Noncoding Segments Research Articles

Gene self-control: when pre-mRNA splicing variants become competing endogenous RNAs.

Since Richard J. Roberts and Phillip A. Sharp discovered split genes (genes are interrupted by RNA-encoding regions called exons and non-coding segments called introns in eukaryotic genome) in 1970's, scientists have been finding many genes can generate more than one mRNA transcripts through AS (alternative splicing, e.g., by different exon-exon combination). This AS strategy increases protein repertoire, encodes proteins with diverse and sometimes even antagonistic activities (Kelemen et al., 2013). A new study led by Dr. Kazuhito Tomizawa and first author Bo Zhou from Kumamoto University in Japan reports that CDKAL1-v1 (Cdk5 Regulator Subunit Associated Protein 1-Like), one splicing variant of CDKAL1, has no coding ability but acts as a miRNA sponge RNA, which regulates its full-length CDKAL1 protein (Zhou et al., 2014). Their results give us a unique paradigm of how AS possesses a regulatory role in controlling gene expression.

Structure and variation of the Anseriformes mitochondrial DNA control region

The control region is the major non-coding segment of animal mitochondrial DNA. To infer the structure and variation of Anseriformes mitochondrial DNA control region, the control region sequences of 52 species were analyzed. The length of the control region sequences ranged from 968 bp (Chenonetta jubata) to 1335 bp (Anseranas semipalmata) and can be separated into three domains. There is a deletion of 100–130 bp in Anatinae, compared to other groups of Anserinae. The average genetic distances among the species within the genera varied from 4.14% (Anser) to 10.58% (Cygnus). The average genetic distances showed insignificantly negative correlation with ts/tv. Domain I is the most variable among the three domains among all the genera. Five conserved sequence boxes in the domain II of Anseriformes sequences were identified. The alignment of the Anseriformes five boxes sequences showed considerable sequence variation. CSB-1, -2 and 3 were not found in the Anseriformes. Maximum-likelihood method was used to construct a phylogenetic tree, which grouped all of the genera into four divergent clades. Anseranas + Chauna and Dendrocygna were identified as early offshoots of the Anatidae. All the remaining taxa fell into two clades that correspond to the two subfamilies Anserinae and Anatiane.

Enhancer variants: evaluating functions in common disease.

Gene enhancer elements are noncoding segments of DNA that play a central role in regulating transcriptional programs that control development, cell identity, and evolutionary processes. Recent studies have shown that noncoding single nucleotide polymorphisms (SNPs) that have been associated with risk for numerous common diseases through genome-wide association studies frequently lie in cell-type-specific enhancer elements. These enhancer variants probably influence transcriptional output, thereby offering a mechanistic basis to explain their association with risk for many common diseases. This review focuses on the identification and interpretation of disease-susceptibility variants that influence enhancer function. We discuss strategies for prioritizing the study of functional enhancer SNPs over those likely to be benign, review experimental and computational approaches to identifying the gene targets of enhancer variants, and highlight efforts to quantify the impact of enhancer variants on target transcript levels and cellular phenotypes. These studies are beginning to provide insights into the mechanistic basis of many common diseases, as well as into how we might translate this knowledge for improved disease diagnosis, prevention and treatments. Finally, we highlight five major challenges often associated with interpreting enhancer variants, and discuss recent technical advances that may help to surmount these challenges.

Biophysical Underpinnings of the Repeat Length Dependence of Polyglutamine Amyloid Formation

