基因表达差异显示实验

The precise location of nucleosomes in functional regulatory regions in chromatin is critical to the regulation of transcription. The nucleosome structure protects DNA from microccocal nuclease (MNase) digestion and leaves a footprint on DNA that indicates the position of nucleo ...

Salt fractionation of nucleosomes, a classical method for defining “active” chromatin based on nucleosome solubility, has recently been adapted for genome-scale profiling. This method has several advantages for profiling chromatin dynamics, including general applicabil ...

Recent high-throughput sequencing technologies have opened the door for genome-wide characterization of chromatin features at an unprecedented resolution. Chromatin accessibility is an important property that regulates protein binding and other nuclear processes. He ...

Genome-wide patterns of nucleosome occupancy and positioning have greatly impacted on studies of chromatin structure, yet these studies require extensive computational analysis which is crucial for the quality of the resulting datasets and inferred conclusions. This chapter ...

Chromatin immunoprecipitation is widely utilized to determine the in vivo binding of factors that regulate transcription. This procedure entails formaldehyde-mediated cross-linking of proteins and isolation of soluble chromatin followed by shearing. The fragmented chr ...

In metazoans transcriptional enhancers and their more complex relatives, locus control regions, are often located at great linear distances from their target genes. In addition, these elements frequently activate different members of gene families in temporal sequence or in diffe ...

Bisulfite genomic sequencing provides a single-molecule view of cytosine methylation states. After deamination, each cloned molecule contains a record of methylation within its sequence. The full power of this technique is harnessed by treating nuclei with an exogenous DNMT prior to ...

We have recently established a system for purifying minichromosomes in a native state from Saccharomyces cerevisiae. This system is extremely efficient, and a single-step purification yields samples with sufficient purity and quantity for mass spectrometry (MS) analysis of hist ...

Site-specific recombinases have been harnessed for a variety of genetic manipulations involving the gain, loss, or rearrangement of genomic DNA in a variety of organisms. The enzymes have been further exploited in the model eukaryote Saccharomyces cerevisiae for mechanistic studi ...

The packaging of eukaryotic DNA into nucleosomes, the fundamental unit of chromatin, creates a barrier to nuclear processes, such as transcription, DNA replication, recombination, and repair. This obstructive nature of chromatin can be overcome by the enzymatic activity of chromat ...

The nucleosome-scanning assay (NuSA) couples isolation of mononucleosomal DNA after micrococcal nuclease (MNase) digestion with quantitative real-time PCR (qPCR) to map nucleosome positions in chromatin. It is a relatively simple, rapid procedure that can produce a high-resol ...

Eukaryotic genomes are wrapped in nucleosomes. These nucleosomes could be a barrier or could help facilitate the binding of transcription or replication factors. To understand what biological role nucleosomes play, an accurate and reliable method for measuring not only the position ...

This article describes QTL analyses for solitary (Nasonia, a parasitoid wasp) and social hymenopteran species (honeybee and bumblebee). These exemplar QTL analyses determined the genetic basis of morphological, behavioral, and colony level traits. Mapping populations were de ...

Quantitative variation underlies normal as well as pathological traits, and large part of this variability is under the control of genetic loci. Thanks to a better understanding of the extent and nature of human genetic variability and the subsequent availability of an increasing number of ...

The goal of mapping expression quantitative trait loci (eQTLs) is to identify genomic regions regulating gene expression traits, which can be gathered through microarrays, RNA-Seq, or related methods. Because thousands of expression traits are analyzed simultaneously, eQTL ana ...

In recent years, a new type of experiment has emerged. It involves genetic crosses and simultaneous measurements of the genome-wide gene expression and genotype information of the offspring. In this chapter, I discuss how to reconstruct gene regulatory networks from this type of data. Subhe ...

Statistical methods for genetic mapping have well been developed for diploid species but are lagging in the more complex polyploids. The genetic mapping of polyploids, where genome number is higher than two, is complicated by uncertainty about the genotype–phenotype correspondenc ...

Functional mapping is a statistical tool for mapping quantitative trait loci (QTLs) that control the developmental pattern and process of a complex trait. Functional mapping has two significant advantages beyond traditional QTL mapping approaches. First, it integrates biologi ...

In this chapter, we consider the problem of jointly analyzing multiple (correlated) complex traits in the context of identifying quantitative trait loci (QTL). The advantages of joint analysis (as opposed independent analysis) is the detection of pleiotropy and improved precision of ...

We introduce this communication with a brief outline of the historical landmarks in genetic modeling, especially concerning epistasis. Then, we present methods for the use of genetic modeling in QTL analyses. In particular, we summarize the essential expressions of the natural and orth ...