scholarly journals A First-Stage Approximation to Identify New Imprinted Genes through Sequence Analysis of Its Coding Regions

2009 ◽  
Vol 2009 ◽  
pp. 1-7 ◽  
Author(s):  
Elias Daura-Oller ◽  
Maria Cabré ◽  
Miguel A. Montero ◽  
José L. Paternáin ◽  
Antoni Romeu
Keyword(s):  
Tandem Repeats ◽  
Cpg Islands ◽  
Imprinted Genes ◽  
Coding Region ◽  
Training Set ◽  
Principle Components Analysis ◽  
Coding Regions ◽  
Gene Coding ◽  
Components Analysis ◽  
Simple Repeats

In the present study, a positive training set of 30 known human imprinted gene coding regions are compared with a set of 72 randomly sampled human nonimprinted gene coding regions (negative training set) to identify genomic features common to human imprinted genes. The most important feature of the present work is its ability to use multivariate analysis to look at variation, at coding region DNA level, among imprinted and non-imprinted genes. There is a force affecting genomic parameters that appears through the use of the appropriate multivariate methods (principle components analysis (PCA) and quadratic discriminant analysis (QDA) to analyse quantitative genomic data. We show that variables, such as CG content, [bp]% CpG islands, [bp]% Large Tandem Repeats, and [bp]% Simple Repeats, are able to distinguish coding regions of human imprinted genes.

scholarly journals Genetic conflict, genomic imprinting and establishment of the epigenotype in relation to growth

Reproduction ◽  
2001 ◽  
pp. 185-193 ◽  
Author(s):  
T Moore
Keyword(s):  
Genomic Imprinting ◽  
Parental Investment ◽  
Tandem Repeats ◽  
Cpg Islands ◽  
Subsequent Development ◽  
Imprinted Genes ◽  
Growth Disorders ◽  
Genetic Loci ◽  
Mammalian Embryo ◽  
Genetic Conflict

Genomic imprinting is the process that differentially modifies the parental alleles at certain genetic loci in the parental germlines. Such modifications of DNA and chromatin are somatically heritable and cause unequal expression of the parental alleles during subsequent development. In mammals, imprinted genes encode a relatively small number of functionally heterogeneous proteins. Nevertheless, imprinted genes exert important effects, primarily on fetal development, and their deregulation is implicated in a variety of pathologies including sporadic, inherited and induced growth disorders. Imprinted loci show several unusual structural and functional characteristics that may be related to mechanistic aspects of mono-allelic expression or to modes of evolution of imprinted genetic loci. Typically, imprinted genes are clustered in certain genomic regions and have relatively reduced intronic DNA content relative to non-imprinted genes. In addition, their regulatory regions frequently contain a combination of features including tandem repeats associated with differentially methylated CpG islands and overlapping transcription of coding or non-coding RNAs. The evolution of imprinting can be understood as the stable outcome of sexual selection acting differently on the parental alleles of genes that influence parental investment in offspring. Consistent with this explanation, imprinted genes are expressed predominantly during embryonic and postnatal development in mammals and in the developing endosperm of plants, and maternal or paternal expression at imprinted loci is associated with reduced or increased parental investment, respectively. Such selective forces have implications for understanding mechanistic aspects of genome reprogramming in the early mammalian embryo.

scholarly journals Structure and evolution of genes encoding polyubiquitin and ubiquitin-like proteins in Arabidopsis thaliana ecotype Columbia.

Genetics ◽  
1995 ◽  
Vol 139 (2) ◽  
pp. 921-939 ◽  
Author(s):  
J Callis ◽  
T Carpenter ◽  
C W Sun ◽  
R D Vierstra
Keyword(s):  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Tandem Repeats ◽  
Synonymous Substitution ◽  
Coding Region ◽  
Coding Regions ◽  
Isolation And Characterization ◽  
Genes Encoding ◽  
Polyubiquitin Gene ◽  
Polyubiquitin Genes

