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1.  Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon 
Domesticated animals provide a unique opportunity to identify genomic targets of artificial selection to the captive environment. Here, we screened three independent domesticated/captive Atlantic salmon (Salmo salar) strains and their wild progenitor populations in an effort to detect potential signals of domestication selection by typing of 261 SNPs and 70 microsatellite loci. By combining information from four different neutrality tests, in total ten genomic regions showed signs of directional selection based on multiple sources of evidence. Most of the identified candidate regions were rather small ranging from zero to a few centimorgans (cM) in the female Atlantic salmon linkage map. We also evaluated how adaptation from standing variation affects adjacent SNP and microsatellite variation along the chromosomes and, by using forward simulations with strong selection, we were able to generate genetic differentiation patterns comparable to the observed data. This study highlights the significance of standing genetic variation during the early stages of adaptation and represents a useful step towards identifying functional variants involved in domestication of Atlantic salmon.
doi:10.1155/2012/628204
PMCID: PMC3544263  PMID: 23326209
2.  Gemi: PCR Primers Prediction from Multiple Alignments 
Designing primers and probes for polymerase chain reaction (PCR) is a preliminary and critical step that requires the identification of highly conserved regions in a given set of sequences. This task can be challenging if the targeted sequences display a high level of diversity, as frequently encountered in microbiologic studies. We developed Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes based on multiple aligned sequences. This tool can be used for the purpose of real-time and conventional PCR and can deal efficiently with large sets of sequences of a large size.
doi:10.1155/2012/783138
PMCID: PMC3535827  PMID: 23316117
3.  The α1AT and TIMP-1 Gene Polymorphism in the Development of Asthma 
Asthma has been an inflammatory disorder accompanied by tissue remodeling and protease-antiprotease imbalance in lungs. The SNPs of alpha-1 antitrypsin (α1AT) and tissue inhibitor of metalloproteinase-1 (TIMP-1) genes were studied for their association with asthma. Genotyping of α1AT and TIMP-1 genes was performed in 202 asthmatics and 204 controls. Serum levels of α1AT, TIMP-1 and cytokines were estimated to find if the interplay between genotypes and cellular biomarkers determines the pathogenesis of asthma. The analysis of results showed significantly low level of α1AT in the serum of asthmatics as compared to controls (P = 0.001), whereas cytokines were elevated in patients. No significant difference was observed in the concentration of TIMP-1 in patients and controls. Genotyping led to the identification of 3 SNPs (Val213Ala, Glu363Lys, and Glu376Asp) in α1AT gene. The novel SNP Glu363Lys of α1AT was found to be associated with asthma (P = 0.001). The analysis of TIMP-1 gene showed the occurrence of seven SNPs, including a novel intronic SNP at base G3774A. The allele frequency of G3774A and Phe124Phe was significantly higher in asthmatics as compared to controls. Thus, the SNP Glu363Lys of α1AT and G3774A and Phe124Phe of TIMP-1 could be important genetic markers for use in better management of the disease.
doi:10.1155/2012/968267
PMCID: PMC3512250  PMID: 23226977
4.  TnpPred: A Web Service for the Robust Prediction of Prokaryotic Transposases 
Transposases (Tnps) are enzymes that participate in the movement of insertion sequences (ISs) within and between genomes. Genes that encode Tnps are amongst the most abundant and widely distributed genes in nature. However, they are difficult to predict bioinformatically and given the increasing availability of prokaryotic genomes and metagenomes, it is incumbent to develop rapid, high quality automatic annotation of ISs. This need prompted us to develop a web service, termed TnpPred for Tnp discovery. It provides better sensitivity and specificity for Tnp predictions than given by currently available programs as determined by ROC analysis. TnpPred should be useful for improving genome annotation. The TnpPred web service is freely available for noncommercial use.
doi:10.1155/2012/678761
PMCID: PMC3506888  PMID: 23251097
5.  Correlation of Aquaporins and Transmembrane Solute Transporters Revealed by Genome-Wide Analysis in Developing Maize Leaf 
Aquaporins are multifunctional membrane channels that facilitate the transmembrane transport of water and solutes. When transmembrane mineral nutrient transporters exhibit the same expression patterns as aquaporins under diverse temporal and physiological conditions, there is a greater probability that they interact. In this study, genome-wide temporal profiling of transcripts analysis and coexpression network-based approaches are used to examine the significant specificity correlation of aquaporins and transmembrane solute transporters in developing maize leaf. The results indicate that specific maize aquaporins are related to specific transmembrane solute transporters. The analysis demonstrates a systems-level correlation between aquaporins, nutrient transporters, and the homeostasis of mineral nutrients in developing maize leaf. Our results provide a resource for further studies into the physiological function of these aquaporins.
