Genes

31 pages, 2373 KiB

Open AccessArticle

Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows

by Federica Torri, Ivo D. Dinov, Alen Zamanyan, Sam Hobel, Alex Genco, Petros Petrosyan, Andrew P. Clark, Zhizhong Liu, Paul Eggert, Jonathan Pierce, James A. Knowles, Joseph Ames, Carl Kesselman, Arthur W. Toga, Steven G. Potkin, Marquis P. Vawter and Fabio Macciardi

Genes 2012, 3(3), 545-575; https://doi.org/10.3390/genes3030545 - 30 Aug 2012

Cited by 44 | Viewed by 21549

Abstract

Whole-genome and exome sequencing have already proven to be essential and powerful methods to identify genes responsible for simple Mendelian inherited disorders. These methods can be applied to complex disorders as well, and have been adopted as one of the current mainstream approaches [...] Read more.

Whole-genome and exome sequencing have already proven to be essential and powerful methods to identify genes responsible for simple Mendelian inherited disorders. These methods can be applied to complex disorders as well, and have been adopted as one of the current mainstream approaches in population genetics. These achievements have been made possible by next generation sequencing (NGS) technologies, which require substantial bioinformatics resources to analyze the dense and complex sequence data. The huge analytical burden of data from genome sequencing might be seen as a bottleneck slowing the publication of NGS papers at this time, especially in psychiatric genetics. We review the existing methods for processing NGS data, to place into context the rationale for the design of a computational resource. We describe our method, the Graphical Pipeline for Computational Genomics (GPCG), to perform the computational steps required to analyze NGS data. The GPCG implements flexible workflows for basic sequence alignment, sequence data quality control, single nucleotide polymorphism analysis, copy number variant identification, annotation, and visualization of results. These workflows cover all the analytical steps required for NGS data, from processing the raw reads to variant calling and annotation. The current version of the pipeline is freely available at http://pipeline.loni.ucla.edu. These applications of NGS analysis may gain clinical utility in the near future (e.g., identifying miRNA signatures in diseases) when the bioinformatics approach is made feasible. Taken together, the annotation tools and strategies that have been developed to retrieve information and test hypotheses about the functional role of variants present in the human genome will help to pinpoint the genetic risk factors for psychiatric disorders. Full article

(This article belongs to the Special Issue Feature Paper 2012)

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24 pages, 292 KiB

Open AccessReview

Radiobiology and Reproduction—What Can We Learn from Mammalian Females?

by Aurora Ruiz-Herrera, Francisca Garcia and Montserrat Garcia-Caldés

Genes 2012, 3(3), 521-544; https://doi.org/10.3390/genes3030521 - 27 Aug 2012

Cited by 4 | Viewed by 7528

Abstract

Ionizing radiation damages DNA and induces mutations as well as chromosomal reorganizations. Although radiotherapy increases survival among cancer patients, this treatment does not come without secondary effects, among which the most problematic is gonadal dysfunction, especially in women. Even more, if radio-induced DNA [...] Read more.

Ionizing radiation damages DNA and induces mutations as well as chromosomal reorganizations. Although radiotherapy increases survival among cancer patients, this treatment does not come without secondary effects, among which the most problematic is gonadal dysfunction, especially in women. Even more, if radio-induced DNA damage occurs in germ cells during spermatogenesis and/or oogenesis, they can produce chromosomal reorganizations associated with meiosis malfunction, abortions, as well as hereditary effects. However, most of our current knowledge of ionizing radiation genotoxic effects is derived from in vitro studies performed in somatic cells and there are only some experimental data that shed light on how germ cells work when affected by DNA alterations produced by ionizing radiation. In addition, these few data are often related to mammalian males, making it difficult to extrapolate the results to females. Here, we review the current knowledge of radiobiology and reproduction, paying attention to mammalian females. In order to do that, we will navigate across the female meiotic/reproductive cycle/life taking into account the radiation-induced genotoxic effects analysis and animal models used, published in recent decades. Full article