Abstract The Arabidopsis thaliana ecotype Columbia ubiquitin gene family consists of 14 members that can be divided into three types of ubiquitin genes; polyubiquitin genes, ubiquitin-like genes and ubiquitin extension genes. The isolation and characterization of eight ubiquitin sequences, consisting of four polyubiquitin genes and four ubiquitin-like genes, are described here, and their relationships to each other and to previously identified Arabidopsis ubiquitin genes were analyzed. The polyubiquitin genes, UBQ3, UBQ10, UBQ11 and UBQ14, contain tandem repeats of the 228-bp ubiquitin coding region. Together with a previously described polyubiquitin gene, UBQ4, they differ in synonymous substitutions, number of ubiquitin coding regions, number and nature of nonubiquitin C-terminal amino acid(s) and chromosomal location, dividing into two subtypes; the UBQ3/UBQ4 and UBQ10/UBQ11/UBQ14 subtypes. Ubiquitin-like genes, UBQ7, UBQ8, UBQ9 and UBQ12, also contain tandem repeats of the ubiquitin coding region, but at least one repeat per gene encodes a protein with amino acid substitutions. Nucleotide comparisons, Ks value determinations and neighbor-joining analyses were employed to determine intra- and intergenic relationships. In general, the rate of synonymous substitution is too high to discern related repeats. Specific exceptions provide insight into gene relationships. The observed nucleotide relationships are consistent with previously described models involving gene duplications followed by both unequal crossing-over and gene conversion events.

scholarly journals Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana

2017 ◽  
Author(s):  
Anuj Kumar ◽  
Aditi Chauhan ◽  
Mansi Sharma ◽  
Sai Kumar Kompelli ◽  
Vijay Gahlaut ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Full Length ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Regions ◽  
Mirna Genes ◽  
Genome Wide ◽  
Varying Length

AbstractSimple Sequence Repeats (SSRs), also known as microsatellites are short tandem repeats of DNA sequences that are 1-6 bp long. In plants, SSRs serve as a source of important class of molecular markers because of their hypervariabile and co-dominant nature, making them useful both for the genetic studies and marker-assisted breeding. The SSRs are widespread throughout the genome of an organism, so that a large number of SSR datasets are available, most of them from either protein-coding regions or untranslated regions. It is only recently, that their occurrence within microRNAs (miRNA) genes has received attention. As is widely known, miRNA themselves are a class of non-coding RNAs (ncRNAs) with varying length of 19-22 nucleotides (nts), which play an important role in regulating gene expression in plants under different biotic and abiotic stresses. In this communication, we describe the results of a study, where miRNA-SSRs in full length pre-miRNA sequences of Arabidopsis thaliana were mined. The sequences were retrieved by annotations available at EnsemblPlants using BatchPrimer3 server with miRNA-SSR flanking primers found to be well distributed. Our analysis shows that miRNA-SSRs are relatively rare in protein-coding regions but abundant in non-coding region. All the observed 147 di-, tri-, tetra-, penta- and hexanucleotide SSRs were located in non-coding regions of all the 5 chromosomes of A. thaliana. While we confirm that miRNA-SSRs were commonly spread across the full length pre-miRNAs, we envisage that such studies would allow us to identify newly discovered markers for breeding studies.

scholarly journals Analysis of the BRCA1 gene coding regions in patients with luminal B breast cancer

2020 ◽  
pp. 22-23
Author(s):  
А.М. Певзнер ◽  
М.К. Ибрагимова ◽  
М.М. Цыганов
Keyword(s):  
Breast Cancer ◽  
Tumor Tissue ◽  
Brca1 Gene ◽  
Germline Mutations ◽  
Coding Region ◽  
Luminal B ◽  
Coding Regions ◽  
Disease Prognosis ◽  
Gene Coding ◽  
Low Expression