doi:10.1155/2012/546930
PMCID: PMC3463914  PMID: 23055821
6.  Comparative Analysis of MicroRNAs between Sporophyte and Gametophyte of Porphyra yezoensis 
Porphyra yezoensis Ueda is an intertidal marine red algae that has received increasing attention as a model organism owing to its important role in biological research and the agronomic industry. The two generations of Porphyra yezoensis, the sporophyte and the gametophyte, have the same genome but show great differences in many aspects, including structural features, habitat, and gene expression. To identify miRNAs and their probable roles in P. yezoensis development, we constructed and sequenced libraries of small RNA from P. yezoensis sporophytes and gametophytes. The sequencing data were analyzed, and 14 miRNAs were identified, with only one common to these two samples. Our results show that P. yezoensis has a complex small RNA processing system containing novel miRNAs that have no identifiable homolog in other organisms. These miRNAs might have important regulatory roles in development of the different generations of P. yezoensis.
doi:10.1155/2012/912843
PMCID: PMC3463926  PMID: 23055822
8.  A Systems Approach and Skeletal Myogenesis 
Skeletal myogenesis depends on the strict regulation of the expression of various gene subsets. Therefore, the understanding of genome wide gene regulation is imperative for elucidation of skeletal myogenesis. In recent years, systems approach has contributed to the understanding of various biological processes. Our group recently revealed the critical genome network of skeletal myogenesis by using a novel systems approach combined with whole-mount in situ hybridization (WISH) database, high-throughput screening, and microarray analysis. In this paper, we introduce our systems approach for understanding the myogenesis regulatory network and describe the advantages of systems approach.
doi:10.1155/2012/759407
PMCID: PMC3443578  PMID: 22991503
9.  Comparative Genome Sequence Analysis Reveals the Extent of Diversity and Conservation for Glycan-Associated Proteins in Burkholderia spp. 
Members of the Burkholderia family occupy diverse ecological niches. In pathogenic family members, glycan-associated proteins are often linked to functions that include virulence, protein conformation maintenance, surface recognition, cell adhesion, and immune system evasion. Comparative analysis of available Burkholderia genomes has revealed a core set of 178 glycan-associated proteins shared by all Burkholderia of which 68 are homologous to known essential genes. The genome sequence comparisons revealed insights into species-specific gene acquisitions through gene transfers, identified an S-layer protein, and proposed that significantly reactive surface proteins are associated to sugar moieties as a potential means to circumvent host defense mechanisms. The comparative analysis using a curated database of search queries enabled us to gain insights into the extent of conservation and diversity, as well as the possible virulence-associated roles of glycan-associated proteins in members of the Burkholderia spp. The curated list of glycan-associated proteins used can also be directed to screen other genomes for glycan-associated homologs.
doi:10.1155/2012/752867
PMCID: PMC3443583  PMID: 22991502
10.  Epigenetic Regulation of B Lymphocyte Differentiation, Transdifferentiation, and Reprogramming 
B cell development is a multistep process that is tightly regulated at the transcriptional level. In recent years, investigators have shed light on the transcription factor networks involved in all the differentiation steps comprising B lymphopoiesis. The interplay between transcription factors and the epigenetic machinery involved in establishing the correct genomic landscape characteristic of each cellular state is beginning to be dissected. The participation of “epigenetic regulator-transcription factor” complexes is also crucial for directing cells during reprogramming into pluripotency or lineage conversion. In this context, greater knowledge of epigenetic regulation during B cell development, transdifferentiation, and reprogramming will enable us to understand better how epigenetics can control cell lineage commitment and identity. Herein, we review the current knowledge about the epigenetic events that contribute to B cell development and reprogramming.
