Chapter title |
Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes
|
---|---|
Chapter number | 12 |
Book title |
Statistical Genomics
|
Published in |
Methods in molecular biology, January 2016
|
DOI | 10.1007/978-1-4939-3578-9_12 |
Pubmed ID | |
Book ISBNs |
978-1-4939-3576-5, 978-1-4939-3578-9
|
Authors |
Songjoon Baek, Myong-Hee Sung, Baek, Songjoon, Sung, Myong-Hee |
Editors |
Ewy Mathé, Sean Davis |
Abstract |
High-throughput sequencing technologies have made it possible for biologists to generate genome-wide profiles of chromatin features at the nucleotide resolution. Enzymes such as nucleases or transposes have been instrumental as a chromatin-probing agent due to their ability to target accessible chromatin for cleavage or insertion. On the scale of a few hundred base pairs, preferential action of the nuclear enzymes on accessible chromatin allows mapping of cell state-specific accessibility in vivo. Such accessible regions contain functionally important regulatory sites, including promoters and enhancers, which undergo active remodeling for cells adapting in a dynamic environment. DNase-seq and the more recent ATAC-seq are two assays that are gaining popularity. Deep sequencing of DNA libraries from these assays, termed genomic footprinting, has been proposed to enable the comprehensive construction of protein occupancy profiles over the genome at the nucleotide level. Recent studies have discovered limitations of genomic footprinting which reduce the scope of detectable proteins. In addition, the identification of putative factors that bind to the observed footprints remains challenging. Despite these caveats, the methodology still presents significant advantages over alternative techniques such as ChIP-seq or FAIRE-seq. Here we describe computational approaches and tools for analysis of chromatin accessibility and genomic footprinting. Proper experimental design and assay-specific data analysis ensure the detection sensitivity and maximize retrievable information. The enzyme-based chromatin profiling approaches represent a powerful and evolving methodology which facilitates our understanding of how the genome is regulated. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 1 | 25% |
Unknown | 3 | 75% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 3 | 75% |
Scientists | 1 | 25% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 20 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 7 | 35% |
Student > Ph. D. Student | 5 | 25% |
Student > Bachelor | 3 | 15% |
Student > Master | 2 | 10% |
Student > Doctoral Student | 1 | 5% |
Other | 1 | 5% |
Unknown | 1 | 5% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 9 | 45% |
Agricultural and Biological Sciences | 5 | 25% |
Neuroscience | 2 | 10% |
Pharmacology, Toxicology and Pharmaceutical Science | 1 | 5% |
Medicine and Dentistry | 1 | 5% |
Other | 1 | 5% |
Unknown | 1 | 5% |