MicroRNA Implications across Neurodevelopment and Neuropathology

MicroRNAs (miRNAs) have rapidly emerged as biologically important mediators of posttranscriptional and epigenetic regulation in both plants and animals. miRNAs function through a variety of mechanisms including mRNA degradation and translational repression; additionally, miRNAs may guide gene expression by serving as transcription factors. miRNAs are highly expressed in human brain. Tissue and cell type-specific enrichments of certain miRNAs within the nervous system argue for a biological significance during neurodevelopmental stages. On the other hand, a large number of studies have reported links between alterations of miRNA homeostasis and pathologic conditions such as cancer, heart diseases, and neurodegeneration. Thus, profiles of distinct or aberrant miRNA signatures have most recently surged as one of the most fascinating interests in current biology. Here, the most recent insights into the involvement of miRNAs in the biology of the nervous system and the occurrence of neuropathological disorders are reviewed and discussed.

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Expression of Hand2 is sufficient for neurogenesis and cell type–specific gene expression in the enteric nervous system

Developmental Dynamics ◽

10.1002/dvdy.20989 ◽

2006 ◽

Vol 236 (1) ◽

pp. 93-105 ◽

Cited By ~ 56

Author(s):

Tyler J. Hendershot ◽

Hongbin Liu ◽

Anjali A. Sarkar ◽

David R. Giovannucci ◽

David E. Clouthier ◽

...

Keyword(s):

Gene Expression ◽

Nervous System ◽

Enteric Nervous System ◽

Specific Gene ◽

Cell Type ◽

Specific Gene Expression ◽

Cell Type Specific

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A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs

10.1101/483461 ◽

2018 ◽

Author(s):

Alexandra L. McCorkindale ◽

Philipp Wahle ◽

Sascha Werner ◽

Irwin Jungreis ◽

Peter Menzel ◽

...

Keyword(s):

Gene Expression ◽

Nervous System ◽

System Development ◽

Cell Types ◽

Nervous System Development ◽

Cell Type ◽

Gene Expression Atlas ◽

Expression Atlas ◽

Gene Expression Dynamics ◽

Cell Type Specific

Summary statementWe present a spatiotemporal transcriptome during early Drosophila embryonic nervous system development, revealing a complex cell type-specific network of mRNAs and lncRNAs.AbstractCell type specification during early nervous system development in Drosophila melanogaster requires precise regulation of gene expression in time and space. Resolving the programs driving neurogenesis has been a major challenge owing to the complexity and rapidity with which distinct cell populations arise. To resolve the cell type-specific gene expression dynamics in early nervous system development, we have sequenced the transcriptomes of purified neurogenic cell types across consecutive time points covering critical events in neurogenesis. The resulting gene expression atlas comprises a detailed resource of global transcriptome dynamics that permits systematic analysis of how cells in the nervous system acquire distinct fates. We resolve known gene expression dynamics and uncover novel expression signatures for hundreds of genes among diverse neurogenic cell types, most of which remain unstudied. We also identified a set of conserved and tissue-specifically regulated long-noncoding RNAs (lncRNAs) that exhibit spatiotemporal expression during neurogenesis with exquisite specificity. LncRNA expression is highly dynamic and demarcates specific subpopulations within neurogenic cell types. Our spatiotemporal transcriptome atlas provides a comprehensive resource to investigate the function of coding genes and noncoding RNAs during critical stages of early neurogenesis.

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Faculty Opinions recommendation of The kinase p38 alpha serves cell type-specific inflammatory functions in skin injury and coordinates pro- and anti-inflammatory gene expression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1135937.593041 ◽

2008 ◽

Author(s):

Lionel Ivashkiv

Keyword(s):

Gene Expression ◽

Cell Type ◽

Skin Injury ◽

Inflammatory Gene Expression ◽

Inflammatory Gene ◽

Cell Type Specific ◽

Anti Inflammatory

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Faculty Opinions recommendation of BMP signaling induces cell-type-specific changes in gene expression programs of human keratinocytes and fibroblasts.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1927959.1482057 ◽

2010 ◽

Author(s):

Ralf Paus

Keyword(s):

Gene Expression ◽

Human Keratinocytes ◽

Bmp Signaling ◽

Cell Type ◽

Cell Type Specific

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An integrated analysis of cell-type specific gene expression reveals genes regulated by REVOLUTA and KANADI1 in the Arabidopsis shoot apical meristem

PLoS Genetics ◽

10.1371/journal.pgen.1008661 ◽

2020 ◽

Vol 16 (4) ◽

pp. e1008661 ◽

Cited By ~ 2

Author(s):

Hasthi Ram ◽

Sudeep Sahadevan ◽

Nittaya Gale ◽

Monica Pia Caggiano ◽

Xiulian Yu ◽

...

