Genetics: Analysis and Principles
6th Edition
ISBN: 9781259616020
Author: Robert J. Brooker Professor Dr.
Publisher: McGraw-Hill Education
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Textbook Question
Chapter 15, Problem 1EQ
Briefly describe the method of chromatin immunoprecipitation sequencing (ChIP-Seq). How is it used to determine nucleosome positions within a genome?
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Outline the procedure of chromatin immunoprecipitation sequencing, and explain how it was used to identify nucleosomefree regions that flank eukaryotic genes.
what is the whole-genome shotgun sequencing? Also briefly explain its strategy to assemble the genome sequence.
A new technique for rapidly determining the nuclesome structure for regions of chromatin is called Mnase-Seq. Briefly, in MNase-Seq experiments, the chromatin is digested with Micrococcal Nuclease (MNase) and then the resulting digest is subjecting to high throughput sequencing to identify sequences digested by enzyme. See this short article for complete explanation.
In the experiment below, researchers conducted an Mnase Seq experiment on a region of a chromosome in the absence (OHT-) and presence (OHT+) of a Protein X. This protein has a dramatic effect on the expression of the Igll1 gene, but no effect on Top3b nor Vpreb1 genes. Based on this information, explain what Protein X is doing to influence the Igll1 gene (limit 4-5 sentences).
Chapter 15 Solutions
Genetics: Analysis and Principles
Ch. 15.1 - 1. Combinatorial control refers to the phenomenon...Ch. 15.1 - 2. A regulatory transcription factor protein...Ch. 15.1 - 3. A bidirectional enhancer has the following...Ch. 15.1 - 4. Regulatory transcription factors can be...Ch. 15.2 - 1. A chromatin-remodeling complex may
a. change...Ch. 15.2 - Prob. 2COMQCh. 15.2 - 3. Which of the following characteristics is...Ch. 15.2 - 4. Transcriptional activation of eukaryotic genes...Ch. 15.3 - How can methylation affect transcription? a. It...Ch. 15.3 - 2. The process in which completely unmethylated...
Ch. 15.4 - Prob. 1COMQCh. 15.5 - The overall goal of the ENCODE Project is a. to...Ch. 15.6 - The binding of iron regulatory protein (IRP) to...Ch. 15 - Discuss the common points of control in eukaryotic...Ch. 15 - 2. Discuss the structure and function of...Ch. 15 - 3. What is meant by the term transcription factor...Ch. 15 - What are the functions of transcriptional...Ch. 15 - 5. Is each of the following statements true or...Ch. 15 - 6. Transcription factors usually contain one or...Ch. 15 - Prob. 7CONQCh. 15 - Prob. 8CONQCh. 15 - 9. Let’s suppose a mutation in the glucocorticoid...Ch. 15 - Prob. 10CONQCh. 15 - Prob. 11CONQCh. 15 - Prob. 12CONQCh. 15 - 13. Transcription factors such as the...Ch. 15 - An enhancer, located upstream from a gene, has the...Ch. 15 - 15. The DNA-binding domain of each CREB protein...Ch. 15 - The gene that encodes the enzyme called tyrosine...Ch. 15 - Prob. 17CONQCh. 15 - 18. What is a histone variant?
Ch. 15 - Prob. 19CONQCh. 15 - 20. What is meant by the term histone code? With...Ch. 15 - Prob. 21CONQCh. 15 - Histones are thought to be displaced as RNA...Ch. 15 - 23. What is an insulator? Describe two different...Ch. 15 - 24. What is DNA methylation? When we say that DNA...Ch. 15 - Lets suppose that a vertebrate organism carries a...Ch. 15 - 26. What is a CpG island? Where would you expect...Ch. 15 - Describe how the binding of iron regulatory...Ch. 15 - 1. Briefly describe the method of chromatin...Ch. 15 - Researchers can isolate a sample of cells, such as...Ch. 15 - Prob. 3EQCh. 15 - Prob. 4EQCh. 15 - Prob. 5EQCh. 15 - 6. As described in Chapter 21, an electrophoretic...Ch. 15 - Prob. 7EQCh. 15 - 1. Explain how DNA methylation could be used to...Ch. 15 - 2. Enhancers can occur almost anywhere in DNA and...
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- Briefly explain how synthetic probes are created to screen a DNA library when the protein encoded by the gene is known.arrow_forwardWhat are site-recombinases? Describe in detail how cre- recombinase can be used to decipher the roles of specific genes and proteins in complex multicellular organisms? Explain how the cre-lox system can be used to examine the role of a particular gene in a specific type of tissue?arrow_forwardBriefly explain why RNA-seq gives more information about the transcriptome than does microarray analysis.arrow_forward
- what are similarities and differences between chain-termination and reversible terminator sequencing?arrow_forwardExplain the sequencing-by synthesis (SBS) approach ?arrow_forwardTranscriptome analysis involves two separate methodologies: gene expression and RNA seq analyses. The 10 items below are a scrambled listing of the steps used in the two procedures. Identify the steps involved in RNA seq from the list below. Use the numbers in the list to refer to each step. Once the steps for RNA seq have been identified, write the steps in the order in which they are performed during the experiment. (1) DNA sequencing (2) Allow for hybridization and wash excess cRNA. (3) Mix labeled cRNA with array chip. (4) PCR amplification (5) Measure fluorescence intensity to determine abundance of transcripts. (6) Add labeled cRNA at each microarray location. (7) Map cDNA sequences to the genome of the organism to determine identity and abundance of transcripts. (8) mRNA isolation from cells (9) Prepare fluorescently labeled cRNA probes (10) cDNA synthesisarrow_forward
- Give a step by step method and diagram of how reversible terminator sequencing works.arrow_forwardWhat is dideoxy sequencing? Explain it please.arrow_forwardMicroarray hybridization is used mostly in transcript profiling or assaying DNA variation. Although the technology for establishing DNA microarrays was developed only recently, numerous applications have already been developed and their impact on future biomedical research and diagnostic approaches is expected to be profound. Give some examples of the practical use of this technique.arrow_forward
- It is desired to isolate genomic DNA from liquid culture of S. cerevisiae yeast. A commercial kit will be used to isolate genomic DNA from this liquid culture. Answer the following questions to understand the strategy used by commercial kits for genomic DNA isolation. a) List all the steps from cell pellet preparation to DNA elution. b) With which feature can the membrane in the column that comes with the commercial kit bind DNA? c) Which component in the kit would you use to recover the DNA from the membrane of the column to which the DNA was attached?arrow_forwardThe technique of fluorescence in situ hybridization (FISH) is described. This is another method for examining sequence complexity within a genome. In this method, a DNA sequence, such as a particular gene sequence, can be detected within an intact chromosome by using a DNA probe that is complementary to the sequence.For example, let’s consider the β-globin gene, which isfound on human chromosome 11. A probe complementary to theβ-globin gene binds to that gene and shows up as a brightly colored spot on human chromosome 11. In this way, researchers can detectwhere the β-globin gene is located within a set of chromosomes. Becausethe β-globin gene is unique and because human cells are diploid(i.e., have two copies of each chromosome), a FISH experimentshows two bright spots per cell; the probe binds to each copy ofchromosome 11. What would you expect to see if you used thefollowing types of probes?A. A probe complementary to the Alu sequenceB. A probe complementary to a tandem array near…arrow_forwardWhat advantages do cDNA libraries provide over genomic DNA libraries? Describe cloning applications where the use of a genomic library is necessary to provide information that a cDNA library cannot.arrow_forward
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