Tandem repeats ubiquitously flank and select translation initiation sites

Abstract Evolutionary divergence in cis-regulatory sequences impacts translation initiation sites (TISs). The implication of tandem repeats (TRs) in TIS selection remains elusive for the most part. Here we employed the TIS homology concept to study a possible link between all categories of TRs and TIS selection. Human and 83 other species were selected, and data was extracted on the entire protein-coding genes (n=1,611,368) and transcripts (n=2,730,515) annotated for those species from Ensembl 102. Two different weighing vectors were employed to assign TIS homology, and the results were assessed in 10-fold validation. On average, every TIS was flanked by 1.19 TRs of various categories within the 120 bp upstream sequence. We detected statistically significant excess of non-homologous TISs co-occurring with human-specific TRs, vice versa. We conclude that TRs are abundant cis elements in the upstream sequences of TISs across species, and there is a link between all categories of TRs and TIS selection.

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Tandem repeats ubiquitously flank and select translation initiation sites.

10.21203/rs.3.rs-832312/v1 ◽

2021 ◽

Author(s):

Ali Maddi ◽

Kaveh Kavousi ◽

Masoud Arabfard ◽

Hamid Ohadi ◽

Mina Ohadi

Keyword(s):

Translation Initiation ◽

Tandem Repeats ◽

Evolutionary Divergence ◽

Regulatory Sequences ◽

Significant Excess ◽

Stem Loop ◽

Protein Coding ◽

Rna Sequence ◽

Protein Coding Genes ◽

Human Specific

Abstract Findings in yeast and human suggest that evolutionary divergence in cis-regulatory sequences impact translation initiation sites (TISs). Here we employed the TIS homology concept to study a possible link between all categories of tandem repeats (TRs) and TIS selection. Human and 83 other species were selected, and data was extracted on the entire protein-coding genes (n = 1,611,368) and transcripts (n = 2,730,515) annotated for those species from Ensembl 102. On average, every transcript was flanked by 1.19 TRs of various categories in their 120 bp upstream RNA sequence. We detected statistically significant excess of non-homologous TISs co-occurring with human-specific TRs, and vice versa. We conclude that TRs are abundant cis elements in the upstream sequences of TISs across species, and there is a link between all categories of TRs and TIS selection. TR-induced symmetric and stem-loop structures may function as genetic marks for TIS selection.

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Link Between Short tandem Repeats and Translation Initiation Site Selection

10.1101/316950 ◽

2018 ◽

Author(s):

M Arabfard ◽

K Kavousi ◽

A Delbari ◽

M Ohadi

Keyword(s):

Amino Acids ◽

Translation Initiation ◽

Short Tandem Repeats ◽

Tandem Repeats ◽

Initiation Site ◽

Translation Initiation Site ◽

Vertebrate Species ◽

Protein Coding ◽

Human Specific ◽

Short Tandem

AbstractRecent work in yeast and humans suggest that evolutionary divergence in cis-regulatory sequences impact translation initiation sites (TISs). Cis-elements can also affect the efficacy and amount of protein synthesis. Despite their vast biological implication, the landscape and relevance of short tandem repeats (STRs)/microsatellites to the human protein-coding gene TISs remain largely unknown. Here we characterized the STR distribution at the 120 bp cDNA sequence upstream of all annotated human protein-coding gene TISs based on the Ensembl database. Furthermore, we performed a comparative genomics study of all annotated orthologous TIS-flanking sequences across 47 vertebrate species (755,956 transcripts), aimed at identifying human-specific STRs in this interval. We also hypothesized that STRs may be used as genetic codes for the initiation of translation. The initial five amino acid sequences (excluding the initial methionine) that were flanked by STRs in human were BLASTed against the initial orthologous five amino acids in other vertebrate species (2,025,817 pair-wise TIS comparisons) in order to compare the number of events in which human-specific and non-specific STRs occurred with homologous and non-homologous TISs (i.e. ≥50% and <50% similarity of the five amino acids). We characterized human-specific STRs and a bias of this compartment in comparison to the overall (human-specific and non-specific) distribution of STRs (Mann Whitney p=1.4 × 10−11). We also found significant enrichment of non-homologous TISs flanked by human-specific STRs (p<0.00001). In conclusion, our data indicate a link between STRs and TIS selection, which is supported by differential evolution of the human-specific STRs in the TIS upstream flanking sequence.AbbreviationscDNAComplementary DNACDSCoding DNA sequenceSTRShort Tandem RepeatTISTranslation Initiation SiteTSSTranscription Start Site

