Special Issue "'Junk DNA' is not Junk"

Guest Editor
Prof. Dr. Mary E. Delany
Department of Animal Science, The University of California, Davis, USA
Website: http://animalscience.ucdavis.edu/faculty/delany/
E-Mail: medelany@ucdavis.edu
Phone: +1 530 752 0233
Fax: +1 530 752 0175

Dear Colleagues,

Since the late Susumu Ohno first introduced the phrase “junk DNA” in 1972 (“So Much Junk DNA in Our Genome”, Brookhaven Symposium on Biology 23:366-370) the concept has captured the imagination of scientists and non-scientists alike leading to much research as well as debate.  Ohno’s original hypothesis regarding the origin and evolutionary significance of “junk DNA” has been modified and refined over the last four decades benefitting from recent comparative and functional genomics analyses and as influenced by the large-scale bioinformatics analysis of sequences. Many have argued we must abandon Ohno’s terminology, but yet it persists, largely because it remains an interesting conceptual framework to explore given the relative enormity of sequence content in the non-protein-coding category and the finding that gene numbers appear surprisingly similar among vertebrates while non-coding sequences range from being widely variable to unexpected conservation.

This special issue seeks to cover a broad range of topics on the types, functions, conservation, evolution and ultimately the biological significance of “junk DNA” broadly defined as “non-protein-coding sequence” found within and among genomes.  We encourage contributions covering the diversity of species. We welcome scientific perspectives, reviews and original research papers on the topic of “junk DNA” and its biological significance.

Prof. Dr. Mary E. Delany
Guest Editor

Submission

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• Junk DNA
• non-coding DNA
• genome evolution
• telomeres
• centromeres
• functional RNA
• siRNA
• piRNA
• lincRNA
• miRNA
• snoRNA
• rRNA
• tRNA
• pseudogenes
• regulatory elements
• introns
• transposons
• retrotransposons
• repetitive DNA
• Heterochromatin
• ENCODE

Type of Paper: Review.
Title: A Model of Evolution of Development Based on Germline Penetration of New "no-junk" DNA.
Authors: Alessandro Fontana ^1,2 and Borys Wrobel ^3,4
Affiliations: ¹ IEEE
² Faculty of Electronics, Telecommunications and Informatics, Technical University of Gdansk, Gdansk, Poland; E-Mail: cnd12001@yahoo.it
³ Evolving Systems Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
⁴ Systems Modeling Laboratory, Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland; E-Mail: wrobel@evosys.org
Abstract: There is a mounting body of evidence that somatic transposition may be involved in normal development of multicellular organisms and in pathology, especially cancer. Epigenetic Tracking (ET) is an abstract model of multicellular development that was designed to take into account these recent observations. Its aim is not to model the development of a particular organism nor to merely summarize mainstream knowledge on genetic regulation of development. Rather, the goal of ET is to provide a theoretical framework to test new postulated genetic mechanisms, not fully established yet in mainstream biology. The first proposal is that some events in development and cancerogenesis are orchestrated by transposition events with specific sources and targets. The second is that these events are affected by somatic mutations in the transposons. The third proposal is that such mutated transposons can enter the germline, and thus affect the fitness of the progeny. In this brief review, we will present the model and link these three postulated mechanisms to biological observations.

Type of Paper: Article
Title: Beyond the Junk — Variable Tandem Repeats as Facilitators of Rapid Evolution of Regulatory and Coding Sequences
Authors: Rita Gemayel ^1,2, Steven Boeynaems ^1,2, Janice Cho ^1,2 and Kevin J. Verstrepen ^1,2
Affiliations: ¹ Laboratory for Systems Biology, VIB, Gaston Geenslaan 1, B-3001 Heverlee, Belgium; E-Mail: Kevin.Verstrepen@biw.vib-kuleuven.be
² Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), K.U.Leuven, Gaston Geenslaan 1, B-3001 Heverlee, Belgium
Abstract: Copy Number Variations (CNVs) and Single Nucleotide Polymorphisms (SNPs) have been the major focus of most large-scale comparative genomics studies to date. Here, we discuss a third, largely ignored, type of genetic variation namely changes in tandem repeat number. Historically, tandem repeats have been designated as non functional ‘junk’ DNA, mostly as a result of their highly unstable nature. With the exception of tandem repeats involved in   human neurodegenerative diseases, repeat variation was believed to be neutral with no phenotypic consequences. Recent studies, however, have shown that as many as 10 % to 20 % of coding and regulatory sequences in eukaryotes contain an unstable repeat tract. Contrary to initial suggestions, tandem repeat variation can have useful phenotypic consequences. Examples include rapid variation in microbial cell surface, tuning of internal molecular clocks in flies and the dynamic morphological plasticity in mammals. As such, tandem repeats can be useful functional elements that facilitate evolvability and rapid adaptation.

