1) Define `transcriptome'. Briefly describe the genome tiling array technology to `visualize' transcriptomes in the genome of an organism. What `startling' observation was noted in the application of the tiling arrays technology to study the human transcriptome?

2) What do nodes and edges represent in system biology? Describe a simple two-node regulatory motif for gene expression.

Answer:

1) a) Define `transcriptome'.

ANSWER: A transcriptome is the full range of messenger RNA, or mRNA, molecules expressed by an organism. The term "transcriptome" can also be used to describe the array of mRNA transcripts produced in a particular cell or tissue type.

DNA microarrays are a well established technology for measuring the gene expression levels. Microarrays designed for the purpose use relatively few probes for each gene and are biased toward known and predicted gene structures. Recently, high-density oligonucleotide based the whole genome microarrays have emerged as a preferred platform for genomic analysis beyond simple gene expression profiling. Potential uses for such whole genome arrays include empirical annotation of the transcriptome, chromatin immunoprecipitation chip studies, analysis of alternative splicing, characterization of the methylome (the methylation state of the genome), polymorphism discovery and genotyping, comparative genome hybridization, and genome resequencing.

The application of whole genome tiling microarrays for studies of global gene expression is providing a more unbiased view of the transcriptional activity within genomes. For example, this approach has led to the identification and isolation of many novel non-protein-coding RNAs (ncRNAs), which have been suggested to comprise a major component of the transcriptome that have novel functions involved in epigenetic regulation of the genome. Additionally, tiling arrays have been recently applied to the study of histone modifications and methylation of cytosine bases (DNA methylation). Surprisingly, recent studies combining the analysis of gene expression (transcriptome) and DNA methylation (methylome) using whole-genome tiling arrays revealed that DNA methylation regulates the expression levels of many ncRNAs.

2) Network biology and bioinformatics Nodes and edges are the basic components of a network. Nodes represent units in the network, while edges represent the interactions between the units. Nodes can represent a wide array of biological units, from individual organisms to individual neurons in the brain.

a)

The feed-forward loop, are known to play an important role in gene regulatory networks.

Boolean networks, which were originally studied in the context of large random networks have emerged as models of specific gene regulatory networks, particularly in the context of plant development and the cell cycle .

Step-by-step explanation

1) The expression "transcriptome" can likewise be utilized to portray the variety of mRNA records delivered in a specific cell or tissue type. Interestingly with the genome, which is described by its strength, the transcriptome effectively changes. Indeed, a life form's transcriptome changes relying upon numerous components, including phase of improvement and ecological conditions.

Tiling array are a subtype of microarray chips. Like conventional microarrays, they work by hybridizing marked DNA or RNA target atoms to tests fixed onto a strong surface. Tiling array exhibits contrast from conventional microarrays in the idea of the tests. Rather than examining for groupings of known or anticipated qualities that might be scattered all through the genome, tiling exhibits test seriously for arrangements which are known to exist in a touching area. This is valuable for describing districts that are sequenced, however whose neighborhood capacities are to a great extent obscure. Tiling exhibits help in transcriptome planning just as in finding locales of DNA/protein collaboration (ChIP-chip, DamID), of DNA methylation (MeDIP-chip) and of affectability to (DNase Chip) and cluster CGH.

 ChIP-chip is one of the most popular usages of tiling arrays. Chromatin immunoprecipitation allows binding sites of proteins to be identified. A genome-wide variation of this is known as ChIP-on-chip. Proteins that bind to chromatin are cross-linked in vivo, usually via fixation with formaldehyde. The chromatin is then fragmented and exposed to antibodies specific to the protein of interest. These complexes are then precipitated. The DNA is then isolated and purified. With traditional DNA microarrays, the immunoprecipitated DNA is hybridized to the chip, which contains probes that are designed to cover representative genome regions. Overlapping probes or probes in very close proximity can be used. This gives an unbiased analysis with high resolution. Besides these advantages, tiling arrays show high reproducibility and with overlapping probes spanning large segments of the genome, tiling arrays can interrogate protein binding sites, which harbor repeats. ChIP-chip experiments have been able to identify binding sites of transcription factors across the genome in yeast, drosophila and a few mammalian species.

2) Nodes can represent genes, proteins, the protein complexes, and the individual states of a protein. A line connecting the two nodes is an edge. The edge can be directed: for example, if A regulates B, we write an arrow - a directed edge - from A to B, whereas if B regulates A we write an arrow from B to A.

Feed forward loop (FFL) motif is one of the most significant one in both E. coli and yeast. The FFL is composed of a transcription factor X, which regulates a second transcription factor Y. X and Y both bind the regulatory region of target gene Z and jointly modulate its transcription rate

A Boolean network consists of a discrete set of boolean variables each of which has a Boolean function (possibly different for each variable) assigned to it which takes inputs from a subset of those variables and output that determines the state of the variable it is assigned to.