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Analyzing and characterization of the chloroplast genome of Salix suchowensis

10.7287/peerj.preprints.2388 ◽

2016 ◽

Author(s):

Congrui Sun ◽

Jie Li ◽

Xiaogang Dai ◽

Yingnan Chen

Keyword(s):

Tandem Repeats ◽

Gene Annotation ◽

Repetitive Sequences ◽

Single Copy ◽

Phylogenetic Position ◽

Shrub Willow ◽

Protein Coding ◽

Protein Coding Genes ◽

Cp Genome ◽

Rna Genes

By screening sequence reads from the chloroplast (cp) genome of S. suchowensis that generated by the next generation sequencing platforms, we built the complete circular pseudomolecule for its cp genome. This pseudomolecule is 155,508 bp in length, which has a typical quadripartite structure containing two single copy regions, a large single copy region (LSC 84,385 bp), and a small single copy region (SSC 16,209 bp) separated by inverted repeat regions (IRs 27,457 bp). Gene annotation revealed that the cp genome of S. suchowensis encoded 119 unique genes, including 4 ribosome RNA genes, 30 transfer RNA genes, 82 protein-coding genes and 3 pseudogenes. Analyzing the repetitive sequences detected 15 tandem repeats, 16 forward repeats and 5 palindromic repeats. In addition, a total of 188 perfect microsatellites were detected, which were characterized as A/T predominance in nucleotide compositions. Significant shifting of the IR/SSC boundaries was revealed by comparing this cp genome with that of other rosids plants. We also built phylogenetic trees to demonstrate the phylogenetic position of S. suchowensis in Rosidae, with 66 orthologous protein-coding genes presented in the cp genomes of 32 species. By sequencing 30 amplicons based on the pseudomolecule, experimental verification achieved accuracy up to 99.84% for the cp genome assembly of S. suchowensis. In conclusion, this study built a high quality pseudomolecule for the cp genome of S. suchowensis, which is a useful resource for facilitating the development of this shrub willow into a more productive bioenergy crop.

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A New Aspergillus fumigatus Typing Method Based on Hypervariable Tandem Repeats Located within Exons of Surface Protein Coding Genes (TRESP)

PLoS ONE ◽

10.1371/journal.pone.0163869 ◽

2016 ◽

Vol 11 (10) ◽

pp. e0163869 ◽

Cited By ~ 6

Author(s):

Rocio Garcia-Rubio ◽

Horacio Gil ◽

Maria Candida Monteiro ◽

Teresa Pelaez ◽

Emilia Mellado

Keyword(s):

Aspergillus Fumigatus ◽

Tandem Repeats ◽

Surface Protein ◽

Typing Method ◽

Protein Coding ◽

Protein Coding Genes

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Recovery of non-reference sequences missing from the human reference genome

10.21203/rs.2.11742/v1 ◽

2019 ◽

Author(s):

Ran Li ◽

Xiaomeng Tian ◽

Peng Yang ◽

Yingzhi Fan ◽

Ming Li ◽

...

Keyword(s):

Tandem Repeats ◽

Reference Genome ◽

De Novo ◽

Precise Location ◽

Protein Coding ◽

Human Reference Genome ◽

Protein Coding Genes ◽

Mhc Haplotype ◽

Reference Sequences ◽

Flanking Regions

Abstract The non-reference sequences (NRS) represent structure variations in human genome with potential functional significance. However, besides the known insertions, it is currently unknown whether other types of structure variations with NRS exist. Here, we compared 31 human de novo assemblies with the current reference genome to identify the NRS and their location. We resolved the precise location of 6,113 NRS adding up to 12.8 Mb. Besides 1,571 insertions, we detected 3,041 alternate alleles, which were defined as having less than 90% (or none) identity with the reference alleles. These alternate alleles overlapped with 1,143 protein-coding genes including a putative novel MHC haplotype. Further, we demonstrated that the alternate alleles and their flanking regions had high content of tandem repeats, indicating that their origin was associated with tandem repeats. Our study enriched the spectrum of human genetic variations.