Наши предыдущие исследования показали, что дефицит гена BRCA1, вызванный изменениями в опухоли, такими как низкая экспрессия, делеция, потеря гетерозиготности, может быть связан с эффективностью химиотерапии и прогнозом заболевания. Однако даже при отсутствии этих факторов эффективность терапии таксотером была переменной. Это может быть связано с наличием других соматических изменениий гена BRCA1 в опухолевой ткани, и их определение поможет определить индивидуальную стратегию лечения для каждого пациента с раком молочной железы. Здесь мы исследовали весь спектр герминальных и соматических мутаций кодирующей области генов BRCA1/2 в опухолевой ткани. В целом, наши результаты показывают, что имеет смысл принимать во внимание не только выявленные герминальные мутации, но и соматические изменения в генах BRCA1/2 при назначении терапии. Our previous studies have shown that BRCA1 gene deficiency caused by changes in the tumor such as low expression, deletion, loss of heterozygosity, etc., can be associated with the effectiveness of chemotherapy and the disease prognosis. However, even in the absence of these factors, the effectiveness of taxotere therapy was variable. This may be due to the availability of another BRCA1 gene somatic changes in the tumor tissue and their determination will help to define the personalize treatment strategy for each breast cancer patient. Here we investigated the entire spectrum germline and somatic mutation of coding region of the BRCA1/2 gene in tumor tissue. Overall, our results suggest that it makes sense to take into account not only identified germline mutations, but also somatic changes in the BRCA1/2 gene when appointment taxotere

scholarly journals Траектории кинков ДНК в последовательностях, содержащих кодирующие области генов

2017 ◽  
Vol 12 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Л.В. Якушевич ◽  
L.V. Yakushevich
Keyword(s):  
Gene Sequence ◽  
Initial Energy ◽  
Energy Profile ◽  
Coding Region ◽  
Quasi Particle ◽  
Coding Regions ◽  
Gene Coding ◽  
Initial Task ◽  
Convenient Approach ◽  
Open States

Coding regions (CDS) being an integral part of any gene sequence, play an important role in the process of transcription. One of the tasks associated with the CDS regions, consists in the modeling of the passage of transcription bubbles named also open states or DNA kinks through the coding regions. In this paper, we present a simple and convenient approach to the modeling of the passage. It includes the calculation of the energy profile of the sequence and reducing the initial task to the modeling of the movement of a quasi particle in the field with this energy profile. To illustrate the method, we present the results of the calculations of the trajectories of the DNA kinks moving in the sequence of gene coding interferon alpha 17 (IFNA17) that consists of the three regions: the coding region and the two regions with unknown functional properties. To analyze the kink dynamics, we apply approximation where the DNA parameters are being averaged separately over each of the three regions. In the absences of dissipation, the total kink energy is constant. At the same time the kink velocity is constant only inside each of the regions. In the presence of dissipation, the total kink energy decreases. It is shown that the greater the total initial energy of the kink, the faster the energy decrease. It is suggested that the proposed approach could be useful in finding the ways to govern the movement of transcription bubbles at the first stage of the process of transcription.

scholarly journals Tandem repeats in the CpG islands of imprinted genes

Genomics ◽  
2006 ◽  
Vol 88 (3) ◽  
pp. 323-332 ◽  
Author(s):  
Barbara Hutter ◽  
Volkhard Helms ◽  
Martina Paulsen
Keyword(s):  
Tandem Repeats ◽  
Cpg Islands ◽  
Imprinted Genes

scholarly journals Structure and Regulation of the Salivary Gland Secretion Protein Gene Sgs-1 of Drosophila melanogaster

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 753-762
Author(s):  
Günther E Roth ◽  
Sigrid Wattler ◽  
Hartmut Bornschein ◽  
Michael Lehmann ◽  
Günter Korge
Keyword(s):  
Drosophila Melanogaster ◽  
Tandem Repeats ◽  
Transcriptional Start Site ◽  
Regulatory Elements ◽  
Coding Region ◽  
Band Shift ◽  
Salivary Gland Secretion ◽  
Enhancer Binding Protein ◽  
Factor Secretion ◽  
Third Instar Larvae

