Transcriptional Regulatory Network (transcriptional + regulatory_network)

Distribution by Scientific Domains


Selected Abstracts


From fibroblasts to iPS cells: Induced pluripotency by defined factors

JOURNAL OF CELLULAR BIOCHEMISTRY, Issue 4 2008
Rui Zhao
Abstract Patient-specific pluripotent cells may serve as a limitless source of transplantable tissue to treat a number of human blood and degenerative diseases without causing immune rejection. Recently, isolation of patient-specific induced pluripotent stem (iPS) cells was achieved by transducing fibroblasts with four transcription factors, Oct4, Sox2, Klf4, and c-Myc. However, the use of oncogenes and retrovirus in the current iPS cell establishment protocol raises safety concerns. To generate clinical quality iPS cells, the development of novel reprogramming methods that avoid permanent genetic modification is highly desired. The molecular mechanisms that mediate reprogramming are essentially unknown. We argue that establishment of a stable and self-sustainable ES-specific transcriptional regulatory network is essential for reprogramming. Such a system should include expression of Oct4, Sox2, Nanog and probably other pluripotenty-promoting factors from endogenous loci and establishment of a permissive epigenetic state to maintain such expression. In addition, though not yet proven experimentally, overcoming cellular senescence of fibroblasts by inactivating Rb and p53 pathways and up-regulating telomerase activity may also be required. J. Cell. Biochem. 105: 949,955, 2008. © 2008 Wiley-Liss, Inc. [source]


Nuclear receptors of the enteric tract: guarding the frontier

NUTRITION REVIEWS, Issue 2008
Daniel R Schmidt
In addition to its classical role in mineral homeostasis, the vitamin D receptor has been implicated in diverse physiologic and pathophysiologic processes including immunoregulation and cancer. Interestingly, the vitamin D receptor has been evolutionarily and functionally linked to a select group of nuclear receptors based on a common organism-wide tissue expression profile. These members of the nuclear receptor superfamily, which include the bile acid receptor, xenobiotic receptors, and several orphan nuclear receptors, comprise a transcriptional regulatory network that functions in nutrient uptake, xenobiotic metabolism, and mucosal protection. The major homeostatic functions of the enteric nuclear receptor network are the topic of this review. [source]


The two faces of short-range evolutionary dynamics of regulatory modes in bacterial transcriptional regulatory networks

BIOESSAYS, Issue 7 2007
S. Balaji
Studies on the conservation of the inferred transcriptional regulatory network of prokaryotes have suggested that specific transcription factors are less-widely conserved in comparison to their target genes. This observation implied that, at large evolutionary distances, the turnover of specific transcription factors through loss and non-orthologous displacement might be a major factor in the adaptive radiation of prokaryotes. However, the recent work of Hershberg and Margalit1 suggests that, at shorter phylogenetic scales, the evolutionary dynamics of the bacterial transcriptional regulatory network might exhibit distinct patterns. The authors find previously unnoticed relationships between the regulatory mode (activation or repression), the number of regulatory interactions and their conservation patterns in ,-proteobacteria. These relationships might be shaped by the differences in the adaptive value and mode of operation of different regulatory interactions. BioEssays 29:625,629, 2007. © 2007 Wiley Periodicals, Inc. [source]


Using ColE1-derived RNA I for suppression of a bacterially encoded gene: implication for a novel plasmid addiction system

BIOTECHNOLOGY JOURNAL, Issue 6 2006
Irene Pfaffenzeller
Abstract The use of plasmid DNA for gene therapeutical purposes is a novel technology with advantages and drawbacks. One of the required improvements is to avoid antibiotic resistance genes or other additional sequences for selection within the plasmid. Here, we describe an alternative approach to equip a ColE1 plasmid with a regulatory function within the cell, which could be used for selection of plasmid carrying cells. No additional sequences are required, since the mechanism is based on RNA/RNA antisense interaction involving the naturally occurring RNA I derived from the plasmid's origin of replication. The plasmid replicational regulatory network was linked to the transcriptional regulatory network of an engineered target gene, present on the bacterial chromosome. Thus, gene suppression of a reporter could be achieved by mere presence of the ColE1-type plasmid pBR322. Proof of this concept was shown in shaker-flask experiments and fed-batch fermentation processes. The strategy of regulating gene expression by plasmid replication implicates a novel strategy for plasmid selection, as the gene to be suppressed could be toxic or growth hampering, providing advantage to plasmid carrying host cells. [source]


Putting numbers on the network connections

BIOESSAYS, Issue 8 2007
Gary D. Stormo
DNA,protein interactions are fundamental to many biological processes, including the regulation of gene expression. Determining the binding affinities of transcription factors (TFs) to different DNA sequences allows the quantitative modeling of transcriptional regulatory networks and has been a significant technical challenge in molecular biology for many years. A recent paper by Maerkl and Quake1 demonstrated the use of microfluidic technology for the analysis of DNA,protein interactions. An array of short DNA sequences was spotted onto a glass slide, which was then covered with a microfluidic device allowing each spot to be within a chamber into which the flow of materials was controlled by valves. By trapping the DNA,protein complexes on the surface and measuring their concentrations microscopically, they could determine the binding affinity to a large number of DNA sequences that were varied systematically. They studied four TFs from the basic helix,loop,helix family of proteins, all of which bind to E-box sites with the consensus CAnnTG (where "n" can be any base), and showed that variations in affinity for different sites allows each TF to regulate different genes. BioEssays 29:717,721, 2007. © 2007 Wiley Periodicals, Inc. [source]


The two faces of short-range evolutionary dynamics of regulatory modes in bacterial transcriptional regulatory networks

BIOESSAYS, Issue 7 2007
S. Balaji
Studies on the conservation of the inferred transcriptional regulatory network of prokaryotes have suggested that specific transcription factors are less-widely conserved in comparison to their target genes. This observation implied that, at large evolutionary distances, the turnover of specific transcription factors through loss and non-orthologous displacement might be a major factor in the adaptive radiation of prokaryotes. However, the recent work of Hershberg and Margalit1 suggests that, at shorter phylogenetic scales, the evolutionary dynamics of the bacterial transcriptional regulatory network might exhibit distinct patterns. The authors find previously unnoticed relationships between the regulatory mode (activation or repression), the number of regulatory interactions and their conservation patterns in ,-proteobacteria. These relationships might be shaped by the differences in the adaptive value and mode of operation of different regulatory interactions. BioEssays 29:625,629, 2007. © 2007 Wiley Periodicals, Inc. [source]


Location analysis of DNA-bound proteins at the whole-genome level: untangling transcriptional regulatory networks

BIOESSAYS, Issue 6 2001
Béatrice Nal
In this post-sequencing era, geneticists can focus on functional genomics on a much larger scale than ever before. One goal is the discovery and elucidation of the intricate genetic networks that co-ordinate transcriptional activation in different regulatory circuitries. High-throughput gene expression measurement using DNA arrays has thus become routine strategy. This approach, however, does not directly identify gene loci that belong to the same regulatory group; e.g., those that are bound by a common (set of) transcription factor(s). Working in yeast, two groups have recently published an elegant method that could circumvent this problem, by combining chromatin immunoprecipitation and DNA microarrays.(1,2) The method is likely to provide a powerful tool for the dissection of global regulatory networks in eukaryotic cells. BioEssays 23:473,476, 2001. © 2001 John Wiley & Sons, Inc. [source]