doi:10.1155/2012/564381
PMCID: PMC3444840  PMID: 22997486
11.  Empirical Bayes Model Comparisons for Differential Methylation Analysis 
A number of empirical Bayes models (each with different statistical distribution assumptions) have now been developed to analyze differential DNA methylation using high-density oligonucleotide tiling arrays. However, it remains unclear which model performs best. For example, for analysis of differentially methylated regions for conservative and functional sequence characteristics (e.g., enrichment of transcription factor-binding sites (TFBSs)), the sensitivity of such analyses, using various empirical Bayes models, remains unclear. In this paper, five empirical Bayes models were constructed, based on either a gamma distribution or a log-normal distribution, for the identification of differential methylated loci and their cell division—(1, 3, and 5) and drug-treatment-(cisplatin) dependent methylation patterns. While differential methylation patterns generated by log-normal models were enriched with numerous TFBSs, we observed almost no TFBS-enriched sequences using gamma assumption models. Statistical and biological results suggest log-normal, rather than gamma, empirical Bayes model distribution to be a highly accurate and precise method for differential methylation microarray analysis. In addition, we presented one of the log-normal models for differential methylation analysis and tested its reproducibility by simulation study. We believe this research to be the first extensive comparison of statistical modeling for the analysis of differential DNA methylation, an important biological phenomenon that precisely regulates gene transcription.
doi:10.1155/2012/376706
PMCID: PMC3432337  PMID: 22956892
12.  Feature Identification of Compensatory Gene Pairs without Sequence Homology in Yeast 
Genetic robustness refers to a compensatory mechanism for buffering deleterious mutations or environmental variations. Gene duplication has been shown to provide such functional backups. However, the overall contribution of duplication-based buffering for genetic robustness is rather small. In this study, we investigated whether transcriptional compensation also exists among genes that share similar functions without sequence homology. A set of nonhomologous synthetic-lethal gene pairs was assessed by using a coexpression network, protein-protein interactions, and other types of genetic interactions in yeast. Our results are notably different from those of previous studies on buffering paralogs. The low expression similarity and the conditional coexpression alone do not play roles in identifying the functionally compensatory genes. Additional properties such as synthetic-lethal interaction, the ratio of shared common interacting partners, and the degree of coregulation were, at least in part, necessary to extract functional compensatory genes. Our network-based approach is applicable to select several well-documented cases of compensatory gene pairs and a set of new pairs. The results suggest that transcriptional reprogramming plays a limited role in functional compensation among nonhomologous genes. Our study aids in understanding the mechanism and features of functional compensation more in detail.
doi:10.1155/2012/653174
PMCID: PMC3431050  PMID: 22952430
13.  Predictive Models of Gene Regulation from High-Throughput Epigenomics Data 
The epigenetic regulation of gene expression involves multiple factors. The synergistic or antagonistic action of these factors has suggested the existence of an epigenetic code for gene regulation. Highthroughput sequencing (HTS) provides an opportunity to explore this code and to build quantitative models of gene regulation based on epigenetic differences between specific cellular conditions. We describe a new computational framework that facilitates the systematic integration of HTS epigenetic data. Our method relates epigenetic signals to expression by comparing two conditions. We show its effectiveness by building a model that predicts with high accuracy significant expression differences between two cell lines, using epigenetic data from the ENCODE project. Our analyses provide evidence for a degenerate epigenetic code, which involves multiple genic regions. In particular, signal changes at the 1st exon, 1st intron, and downstream of the polyadenylation site are found to associate strongly with expression regulation. Our analyses also show a different epigenetic code for intron-less and intron-containing genes. Our work provides a general methodology to do integrative analysis of epigenetic differences between cellular conditions that can be applied to other studies, like cell differentiation or carcinogenesis.
doi:10.1155/2012/284786
PMCID: PMC3424690  PMID: 22924024
14.  Multidimensional Scaling Applied to Histogram-Based DNA Analysis 
This paper aims to study the relationships between chromosomal DNA sequences of twenty species. We propose a methodology combining DNA-based word frequency histograms, correlation methods, and an MDS technique to visualize structural information underlying chromosomes (CRs) and species. Four statistical measures are tested (Minkowski, Cosine, Pearson product-moment, and Kendall τ rank correlations) to analyze the information content of 421 nuclear CRs from twenty species. The proposed methodology is built on mathematical tools and allows the analysis and visualization of very large amounts of stream data, like DNA sequences, with almost no assumptions other than the predefined DNA “word length.” This methodology is able to produce comprehensible three-dimensional visualizations of CR clustering and related spatial and structural patterns. The results of the four test correlation scenarios show that the high-level information clusterings produced by the MDS tool are qualitatively similar, with small variations due to each correlation method characteristics, and that the clusterings are a consequence of the input data and not method's artifacts.