(This article belongs to the Special Issue Feature Paper 2012)

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16 pages, 684 KiB

Open AccessArticle

Regulation of Fibroblast Growth Factor-2 Expression and Cell Cycle Progression by an Endogenous Antisense RNA

by Mark Baguma-Nibasheka, Leigh Ann MacFarlane and Paul R. Murphy

Genes 2012, 3(3), 505-520; https://doi.org/10.3390/genes3030505 - 16 Aug 2012

Cited by 11 | Viewed by 8907

Abstract

Basic fibroblast growth factor (FGF2) is a potent wide-spectrum mitogen whose overexpression is associated with immortalization and unregulated cell proliferation in many tumors. The FGF2 gene locus is bi-directionally transcribed to produce FGF2 mRNA from the “sense” strand and a cis-antisense RNA [...] Read more.

Basic fibroblast growth factor (FGF2) is a potent wide-spectrum mitogen whose overexpression is associated with immortalization and unregulated cell proliferation in many tumors. The FGF2 gene locus is bi-directionally transcribed to produce FGF2 mRNA from the “sense” strand and a cis-antisense RNA (NUDT6) from the NUDT6 gene on the “antisense” strand. The NUDT6 gene encodes a nudix motif protein of unknown function, while its mRNA has been implicated in the post-transcriptional regulation of FGF2 expression. FGF2 and NUDT6 are co-expressed in rat C6 glioma cells, and ectopic overexpression of NUDT6 suppresses cellular FGF2 accumulation and cell cycle progression. However, the role of the endogenous antisense RNA in regulation of FGF2 is unclear. In the present study, we employed siRNA-mediated gene knockdown to examine the role of the endogenous NUDT6 RNA in regulation of FGF2 expression and cell cycle progression. Knockdown of either FGF2 or NUDT6 mRNA was accompanied by a significant (>3 fold) increase in the complementary partner RNA. Similar reciprocal effects were observed at the protein level, indicating that these two transcripts are mutually regulatory. Remarkably, knockdown of either FGF2 or NUDT6 significantly reduced cell proliferation and inhibited S-phase re-entry following serum deprivation, implicating both FGF2 and NUDT6 in the regulation of cell transformation and cell cycle progression. Full article

(This article belongs to the Special Issue RNA Interference)

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13 pages, 408 KiB

Open AccessArticle

A Model of Evolution of Development Based on Germline Penetration of New “No-Junk” DNA

by Alessandro Fontana and Borys Wróbel

Genes 2012, 3(3), 492-504; https://doi.org/10.3390/genes3030492 - 2 Aug 2012

Cited by 9 | Viewed by 6942

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, able to generate complex 3-dimensional structures. Its aim is [...] Read more.

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, able to generate complex 3-dimensional structures. Its aim is not to model the development of a particular organism nor to merely summarise 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 development is orchestrated through a subset of cells which we call driver cells. In these cells, the cellular state determines a specific pattern of gene activation which leads to the occurrence of developmental events. The second proposal is that evolution of development is affected by somatic transposition events. We postulate that when the genome of a driver cell does not specify what developmental event should be undertaken when the cell is in a particular cellular state, somatic transposition events can reshape the genome, build new regulatory regions, and lead to a new pattern of gene activation in the cell. Our third hypothesis, not supported yet by direct evidence, but consistent with some experimental observations, is that these new “no-junk” sequences—regulatory regions created by transposable elements at new positions in the genome—can exit the cell and enter the germline, to be incorporated in the genome of the progeny. We call this mechanism germline penetration. This process allows heritable incorporation of novel developmental events in the developmental trajectory. In this paper we will present the model and link these three postulated mechanisms to biological observations. Full article

(This article belongs to the Special Issue Junk DNA' is not Junk)

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11 pages, 119 KiB

Open AccessReview

Transgenic Models of Spinocerebellar Ataxia Type 10: Modeling a Repeat Expansion Disorder

by Karen N. McFarland and Tetsuo Ashizawa

Genes 2012, 3(3), 481-491; https://doi.org/10.3390/genes3030481 - 30 Jul 2012

Cited by 5 | Viewed by 6265

Abstract

Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurodegenerative disease with a spectrum of phenotypes. SCA10 is caused by a pentanucleotide repeat expansion of the ATTCT motif within intron 9 of ATAXIN 10 (ATXN10). Patients present with cerebellar ataxia; however, a [...] Read more.

Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant neurodegenerative disease with a spectrum of phenotypes. SCA10 is caused by a pentanucleotide repeat expansion of the ATTCT motif within intron 9 of ATAXIN 10 (ATXN10). Patients present with cerebellar ataxia; however, a subset also develops epileptic seizures which significantly contribute to the morbidity and mortality of the disease. Past research from our lab has demonstrated that epileptic SCA10 patients predominantly originate from or have ancestral ties to Mexico. In addition, a large proportion of epileptic SCA10 patients carry repeat interruptions within their SCA10 expansion. This paper outlines the variability in SCA10 phenotypes and our attempts to model these phenotypes using transgenic mouse models and highlights the benefits of using a transgenic model organism to understand the pathological mechanisms of a human disease. Full article

(This article belongs to the Special Issue Transgenic Technology: Benefits or Dangers?)

20 pages, 429 KiB

Open AccessReview

Beyond Junk-Variable Tandem Repeats as Facilitators of Rapid Evolution of Regulatory and Coding Sequences

by Rita Gemayel, Janice Cho, Steven Boeynaems and Kevin J. Verstrepen

Genes 2012, 3(3), 461-480; https://doi.org/10.3390/genes3030461 - 26 Jul 2012

Cited by 109 | Viewed by 14291

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 [...] Read more.

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 often 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. Full article

(This article belongs to the Special Issue Junk DNA' is not Junk)

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17 pages, 413 KiB

Open AccessReview

Microsatellites with Macro-Influence in Ewing Sarcoma

by Michael J. Monument, Kirsten M. Johnson, Allie H. Grossmann, Joshua D. Schiffman, R. Lor Randall and Stephen L. Lessnick

Genes 2012, 3(3), 444-460; https://doi.org/10.3390/genes3030444 - 23 Jul 2012

Cited by 15 | Viewed by 10200

Abstract

Numerous molecular abnormalities contribute to the genetic derangements involved in tumorigenesis. Chromosomal translocations are a frequent source of these derangements, producing unique fusion proteins with novel oncogenic properties. EWS/ETS fusions in Ewing sarcoma are a prime example of this, resulting in potent chimeric [...] Read more.

Numerous molecular abnormalities contribute to the genetic derangements involved in tumorigenesis. Chromosomal translocations are a frequent source of these derangements, producing unique fusion proteins with novel oncogenic properties. EWS/ETS fusions in Ewing sarcoma are a prime example of this, resulting in potent chimeric oncoproteins with novel biological properties and a unique transcriptional signature essential for oncogenesis. Recent evidence demonstrates that EWS/FLI, the most common EWS/ETS fusion in Ewing sarcoma, upregulates gene expression using a GGAA microsatellite response element dispersed throughout the human genome. These GGAA microsatellites function as enhancer elements, are sites of epigenetic regulation and are necessary for EWS/FLI DNA binding and upregulation of principal oncogenic targets. An increasing number of GGAA motifs appear to substantially enhance EWS/FLI-mediated gene expression, which has compelling biological implications as these GGAA microsatellites are highly polymorphic within and between ethnically distinct populations. Historically regarded as junk DNA, this emerging evidence clearly demonstrates that microsatellite DNA plays an instrumental role in EWS/FLI-mediated transcriptional regulation and oncogenesis in Ewing sarcoma. This unprecedented role of GGAA microsatellite DNA in Ewing sarcoma provides a unique opportunity to expand our mechanistic understanding of how EWS/ETS fusions influence cancer susceptibility, prognosis and transcriptional regulation. Full article

(This article belongs to the Special Issue Junk DNA' is not Junk)

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21 pages, 550 KiB

Open AccessArticle

REGEN: Ancestral Genome Reconstruction for Bacteria

by Kuan Yang, Lenwood S. Heath and João C. Setubal

Genes 2012, 3(3), 423-443; https://doi.org/10.3390/genes3030423 - 18 Jul 2012

Cited by 6 | Viewed by 10215

Abstract

Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, [...] Read more.

Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order. Full article

(This article belongs to the Special Issue Feature Paper 2012)

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14 pages, 235 KiB

Open AccessReview

Transposable Elements: From DNA Parasites to Architects of Metazoan Evolution

by Oliver Piskurek and Daniel J. Jackson

Genes 2012, 3(3), 409-422; https://doi.org/10.3390/genes3030409 - 12 Jul 2012

Cited by 26 | Viewed by 9626

Abstract

One of the most unexpected insights that followed from the completion of the human genome a decade ago was that more than half of our DNA is derived from transposable elements (TEs). Due to advances in high throughput sequencing technologies it is now [...] Read more.

One of the most unexpected insights that followed from the completion of the human genome a decade ago was that more than half of our DNA is derived from transposable elements (TEs). Due to 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 stimulate the evolution of metazoan genomes. This review highlights several 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. Full article

(This article belongs to the Special Issue Junk DNA' is not Junk)

18 pages, 240 KiB

Open AccessArticle

siRNAs Trigger Efficient Silencing of a Parasitism Gene in Plant Parasitic Root-Knot Nematodes

by Marie-Jeanne Arguel, Maëlle Jaouannet, Marc Magliano, Pierre Abad and Marie-Noëlle Rosso

Genes 2012, 3(3), 391-408; https://doi.org/10.3390/genes3030391 - 10 Jul 2012

Cited by 22 | Viewed by 11048

Abstract

Expanding genomic data on plant pathogens open new perspectives for the development of specific and environment friendly pest management strategies based on the inhibition of parasitism genes that are essential for the success of infection. Identifying such genes relies on accurate reverse genetics [...] Read more.

Expanding genomic data on plant pathogens open new perspectives for the development of specific and environment friendly pest management strategies based on the inhibition of parasitism genes that are essential for the success of infection. Identifying such genes relies on accurate reverse genetics tools and the screening of pathogen knock-down phenotypes. Root-knot nematodes are major cosmopolitan crop pests that feed on a wide range of host plants. Small interfering RNAs (siRNAs) would provide a powerful tool for reverse genetics of nematode parasitism genes provided that they could (1) target genes expressed in inner tissues of infective nematodes and (2) target genes expressed during parasitism. In this study, we show that siRNAs can access inner tissues of the infective juveniles during soaking and accumulate in the esophagus, amphidial pouches and related neurons of the nematode. We provide evidence that siRNAs can trigger knock-down of the parasitism gene Mi-CRT, a calreticulin gene expressed in the esophageal glands of Meloidogyne incognita. Mi-CRT knock-down in infective juveniles affected nematode virulence. However, Mi-CRT knock-down was not persistent after plant infection, indicating that siRNA-mediated RNAi is best suited for functional analysis of genes involved in pre-parasitic stages or in the early steps of infection. Full article

(This article belongs to the Special Issue RNA Interference)

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13 pages, 3062 KiB

Open AccessArticle

Clustering Rfam 10.1: Clans, Families, and Classes

by Felipe A. Lessa, Tainá Raiol, Marcelo M. Brigido, Daniele S. B. Martins Neto, Maria Emília M. T. Walter and Peter F. Stadler

Genes 2012, 3(3), 378-390; https://doi.org/10.3390/genes3030378 - 5 Jul 2012

Cited by 5 | Viewed by 8980

Abstract

The Rfam database contains information about non-coding RNAs emphasizing their secondary structures and organizing them into families of homologous RNA genes or functional RNA elements. Recently, a higher order organization of Rfam in terms of the so-called clans was proposed along with its [...] Read more.

