wikipedia. The only text we included is bolded and italicized and functions to clarify that POU3F2 is also referred to as BRN2. This was a suggestion you had made previously, and therefore it was included to improve the current article but was not part of our original outline. We have added additional edits to improve this section as you suggested below.

*1* This sentence is pretty awkward. "Generate"? in place of "develops"? Terrible. 

*2* Prior sentences talk about normal development and this sentence talks about development in a mutant. People will assume that this sentence is part of normal development and that deletion of part of PRC2 is a normal developmental process. This is what you led them to think. Please fix.

*3* There is a lot more that should be cleaned up about this paragraph. In general as constructed I think that the separation between the description of normal development and the mutant phenotype is nonexistant. Really you just need some transition phrases here and there that help the reader. For instance, you could rewrite sentence 3 like this: Mutant analysis has shown that histone methylation modulates the production of deep layer and upper layer neurons.

Adult neurogenesis

Astrocyte reprogramming: (addition)

Astrocytes are specialized glial cells that vastly outnumber neurons in the adult brain, due to their ability to multiply as needed to sustain proper levels for brain function through multiple functions, including blood brain barrier control, supporting synapses as well as axon pathfinding. <- there are a lot of residues Unlike neurons, these specialized glial cells are able to alter their cell fate prior to reaching full maturation and “dedifferentiate,” in large part due to epigenetic factors. This dedifferentiation allows astrocytes to potentially reach a different cell fate entirely, so long as this dedifferentiation occurs before complete maturation occurs, and can lead to their consequent differentiation and conversion from glial cells into neurons in the adult brain. Prior to complete maturation while dedifferentiation is still possible, the expression of genes Mash1, NeuroG1 and NeuroG2 can allow for reprogramming of astrocytes into neurons. In addition to the expression of these genes in brain cells, multiple epigenetic factors play a role in these gene’s expression patterns. An up-regulation of acetylation at H3K9 and H3K14 <- is this acetylation at both these residues? residues adjacent to both NeuroG1 and NeuroG2 genes has been shown to accompany astrocyte dedifferentiation, over-expression and/or forced expression of these genes can directly induce the differentiation of astrocytes. In addition, silencing of methylation mechanisms, specifically the silencing of many classes of DNA methyltransferases which themselves are involved in silencing expression, inhibits the progenitor cells of astrocytes from differentiating back to their original fate as glial cells. Despite this knowledge of the mechanism of methylation repression, the identity of these silenced genes is not yet fully known. While this overall repression of methylation is necessary to prevent expression of specific genes needed to allow an astrocyte to fully mature and reach an astrocytic cell fate, it was found that the over-expression of one specific DNA methyltransferase, Ezh2, which catalyzes the tri-methylation of H3K27, represses genes needed for astrocyte maintenance, thus allowing the cell to retain its neural stem cell morphology. This demonstrates that differential methylation by distinct methyltransferases and their consequent repression or over-expression have differing roles in the dedifferentiation of astrocytes to form neurons. Furthermore, while not sufficient to induce astrocyte dedifferentiation alone, Ezh2 is necessary for astrocytes to dedifferentiate as they are inhibited from reaching complete maturity into their original cell fate. Once in this inhibited stage, expression of the gene NeuroD4 in these specified glial cells has been shown to lead to neuronal formation, and thus neurogenesis, from the dedifferentiated astrocytes in adult mammalian brains.

I'm a little confused about the timing of things here. It initially sounds like astrocytes can be reprogrammed at any point, but then later it's written as if this has to happen before final maturation steps. Can you clear up some of the timing of when this happens and also when astrocytes are committed to their cell fate (if at all)?

-Clarified in the second sentence that dedifferentiation can occur only before the astrocyte's final cell fate has been reached and prior to full maturation. In the following sentences I reiterated that dedifferentiation must occur prior to maturation if it is to occur at all.

-Originally I had referenced H3K9K14 acetylation, and upon further research in reference of the review article discussing this topic, I found that co-acetylation occurs at both residues. As a result, I separated the two sites as "H3K9 and H3K14" for clarity.

Expand on the epigenetic aspect here a little more.

-Expanded on the epigenetic mechanisms to highlight how differential methylation and repression of those methylation mechanisms function in tandem with acetylation mechanisms to lead to the dedifferentiation of astrocytes, allowing them to become neurons through expression of specific genes.