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Genetic characterization of mitochondrial genome of the small intestinal fluke, Haplorchis taichui (Trematoda: Heterophyidae), Vietnamese sample

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/14/2/9333 ◽

2016 ◽

Vol 14 (2) ◽

pp. 215-224

Author(s):

Lê Thanh Hòa ◽

Nguyễn Thị Khuê ◽

Nguyễn Thị Bích Nga ◽

Đỗ Thị Roan ◽

Đỗ Trung Dũng ◽

...

Keyword(s):

Mitochondrial Genome ◽

Tandem Repeats ◽

Transfer Rna ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Mtdna Sequence ◽

Small Intestinal ◽

Haplorchis Taichui ◽

Rna Genes

The small intestinal fluke, Haplorchis taichui Nishigori, 1924, belonging to genus Haplorchis (family Heterophyidae, class Trematoda, phylum Platyhelminthes), is a zoonotic pathogen causing disease in humans and animals. Complete mitochondrial genome (mtDNA) of H. taichui (strain HTAQT, collected from Quang Tri) was obtained and characterized for structural genomics providing valuable data for studies on epidemiology, species identification, diagnosis, classification, molecular phylogenetic relationships and prevention of the disease. The entire nucleotide mtDNA sequence of H. taichui (HTAQT) is 15.119 bp in length, containing 36 genes, including 12 protein-coding genes (cox1, cox2, cox3, nad1, nad2, nad3, nad4L, nad4, nad5, nad6, atp6 and cob); 2 ribosomal RNA genes, rrnL (16S) and rrnS (12S); 22 transfer RNA genes (tRNA or trn), and a non-coding region (NR), divided into two sub-regions of short non-coding (short, SNR) and long non-coding (long, LNR). LNR region, 1.692 bp in length, located between the position of trnG (transfer RNA-Glycine) and trnE (Glutamic acid), contains 6 tandem repeats (TR), arranged as TR1A, TR2A, TR1B, TR2B, TR3A, TR3B, respectively. Each protein coding gene (overall, 12 genes), ribosomal rRNA (2 genes) and tRNA (22 genes) were analyzed, in particular, protein-coding genes were defined in length, start and stop codons, and rRNA and tRNA genes for secondary structure.

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Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera: Sphingidae)

ZooKeys ◽

10.3897/zookeys.754.23404 ◽

2018 ◽

Vol 754 ◽

pp. 127-139 ◽

Cited By ~ 1

Author(s):

Jun Li ◽

Rui-Rui Lin ◽

Yao-Yao Zhang ◽

Kun-Jie Hu ◽

Ya-Qi Zhao ◽

...

Keyword(s):

Tandem Repeats ◽

Phylogenetic Analyses ◽

Rrna Genes ◽

Phylogenetic Position ◽

Trna Genes ◽

Rich Region ◽

Protein Coding ◽

Protein Coding Genes ◽

Oxidase Subunit ◽

Relationship Of

In the present study, the complete mitogenome of Theretrajaponica was sequenced and compared with other sequenced mitogenomes of Sphingidae species. The mitogenome of T.japonica, containing 37 genes (13 protein-coding genes, 22 tRNA genes, and two rRNA genes) and a region rich in adenine and thymine (AT-rich region), is a circular molecule with 15,399 base pairs (bp) in length. The order and orientation of the genes in the mitogenome are similar to those of other sequenced mitogenomes of Sphingidae species. All 13 protein-coding genes (PCGs) are initiated by ATN codons except for the cytochrome C oxidase subunit 1 gene (cox1) which is initiated by the codon CGA as observed in other lepidopteran insects. Cytochrome C oxidase subunit 2 gene (cox2) has the incomplete termination codon T and NADH dehydrogenase subunit 1 gene (nad1) terminates with TAG while the remainder terminates with TAA. Additionally, the codon distributions of the 13 PCGs revealed that Ile and Leu2 are the most frequently used codon families and codons CGG, CGC, CCG, CAG, and AGG are absent. The 431 bp AT-rich region includes the motif ATAGA followed by a 23 bp poly-T stretch, short tandem repeats (STRs) of TC and TA, two copies of a 28 bp repeat ‘ATTAAATTAATAAATTAA TATATTAATA’ and a poly-A element. Phylogenetic analyses within Sphingidae confirmed that T.japonica belongs to the Macroglossinae and showed that the phylogenetic relationship of T.japonica is closer to Ampelophagarubiginosa than Daphnisnerii. Phylogenetic analyses within Theretra demonstrate that T.japonica, T.jugurtha, T.suffusa, and T.capensis are clustered into one clade.

