scholarly journals The DREAM complex: master coordinator of cell cycle-dependent gene expression

2013 ◽  
Vol 13 (8) ◽  
pp. 585-595 ◽  
Author(s):  
Subhashini Sadasivam ◽  
James A. DeCaprio
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Cycle Dependent

scholarly journals Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

2019 ◽  
Vol 116 (39) ◽  
pp. 19490-19499 ◽  
Author(s):  
Chenglong Xia ◽  
Jean Fan ◽  
George Emanuel ◽  
Junjie Hao ◽  
Xiaowei Zhuang
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Spatial Information ◽  
Detection Efficiency ◽  
Expression Profiles ◽  
Regulation Of Gene Expression ◽  
Rna Profiling ◽  
Spatially Resolved ◽  
Cycle Dependent

The expression profiles and spatial distributions of RNAs regulate many cellular functions. Image-based transcriptomic approaches provide powerful means to measure both expression and spatial information of RNAs in individual cells within their native environment. Among these approaches, multiplexed error-robust fluorescence in situ hybridization (MERFISH) has achieved spatially resolved RNA quantification at transcriptome scale by massively multiplexing single-molecule FISH measurements. Here, we increased the gene throughput of MERFISH and demonstrated simultaneous measurements of RNA transcripts from ∼10,000 genes in individual cells with ∼80% detection efficiency and ∼4% misidentification rate. We combined MERFISH with cellular structure imaging to determine subcellular compartmentalization of RNAs. We validated this approach by showing enrichment of secretome transcripts at the endoplasmic reticulum, and further revealed enrichment of long noncoding RNAs, RNAs with retained introns, and a subgroup of protein-coding mRNAs in the cell nucleus. Leveraging spatially resolved RNA profiling, we developed an approach to determine RNA velocity in situ using the balance of nuclear versus cytoplasmic RNA counts. We applied this approach to infer pseudotime ordering of cells and identified cells at different cell-cycle states, revealing ∼1,600 genes with putative cell cycle-dependent expression and a gradual transcription profile change as cells progress through cell-cycle stages. Our analysis further revealed cell cycle-dependent and cell cycle-independent spatial heterogeneity of transcriptionally distinct cells. We envision that the ability to perform spatially resolved, genome-wide RNA profiling with high detection efficiency and accuracy by MERFISH could help address a wide array of questions ranging from the regulation of gene expression in cells to the development of cell fate and organization in tissues.

scholarly journals Protein Kinase C Regulates Late Cell Cycle-Dependent Gene Expression

2012 ◽  
Vol 32 (22) ◽  
pp. 4651-4661 ◽  
Author(s):  
Z. Darieva ◽  
N. Han ◽  
S. Warwood ◽  
K. S. Doris ◽  
B. A. Morgan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Protein Kinase C ◽  
Protein Kinase ◽  
Kinase C ◽  
Cycle Dependent

Cell-cycle-dependent localization of human cytomegalovirus UL83 phosphoprotein in the nucleolus and modulation of viral gene expression in human embryo fibroblasts in vitro

2011 ◽  
Vol 112 (1) ◽  
pp. 307-317 ◽  
Author(s):  
Maria-Cristina Arcangeletti ◽  
Isabella Rodighiero ◽  
Prisco Mirandola ◽  
Flora De Conto ◽  
Silvia Covan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Human Cytomegalovirus ◽  
Human Embryo ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
Embryo Fibroblasts ◽  
Cycle Dependent
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