scholarly journals Transposition-Driven Genomic Heterogeneity in the Drosophila Brain

Science ◽  
2013 ◽  
Vol 340 (6128) ◽  
pp. 91-95 ◽  
Author(s):  
Paola N. Perrat ◽  
Shamik DasGupta ◽  
Jie Wang ◽  
William Theurkauf ◽  
Zhiping Weng ◽  
...  
Keyword(s):  
Expression Profiling ◽  
Mushroom Body ◽  
De Novo ◽  
Brain Cell ◽  
Specific Gene ◽  
Cell Type ◽  
Drosophila Brain ◽  
Cell Type Specific ◽  
Transposon Insertions ◽  
The Brain

Recent studies in mammals have documented the neural expression and mobility of retrotransposons and have suggested that neural genomes are diverse mosaics. We found that transposition occurs among memory-relevant neurons in the Drosophila brain. Cell type–specific gene expression profiling revealed that transposon expression is more abundant in mushroom body (MB) αβ neurons than in neighboring MB neurons. The Piwi-interacting RNA (piRNA) proteins Aubergine and Argonaute 3, known to suppress transposons in the fly germline, are expressed in the brain and appear less abundant in αβ MB neurons. Loss of piRNA proteins correlates with elevated transposon expression in the brain. Paired-end deep sequencing identified more than 200 de novo transposon insertions in αβ neurons, including insertions into memory-relevant loci. Our observations indicate that genomic heterogeneity is a conserved feature of the brain.

scholarly journals A regulatory element is characterized by purine-mediated and cell-type-specific gene transcription.

1990 ◽  
Vol 10 (8) ◽  
pp. 4356-4364 ◽  
Author(s):  
M J Walsh ◽  
A Sanchez-Pozo ◽  
N S Leleiko
Keyword(s):  
De Novo ◽  
Cell Types ◽  
High Rate ◽  
Specific Gene ◽  
Intestinal Epithelial ◽  
Purine Nucleotide ◽  
Cell Type ◽  
Hprt Gene ◽  
Purine Nucleotides ◽  
Cell Type Specific

Purines and purine nucleotides were found to affect transcription of the hypoxanthine-guanine phosphoribosyltransferase (HPRT) gene in whole nuclei isolated from intestinal mucosa of adult rats fed a purine- and purine nucleotide-free diet. Nuclear run-on transcription assays, performed on whole nuclei from different tissues and cell types, identified an intestine-specific decrease in the overall incorporation of [alpha-32P]UTP in HPRT transcripts from intestinal epithelial cell nuclei when exogenous purines or purine nucleotides were omitted from either the diet or culture medium. Using a 990-base-pair genomic fragment that contains the 5'-flanking region from the HPRT gene, we generated plasmid constructs with deletions, transfected the DNA into various cell types, and assayed for chloramphenicol acetyltransferase (CAT) reporter activity in vitro. We determined that an element upstream from the putative transcriptional start site is necessary to maintain the regulatory response to purine and nucleotide levels in cultured intestinal epithelial cells. These results were tissue and cell type specific and suggest that in the absence of exogenous purines, the presence of specific factors influences transcriptional initiation of HPRT. This information provides evidence for a mechanism by which the intestinal epithelium, which has been reported to lack constitutive levels of de novo purine nucleotide biosynthetic activity, could maintain and regulate the salvage of purines and nucleotides necessary for its high rate of cell and protein turnover during fluctuating nutritional and physiological conditions. Furthermore, this information may provide more insight into regulation of the broad class of genes recognized by their lack of TATA and CCAAT box consensus sequences within the region proximal to the promoter.

scholarly journals Brain Cell Type Specific Gene Expression and Co-expression Network Architectures

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Andrew T. McKenzie ◽  
Minghui Wang ◽  
Mads E. Hauberg ◽  
John F. Fullard ◽  
Alexey Kozlenkov ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brain Cell ◽  
Specific Gene ◽  
Network Architectures ◽  
Cell Type ◽  
Specific Gene Expression ◽  
Cell Type Specific

scholarly journals Cell-Type-Specific Gene Expression Profiling in Adult Mouse Brain Reveals Normal and Disease-State Signatures

