scholarly journals MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis

2019 ◽  
Author(s):  
Alexandra Plotnikova ◽  
Max J. Kellner ◽  
Magdalena Mosiolek ◽  
Michael A. Schon ◽  
Michael D. Nodine
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
High Throughput ◽  
Cellular Differentiation ◽  
High Throughput Sequencing ◽  
Profound Impact ◽  
Plant Body ◽  
Non Coding Rnas ◽  
Arabidopsis Embryogenesis

SummaryMicroRNAs (miRNAs) are short non-coding RNAs that mediate the repression of target transcripts in plants and animals. Although miRNAs are required throughout plant development, relatively little is known regarding their embryonic functions. To systematically characterize embryonic miRNAs in Arabidopsis thaliana, we developed or applied high-throughput sequencing based methods to profile hundreds of miRNAs and associated targets throughout embryogenesis. We discovered dozens of miRNAs that dynamically cleave and repress target transcripts including 30 that encode transcription factors. Transcriptome analyses indicated that these miRNA:target interactions have a profound impact on embryonic gene expression programs, and we further demonstrated that the miRNA-mediated repression of six transcription factors were individually required for embryo morphogenesis. These data indicate that the miRNA-directed repression of multiple transcription factors is critically important for the establishment of the plant body plan, and provide a foundation to further investigate how miRNAs contribute to these initial cellular differentiation events.

scholarly journals Behavior Individuality: A Focus on Drosophila melanogaster

2021 ◽  
Vol 12 ◽  
Author(s):  
Rubén Mollá-Albaladejo ◽  
Juan A. Sánchez-Alcañiz
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Great Effort ◽  
Behavioral Differences ◽  
Adult Behavior ◽  
Large Numbers ◽  
Environmental Variations ◽  
And Function

Among individuals, behavioral differences result from the well-known interplay of nature and nurture. Minute differences in the genetic code can lead to differential gene expression and function, dramatically affecting developmental processes and adult behavior. Environmental factors, epigenetic modifications, and gene expression and function are responsible for generating stochastic behaviors. In the last decade, the advent of high-throughput sequencing has facilitated studying the genetic basis of behavior and individuality. We can now study the genomes of multiple individuals and infer which genetic variations might be responsible for the observed behavior. In addition, the development of high-throughput behavioral paradigms, where multiple isogenic animals can be analyzed in various environmental conditions, has again facilitated the study of the influence of genetic and environmental variations in animal personality. Mainly, Drosophila melanogaster has been the focus of a great effort to understand how inter-individual behavioral differences emerge. The possibility of using large numbers of animals, isogenic populations, and the possibility of modifying neuronal function has made it an ideal model to search for the origins of individuality. In the present review, we will focus on the recent findings that try to shed light on the emergence of individuality with a particular interest in D. melanogaster.

scholarly journals High-throughput sequencing identifies STAT3 as the DNA-associated factor for p53 - NF-kappaB - complex-dependent gene expression in human heart failure

10.1186/gm158 ◽  
2010 ◽  
Vol 2 (6) ◽  
pp. 37 ◽  
Author(s):  
Mun-Kit Choy ◽  
Mehregan Movassagh ◽  
Lee Siggens ◽  
Ana Vujic ◽  
Martin Goddard ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
High Throughput ◽  
Human Heart ◽  
High Throughput Sequencing ◽  
Human Heart Failure ◽  
Associated Factor ◽  
Nf Kappab

scholarly journals Ribosomes act as cryosensors in plants

2020 ◽  
Author(s):  
Philip Anthony Wigge ◽  
David Guillaume-Schoepfer ◽  
Katja E Jaeger ◽  
Feng Geng ◽  
Fabrizio G Doccula ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Cold Stress ◽  
Protein Translation ◽  
Free Calcium ◽  
Cold Temperatures ◽  
Stunted Growth ◽  
Subzero Temperatures ◽  
Delayed Flowering