There are now 10 expanded CAG repeat diseases in which both disease risk and age of onset are strongly dependent on the repeat length of the polyglutamine (polyQ) sequence in the disease protein. Large, polyQ-rich inclusions in patient brains and in cell and animal models are consistent with the involvement of polyQ aggregation in the disease mechanism. This possibility is reinforced by studies showing strong repeat length dependence to the aggregation process, qualitatively mirroring the repeat length dependence of disease risk. Our understanding of the underlying biophysical principles that mediate the repeat length dependence of aggregation, however, is far from complete. A previous study of simple polyQ peptides showed that N*, the size of the critical nucleus that controls onset of aggregation, decreases from unfavorable tetramer to favorable monomer over the range Q23 to Q26. These data, however, do not explain why, for all peptides exhibiting N* ∼ 1, spontaneous aggregation rates continue to increase with increasing repeat length. Here we describe a novel kinetics analyses that maps out the nonlinear dependence with repeat length of a nucleation efficiency term that is likely related to aspects of nucleus structure. This trend accounts for why nucleus size increases to tetrameric at repeat lengths of Q23 or below. Intriguingly, both aggregation and age of onset trend with repeat length in similar ways, exhibiting large changes per added Gln at low repeat lengths and small changes per added Gln at relatively long repeat lengths. Fibril stability also increases with repeat length in a nonlinear fashion.

MP23-13 MICRO-RNA DIFFERENTIATES TUMOR TYPE & METASTATIC POTENTIAL IN RCC

You have accessJournal of UrologyKidney Cancer: Basic Research I1 Apr 2014MP23-13 MICRO-RNA DIFFERENTIATES TUMOR TYPE & METASTATIC POTENTIAL IN RCC Michael Garcia-Roig, Nicolas Ortiz, and Vinata Lokeshwar Michael Garcia-RoigMichael Garcia-Roig More articles by this author , Nicolas OrtizNicolas Ortiz More articles by this author , and Vinata LokeshwarVinata Lokeshwar More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2014.02.881AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Small renal tumors (<4 cm) pose a challenge as 16-28% are benign, indistinguishable from malignant lesions on imaging & pose a metastatic risk. Percutaneous biopsy has regained popularity for small masses by using histology, immunology or molecular markers for diagnosis and prognosis. miRNAs are 22-nucleotide noncoding segments regulating gene expression by causing degradation of target mRNAs. We examined the differential expression of microRNAs (miRs) in renal cell carcinoma (RCC) & normal kidney specimens. Our objective was to examine whether miRNA expression can identify tumor type & predict metastasis. METHODS RCC & normal kidney specimens were collected from 86 patients at the time of nephrectomy. miR enriched total RNA was isolated from 46 RCC & 59 normal specimens. Clinical & pathologic data were collected including histology (oncocytoma 6, chromophobe 4, papillary 6, clear cell 25, sarcoma 4, & collecting duct 1), stage (T1a, 11; T1b, 9; T2, 9; T3, 10; T4, 1), renal vein involvement (+: 5; −: 41), & lymph node status (+: 4; −: 41). At 14 months median follow−up, 6 patients were positive for metastasis. Microarray (Thermo Fisher Scientific 10.1) was performed on 30 samples to characterize 554 miRNA targets. 7 miRs were chosen (mir−21, 150, 155, 142−3p, 142−5p, 192, & 194) based on the fold change in tumor samples. Their expression was quantified by quantitative PCR, & normalized to a housekeeping miR. Statistical analysis was performed using the Mann−Whiteny U−test & multivariate analysis. RESULTS miR microarray of RCC vs non-RCC specimens identified significant upregulation of 65 (mean fold change (FC) 2.13), & downregulation of 47 (mean FC 1.7) miRNAs in (p<0.05), respectively. Q-PCR of RCC specimens showed differential expression of miRs-21, 155, 192 & 194. miR-150 & miR-155 levels were 5.8-8.2-fold upregulated in chromophobe (25.8±21; 2.3±2.9) vs. oncocytomas (4.4±2.0; 0.28±0.36; P=0.038). miR-21, miR-1423P, miR-1425P & miR-155 were 3-10-fold upregulated in CC-RCC (1731±1145; 77±174; 4.2±5.2; 2.2±2.7) vs oncocytoma (553±523; 7.3±8.2; 0.43±0.42; 0.28±0.36), respectively (P ≤0.01). Only miR-155 was 5.5-fold upregulated in papillary tumors vs oncocytoma (P=0.015). In multivariate analysis including TNM stage, renal vein invasion, age, gender & miR levels, only mir−194 expression correlated with metastasis (p=0.034; Xˆ2 = 4.5). CONCLUSIONS miR−155, 192, 194, & 21 are differentially expressed in kidney cancer. miR−194 expression independently associates with metastasis. miR-155 was differentially expressed in all RCC types when compared to normal kidney & oncocytomas. © 2014FiguresReferencesRelatedDetails Volume 191Issue 4SApril 2014Page: e248 Advertisement Copyright & Permissions© 2014MetricsAuthor Information Michael Garcia-Roig More articles by this author Nicolas Ortiz More articles by this author Vinata Lokeshwar More articles by this author Expand All Advertisement Advertisement PDF DownloadLoading ...