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Molecular phylogeny inferred from the mitochondrial genomes of Plecoptera with Oyamia nigribasis (Plecoptera: Perlidae)

Scientific Reports ◽

10.1038/s41598-020-78082-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Meng-Yuan Zhao ◽

Qing-Bo Huo ◽

Yu-Zhou Du

Keyword(s):

Ribosomal Rna ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

The Other ◽

Mitochondrial Genomes ◽

Stem Loop ◽

Protein Coding ◽

Protein Coding Genes ◽

Noncoding Control Region ◽

Rna Genes

AbstractIn this study, the mitochondrial genome of the stonefly, Oyamia nigribasis Banks, 1920 (Plecoptera: Perlidae), was sequenced and compared with the mtDNA genomes of 38 other stoneflies and two Ephemerae. The O. nigribasis mitogenome is a circular 15,923 bp molecule that encodes a large, noncoding control region (CR) and 37 typical mtDNA genes; these include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), respectively. Most of the PCGs initiated with ATN and terminated with TAN. The dihydrouridine (DHU) arm of tRNASer (AGN) was missing, whereas the other 21 tRNAs all exhibited the typical cloverleaf secondary structure. Stem-loop (SL) structures and tandem repeats were identified in the CR. Phylogenetic analyses using Bayesian inference and maximum likelihood were undertaken to determine relationships between stoneflies. Results indicated that the Antarctoperlaria, which contains Gripopterygidae, was absolutely separated from Arctoperlaria; this finding agrees with morphology. Finally, the overall relationships could be summarized as follows ((((Notonemouridae + Nemouridae) + Leuctridae) + (Scopuridae + (Capniidae + Taeniopterygidae))) + (((Perlodidae + Chloroperlidae) + Perlidae) + (Pteronarcyidae + (Peltoperlidae + Styloperlidae))) + ((Diamphipnoidae + Eustheniidae) + Gripopterygidae)).

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The role of transposable elements in the ecological morphogenesis under the influence of stress

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj19.506 ◽

2019 ◽

Vol 23 (4) ◽

pp. 380-389 ◽

Cited By ~ 3

Author(s):

R. N. Mustafin ◽

E. K. Khusnutdinova

Keyword(s):

Transcription Factors ◽

Regulatory Networks ◽

Insertional Mutagenesis ◽

Specific Protein ◽

Regulatory Sequences ◽

Rapid Variability ◽

Protein Coding ◽

Genome Variability ◽

Protein Coding Genes ◽

Non Coding Rna

In natural selection, insertional mutagenesis is an important source of genome variability. Transposons are sensors of environmental stress effects, which contribute to adaptation and speciation. These effects are due to changes in the mechanisms of morphogenesis, since transposons contain regulatory sequences that have cis and trans effects on specific protein-coding genes. In variability of genomes, the horizontal transfer of transposons plays an important role, because it contributes to changing the composition of transposons and the acquisition of new properties. Transposons are capable of site-specific transpositions, which lead to the activation of stress response genes. Transposons are sources of non-coding RNA, transcription factors binding sites and protein-coding genes due to domestication, exonization, and duplication. These genes contain nucleotide sequences that interact with non-coding RNAs processed from transposons transcripts, and therefore they are under the control of epigenetic regulatory networks involving transposons. Therefore, inherited features of the location and composition of transposons, along with a change in the phenotype, play an important role in the characteristics of responding to a variety of environmental stressors. This is the basis for the selection and survival of organisms with a specific composition and arrangement of transposons that contribute to adaptation under certain environmental conditions. In evolution, the capability to transpose into specific genome sites, regulate gene expression, and interact with transcription factors, along with the ability to respond to stressors, is the basis for rapid variability and speciation by altering the regulation of ontogenesis. The review presents evidence of tissue-specific and stage-specific features of transposon activation and their role in the regulation of cell differentiation to confirm their role in ecological morphogenesis.

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