Cold temperatures are a threat to temperate plants, and Arabidopsis thaliana has acquired an adaptive gene expression network controlled by CBF transcription factors. The CBFs are sufficient to enable plants to survive otherwise lethal subzero temperatures. Constitutive CBF expression causes delayed flowering and stunted growth, and plants have evolved the ability to restrict CBF expression to occur only in the cold. This allows plants to anticipate likely freezing events and selectively deploy cold tolerance. The mechanism by which cold stress is sensed is however unknown. Here we show that protein translation rates in plants are proportional to temperature, and reduced translation rates trigger a rise in intracellular free calcium that activates the CAMTA transcription factors, and these directly activate cold-induced gene expression.

scholarly journals The biological characteristics of transcription factors AP-2α and AP-2γ and their importance in various types of cancers

2019 ◽  
Vol 39 (3) ◽  
Author(s):  
Damian Kołat ◽  
Żaneta Kałuzińska ◽  
Andrzej K. Bednarek ◽  
Elżbieta Płuciennik
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Regulation Of Gene Expression ◽  
Cancer Tissue ◽  
Diagnostic Biomarkers ◽  
Oncological Patients ◽  
Wide Range ◽  
Non Coding Rnas

Abstract The Activator Protein 2 (AP-2) transcription factor (TF) family is vital for the regulation of gene expression during early development as well as carcinogenesis process. The review focusses on the AP-2α and AP-2γ proteins and their dualistic regulation of gene expression in the process of carcinogenesis. Both AP-2α and AP-2γ influence a wide range of physiological or pathological processes by regulating different pathways and interacting with diverse molecules, i.e. other proteins, long non-coding RNAs (lncRNA) or miRNAs. This review summarizes the newest information about the biology of two, AP-2α and AP-2γ, TFs in the carcinogenesis process. We emphasize that these two proteins could have either oncogenic or suppressive characteristics depending on the type of cancer tissue or their interaction with specific molecules. They have also been found to contribute to resistance and sensitivity to chemotherapy in oncological patients. A better understanding of molecular network of AP-2 factors and other molecules may clarify the atypical molecular mechanisms occurring during carcinogenesis, and may assist in the recognition of new diagnostic biomarkers.

scholarly journals Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding Datasets

Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1321 ◽  
Author(s):  
Mahmoud Ahmed ◽  
Trang Huyen Lai ◽  
Jin Seok Hwang ◽  
Sahib Zada ◽  
Trang Minh Pham ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Transcription Factors ◽  
High Throughput Sequencing ◽  
Cell Model ◽  
Cell Types ◽  
Autophagy Gene ◽  
Occupancy Patterns ◽  
Differentiation Stage

Autophagy is the cell self-eating mechanism to maintain cell homeostasis by removing damaged intracellular proteins or organelles. It has also been implicated in the development and differentiation of various cell types including the adipocyte. Several links between adipogenic transcription factors and key autophagy genes has been suggested. In this study, we tried to model the gene expression and their transcriptional regulation during the adipocyte differentiation using high-throughput sequencing datasets of the 3T3-L1 cell model. We applied the gene expression and co-expression analysis to all and the subset of autophagy genes to study the binding, and occupancy patterns of adipogenic factors, co-factors and histone modifications on key autophagy genes. We also analyzed the gene expression of key autophagy genes under different transcription factor knockdown adipocyte cells. We found that a significant percent of the variance in the autophagy gene expression is explained by the differentiation stage of the cell. Adipogenic master regulators, such as CEBPB and PPARG target key autophagy genes directly. In addition, the same factor may also control autophagy gene expression indirectly through autophagy transcription factors such as FOXO1, TFEB or XBP1. Finally, the binding of adipogenic factors is associated with certain patterns of co-factors binding that might modulate the functions. Some of the findings were further confirmed under the knockdown of the adipogenic factors in the differentiating adipocytes. In conclusion, autophagy genes are regulated as part of the transcriptional programs through adipogenic factors either directly or indirectly through autophagy transcription factors during adipogenesis.

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