Histone modification (edit)

Histone acetylation, deacetylation, as well as the inhibition of histone deacetylation mechanisms also play large roles in the proliferation and self-renewal of post-natal neural stem cells, in contrasting ways. <- I'm not sure what you mean by "in contrasting ways" Neural-expressed HDACs interact with Tlx, an essential neural stem cell regulator, to suppress TLX target genes. This includes the cyclin-dependent kinase inhibitor P21 and the tumor suppressor gene Pten to promote neural stem cell proliferation. The most prominently studied and well-understood regulators of chromatin remodeling, which play an important role in adult neurogenesis are histone acetyltransferases (HATs) and histone deacetylases (HDACs). HATs add acetyl groups to nucleosomes, while HDACs remove them. The acetylation of histones leads to decreased condensation of the nucleosomes to target DNA, and increases the likelihood that gene expression may occur by freeing up the DNA targets to bind to their respective transcriptional factors. This process is involved in neural proliferation regulation, as different neuronal cell genes are expressed and repressed. Deacetylation of histones leads to the reverse, and increases the likelihood for the repression of gene expression. HDAC inhibitors (HDACi), such as valproic acid (VPA) and trichostatin A can promote proliferation of adult neurogenesis through the reversal of HDAC activity, inducing differentiation of adult progenitor cells. <- It feels like this should come before the second sentence of the paragraph since it starts to discuss HDACs -- it would make sense to have this background info before the details. It might also be good to split this up into a background paragraph and a paragraph talking about the role of histone modifications in neurogenesis. Inhibition of HDACS by the antiepileptic drug valproic acid induces neuronal differentiation as in embryonic neurogenesis, but also inhibits glial cell differentiation of adult neural stem cells. This is likely mediated through upregulation of neuronal specific genes such as the neurogeneic basic helix-loop-helix transcription factors NEUROD, NEUROGENENIN1, and Math1. Conditional loss of HDAC1, HDAC2 in neural progenitor cells prevented them from differentiating into neurons and their loss in oligodendrytic progenitor cells disrupted oligodendrocyte formations, suggesting that histone deacetlyation plays important but varying roles in different stages of neuronal development.

This section is titled "histone modifications" but only really focuses on histone acetylation, specifically the role of HDACs. Can you expand this a little more? Also, the model you're working with of histone acetylation making chromatin more accessible is pretty simplistic - consider the other things histone acetylation does like recruitment of chromatin proteins, reinforcement and expansion of acetylation, etc.

miRNAs (edit)

MicroRNAs (miRNAs) are small noncoding RNAs that play a significant role in eukaryotic epigenetic regulation. miRNAs function to modulate protein expression levels of their mRNA targets without affecting the sequences of the genes of interest. While miRNAs play a large role in the modulation of epigenetic mechanisms, they are also modified and regulated by other epigenetic factors including DNA methylation, histone modifications and other RNA modifications. Together, miRNAs create an epigenetic feedback loop with other epigenetic factors to affect the expression levels of specific genes. A number of specific miRNAs have been implicated as agents of epigenetic regulation in adult neurogenesis. miR-9 targets the nuclear receptor TLX in adult neurogenesis to promote neural differentiation and inhibit neural stem cell proliferation. It also influences neuronal subtype specification and regulates axonal growth, branching, and targeting in the central nervous system through interactions with HES1, a neural stem cell homeostasis molecule. miR-124 promotes cell cycle exit and neuronal differentiation in adult neurogenesis. Mouse studies have shown that ectopic expression of miR-124 showed premature neural progenitor cell differentiation and exhaustion in the subventricular zone. In addition to miR-9 and miR-124, other miRNAs play essential roles in regulation of adult neurogenesis. miR-137, miR-184 and miR-195 regulate adult neural stem cell proliferation, with their over-expression leading to up-regulated proliferation while their down-regulation leads to a decrease in neuronal proliferation. Methyl-CpG binding protein 1 (MBD1) represses miR-184, which is a microRNA responsible for proliferation of adult neural stem/progenitor cells (aNSCs) along with the inhibition of differentiating these cells. miR-184 regulates embryonic brain development by binding to the mRNA for the Numblike (Numbl) protein and altering its expression. MBD1, Numbl, and miR-184 all work together to regulate the proliferation and differentiation of aNSCs. In addition, miR-195 works closely with MBD1 to regulate aNSC proliferation and differentiation. mIR-194 and MBD1 form a negative regulatory loop in aNSCs and work to repress the expression of each other. Inhibition of miR-195 promotes aNSC differentiation. Once differentiation has occurred, levels of miR-195 decreases.

Might be a good idea to break up this paragraph too.

Epigenetic dysregulation and neurological disorders (section addition)

Epigenetic dysregulation, or alterations on epigenomic machinery, can cause DNA methylation and histone acetylation processes to go rogue. The epigenetic machinery influence neural differentiation regulation (i.e. neurogenesis) and are also involved in processes related to memory consolidation and learning in healthy individuals. As aging is the main risk for many neurological disorders, epigenetic dysregulation can in turn lead to alterations on the transcriptional level of genes involved in the pathogenesis of neural degenerative diseases such as Parkinson's disease, Alzheimer's disease, Huntington's disease, schizophrenia, and bipolar disease.

Can you draw a general link between aging and altered epigenetic mechanisms? Feels like that would help strengthen your claim about aging risk and epigenetic mechanisms.