MicroRNA function and dysregulation in bone tumors: the evidence to date

Micro ribonucleic acids (miRNAs) are small non-coding RNA segments that have a role in the regulation of normal cellular development and proliferation including normal osteogenesis. They exert their effects through inhibition of specific target genes at the post-transcriptional level. Many miRNAs have altered expression levels in cancer (either increased or decreased depending on the specific miRNA). Altered miRNA expression profiles have been identified in several malignancies including primary bone tumors such as osteosarcoma and Ewing’s sarcoma. It is thought that they may function as tumor suppressor genes or oncogenes and hence when dysregulated contribute to the initiation and progression of malignancy. miRNAs are also thought to have a role in the development of bone metastases in other malignancies. In addition, evidence increasingly suggests that miRNAs may play a part in determining the response to chemotherapy in the treatment of osteosarcoma. These molecules are readily detectable in tissues, both fresh and formalin fixed paraffin embedded and, more recently, in blood. Although there are fewer published studies regarding circulating miRNA profiles, they appear to reflect changes in tissue expression. Thus miRNAs may serve as potential indicators of disease presence but more importantly, may have a role in disease characterization or as potential therapeutic targets. This review gives a brief overview of miRNA biochemistry and explores the evidence to date implicating these small molecules in the pathogenesis of bone tumors.

Alternatives Spleißen – Prinzipien, funktionelle Konsequenzen und therapeutische Relevanz

Protein-coding genes in higher eukaryotes are transcribed as pre-mRNA in which the coding regions (exons) are separated by non-coding segments (introns). The exons are connected to form the mature mRNA in a process called splicing. In the case of alternative splicing an exon can be either included or skipped from the mature transcript leading to formation of several mRNAs from a single pre-mRNA. As over 90 % of all human genes are alternatively spliced, alternative splicing dramatically increases proteome diversity and fulfills important regulatory functions. This is underlined by mutations that interfere with splicing regulation and directly correlate with the formation of several diseases. Correction of these disturbed splicing processes has emerged as a promising therapeutic concept and has led to the development of several drugs that are currently being tested in clinical trials.

The complete mitochondrial genome of Ircinia sp. (Dictyoceratida: Irciniidae)

The mitochondrial genome of Ircinia sp. (Dictyoceratida: Irciniidae) is a circular molecule of 16,037 bp in length, containing 14 protein-coding genes, 2 ribosomal RNA genes, 2 transfer RNA genes (trnW and trnM) and 13 non-coding segments. All genes are distributed in the same strand (H-strand). The overall base composition of the H-strand is as follows: T (37.84%), C (11.22%), A (24.81%), G (26.13%), with GC- and AT-skew of 0.399 and −0.208, respectively, reflecting unbalanced base composition between the two strands. The non-coding regions are 1190 bp in total length, with high AT content (76.31%). The current mitochondrial genome is identical to that of sibling species I. strobilina in gene order and contents, but differs from the latter in the presence of two kinds of repetitive sequences in the non-coding regions, of which one could form repetitive hairpin-forming elements.

