遗传学实验技术

Retrotransposons are a major agent of genome evolution. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within speci ...

The recent development of next-generation sequencing (NGS) technologies allowed various authors to imagine, test, and validate new approaches for TE analysis, in their nature, type, activity, or quantity. In this chapter, we describe briefly the technologies used, then the various app ...

We describe here the use of the ISfinder database and its associated software. ISfinder was conceived �initially as a comprehensive database for prokaryotic insertion sequences (ISs). It now includes software for visualising complete and partial IS copies in whole genomes (ISbrows ...

The development of numerous programs for the identification of mobile elements raises the issue of the founding concepts that are shared in their design. This is necessary for at least three reasons. First, the cost of designing, developing, debugging, and maintaining software could prese ...

Current high-throughput techniques have made it feasible to sequence even the genomes of non-model organisms. However, the annotation process now represents a bottleneck to genome analysis, especially when dealing with transposable elements (TE). Combined approaches, using bo ...

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low-complexity DNA sequences. In this chapter, we present the procedure to routinely use this program on a personal computer.

Transposable elements (TEs) are discrete pieces of DNA that can move from one site to another within genomes and sometime between genomes. They are found in all major branches of life. Because of their wide distribution and considerable diversity, they are a considerable source of genomic vari ...

Molecular domestication of several DNA transposons has occurred during the evolution of the primate lineage, and has led to the emergence of at least 42 new genes known as neogenes. Because these genes are derived from transposons, they encode proteins that are related to certain recombinas ...

Hypomethylation of repetitive DNA elements is a common epigenetics event in cancer. Although it is believed that this hypomethylation impacts chromosomal and transcriptional stability of the genome, the extent of repetitive sequences contribution to the development and progr ...

In gene therapy, viral or nonviral integrating vectors are used to deliver a corrected gene to replace the corresponding defective cellular gene. As vector delivery is (yet) commonly not targeted to a specific site in the host genome, and vector integration may lead to unwanted cellular gene der ...

The PiggyBac (PB) transposon system was originally derived from the cabbage looper moth Trichoplusia ni and represents one of the most promising transposon systems to date. Engineering of the PB transposase enzyme (PBase) and its cognate transposon DNA elements resulted in a substanti ...

The mobility of class II transposable elements (DNA transposons) can be experimentally controlled by separating the two functional components of the transposon: the terminal inverted repeat sequences that flank a gene of interest to be mobilized and the transposase protein that can be c ...

Transposable elements, the Flp recombinase, and the ΦC31 integrase are used in Drosophila melanogaster for numerous genome-wide manipulations. Often, their use is combined in a synergistic fashion to alter and engineer the fruit fly genome. Transposons are the foundation for all trans ...

Mos1-induced transgene-instructed gene conversion (MosTIC) is a technique of choice to engineer the genome of the nematode Caenorhabditis elegans. MosTIC is initiated by the excision of Mos1, a DNA transposon of the Tc1/Mariner super family that can be mobilized in the germ line of C. elegans. M ...

Rice is the model plant for monocotyledons. Since the completion of the high-quality sequence of its genome, the international community is deploying efforts to identify the function of the 30–40,000 nontransposable element genes of rice. These efforts comprise the creation of large col ...

Avian eggshell fragments recovered from both paleontological and archaeological deposits contain a cache of well-preserved ancient DNA. Here, we describe an extraction protocol that has been optimized to maximize the recovery of ancient DNA from fossil eggshell and minimize the co- ...

DNA contained in soils and sediments can provide novel insights into past environments and ecosystems. In this chapter, I describe an efficient and effective technique to extract total DNA from sediments in a manner that minimizes the coextraction of PCR-inhibitory compounds. I describe ...

Ancient hair, which has proved to be an excellent source of well-preserved ancient DNA, is often preserved in paleofeces. Here, we separate and wash hair shafts preserved in a paleofecal specimen believed to be from a Darwin’s ground sloth, Mylodon darwinii. After extracting DNA from the recover ...

DNA extracted from keratinous and chitinous materials can be a useful source of genetic information. To effectively liberate the DNA from these materials, buffers containing relatively high levels of DTT, proteinase K, and detergent are recommended, followed by purification using e ...

Paleofeces are the nonmineralized remains of dung from extant and extinct fauna. They represent a surprisingly large proportion of fossil remains recovered from cave sites across the world. Paleofeces contain the DNA of the defecator as well as the DNA of ingested plant and animal remains. To s ...