Transcriptional Complexity from Dynamic Interaction Networks In Vivo

2004 ◽  
Vol 5 (7) ◽  
pp. 559-566 ◽  
Author(s):  
Miroslav Dundr ◽  
Tom Misteli
Keyword(s):  
Dynamic Interaction ◽  
Interaction Networks

scholarly journals Global Nature of Dynamic Protein-Chromatin Interactions In Vivo: Three-Dimensional Genome Scanning and Dynamic Interaction Networks of Chromatin Proteins

2004 ◽  
Vol 24 (14) ◽  
pp. 6393-6402 ◽  
Author(s):  
Robert D. Phair ◽  
Paola Scaffidi ◽  
Cem Elbi ◽  
Jaromíra Vecerová ◽  
Anup Dey ◽  
...  
Keyword(s):  
Residence Time ◽  
Binding Proteins ◽  
Three Dimensional ◽  
Dynamic Interaction ◽  
Interaction Networks ◽  
High Plasticity ◽  
Chromatin Binding ◽  
Associated Proteins ◽  
Chromatin Proteins

ABSTRACT Genome structure and gene expression depend on a multitude of chromatin-binding proteins. The binding properties of these proteins to native chromatin in intact cells are largely unknown. Here, we describe an approach based on combined in vivo photobleaching microscopy and kinetic modeling to analyze globally the dynamics of binding of chromatin-associated proteins in living cells. We have quantitatively determined basic biophysical properties, such as off rate constants, residence time, and bound fraction, of a wide range of chromatin proteins of diverse functions in vivo. We demonstrate that most chromatin proteins have a high turnover on chromatin with a residence time on the order of seconds, that the major fraction of each protein is bound to chromatin at steady state, and that transient binding is a common property of chromatin-associated proteins. Our results indicate that chromatin-binding proteins find their binding sites by three-dimensional scanning of the genome space and our data are consistent with a model in which chromatin-associated proteins form dynamic interaction networks in vivo. We suggest that these properties are crucial for generating high plasticity in genome expression.

The study of protein–protein interactions in bacteria

2012 ◽  
Vol 58 (11) ◽  
pp. 1241-1257 ◽  
Author(s):  
Roberto Velasco-García ◽  
Rocío Vargas-Martínez
Keyword(s):  
Hybrid System ◽  
High Throughput ◽  
Protein Interactions ◽  
Specific Protein ◽  
False Positives ◽  
Interaction Networks ◽  
Protein Protein Interactions ◽  
Extensive Data ◽  
False Positives And Negatives

Many of the functions fulfilled by proteins in the cell require specific protein–protein interactions (PPI). During the last decade, the use of high-throughput experimental technologies, primarily based on the yeast 2-hybrid system, generated extensive data currently located in public databases. This information has been used to build interaction networks for different species. Unfortunately, due to the nature of the yeast 2-hybrid system, these databases contain many false positives and negatives, thus they require purging. A method for confirming these PPI is to test them using a technique that operates in vivo and detects binary PPI. This article comprises an overview of the study of PPI and describes the main techniques that have been used to identify bacterial PPI, prioritizing those that can be used for their verification, and it also mentions a number of PPI that have been identified or confirmed using these methods.

Cardiac fibroblasts: friend or foe?

2006 ◽  
Vol 291 (3) ◽  
pp. H1015-H1026 ◽  
Author(s):  
Troy A. Baudino ◽  
Wayne Carver ◽  
Wayne Giles ◽  
Thomas K. Borg
Keyword(s):  
Cardiac Function ◽  
Cardiac Fibroblasts ◽  
Cell Types ◽  
Dynamic Interaction ◽  
Normal Function ◽  
Complex Signals ◽  
Stage Of Development ◽  
Electrical Stimuli

Cardiac function is determined by the dynamic interaction of various cell types and the extracellular matrix that composes the heart. This interaction varies with the stage of development and the degree and duration of mechanical, chemical, and electrical signals between the various cell types and the ECM. Understanding how these complex signals interact at the molecular, cellular, and organ levels is critical to understanding the function of the heart under a variety of physiological and pathophysiological conditions. Quantitative approaches, both in vivo and in vitro, are essential to understand the dynamic interaction of mechanical, chemical, and electrical stimuli that govern cardiac function. The fibroblast can thus be a friend in normal function or a foe in pathophysiological conditions.