The complete mitochondrial genome of Hyattella sinuosa (Dictyoceratida: Spongiidae)

The mitochondrial genome of Hyattella sinuosa (Dictyoceratida: Spongiidae) is a circular molecule of 16,422 bp in length, containing 14 protein-coding genes, 2 ribosomal RNA genes, 2 transfer RNA genes(trnW and trnM) and 13 non-coding segments. All genes are distributed in the same strand (H-strand). The overall base composition of the H-strand is as follows: T (37.72%), C (11.27%), A (25.14%), G (25.86%), with GC- and AT-skew of 0.393 and −0.2, respectively, reflecting unbalanced base composition between the two strands. The non-coding regions are 1240 bp in total length, with high-AT content (73.72%). The current mitochondrial genome is identical to that of Hippospongia Lachne (Family Spongiidae) in gene order and contents, except for the absence of the repeat hairpin-forming element (RHE) in the non-coding regions.

Reproduction and immunity-driven natural selection in the human WFDC locus.

The whey acidic protein (WAP) four-disulfide core domain (WFDC) locus located on human chromosome 20q13 spans 19 genes with WAP and/or Kunitz domains. These genes participate in antimicrobial, immune, and tissue homoeostasis activities. Neighboring SEMG genes encode seminal proteins Semenogelin 1 and 2 (SEMG1 and SEMG2). WFDC and SEMG genes have a strikingly high rate of amino acid replacement (dN/dS), indicative of responses to adaptive pressures during vertebrate evolution. To better understand the selection pressures acting on WFDC genes in human populations, we resequenced 18 genes and 54 noncoding segments in 71 European (CEU), African (YRI), and Asian (CHB + JPT) individuals. Overall, we identified 484 single-nucleotide polymorphisms (SNPs), including 65 coding variants (of which 49 are nonsynonymous differences). Using classic neutrality tests, we confirmed the signature of short-term balancing selection on WFDC8 in Europeans and a signature of positive selection spanning genes PI3, SEMG1, SEMG2, and SLPI. Associated with the latter signal, we identified an unusually homogeneous-derived 100-kb haplotype with a frequency of 88% in Asian populations. A putative candidate variant targeted by selection is Thr56Ser in SEMG1, which may alter the proteolytic profile of SEMG1 and antimicrobial activities of semen. All the well-characterized genes residing in the WDFC locus encode proteins that appear to have a role in immunity and/or fertility, two processes that are often associated with adaptive evolution. This study provides further evidence that the WFDC and SEMG loci have been under strong adaptive pressure within the short timescale of modern humans.

Estimating intrinsic structural preferences of de novo emerging random-sequence proteins: Is aggregation the main bottleneck?

Present-day proteins are believed to have evolved features to reduce the risk of aggregation. However, proteins can emerge de novo by translation of non-coding DNA segments. In this study we assess the aggregation, disorder and transmembrane propensity of protein sequences generated by translating random nucleotide sequences of varying GC-content. Potential de novo random-sequence proteins translated from regions with GC content between 40% and 60% do not show stronger aggregation propensity than existing ones and exhibit similar tendency to be disordered. We suggest that de novo emerging proteins do not mean an unavoidable aggregation threat to evolving organisms.

Circulating miR‐34a levels are reduced in colorectal cancer

MicroRNAs (miRNAs) are small, non-coding RNA segments that regulate gene expression via post-transcriptional inhibition and have roles in cell differentiation, proliferation, and apoptosis. Expression differs between tumor and normal tissue in several malignancies. Most work has focused on tissue and cell expression with few reports of circulating miRNAs in colorectal cancer. Available biomarkers for colorectal cancer have limited sensitivity and specificity, thus there is a need for new markers. This study aimed to identify miRNAs that are differentially expressed in the blood of colorectal cancer patients compared to controls and to establish if this is specific to colorectal cancer and thus could be utilized as potential tumor markers. Blood samples were collected from 63 colorectal cancer patients and 45 controls. Expression of 7 target miRNAs (miR-143, miR-145, miR-21, miR-30a-3p, miR-31, miR-34a, and miR-92) was measured using RQ-PCR. Results were correlated with clinicopathological data and analyzed. Analysis of differentially expressed circulating miRNAs was expanded to include 62 patients with prostate, renal, breast, and melanoma cancers. Analysis of the relative quantification of the target miRNAs showed significantly reduced expression (P = 0.004) of miR-34a in colorectal cancer. MiR-34a was also significantly reduced in breast cancer (P = 0.019). This study demonstrates significantly reduced expression of circulating miR-34a in colorectal and breast cancer. This may have future application as part of a biomarker profile.