Huntington’s disease (addition)

Histone acetylation has received increasing support over the years as a proposed mechanism for the dysregulation of HD.

Preclinical studies have been performed using various HDACi’s [such as suberoxylanilide hydroxamic acid (SAHA), Trichostatin A (TSA), phenylbutyrate, and sodium butyrate (NaB)] that target HDACI and HDACII. Although these inhibitors improve some phenotypes of HD in mice, such as neuropathology and motor function, the beneficial effects do not provide a clear indication of the necessity of an increase in histone acetylation. However, inactivation of a target of SAHA, Hdac 4, alleviates neurodegenerative complications in mice with HD through a transcription-independent mechanism which acts upon mutant Htt aggregation processes-which may indicate that there is a mechanism involving non-histone proteins. <- This is super important! Say more about this mechanism, especially since almost all of your discussion of HDACs and histone acetylation has been focused on transcription, mentioning a transcription-independent mechanism and then not explaining it is going to bug your readers (like it did me).You pique our curiosity and then leave us hanging!

HDACi treatment still does not have clear results in regards to the restoration of neuronal identity genes. However clinical studies using HDACi are currently ongoing and the results are pending, with the Phase II studies showing promise for safe and tolerable use of several compounds such as phenylbutyrate.

Non-histone-mediated beneficial effects of HDACi have also been documented in models of Parkinson disease, suggesting common mechanisms between several neurodegenerative diseases.

Parkinson’s disease (addition)

DNA methylation analysis showed that there is significant dysregulation of methylation on CpG islands on patients with PD when compared to healthy individuals. Although this was genome-wide, this also occurred on many PD risk genes.

Mitochondrial DNA methylation has also been shown to have variance over time due to age variance. As mitochondria plays a role in the development of the PD, further research into the area will help uncover any implications that mitochondrial DNA methylation plays in the pathogenesis of PD.

Can you draw any stronger of a link here? What does methylation of mitochondrial DNA do (as far as I know mtDNA doesn't really get packaged into chromatin)? Would this methylation reasonably affect mitochondrial function in a similar manner to what's seen in PD?

The use of dopaminergic neurons that have been isolated from the PD patients indicated that there were increases in acetylation (at H2A, H3 and H4) when compared to the age-control group. Beyond this, HDAC levels are reduced in 1-methyl-4-phenylpyridinium (MPP+)-treated cells and in MPTP-treated mouse brains, as well as in midbrain samples from patients with PD. <- what's this treatment? what does it do, and why do you see these changes? These results point towards the stress of  histone modifications in regards to chromatin remodeling and its implication in the pathogenesis of PD.

miRNAs are also emerging as relevant contributors to neurodegeneration in PD. In particular, the frontal cortex PD patients have shown higher levels of LRRK2 and lower levels of miR-205 when compared to healthy individuals. Connecting this to the findings of miR-205’s ability to bind to the 3′ UTR of LRRK2 mRNA and suppress expression, as well as miR-205’s prevention of defects after introduction to a R1441G LRRK2 mutation, these results point towards miR-205 and its regulatory role in LRRK2 expression-which in turn suggest a regulatory role in the pathogenesis of PD.

You don't link to this the HDACi effects you mentioned in the HD section. I think you should expand on that link since you claim it exists.

Bipolar Disorder (addition)

Bipolar disorders are both highly complex and heritable, which makes it an interesting disorder to examine for epigenetic modifications. DNA methylation, DNA hydroxymethylation, and histone modifications are all capable of contributing to the formation of bipolar disorder.  

For example, studies of monozygotic twins revealed that individuals with bipolar disorder had lower methylation of the peptidylprolyl isomerase E-like (PPIEL) gene, which can be attributed to the dopamine transmission. The studies indicated that hypermethylation of SLC6A4, a serotinin transporter gene, is also involved with bipolar disorder. The methylation of CpG regions are relevant to bipolar disorders. Patients with bipolar disorder showed lower methylation levels for the CpG region of the KCNQ3 gene, which is responsible for the voltage-gated K+ channel. Childhood maltreatment contributed to the methylation status of CpG2 III of 5-hydroxytryptamine 3A, which alters how maltreatment affects bipolar disorder.

Explain these mechanisms a little more. Why are these changes in methylation associated with bipolar? What causes them?

Moreover, therapeutic interventions such as engineered transcription factors could modify chromatin structure. DNA methyltransferase (DNMT) inhibitors and histone deacetylase (HDAC) inhibitors could possibly reverse epigenetic modifications in order to therapeutically address bipolar disorder.

Dive into these treatments a little more. I think this comment applies for all the sections here.

~~General comments~~

This looks to be in pretty good shape. I think just expanding on a lot of these topics is the focus at this point. I don't really have much more to say than to think about mechanisms more and the structures of these paragraphs.