scholarly journals Dynamic interaction networks in a hierarchically organized tissue

2010 ◽  
Vol 6 (1) ◽  
pp. 417 ◽  
Author(s):  
Daniel C Kirouac ◽  
Caryn Ito ◽  
Elizabeth Csaszar ◽  
Aline Roch ◽  
Mei Yu ◽  
...  
Keyword(s):  
Dynamic Interaction ◽  
Interaction Networks

200 IN VITRO EMBRYO PRODUCTION IS ASSOCIATED WITH DISTINCT ALTERATIONS IN THE TRANSCRIPTOME BETWEEN THE BLASTOCYST STAGE AND THE INITIATION OF ELONGATION IN CATTLE

2011 ◽  
Vol 23 (1) ◽  
pp. 199
Author(s):  
M. Clemente ◽  
I. Lopez-Vidriero ◽  
P. O'Gaora ◽  
J. P. Mehta ◽  
N. Forde ◽  
...  
Keyword(s):  
Embryonic Development ◽  
System Development ◽  
Cell Communication ◽  
Blastocyst Stage ◽  
Interaction Networks ◽  
Differentially Expressed ◽  
Canonical Pathways ◽  
Cellular Development

The majority of embryonic loss in cattle occurs before maternal recognition of pregnancy around Day 16 postconception. The origin of the embryo can have a significant impact on the dynamics of embryo mortality. The aim of the present study was to compare transcript profiles between Day 7 (spherical blastocyst) and Day 13 (ovoid conceptus) bovine embryos derived in vitro or in vivo using the bovine Affymetrix microarray. Subsequent mapping of these differentially expressed genes (DEG) into relevant functional groups and pathways using ingenuity pathway analysis would identify the most important pathways involved in conceptus elongation in cattle. All embryos were produced either in vitro or in vivo by superovulation. A proportion of Day 7 blastocysts were snap frozen and the remainder were transferred (n = 10 per recipient) to synchronized heifers, recovered on Day 13, and snap frozen individually. Three pools of Day 7 blastocysts (n = 25 per pool) and Day 13 conceptuses (n = 5 per pool) were used for microarray analysis. A total of 909 and 1806 transcripts were differentially expressed between Day 7 and 13 in in vivo- and in vitro-derived embryos, respectively, of which a core of 465 transcripts was common to both groups. These 465 genes, likely to be crucial for the transition from blastocyst to the initiation of elongation, were associated with 5 canonical pathways, including interleukin (IL)-6 and IL-10 signalling, the endoplasmic reticulum stress pathway, and nitrogen metabolism. The top networks identified genes associated with 1) cellular development, lipid metabolism, and small molecular biochemistry; 2) cell-to-cell signaling; and 3) amino acid metabolism, including transcripts such as MYC, SLC25A12, HSPH1, LXN, ALDH18A1, PMP22, PEG3, CDH2, and Hsp70, which were up-regulated in the conceptus on Day 13. The top canonical pathways among the 444 DEG unique to in vivo embryos were 1) glycerolipid metabolism, 2) steroid biosynthesis, and 3) acute phase response signalling. One of the interaction networks identified was associated with cardiovascular system development and function, gene expression, and organismal development, including transcripts of proteins such as laminins and claudins, which are important for cell communication and morphogenesis during embryonic development. Among the 1341 DEG unique to in vitro-produced embryos, the top pathways were 1) glycerophospholipid metabolism, 2) IL-6 signalling, and 3) endothelial-1 signalling, whereas one of the interaction networks identified was associated with hematological disease, organismal injury, and abnormalities and cellular development, including POU5F1, a transcription factor known to bind to DNA and activate or repress transcription of several genes important for early embryonic development. In conclusion, this analysis has identified genes and pathways crucial to the transition from a spherical blastocyst to an ovoid conceptus as well as those uniquely associated with a greater likelihood of embryonic survival (those unique to in vivo embryos) or loss (those unique to in vitro embryos).

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