446 RENAL CELL CARCINOMA MICRO-RNA A MOLECULAR DETERMINANT OF METASTASIS

You have accessJournal of UrologyKidney Cancer: Basic Research III1 Apr 2012446 RENAL CELL CARCINOMA MICRO-RNA A MOLECULAR DETERMINANT OF METASTASIS Michael Garcia-Roig, Kateryna Kiselora, Travis Yates, Soum Lokeshwar, Ezekiel Young, Vincent Bird, Murugesan Manoharan, and Vinita Lokeshwar Michael Garcia-RoigMichael Garcia-Roig Miami, FL More articles by this author , Kateryna KiseloraKateryna Kiselora Miami, FL More articles by this author , Travis YatesTravis Yates Miami, FL More articles by this author , Soum LokeshwarSoum Lokeshwar Miami, FL More articles by this author , Ezekiel YoungEzekiel Young Miami, FL More articles by this author , Vincent BirdVincent Bird Gainesville, FL More articles by this author , Murugesan ManoharanMurugesan Manoharan Miami, FL More articles by this author , and Vinita LokeshwarVinita Lokeshwar Miami, FL More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2012.02.513AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Up to 25% of patients with renal cell carcinoma (RCC) present with metastasis at initial diagnosis. Molecular determinants of RCC growth & metastasis may be accurate prognostic markers for metastasis. miRNAs (miRs) are 22-nucleotide non-coding segments that regulate gene expression by degrading target mRNAs. Therefore, specific miRs are molecular determinants of tumor growth & metastasis. We examined expression of seven miRs in kidney tumor & normal specimens & correlated the expression with metastasis. METHODS RCC & normal kidney specimens were collected from 86 patients undergoing nephrectomy. miR enriched total RNA was successfully isolated from 46 RCC & 59 normal kidney tissues. Clinical data was collected including tumor histology (oncocytoma 6, chromophobe 4, papillary 6, clear cell 25, sarcoma 4, & collecting duct 1), stage (T1: 20; T2: 9; T3: 10; T4: 1), renal vein involvement (+: 5; −: 41), & lymph node positivity (+: 4; −: 41). At 14 months median follow-up, 6 patients were positive for metastasis. Microarray (Thermo Fisher Scientific 10.1) was performed on 30 samples to identify 554 miR targets. Seven miRs were chosen (mir-21, 150, 155, 142-3p, 142-5p, 192, & 194) based on the fold change in tumor samples. Their expression was quantified by quantitative PCR, & normalized to a housekeeping miR. Statistical analysis was performed using the Mann-Whiteny U-test & multivariate analysis. RESULTS Microarray analysis identified significant upregulation of 65 & down-regulation of 47 miRs in RCC tissues (p<0.05). When compared to normal kidney, RCC specimens demonstrated that miR-155 levels were up-regulated by 4-fold (0.67±0.87 vs 2.7±4.5; P=0.0003) & miR-194 levels were 6.5-fold downregulated (320±352 vs 49.1±74.6; P<0.0001). Similarly, miR-192 expression was downregulated by 5.5-fold in RCC specimens (P<0.0001). miR-142-3p & miR-142-5p levels significantly correlated with tumor grade; median levels in high-grade (3p: 52.97; 5p: 6.2) were 6.8-13.7-fold elevated when compared to low-grade tumors (3p: 7.8; p=0.028; chi-sq =4.8; 5p: 0.45; p=0.003; chi-sq: 8.7). In multivariate analysis which included TMN, renal vein, lymphovascular invasion, age, gender & miR levels, only mir-194 expression was associated with metastasis (p=0.034; chi-sq: 4.5). None of the miRs studied correlated with tumor size or lymphovascular invasion, but miR194 correlated with renal vein involvement (P=0.05). CONCLUSIONS miR-155, 192, 194, & 21 are differentially expressed in kidney cancer. While miR-142 (3p, 5p) associates with tumor grade, miR-194 expression independently associates with metastasis. © 2012 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 187Issue 4SApril 2012Page: e183 Advertisement Copyright & Permissions© 2012 by American Urological Association Education and Research, Inc.MetricsAuthor Information Michael Garcia-Roig Miami, FL More articles by this author Kateryna Kiselora Miami, FL More articles by this author Travis Yates Miami, FL More articles by this author Soum Lokeshwar Miami, FL More articles by this author Ezekiel Young Miami, FL More articles by this author Vincent Bird Gainesville, FL More articles by this author Murugesan Manoharan Miami, FL More articles by this author Vinita Lokeshwar Miami, FL More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

