scholarly journals A transcriptomic taxonomy of Drosophila circadian neurons around the clock

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Dingbang Ma ◽  
Dariusz Przybylski ◽  
Katharine C Abruzzi ◽  
Matthias Schlichting ◽  
Qunlong Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Synapse Formation ◽  
Regulation Of Gene Expression ◽  
Surface Proteins ◽  
Circadian Oscillation ◽  
Functional Studies ◽  
Spatial Regulation ◽  
Sequencing Method ◽  
Transcription Factor Regulation ◽  
The Many

Many different functions are regulated by circadian rhythms, including those orchestrated by discrete clock neurons within animal brains. To comprehensively characterize and assign cell identity to the 75 pairs of Drosophila circadian neurons, we optimized a single-cell RNA sequencing method and assayed clock neuron gene expression at different times of day. The data identify at least 17 clock neuron categories with striking spatial regulation of gene expression. Transcription factor regulation is prominent and likely contributes to the robust circadian oscillation of many transcripts, including those that encode cell-surface proteins previously shown to be important for cell recognition and synapse formation during development. The many other clock-regulated genes also constitute an important resource for future mechanistic and functional studies between clock neurons and/or for temporal signaling to circuits elsewhere in the fly brain.

scholarly journals A transcriptomic taxonomy of Drosophila circadian neurons around the clock

2020 ◽  
Author(s):  
Dingbang Ma ◽  
Dariusz Przybylski ◽  
Katharine C. Abruzzi ◽  
Matthias Schlichting ◽  
Qunlong Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Synapse Formation ◽  
Regulation Of Gene Expression ◽  
Surface Proteins ◽  
Circadian Oscillation ◽  
Temporal Regulation ◽  
Functional Studies ◽  
Spatial Regulation ◽  
Sequencing Method ◽  
The Many

AbstractMany different functions are regulated by circadian rhythms, including those orchestrated by discrete clock neurons within animal brains. To comprehensively characterize and assign cell identity to the 75 pairs of Drosophila circadian neurons, we optimized a single cell RNA sequencing method and assayed clock neuron gene expression at different times of day. The data identify at least 17 clock neuron categories with striking spatial regulation of gene expression. Transcription factor regulation is prominent and likely contributes to the robust circadian oscillation of many transcripts, including those that encode cell-surface proteins previously shown to be important for cell recognition and synapse formation during development. We suggest that these molecules orchestrate the temporal regulation of synapse formation and/or strength. The many other clock-regulated genes also constitute an important resource for future mechanistic and functional studies between clock neurons and/or for temporal signaling to circuits elsewhere in the fly brain.

scholarly journals Circadian variations in gene expression in rat abdominal adipose tissue and relationship to physiology

2010 ◽  
Vol 42A (2) ◽  
pp. 141-152 ◽  
Author(s):  
Siddharth Sukumaran ◽  
Bai Xue ◽  
William J. Jusko ◽  
Debra C. DuBois ◽  
Richard R. Almon
Keyword(s):  
Gene Expression ◽  
Adipose Tissue ◽  
Circadian Rhythms ◽  
Regulation Of Gene Expression ◽  
Gene Array ◽  
Circadian Oscillation ◽  
Peripheral Tissues ◽  
Physiological Processes ◽  
Expression Of Genes ◽  
Rat Adipose Tissue

Circadian rhythms occur in all levels of organization from expression of genes to complex physiological processes. Although much is known about the mechanism of the central clock in the suprachiasmatic nucleus, the regulation of clocks present in peripheral tissues as well as the genes regulated by those clocks is still unclear. In this study, the circadian regulation of gene expression was examined in rat adipose tissue. A rich time series involving 54 animals euthanized at 18 time points within the 24-h cycle (12:12 h light-dark) was performed. mRNA expression was examined with Affymetrix gene array chips and quantitative real-time PCR, along with selected physiological measurements. Transcription factors involved in the regulation of central rhythms were examined, and 13 showed circadian oscillations. Mining of microarray data identified 190 probe sets that showed robust circadian oscillations. Circadian regulated probe sets were further parsed into seven distinct temporal clusters, with >70% of the genes showing maximum expression during the active/dark period. These genes were grouped into eight functional categories, which were examined within the context of their temporal expression. Circadian oscillations were also observed in plasma leptin, corticosterone, insulin, glucose, triglycerides, free fatty acids, and LDL cholesterol. Circadian oscillation in these physiological measurements along with the functional categorization of these genes suggests an important role for circadian rhythms in controlling various functions in white adipose tissue including adipogenesis, energy metabolism, and immune regulation.

scholarly journals Genetic Subtraction Profiling Identifies Candidate miRNAs Involved in Rice Female Gametophyte Abortion

2017 ◽  
Vol 7 (7) ◽  
pp. 2281-2293 ◽  
Author(s):  
Liyu Yang ◽  
Ya Wu ◽  
Wenliang Wang ◽  
Bigang Mao ◽  
Bingran Zhao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sexual Reproduction ◽  
Female Gametophyte ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Ovule Development ◽  
Sequencing Method ◽  
Transcription Factor Regulation ◽  
Regulatory Effects ◽  
Functional Analyses

Abstract The female gametophyte is an important participant in the sexual reproduction of plants. The molecular mechanism of its development has received much attention in recent years. As important regulators of gene expression, miRNAs have been certified to play a significant role in many biological processes of plants, including sexual reproduction. In this study, to investigate the potential regulatory effects of miRNAs on rice female gametophyte abortion, we used the high-throughput sequencing method to compare the miRNA transcriptome in ovules of a high frequency female-sterile line (fsv1) and a rice wild-type line (Gui 99) during ovule development. As a result, 522 known miRNAs and 295 novel miRNAs were expressed in the developing ovule of rice, while 100 known miRNAs were significantly differentially expressed between these two rice lines during ovule development. Combining with gene expression information, a total of 627 coherent target genes of these differential expressed known miRNAs between fsv1 and Gui 99 were identified. The functional analyses of these coherent target genes revealed that the coherent target genes of differential expressed known miRNAs between the two rice lines are involved in many biological pathways, such as protein degradation, auxin signal transduction, and transcription factor regulation. These results provide us with important clues to investigate the regulatory roles of miRNAs in rice female gametophyte abortion.

scholarly journals Spatial regulation of gene expression during growth of articular cartilage in juvenile mice

2014 ◽  
Vol 77 (3) ◽  
pp. 406-415 ◽  
Author(s):  
Julian C. Lui ◽  
Michael Chau ◽  
Weiping Chen ◽  
Crystal S. F. Cheung ◽  
Jeffrey Hanson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Articular Cartilage ◽  
Regulation Of Gene Expression ◽  
Spatial Regulation

Regulatory noncoding RNAs at Hox lociThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (1) ◽  
pp. 27-34 ◽  
Author(s):  
Hugh W. Brock ◽  
Jacob W. Hodgson ◽  
Svetlana Petruk ◽  
Alexander Mazo
Keyword(s):  
Gene Expression ◽  
Hox Genes ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Chromatin Dynamics ◽  
Spatial Regulation ◽  
Positional Identity ◽  
In Trans ◽  
In Cis

There is growing awareness of the importance of noncoding (nc)RNAs in the regulation of gene expression during pattern formation in development. Spatial regulation of Hox gene expression in development controls positional identity along the antero–posterior axis. In this review, we will focus on the role of short ncRNAs that repress Hox genes in Drosophila and mammals by RNA interference (RNAi), on long ncRNAs that may repress a Hox in cis in Drosophila by transcriptional interference, and on a novel long ncRNA that functions in trans to regulate Hox genes mammals.

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