scholarly journals A Genome-Wide Analysis of the Effects of Sucrose on Gene Expression in Arabidopsis Seedlings under Anoxia

2005 ◽  
Vol 137 (3) ◽  
pp. 1130-1138 ◽  
Author(s):  
Elena Loreti ◽  
Alessandra Poggi ◽  
Giacomo Novi ◽  
Amedeo Alpi ◽  
Pierdomenico Perata
Keyword(s):  
Gene Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-Wide Analysis of Dof Genes and Their Response to Abiotic Stress in Rose (Rosa chinensis)

2021 ◽  
Vol 12 ◽  
Author(s):  
Hong Nan ◽  
Richard A. Ludlow ◽  
Min Lu ◽  
Huaming An
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Stress Conditions ◽  
Genome Wide Analysis ◽  
Rosa Chinensis ◽  
Genome Wide ◽  
A Genome

Dof (DNA binding with one finger) proteins play important roles in plant development and defense regulatory networks. In the present study, we report a genome-wide analysis of rose Dof genes (RchDof), including phylogenetic inferences, gene structures, chromosomal locations, gene duplications, and expression diversity. A total of 24 full-length RchDof genes were identified in Rosa chinensis, which were assigned to nine distinct subgroups. These RchDof genes were unevenly distributed on rose chromosomes. The genome-scale analysis of synteny indicated that segmental duplication events may have played a major role in the evolution of the RchDof gene family. Analysis of cis-acting elements revealed putative functions of Dofs in rose during development as well as under numerous biotic and abiotic stress conditions. Moreover, the expression profiles derived from qRT-PCR experiments demonstrated distinct expression patterns in various tissues, and gene expression divergence existed among the duplicated RchDof genes, suggesting a fundamentally functional divergence of the duplicated Dof paralogs in rose. The gene expression analysis of RchDofs under drought and salt stress conditions was also performed. The present study offered novel insights into the evolution of RchDofs and can aid in the further functional characterization of its candidate genes.

scholarly journals Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells

2019 ◽  
Author(s):  
Hiroshi Ochiai ◽  
Tetsutaro Hayashi ◽  
Mana Umeda ◽  
Mika Yoshimura ◽  
Akihito Harada ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mammalian Cells ◽  
Molecular Mechanisms ◽  
Transcription Elongation ◽  
Mapk Signaling ◽  
Kinetic Properties ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Transcriptional Bursting

AbstractTranscriptional bursting is stochastic activation and inactivation of promoters, leading to discontinuous production of mRNA, and is considered to be a contributing factor to cell-to-cell heterogeneity in gene expression. However, it remains elusive how the kinetic properties of transcriptional bursting (e.g., burst size, burst frequency, and noise induced by transcriptional bursting) are regulated in mammalian cells. In this study, we performed a genome-wide analysis of transcriptional bursting in mouse embryonic stem cells (mESCs) using single-cell RNA-sequencing. We found that the kinetics of transcriptional bursting was determined by a combination of promoter and gene body binding proteins, including polycomb repressive complex 2 and transcription elongation-related factors. Furthermore, large-scale CRISPR-Cas9-based screening and functional analysis revealed that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncover key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.

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