doi:10.1155/2012/289694
PMCID: PMC3418642  PMID: 22919286
15.  Comparative Analysis of SWIRM Domain-Containing Proteins in Plants 
Chromatin-remodeling complexes affect gene expression by using the energy of ATP hydrolysis to locally disrupt or alter the association of histones with DNA. SWIRM (Swi3p, Rsc8p, and Moira) domain is an alpha-helical domain of about 85 residues in chromosomal proteins. SWIRM domain-containing proteins make up large multisubunit complexes by interacting with other chromatin modification factors and may have an important function in plants. However, little is known about SWIRM domain-containing proteins in plants. In this study, 67 SWIRM domain-containing proteins from 6 plant species were identified and analyzed. Plant SWIRM domain proteins can be divided into three distinct types: Swi-type, LSD1-type, and Ada2-type. Generally, the SWIRM domain forms a helix-turn-helix motif commonly found in DNA-binding proteins. The genes encoding SWIRM domain proteins in Oryza sativa are widely expressed, especially in pistils. In addition, OsCHB701 and OsHDMA701 were downregulated by cold stress, whereas OsHDMA701 and OsHDMA702 were significantly induced by heat stress. These observations indicate that SWIRM domain proteins may play an essential role in plant development and plant responses to environmental stress.
doi:10.1155/2012/310402
PMCID: PMC3424641  PMID: 22924025
16.  Evolutionary Conservation and Diversification of the Translation Initiation Apparatus in Trypanosomatids 
Trypanosomatids are ancient eukaryotic parasites that migrate between insect vectors and mammalian hosts, causing a range of diseases in humans and domestic animals. Trypanosomatids feature a multitude of unusual molecular features, including polycistronic transcription and subsequent processing by trans-splicing and polyadenylation. Regulation of protein coding genes is posttranscriptional and thus, translation regulation is fundamental for activating the developmental program of gene expression. The spliced-leader RNA is attached to all mRNAs. It contains an unusual hypermethylated cap-4 structure in its 5′ end. The cap-binding complex, eIF4F, has gone through evolutionary changes in accordance with the requirement to bind cap-4. The eIF4F components in trypanosomatids are highly diverged from their orthologs in higher eukaryotes, and their potential functions are discussed. The cap-binding activity in all eukaryotes is a target for regulation and plays a similar role in trypanosomatids. Recent studies revealed a novel eIF4E-interacting protein, involved in directing stage-specific and stress-induced translation pathways. Translation regulation during stress also follows unusual regulatory cues, as the increased translation of Hsp83 following heat stress is driven by a defined element in the 3′ UTR, unlike higher eukaryotes. Overall, the environmental switches experienced by trypanosomatids during their life cycle seem to affect their translational machinery in unique ways.
doi:10.1155/2012/813718
PMCID: PMC3399392  PMID: 22829751
17.  Identification and Characterization of MicroRNAs in Macaca fascicularis by EST Analysis 
MicroRNAs (miRNAs) are small noncoding RNAs which repress gene expression at the posttranscriptional level. In this study, an expressed sequence tag (EST)-based combined method was applied for the detection of miRNAs in Macaca fascicularis which is used as a model animal extensively in medical experiments, particularly those involved with neuroscience and disease. Initially, previously known miRNA sequences from metazoans were used to blast with the EST databases of Macaca fascicularis, and then a range of filtering criteria was conducted to remove some pseudo ones. At last a total of 8 novel conserved miRNAs were identified; their functions were further predicted and analyzed. Together, our study provides insight into miRNAs and their functions in Macaca fascicularis, indicating that the EST analysis is an efficient and affordable alternative approach for identifying novel miRNA candidates.
doi:10.1155/2012/957607
PMCID: PMC3398586  PMID: 22829752
18.  Turning on Myogenin in Muscle: A Paradigm for Understanding Mechanisms of Tissue-Specific Gene Expression 
Expression of the myogenin (Myog) gene is restricted to skeletal muscle cells where the transcriptional activator turns on a gene expression program that permits the transition from proliferating myoblasts to differentiating myotubes. The strict temporal and spatial regulation on Myog expression in the embryo makes it an ideal gene to study the developmental regulation of tissue-specific expression. Over the last 20 years, our knowledge of the regulation of Myog expression has evolved from the identification of the minimal promoter elements necessary for the gene to be transcribed in muscle, to a mechanistic understanding of how the proteins that bind these DNA elements work together to establish transcriptional competence. Here we present our current understanding of the developmental regulation of gene expression gained from studies of the Myog gene.
