Pseudogenes-functions and protocols

Discovered a few decades ago, pseudogenes have been dismissed as "junk DNA" on the basis of the wrong assumption that absence of full coding potential means complete lack of functionality. However, in the past few years, pseudogenic DNA, RNA, and peptides/proteins have been shown to be involved in complex regulatory circuits that can affect not only their highly homologous parental genes but also unrelated genes. Therefore, it has become evident that these previously neglected molecules can contribute to the understanding of the physiological functions of the noncoding genome as well as to its alterations in disease, and for these reasons they have risen to the status of a new class of regulatory long noncoding RNAs. The main purpose of this volume is to increase the awareness of molecular, cellular, and computational biologists on the subject of pseudogenes, as well as to provide a list of methods that can be useful both to those who indeed want to study pseudogenes and to those who actually want to avoid their inadvertent detection. The introductory chapters give an overview of the functions that have been so far attributed to pseudogenes. After a section collecting methods for pseudogene identifi cation, the volume describes methods for the detection of pseudogene transcription and translation, both in the case that a specifi c pseudogene is under study and in the case that a high-throughput approach is undertaken. Two sections collecting methods to study the functions of pseudogenic RNA and proteins are then presented. The last section is composed of methods to avoid pseudogene detection when the targets of the study are their highly homologous parental counterparts. It is our hope that this volume will contribute to maintaining the high interest of the scientifi c community toward pseudogenes, while stimulating the conception of pseudogene- centered research projects and providing experimental protocols that can facilitate their execution.