Pattern Discovery in Genomic Coding Sequences Based on Protein Motifs

Pattern recognition and identification on non-coding segments of the genome has been facilitated by presence of vast and diversified regular patterns in these regions. On the other hand, coding segments of the genome has been mostly resistant to pattern discovery efforts due to the lack of easily recognizable patterns in these regions. We have developed a novel algorithm for discovery and identification of patterns in the coding segments of the genome based on regular expressions in corresponding proteins. The algorithm reads pre-identified patterns in proteins, such as those in Prosite, and generates a Consecutive Positions Specific Scoring Matrix (CPSSM). CPSSMs are then aligned to genomics sequences to find hits. CPSSMs may be considered as alternatives to usual protein patterns, but on genomes. We have designed a novel CPSSM-genome alignment algorithm that supports affine gaps, introns, and mismatches based on dynamic programming. Methods have been tested against the real data. Results show 63% more true positives and no false negatives on Saccharomyces cerevisiae's genome, and 99.97% less false negatives and three times more true positives on Human's genome in comparison to previous works.

Overexpression of the CHRNA5/A3/B4 genomic cluster in mice increases the sensitivity to nicotine and modifies its reinforcing effects

Nicotinic acetylcholine receptors (nAChRs) are ligand-gated pentameric ion channels that account for the effects of nicotine. Recent genetic studies have highlighted the importance of variants of the CHRNA5/A3/B4 genomic cluster in human nicotine dependence. Among these genetic variants those found in non-coding segments of the cluster may contribute to the pathophysiology of tobacco use through alterations in the expression of these genes. To discern the in vivo effects of the cluster, we generated a transgenic mouse overexpressing the human CHRNA5/A3/B4 cluster using a bacterial artificial chromosome. Transgenic mice showed increased functional α3β4-nAChRs in brain regions where these subunits are highly expressed under normal physiological conditions. Moreover, they exhibited increased sensitivity to the pharmacological effects of nicotine along with higher activation of the medial habenula and reduced activation of dopaminergic neurons in the ventral tegmental area after acute nicotine administration. Importantly, transgenic mice showed increased acquisition of nicotine self-administration (0.015 mg/kg per infusion) and a differential response in the progressive ratio test. Our study provides the first in vivo evidence of the involvement of the CHRNA5/A3/B4 genomic cluster in nicotine addiction through modifying the activity of brain regions responsible for the balance between the rewarding and the aversive properties of this drug.

Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma

Although expression of non-protein-coding RNA (ncRNA) can be altered in human cancers, their functional relevance is unknown. Ultraconserved regions are noncoding genomic segments that are 100% conserved across humans, mice, and rats. Conservation of gene sequences across species may indicate an essential functional role, and therefore we evaluated the expression of ultraconserved RNAs (ucRNA) in hepatocellular cancer (HCC). The global expression of ucRNAs was analyzed with a custom microarray. Expression was verified in cell lines by real-time PCR or in tissues by in situ hybridization using tissue microarrays. Cellular ucRNA expression was modulated with siRNAs, and the effects on global gene expression and growth of human and murine HCC cells were evaluated. Fifty-six ucRNAs were aberrantly expressed in HepG2 cells compared with nonmalignant hepatocytes. Among these ucRNAs, the greatest change was noted for ultraconserved element 338 (uc.338), which was dramatically increased in human HCC compared with noncancerous adjacent tissues. Although uc.338 is partially located within the poly(rC) binding protein 2 (PCBP2) gene, the transcribed ncRNA encoding uc.338 is expressed independently of PCBP2 and was cloned as a 590-bp RNA gene, termed TUC338. Functional gene annotation analysis indicated predominant effects on genes involved in cell growth. These effects were experimentally demonstrated in both human and murine cells. siRNA to TUC338 decreased both anchorage-dependent and anchorage-independent growth of HCC cells. These studies identify a critical role for TUC338 in regulation of transformed cell growth and of transcribed ultraconserved ncRNA as a unique class of genes involved in the pathobiology of HCC.