doi:10.1155/2012/836374
PMCID: PMC3395204  PMID: 22811619
19.  Interactome of Radiation-Induced microRNA-Predicted Target Genes 
The microRNAs (miRNAs) function as global negative regulators of gene expression and have been associated with a multitude of biological processes. The dysfunction of the microRNAome has been linked to various diseases including cancer. Our laboratory recently reported modulation in the expression of miRNA in a variety of cell types exposed to ionizing radiation (IR). To further understand miRNA role in IR-induced stress pathways, we catalogued a set of common miRNAs modulated in various irradiated cell lines and generated a list of predicted target genes. Using advanced bioinformatics tools we identified cellular pathways where miRNA predicted target genes function. The miRNA-targeted genes were found to play key roles in previously identified IR stress pathways such as cell cycle, p53 pathway, TGF-beta pathway, ubiquitin-mediated proteolysis, focal adhesion pathway, MAPK signaling, thyroid cancer pathway, adherens junction, insulin signaling pathway, oocyte meiosis, regulation of actin cytoskeleton, and renal cell carcinoma pathway. Interestingly, we were able to identify novel targeted pathways that have not been identified in cellular radiation response, such as aldosterone-regulated sodium reabsorption, long-term potentiation, and neutrotrophin signaling pathways. Our analysis indicates that the miRNA interactome in irradiated cells provides a platform for comprehensive modeling of the cellular stress response to IR exposure.
doi:10.1155/2012/569731
PMCID: PMC3424689  PMID: 22924026
20.  Transposable Elements Are a Significant Contributor to Tandem Repeats in the Human Genome 
Sequence repeats are an important phenomenon in the human genome, playing important roles in genomic alteration often with phenotypic consequences. The two major types of repeat elements in the human genome are tandem repeats (TRs) including microsatellites, minisatellites, and satellites and transposable elements (TEs). So far, very little has been known about the relationship between these two types of repeats. In this study, we identified TRs that are derived from TEs either based on sequence similarity or overlapping genomic positions. We then analyzed the distribution of these TRs among TE families/subfamilies. Our study shows that at least 7,276 TRs or 23% of all minisatellites/satellites is derived from TEs, contributing ∼0.32% of the human genome. TRs seem to be generated more likely from younger/more active TEs, and once initiated they are expanded with time via local duplication of the repeat units. The currently postulated mechanisms for origin of TRs can explain only 6% of all TE-derived TRs, indicating the presence of one or more yet to be identified mechanisms for the initiation of such repeats. Our result suggests that TEs are contributing to genome expansion and alteration not only by transposition but also by generating tandem repeats.
doi:10.1155/2012/947089
PMCID: PMC3389668  PMID: 22792041
21.  Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists 
The greatest diversity of eukaryotic species is within the microbial eukaryotes, the protists, with plants and fungi/metazoa representing just two of the estimated seventy five lineages of eukaryotes. Protists are a diverse group characterized by unusual genome features and a wide range of genome sizes from 8.2 Mb in the apicomplexan parasite Babesia bovis to 112,000-220,050 Mb in the dinoflagellate Prorocentrum micans. Protists possess numerous cellular, molecular and biochemical traits not observed in “text-book” model organisms. These features challenge some of the concepts and assumptions about the regulation of gene expression in eukaryotes. Like multicellular eukaryotes, many protists encode multiple eIF4Es, but few functional studies have been undertaken except in parasitic species. An earlier phylogenetic analysis of protist eIF4Es indicated that they cannot be grouped within the three classes that describe eIF4E family members from multicellular organisms. Many more protist sequences are now available from which three clades can be recognized that are distinct from the plant/fungi/metazoan classes. Understanding of the protist eIF4Es will be facilitated as more sequences become available particularly for the under-represented opisthokonts and amoebozoa. Similarly, a better understanding of eIF4Es within each clade will develop as more functional studies of protist eIF4Es are completed.
doi:10.1155/2012/134839
PMCID: PMC3388326  PMID: 22778692
22.  Epigenetic Alterations in Muscular Disorders 
Epigenetic mechanisms, acting via chromatin organization, fix in time and space different transcriptional programs and contribute to the quality, stability, and heritability of cell-specific transcription programs. In the last years, great advances have been made in our understanding of mechanisms by which this occurs in normal subjects. However, only a small part of the complete picture has been revealed. Abnormal gene expression patterns are often implicated in the development of different diseases, and thus epigenetic studies from patients promise to fill an important lack of knowledge, deciphering aberrant molecular mechanisms at the basis of pathogenesis and diseases progression. The identification of epigenetic modifications that could be used as targets for therapeutic interventions could be particularly timely in the light of pharmacologically reversion of pathological perturbations, avoiding changes in DNA sequences. Here I discuss the available information on epigenetic mechanisms that, altered in neuromuscular disorders, could contribute to the progression of the disease.
