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@PHDTHESIS{Sakib:282312,
author = {Sakib, Sadman},
title = {{E}pigenomic and transcriptomic analysis of developing,
adult and aging brain: mechanisms of brain folding, neuronal
function and finding novel therapy for dementia},
school = {Georg-August-Universität Göttingen},
type = {Dissertation},
reportid = {DZNE-2025-01282},
pages = {188 p.},
year = {2021},
note = {Dissertation, Georg-August-Universität Göttingen, 2021},
abstract = {Histone modifications and gene expression are tightly
regulated processes in the brain that has been shown to play
crucial role from the beginning of brain development,
learning-memory formation and aging. While brain comprises
of numerous types of neurons and non-neuronal cells, this
regulation is highly cell type specific. To gain more
mechanistic insights on cell type specific epigenetic and
transcriptomic processes, in this thesis, I demonstrated
brain nuclei isolation, cell nuclei specific antibody
staining and FACS sorting can be successfully utilized to
perform cell type specific genome wide histone mark
characterization, gene expression and single nuclei RNA
sequencing. I have applied these tools to gain valuable
mechanistic insights of the causal epigenetic mechanism for
cortical folding, functional role of a histone
methyltransferase in memory impairment, and multi
omics-based characterization of aged induced cognitive
decline model. In the first manuscript, we found that
embryonic mice treated with histone deacetylase inhibitors
(therefore, increasing histone acetylation) led to higher
amounts of basal progenitor (BP) cells in their cortex. This
resulted into higher number of mature neurons, thereby
producing cortical gyration phenotypes in lissencephalic
rodent brains. To understand causal mechanisms, I
established and performed for the first time, BP nuclei
specific gene expression and histone 3 lysine 9(H3K9)
acetylation dataset from embryonic mice cortex. This cell
type specific analysis led to discovering distinct increased
H3K9ac induced gene expression signature, that contained key
regulatory transcription factor, resulting into higher
amount of BP proliferation. Further validation experiments
via epigenome editing confirmed the epigenetic basis of
cortical gyrification in a lissencephalic brain via
increasing histone acetylation. For the second manuscript, I
investigated the molecular role of a histone
methyltransferase (HMT), Setd1b in mature neurons. Forebrain
excitatory neuron specific Setd1B conditional knockout (cKO)
resulted into severe memory impairment which required
further characterization of neuron specific epigenetic and
transcriptomic perturbation due to this cKO. To understand
molecular function of Setd1b cKO in neurons, I isolated
neuron specific nuclei from WT vs cKO mice hippocampal CA
region and performed 4 different histone modification
ChIPseq (H3K4me3, H3K4me1, H3K9ac, H3K27ac) and neuron
specific nuclear RNA seq. Bioinformatic data analysis
revealed promoter specific alteration of all 4 marks and
significant down regulation of memory forming genes.
Comparison with other two previously studied HMT revealed
Setd1b to be having broadest H3K4me3 peaks and regulating
distinct sets of genes, which manifested to the severe most
behavioral deficit. To understand expression pattern of
those three HMTs, I performed single nuclei RNA sequencing
of sorted neurons from wild type mice and found, even though
Setd1b is expressed in a small subset of neurons, those
neurons had the highest level of neuronal function and
memory forming gene expression, compared to other two HMT
expressing neurons studied previously by our group. Overall,
our work shows neuron specific role of Setd1b and its
contribution towards hippocampal memory formation. In the
third manuscript, I applied neuronal and non-neuronal
epigenome and transcriptome data generation and analysis of
3 vs 16 months old mice. As it is well known that memory
impairment starts during the middle of life, and previous
gene expression studies in mice showed very little to no
changes while having cognitive deficit, I utilized nuclei
based cell sorting method to study two promoter epigenetic
marks(H3K4me3, H3K27me3) and RNA expression (including
coding and non-coding) in neuronal and non-neuronal cells
separately. Due to the novelty of the data, I first
characterized the basal activatory H3K4me3, inhibitory
H3K27me3, bivalent regions and gene expression in neuronal
and non-neuronal nuclei. These epigenomic and transcriptomic
datasets would be a valuable resource to the community to
compare cell type specific gene expression and epigenomes
with their datasets. Moreover, profiling epigenetic marks in
old hippocampal CA1 neurons and non-neurons revealed massive
decrease of epigenetic marks mostly in the non-neurons,
while neurons only had decreased inhibitory H3K27me3 mark.
Mechanistically, these epigenome changes correspond to
probable non-neuronal dysfunction and neuronal upregulation
of aberrant developmental pathways. Surprisingly, nuclear
RNAseq revealed significant number of genes deregulated in
non-neuronal cells, compared to neurons. By integrating
transcriptome and epigenome, I found decreased H3K4me3
leading to decreased gene expression in non-neuronal cells,
that resulted into probably downregulated neuronal support
function and downregulated important glial metabolic
pathways related to extra cellular matrix. Therefore, in
this thesis, I have described cell type specific
neurodevelopmental, neuronal and cognitive decline related
epigenetic and transcriptional pathways that would add
valuable knowledge and resources to the neuroscientific
community.},
cin = {AG Fischer},
cid = {I:(DE-2719)1410002},
pnm = {352 - Disease Mechanisms (POF4-352)},
pid = {G:(DE-HGF)POF4-352},
typ = {PUB:(DE-HGF)11},
url = {https://pub.dzne.de/record/282312},
}
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