Cell Reports ◽  
2019 ◽  
Vol 26 (9) ◽  
pp. 2477-2493.e9 ◽  
Author(s):  
Nicolas Merienne ◽  
Cécile Meunier ◽  
Anne Schneider ◽  
Jonathan Seguin ◽  
Satish S. Nair ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Mouse Brain ◽  
Expression Profiling ◽  
Adult Mouse ◽  
Specific Gene ◽  
Cell Type ◽  
Adult Mouse Brain ◽  
Specific Gene Expression ◽  
Cell Type Specific

scholarly journals Evidence of wiring development processes from the connectome of adult Drosophila

2021 ◽  
Author(s):  
Louis K Scheffer
Keyword(s):  
Mushroom Body ◽  
Development Process ◽  
Synapse Formation ◽  
Cell Types ◽  
Surface Proteins ◽  
Cell Type ◽  
Drosophila Brain ◽  
Development Processes ◽  
The Brain ◽  
Adult Drosophila

How is the brain wired during development? Here we look at some of the characteristics of the adult Drosophila brain, a result of this development process. From this we can speculate on at least some aspects of how the wiring was done. A common hypothesis is that surface proteins direct synapse formation among touching neurons. Assuming that surface proteins are specific to cell types, we find support for this hypothesis. The brain in general supports a wide variety of connections of different degrees of reciprocity, with ratios up to a thousand to one in the two directions of synapses between types. However, contacts between cells of the same type are always bi-directional and nearly equal strength. Furthermore, among similar cell types, at least in the mushroom body, the closer the cell type by morphology, the closer the inter-type contacts are to symmetrical. These findings are all consistent with the hypothesis that surface proteins specific to cell types determine the directivity of connections. Next we look at synapses per area, and find this varies widely and is roughly log-normally distributed. In most cases, the number of synapses saturates at higher areas, though other forms are seen - linear, flat, or decreasing with increasing area. Evidence suggests that at least some of this distinction is post-synaptic.

scholarly journals Cross-laboratory analysis of brain cell type transcriptomes with applications to interpretation of bulk tissue data

2016 ◽  
Author(s):  
B. Ogan Mancarci ◽  
Lilah Toker ◽  
Shreejoy J Tripathy ◽  
Brenna Li ◽  
Brad Rocco ◽  
...  
Keyword(s):  
Nervous System ◽  
Cell Types ◽  
Brain Cell ◽  
Marker Genes ◽  
Specific Gene ◽  
Published Data ◽  
Specific Marker ◽  
Cell Type ◽  
Cell Type Specific ◽  
Bulk Tissue

AbstractEstablishing the molecular diversity of cell types is crucial for the study of the nervous system. We compiled a cross-laboratory database of mouse brain cell type-specific transcriptomes from 36 major cell types from across the mammalian brain using rigorously curated published data from pooled cell type microarray and single cell RNA-sequencing studies. We used these data to identify cell type-specific marker genes, discovering a substantial number of novel markers, many of which we validated using computational and experimental approaches. We further demonstrate that summarized expression of marker gene sets in bulk tissue data can be used to estimate the relative cell type abundance across samples. To facilitate use of this expanding resource, we provide a user-friendly web interface at Neuroexpresso.org.Significance StatementCell type markers are powerful tools in the study of the nervous system that help reveal properties of cell types and acquire additional information from large scale expression experiments. Despite their usefulness in the field, known marker genes for brain cell types are few in number. We present NeuroExpresso, a database of brain cell type specific gene expression profiles, and demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression. The database will prove itself as a useful resource for researchers aiming to reveal novel properties of the cell types and aid both laboratory and computational scientists to unravel the cell type specific components of brain disorders.

Sign in / Sign up

Export Citation Format

Share Document