Keyword(s):

Gene Expression ◽

Shoot Apical Meristem ◽

Apical Meristem ◽

Integrated Analysis ◽

Specific Gene ◽

Cell Type ◽

Specific Gene Expression ◽

Cell Type Specific

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Cortical structural differences in major depressive disorder correlate with cell type-specific transcriptional signatures

Nature Communications ◽

10.1038/s41467-021-21943-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Jiao Li ◽

Jakob Seidlitz ◽

John Suckling ◽

Feiyang Fan ◽

Gong-Jun Ji ◽

...

Keyword(s):

Gene Expression ◽

Major Depressive Disorder ◽

Depressive Disorder ◽

Structural Changes ◽

Brain Regions ◽

Cell Type ◽

Major Depressive ◽

Structural Differences ◽

Neuroimaging Data ◽

Cell Type Specific

AbstractMajor depressive disorder (MDD) has been shown to be associated with structural abnormalities in a variety of spatially diverse brain regions. However, the correlation between brain structural changes in MDD and gene expression is unclear. Here, we examine the link between brain-wide gene expression and morphometric changes in individuals with MDD, using neuroimaging data from two independent cohorts and a publicly available transcriptomic dataset. Morphometric similarity network (MSN) analysis shows replicable cortical structural differences in individuals with MDD compared to control subjects. Using human brain gene expression data, we observe that the expression of MDD-associated genes spatially correlates with MSN differences. Analysis of cell type-specific signature genes suggests that microglia and neuronal specific transcriptional changes account for most of the observed correlation with MDD-specific MSN differences. Collectively, our findings link molecular and structural changes relevant for MDD.

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Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle

Scientific Reports ◽

10.1038/s41598-021-82539-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

John A. Halsall ◽

Simon Andrews ◽

Felix Krueger ◽

Charlotte E. Rutledge ◽

Gabriella Ficz ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Histone Modifications ◽

Expression Patterns ◽

Cell Types ◽

Cell Type ◽

Bar Code ◽

Genes Encoding ◽

Cell Type Specific ◽

Rolling Windows

AbstractChromatin configuration influences gene expression in eukaryotes at multiple levels, from individual nucleosomes to chromatin domains several Mb long. Post-translational modifications (PTM) of core histones seem to be involved in chromatin structural transitions, but how remains unclear. To explore this, we used ChIP-seq and two cell types, HeLa and lymphoblastoid (LCL), to define how changes in chromatin packaging through the cell cycle influence the distributions of three transcription-associated histone modifications, H3K9ac, H3K4me3 and H3K27me3. We show that chromosome regions (bands) of 10–50 Mb, detectable by immunofluorescence microscopy of metaphase (M) chromosomes, are also present in G1 and G2. They comprise 1–5 Mb sub-bands that differ between HeLa and LCL but remain consistent through the cell cycle. The same sub-bands are defined by H3K9ac and H3K4me3, while H3K27me3 spreads more widely. We found little change between cell cycle phases, whether compared by 5 Kb rolling windows or when analysis was restricted to functional elements such as transcription start sites and topologically associating domains. Only a small number of genes showed cell-cycle related changes: at genes encoding proteins involved in mitosis, H3K9 became highly acetylated in G2M, possibly because of ongoing transcription. In conclusion, modified histone isoforms H3K9ac, H3K4me3 and H3K27me3 exhibit a characteristic genomic distribution at resolutions of 1 Mb and below that differs between HeLa and lymphoblastoid cells but remains remarkably consistent through the cell cycle. We suggest that this cell-type-specific chromosomal bar-code is part of a homeostatic mechanism by which cells retain their characteristic gene expression patterns, and hence their identity, through multiple mitoses.

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