The Rfam database contains information about non-coding RNAs emphasizing their secondary structures and organizing them into families of homologous RNA genes or functional RNA elements. Recently, a higher order organization of Rfam in terms of the so-called clans was proposed along with its “decimal release”. In this proposition, some of the families have been assigned to clans based on experimental and computational data in order to find related families. In the present work we investigate an alternative classification for the RNA families based on tree edit distance. The resulting clustering recovers some of the Rfam clans. The majority of clans, however, are not recovered by the structural clustering. Instead, they get dispersed into larger clusters, which correspond roughly to well-described RNA classes such as snoRNAs, miRNAs, and CRISPRs. In conclusion, a structure-based clustering can contribute to the elucidation of the relationships among the Rfam families beyond the realm of clans and classes. Full article

(This article belongs to the Special Issue Feature Paper 2012)

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17 pages, 691 KiB

Open AccessCommunication

Genome-Wide Sequencing Reveals Two Major Sub-Lineages in the Genetically Monomorphic Pathogen Xanthomonas Campestris Pathovar Musacearum

by Arthur Wasukira, Johnbosco Tayebwa, Richard Thwaites, Konrad Paszkiewicz, Valente Aritua, Jerome Kubiriba, Julian Smith, Murray Grant and David J. Studholme

Genes 2012, 3(3), 361-377; https://doi.org/10.3390/genes3030361 - 4 Jul 2012

Cited by 39 | Viewed by 12004

Abstract

The bacterium Xanthomonas campestris pathovar musacearum (Xcm) is the causal agent of banana Xanthomonas wilt (BXW). This disease has devastated economies based on banana and plantain crops (Musa species) in East Africa. Here we use genome-wide sequencing to discover a [...] Read more.

The bacterium Xanthomonas campestris pathovar musacearum (Xcm) is the causal agent of banana Xanthomonas wilt (BXW). This disease has devastated economies based on banana and plantain crops (Musa species) in East Africa. Here we use genome-wide sequencing to discover a set of single-nucleotide polymorphisms (SNPs) among East African isolates of Xcm. These SNPs have potential as molecular markers for phylogeographic studies of the epidemiology and spread of the pathogen. Our analysis reveals two major sub-lineages of the pathogen, suggesting that the current outbreaks of BXW on Musa species in the region may have more than one introductory event, perhaps from Ethiopia. Also, based on comparisons of genome-wide sequence data from multiple isolates of Xcm and multiple strains of X. vasicola pathovar vasculorum, we identify genes specific to Xcm that could be used to specifically detect Xcm by PCR-based methods. Full article

(This article belongs to the Special Issue Feature Paper 2012)

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17 pages, 374 KiB

Open AccessReview

The Human Transcriptome: An Unfinished Story

by Mihaela Pertea

Genes 2012, 3(3), 344-360; https://doi.org/10.3390/genes3030344 - 29 Jun 2012

Cited by 116 | Viewed by 14767

Abstract

Despite recent technological advances, the study of the human transcriptome is still in its early stages. Here we provide an overview of the complex human transcriptomic landscape, present the bioinformatics challenges posed by the vast quantities of transcriptomic data, and discuss some of [...] Read more.

Despite recent technological advances, the study of the human transcriptome is still in its early stages. Here we provide an overview of the complex human transcriptomic landscape, present the bioinformatics challenges posed by the vast quantities of transcriptomic data, and discuss some of the studies that have tried to determine how much of the human genome is transcribed. Recent evidence has suggested that more than 90% of the human genome is transcribed into RNA. However, this view has been strongly contested by groups of scientists who argued that many of the observed transcripts are simply the result of transcriptional noise. In this review, we conclude that the full extent of transcription remains an open question that will not be fully addressed until we decipher the complete range and biological diversity of the transcribed genomic sequences. Full article

(This article belongs to the Special Issue Junk DNA' is not Junk)

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Genes, Volume 3, Issue 3 (September 2012) – 13 articles , Pages 344-575

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