Question

In: Biology

Describe the whole genome tiling and ChIP assays.

Describe the whole genome tiling and ChIP assays.

Solutions

Expert Solution

Whole Genome Tiling Array: Whole genome tiling array is a variation of microarray and is used for whole genome analysis. Whole genome tiling array for humans For the human genome, tiling arrays have been are designed for chromosomes 21 and 22. 25-mer oligonucleotides are used which are spaced 35 bp apart along the sequences. Tiling arrays can identify known genes, novel transcribed genes, or non translated RNA. The arrays can monitor gene expression, splicing pattern differences, identify new genes, and analyze for RNA-binding protein target sequences.

The tiling probe is designed against known contiguous sequences, whose transcriptional expression may not be known. Probe design (overlapping or gapped probes) determine the resolution of the tiling arrays. Immunoprecipitated DNA is used for tiling arrays. Total RNA is first isolated and reverse transcribed to double strand DNA. This DNA is in vitro transcribed to cRNA. The cRNA sample is split into triplicates, fragmented and labeled and then hybridized to the array. Arrays are scanned and then analyzed by bioinformatics. As the entire genome is covered, new genes that are expressed will be identified. The arrays involves hybridization with probes either at regular interval (TA) or probes that are overlapping along the entire length of the genome. Whole genome tiling arrays can be used after ChIP using overlapping probes too.

ChIP Arrays: Chromatin immunoprecipitation (ChIP) is an array that identifies in vivo binding sites on a genome wide basis. In ChIP, the DNA binding protein is covalently linked to its DNA binding sites invivo by a crosslinker. The crosslinking reagent penetrates the cell membrane and link both DNA and protein in a reversible manner. Cells are treated with formaldehyde and subjected to sonic oscillation. As a result, the length of each DNA molecule us reduced to fragment of several 100 base pairs. The mixture of DNA fragments is treated with an antibody to the protein of interest. The DNA protein complexes are immunoprecipitated and cross-links are broken. The DNA with the protein is PCR amplified and then sequenced. The DNA fragments can also be cloned and ligated to flanking sequences in the vector using PCR primers and then sequenced. ChIP-sequencing is a next generation sequencing technique where the immunoprecipitated DNA is subjected to sequence analysis for thousands of genes


Related Solutions

How does Whole Genome Sequencing work? Why is Whole Genome Sequencing useful for tracking the spread...
How does Whole Genome Sequencing work? Why is Whole Genome Sequencing useful for tracking the spread of S. Aureus infections? What is a 'clone' of S. aureus? Which clone is most common in the US, Canada, and South America? What is an 'endemic' disease? What are 'reservoirs' of disease? Which reservoirs play the greatest role in spreading MRSA in households? What are some ways MRSA may be spread through the household? What was one method used to reduce the rate...
ChIP-seq is widely used to analyze the distribution of specific proteins throughout the genome. Which is...
ChIP-seq is widely used to analyze the distribution of specific proteins throughout the genome. Which is NOT a requirement for doing ChIP-seq? Group of answer choices Next Generation Sequencing (ie Illumina sequencing) is required to analyze the sequence composition of the DNA recovered from the immunoprecipitate. The sequence of the genome for the organism you are studying must be known. An antibody must be available to immunoprecipitate the protein of interest. The protein of interest must crosslink either directly or...
Describe the general principles of antibody based assays in cohesive sentences
Describe the general principles of antibody based assays in cohesive sentences
System on Chip designs are made possible by deep submicron technology. This technology presents a whole...
System on Chip designs are made possible by deep submicron technology. This technology presents a whole set of design challenges including: (1) interconnect delays, (2) clock and power distribution, and (3) the placement and routing of millions of gates. Explain in details your answer.
Describe the use of microarrays in plant research. In your answer define what a Tiling Array...
Describe the use of microarrays in plant research. In your answer define what a Tiling Array is.
Whole genome analyses reveal millions of variants; however, at the present time only a very small...
Whole genome analyses reveal millions of variants; however, at the present time only a very small number of genetic variations exist for which there are firm associations with disease or a high risk for disease and where morbidity and mortality are increased. However, science is continuously updating the list of clinically relevant variants (Evans & Rothschild, 2012). The requirements for monitoring of whole genome analyses over time are not yet established. Since existence of a known deleterious variant can change...
What is the principle of Genome-Wide Expression Patterns Analysis using PCR and how DNA chip can...
What is the principle of Genome-Wide Expression Patterns Analysis using PCR and how DNA chip can be used in this process.
Describe what is meant by the terms ‘pan genome’ and ‘core genome.’ What sorts of genes...
Describe what is meant by the terms ‘pan genome’ and ‘core genome.’ What sorts of genes do you expect to be present in the core genome? What sorts of genes are found in the pan genome but outside the core genome? What processes of genetic exchange give rise to the great diversity of genome sequences in the various strains of a given species?
State a clinical diagnosis for the results of the laboratory assays/tests below and describe the relevant...
State a clinical diagnosis for the results of the laboratory assays/tests below and describe the relevant sonographic findings of each condition. i. ↑Ca2+, ↑PTH ii. FT4/FT3↓, TSH↑ iii. FT4/FT3↑, TSH↓
Read the paper below and answer the accompanying questions. ‘Whole-genome sequencing expands diagnostic utility and improves...
Read the paper below and answer the accompanying questions. ‘Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine’ Stavropoulos et al. npj Genomic Medicine 1, Article number: 15012 (2016) doi:10.1038/npjgenmed.2015.12 How successful was the study at reaching conclusive clinically useful diagnoses? Briefly describe the relationship between the CNV found and one disease phenotype – why does discovery of the variant provide a diagnosis (what gene is affected, how, what has that got to do with the disease?)...
ADVERTISEMENT
ADVERTISEMENT
ADVERTISEMENT