doi:10.1155/2012/256892
PMCID: PMC3385594  PMID: 22761545
23.  Global Transcriptional Analysis of Olfactory Genes in the Head of Pine Shoot Beetle, Tomicus yunnanensis 
The most important proteins involved in olfaction include odorant binding protein (OBP), chemosensory protein (CSP), olfactory receptor (OR), and gustatory receptor (GR). Despite that the exhaustive genomic analysis has revealed a large number of olfactory genes in a number of model insects, it is still poorly understood for most nonmodel species. This is mostly due to the reason that the small antenna is challenging for collection. We can generally isolate one or few genes at a time by means of the traditional method. Here, we present the large-scale identifying members of the main olfactory genes from the head of Tomicus yunnanensis using Illumina sequencing. In a single run, we obtained over 51.8 million raw reads. These reads were assembled into 57,142 unigenes. Nearly 29,384 of them were functionally annotated in the NCBI nonredundant database. By depth analysis of the data, 11 OBPs, 8 CSPs, 18 ORs, and 8 GRs were retrieved. Sequences encoding full length proteins were further characterised for one OBP and two CSPs. The obtained olfactory genes provide a major resource in further unraveling the molecular mechanisms of T. yunnanensis chemoperception. This study indicates that the next generation sequencing is an attractive approach for efficient identification of olfactory genes from insects, for which the genome sequence is unavailable.
doi:10.1155/2012/491748
PMCID: PMC3385610  PMID: 22761546
24.  Peanut (Arachis hypogaea) Expressed Sequence Tag Project: Progress and Application 
Many plant ESTs have been sequenced as an alternative to whole genome sequences, including peanut because of the genome size and complexity. The US peanut research community had the historic 2004 Atlanta Genomics Workshop and named the EST project as a main priority. As of August 2011, the peanut research community had deposited 252,832 ESTs in the public NCBI EST database, and this resource has been providing the community valuable tools and core foundations for various genome-scale experiments before the whole genome sequencing project. These EST resources have been used for marker development, gene cloning, microarray gene expression and genetic map construction. Certainly, the peanut EST sequence resources have been shown to have a wide range of applications and accomplished its essential role at the time of need. Then the EST project contributes to the second historic event, the Peanut Genome Project 2010 Inaugural Meeting also held in Atlanta where it was decided to sequence the entire peanut genome. After the completion of peanut whole genome sequencing, ESTs or transcriptome will continue to play an important role to fill in knowledge gaps, to identify particular genes and to explore gene function.
doi:10.1155/2012/373768
PMCID: PMC3382957  PMID: 22745594
25.  Intron Retention and TE Exonization Events in ZRANB2 
The Zinc finger, RAN-binding domain-containing protein 2 (ZRANB2), contains arginine/serine-rich (RS) domains that mediate its function in the regulation of alternative splicing. The ZRANB2 gene contains 2 LINE elements (L3b, Plat_L3) between the 9th and 10th exons. We identified the exonization event of a LINE element (Plat_L3). Using genomic PCR, RT-PCR amplification, and sequencing of primate DNA and RNA samples, we analyzed the evolutionary features of ZRANB2 transcripts. The results indicated that 2 of the LINE elements were integrated in human and all of the tested primate samples (hominoids: 3 species; Old World monkey: 8 species; New World monkey: 6 species; prosimian: 1 species). Human, rhesus monkey, crab-eating monkey, African-green monkey, and marmoset harbor the exon derived from LINE element (Plat_L3). RT-PCR amplification revealed the long transcripts and their differential expression patterns. Intriguingly, these long transcripts were abundantly expressed in Old World monkey lineages (rhesus, crab-eating, and African-green monkeys) and were expressed via intron retention (IR). Thus, the ZRANB2 gene produces 3 transcript variants in which the Cterminus varies by transposable elements (TEs) exonization and IR mechanisms. Therefore, ZRANB2 is valuable for investigating the evolutionary mechanisms of TE exonization and IR during primate evolution.
doi:10.1155/2012/170208
PMCID: PMC3384923  PMID: 22778693

Results 1-25 (556)