Abstract The Drosophila melanogaster gene Sgs-1 belongs to the secretion protein genes, which are coordinately expressed in salivary glands of third instar larvae. Earlier analysis had implied that Sgs-1 is located at the 25B2-3 puff. We cloned Sgs-1 from a YAC covering 25B2-3. Despite using a variety of vectors and Escherichia coli strains, subcloning from the YAC led to deletions within the Sgs-1 coding region. Analysis of clonable and unclonable sequences revealed that Sgs-1 mainly consists of 48-bp tandem repeats encoding a threonine-rich protein. The Sgs-1 inserts from single λ clones are heterogeneous in length, indicating that repeats are eliminated. By analyzing the expression of Sgs-1/lacZ fusions in transgenic flies, cis-regulatory elements of Sgs-1 were mapped to lie within 1 kb upstream of the transcriptional start site. Band shift assays revealed binding sites for the transcription factor fork head (FKH) and the factor secretion enhancer binding protein 3 (SEBP3) at positions that are functionally relevant. FKH and SEBP3 have been shown previously to be involved in the regulation of Sgs-3 and Sgs-4. Comparison of the levels of steady state RNA and of the transcription rates for Sgs-1 and Sgs-1/lacZ reporter genes indicates that Sgs-1 RNA is 100-fold more stable than Sgs-1/lacZ RNA. This has implications for the model of how Sgs transcripts accumulate in late third instar larvae.

scholarly journals Identification of NURR1 (Exon 4) and FOXA1 (Exon 3) Haplotypes Associated with mRNA Expression Levels in Peripheral Blood Lymphocytes of Parkinson’s Patients in Small Indian Population

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Jayakrishna Tippabathani ◽  
Jayshree Nellore ◽  
Vaishnavie Radhakrishnan ◽  
Somashree Banik ◽  
Sonia Kapoor
Keyword(s):  
Mrna Expression ◽  
Peripheral Blood ◽  
Peripheral Blood Lymphocytes ◽  
Coding Region ◽  
Male And Female ◽  
Blood Lymphocytes ◽  
Coding Regions ◽  
Significant Difference ◽  
Exon 4 ◽  
Foxa1 Expression

Here, we study the expression of NURR1 and FOXA1 mRNA in peripheral blood lymphocytes and its haplotypes in coding region in a small Chennai population of India. Thirty cases of Parkinson’s patients (PD) with anti-PD medications (20 males aged65.85±1.19and 10 females aged65.7±1.202) and 30 age matched healthy people (20 males aged68.45±1.282and 10 females aged65.8±1.133) were included. The expression of NURR1 and FOXA1 in PBL was detected by Q-PCR and haplotypes were identified by PCR-SSCP. In the 30 PD cases examined, NURR1 and FOXA1 expression was significantly reduced in both male and female PD patients. However, NURR1 (57.631% reduced in males; 28.93% in females) and FOXA1 (64.42% in males; 55.76% in females) mRNA expression did differ greatly between male and female PD patients. Polymorphisms were identified at exon 4 of the NURR1 and at exon 3 of the FOXA1, respectively, in both male and female patients. A near significant difference in SSCP patterns between genders of control and PD population was analyzed suggesting that further investigations of more patients, more molecular markers, and coding regions should be performed. Such studies could potentially reveal peripheral molecular marker of early PD and different significance to the respective genders.

Structure and expression of canary myc family genes

1991 ◽  
Vol 11 (3) ◽  
pp. 1770-1776
Author(s):  
R G Collum ◽  
D F Clayton ◽  
F W Alt
Keyword(s):  
Untranslated Region ◽  
Untranslated Regions ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Regions ◽  
Neuronal Precursors ◽  
Myc Gene ◽  
Mature Neurons

We found that the canary N-myc gene is highly related to mammalian N-myc genes in both the protein-coding region and the long 3' untranslated region. Examined coding regions of the canary c-myc gene were also highly related to their mammalian counterparts, but in contrast to N-myc, the canary and mammalian c-myc genes were quite divergent in their 3' untranslated regions. We readily detected N-myc and c-myc expression in the adult canary brain and found N-myc expression both at sites of proliferating neuronal precursors and in mature neurons.

scholarly journals Transposons, Tandem Repeats, and the Silencing of Imprinted Genes

2004 ◽  
Vol 69 (0) ◽  
pp. 371-380 ◽  
Author(s):  
R. MARTIENSSEN ◽  
Z. LIPPMAN ◽  
B. MAY ◽  
M. RONEMUS ◽  
M. VAUGHN
Keyword(s):  
Tandem Repeats ◽  
Imprinted Genes
Sign in / Sign up

Export Citation Format

Share Document