Type of Paper: Review
Title: Involvement of Small RNAs in Host defense and Immunity in Plants and Animals
Authors: Julie Hicks and Hsiao-Ching Liu
Affiliation: North Carolina State University, Raleigh, NC 27695, USA; E-Mail: hc_liu@ncsu.edu
Abstract: Post-transcriptional gene regulation by small RNAs is now established as an important branch of the gene regulatory system. Many different classes of small RNAs have been discovered, and among these are short interfering RNAs (siRNAs) and microRNA (miRNAs). Though differences exist in the processing and function of small RNAs between plants and animals, both groups utilize small RNA-mediated gene regulation in response to pathogens. In plants host encoded miRNAs and siRNAs generated from viral RNA function in host defense and pathogenic resistance. In animals miRNAs are key regulators of both immune system development and immune function.  Many pathogens, and especially viruses, have evolved mechanisms to usurp the host's small RNA mediated regulatory system. Overall, small RNAs are a major component of eukaryotic host defense and immunity.

Type of Paper: Review
Title: Factors Behind Junk DNA in Bacteria
Authors: Rosario Gil^1,2 and Amparo Latorre^1,2,3
Affiliations: ¹Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, 46071 València, Spain; E-Mail: Amparo.Latorre@uv.es
²Departament de Genètica, Universitat de València, Dr. Moliner, 50, 46100 Burjassot (València), Spain
³Área de Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP), Avenida de Cataluña 21, 46020 Valencia, Spain
Abstract: Although bacterial genomes have been traditionally viewed as being very compact, with relatively low amounts of repetitive and non-coding DNA, this view has dramatically changed in recent years.  The increase of available complete bacterial genomes has revealed that many species present abundant repetitive DNA (i.e. insertion sequences, prophages or paralogous genes), and that many of these sequences are not functional but the consequence of evolution to adapt to specialized host-related ecological niches. Comparative genomics analyses with close relatives that live in non-specialized environments reveal the nature and fate of this bacterial junk DNA.

Type of Paper: Review
Title: Identifying and Characterizing Regulatory Sequences in the Human Genome
Authors: Nathan Sheffield ¹, Terrence S. Furey ²
Affiliation: ¹ Institute for Genome Sciences & Policy, Duke University, Durham, NC, USA
² Carolina Center for Genome Sciences, Depts. of Genetics and Biology, University of North Carolina, Chapel Hill, NC, USA; E-Mail: tsfurey@email.unc.edu
Abstract: After finishing a nearly complete human genome reference sequence in 2002, the genomics community turned to the task of interpreting it, especially the non-coding portions. This effort has been led by both large scale-projects, such as the Encyclopedia of DNA Elements (ENCODE) project, and individual investigators working to identify and characterize the functional elements in the genome. As part of the ENCODE project, our group and others have identified millions of regulatory elements in hundreds of human cell-types using DNase-seq and FAIRE-seq experiments that detect regions of nucleosome-free open chromatin. Nearly all identified elements are found in non-coding DNA, hypothesizing a function for previously unannotated sequence. In this review, we provide details of the ENCODE effort to define regulatory elements, summarize the main results, and discuss implications of the millions of novel regulatory elements distributed throughout the genome.

Type of Paper: Review
Title: Transposable Elements: From DNA Parasites to Architects of Evolution
Authors: Oliver Piskurek and Daniel J. Jackson
Affiliation: Courant Research Centre Geobiology, Georg-August-University of Göttingen, Goldschmidtstr. 3, 37077 Göttingen, Germany; E-Mail: djackso@uni-goettingen.de
Abstract: Following the completion of the human genome a decade ago, scientists realized that nearly half of our DNA is derived from transposable elements (TEs). Due to recent advances in high throughput sequencing technologies, it is now clear that TEs comprise the largest molecular class within most metazoan genomes. TEs, once categorised as "junk DNA", are now known to influence genomic structure and function by increasing the coding and non-coding genetic repertoire of the host. In this way TEs are key elements that have stimulated the evolution of metazoan genomes. This review highlights several exciting lines of TE research including the horizontal transfer of TEs through host-parasite interactions, the vertical maintenance of TEs over long periods of evolutionary time, and the direct role that TEs have played in generating morphological novelty.