Perspectives in Implementing Radiogenomics to Radiotherapy

Genomics is the study of all nucleotide sequences, including structural genes, regulatory sequences and noncoding DNA segments, in the chromosomes of an organism. Radiogenomics focuses on the underlying genetic causes of cellular responses to radiation and its applications to radiation oncology practice. The purpose of this review is to introduce the technology behind radiogenomics and discuss how it may impact radiotherapy practice for practitioners. A literature search was conducted on PubMed using the key words genomics, genes, pharmacogenomics, radiogenomics, dose painting and dose sculpting. A review of the literature shows much promise for future radiation oncology health care practices. Current findings from radiogenomics research require much work in translational research via rigorous testing, evaluation and validation to corroborate data and research methodologies. This review consolidates the theoretical basis of radiogenomics research and discusses the considerations of genomics technology in the context of how it will impact radiotherapy practice. The promise of radiogenomics applications holds a future role in identifying tissue-specific radiation resistance and tolerance by identifying genes responsible for radiobiological response.

DIFFERENTIATING THE PROTEIN CODING AND NONCODING RNA SEGMENTS OF DNA USING SHANNON ENTROPY

The complexity of DNA sequences is evaluated in order to differentiate between protein-coding and noncoding RNA segments. The method is based on computing the Shannon entropy of the sequences. By comparing the entropy of the original sequence with that of its shuffled one, we identify the source of the difference between the two segments and their relative contributions to the sequence. To demonstrate the method, the DNA sequences of the bacterium Clostridium difficile 630(G + C = 29.1%) and Bdellovibrio bacteriovorus(G + C = 50.6%) are analyzed, which are representatives of bacteria with unbalanced and balanced nucleotide content, respectively. It is shown that in both bacteria, regardless of nucleotide content, ΔrS — the relative difference of the two entropies — is significantly greater in protein-coding regions, when compared with noncoding RNA segments.

Origins and functional impact of copy number variation in the human genome.

Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.

The word landscape of the non-coding segments of the Arabidopsis thaliana genome

BackgroundGenome sequences can be conceptualized as arrangements of motifs or words. The frequencies and positional distributions of these words within particular non-coding genomic segments provide important insights into how the words function in processes such as mRNA stability and regulation of gene expression.ResultsUsing an enumerative word discovery approach, we investigated the frequencies and positional distributions of all 65,536 different 8-letter words in the genome of Arabidopsis thaliana. Focusing on promoter regions, introns, and 3' and 5' untranslated regions (3'UTRs and 5'UTRs), we compared word frequencies in these segments to genome-wide frequencies. The statistically interesting words in each segment were clustered with similar words to generate motif logos. We investigated whether words were clustered at particular locations or were distributed randomly within each genomic segment, and we classified the words using gene expression information from public repositories. Finally, we investigated whether particular sets of words appeared together more frequently than others.ConclusionOur studies provide a detailed view of the word composition of several segments of the non-coding portion of the Arabidopsis genome. Each segment contains a unique word-based signature. The respective signatures consist of the sets of enriched words, 'unwords', and word pairs within a segment, as well as the preferential locations and functional classifications for the signature words. Additionally, the positional distributions of enriched words within the segments highlight possible functional elements, and the co-associations of words in promoter regions likely represent the formation of higher order regulatory modules. This work is an important step toward fully cataloguing the functional elements of the Arabidopsis genome.