Genomes and Genes
inverted repeat sequences
Summary: Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.
- Aktas T, Avşar Ilık İ, Maticzka D, Bhardwaj V, Pessoa Rodrigues C, Mittler G, et al. DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome. Nature. 2017;544:115-119 pubmed publisher..We propose that it acts as a nuclear RNA resolvase that neutralizes the immediate threat posed by transposon insertions and allows these elements to evolve as tools for the post-transcriptional regulation of gene expression. ..
- Nguyen J, Viterbo D, Anand R, Verra L, Sloan L, Richard G, et al. Differential requirement of Srs2 helicase and Rad51 displacement activities in replication of hairpin-forming CAG/CTG repeats. Nucleic Acids Res. 2017;45:4519-4531 pubmed publisher..These results clarify the many roles of Srs2 in facilitating replication through fork-blocking hairpin lesions. ..
- Nock C, Baten A, King G. Complete chloroplast genome of Macadamia integrifolia confirms the position of the Gondwanan early-diverging eudicot family Proteaceae. BMC Genomics. 2014;15 Suppl 9:S13 pubmed publisher..Genomic resources for the family are limited, and until now it is one of the few early-diverging 'basal eudicot' lineages not represented in chloroplast phylogenomic analyses...
- Liu N, Parisien M, Dai Q, Zheng G, He C, Pan T. Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA. 2013;19:1848-56 pubmed publisher..We also found that many m(6)A candidate sites in these RNAs are however not modified. The precise determination of m(6)A status in a long noncoding RNA also enables the identification of an m(6)A-containing RNA structural motif. ..
- Cantero Camacho Á, Fan L, Wang Y, Gallego J. Three-dimensional structure of the 3'X-tail of hepatitis C virus RNA in monomeric and dimeric states. RNA. 2017;23:1465-1476 pubmed publisher..Formation of these dimers could initialize and/or regulate the packaging of viral RNA genomes into virions. ..
- Huang L, Wang J, Lilley D. The Structure of the Guanidine-II Riboswitch. Cell Chem Biol. 2017;24:695-702.e2 pubmed publisher..One side of the pocket has an opening to the solvent, slightly lowering the specificity of ligand binding, and structures with bound methylguanidine, aminoguanidine, and agmatine show how this is possible. ..
- Ritchie D, Cappellano T, Tittle C, Rezajooei N, Rouleau L, Sikkema W, et al. Conformational dynamics of the frameshift stimulatory structure in HIV-1. RNA. 2017;23:1376-1384 pubmed publisher..The unusual heterogeneity of the hairpin dynamics under tension suggests a possible functional role in PRF similar to the dynamics of other stimulatory structures. ..
- Guo P, Chan H, Lam S. Conformational flexibility in the RNA stem-loop structures formed by CAG repeats. FEBS Lett. 2017;591:1752-1760 pubmed publisher..Our results show the formation of a type III AGCA tetraloop and reveal the effect of stem rigidity on the loop conformational flexibility. ..
- Liu K, Wessler S. Transposition of Mutator-like transposable elements (MULEs) resembles hAT and Transib elements and V(D)J recombination. Nucleic Acids Res. 2017;45:6644-6655 pubmed publisher..Collectively, our data provides new insights to understand the evolutionary relationships between MULE, hAT and Transib elements and the V(D)J recombinase. ..
- Bertels F, Gallie J, Rainey P. Identification and Characterization of Domesticated Bacterial Transposases. Genome Biol Evol. 2017;9:2110-2121 pubmed publisher..Overall, the genomic distribution of RAYTs suggests that they have been coopted by host genomes to perform a function that benefits the host cell...
- Brogie J, Price D. Reconstitution of a functional 7SK snRNP. Nucleic Acids Res. 2017;45:6864-6880 pubmed publisher..Inhibition of MEPCE is dependent on the structure of the 3? stem loop and the closed form of 7SK RNA. This study provides important insights into intramolecular interactions within the 7SK snRNP...
- Wang Y, Huang J. Lirex: A Package for Identification of Long Inverted Repeats in Genomes. Genomics Proteomics Bioinformatics. 2017;15:141-146 pubmed publisher..Our tool can identify more LIRs than other LIR searching tools. Lirex is publicly available at http://126.96.36.199/Lirex. ..
- Whittum M, Blose J. Effects of osmolytes on stable UUCG tetraloops and their preference for a CG closing base pair. Nucleosides Nucleotides Nucleic Acids. 2017;36:583-597 pubmed publisher..These results reveal that relatively small structural changes may influence how osmolytes tune the stability, and thus the function of a secondary structure motif in vivo...
- Porter J, Sun M, Xie H, Zhang L. Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data. BMC Genomics. 2015;16 Suppl 11:S2 pubmed publisher..Such improvement in mapping efficiency is related to sequence entropy. The hairpin recovery technique improves mapping efficiency, and sequence entropy relates to mapping efficiency. ..
- Coons L, Hewitt S, Burkholder A, McDonnell D, Korach K. DNA Sequence Constraints Define Functionally Active Steroid Nuclear Receptor Binding Sites in Chromatin. Endocrinology. 2017;158:3212-3234 pubmed publisher..These findings define the transcriptional grammar necessary to predict functionality from regulatory sequences, with a multitude of future implications...
- Mojica F, Díez Villaseñor C. The on-off switch of CRISPR immunity against phages in Escherichia coli. Mol Microbiol. 2010;77:1341-5 pubmed
- Morita T, Nishino R, Aiba H. Role of the terminator hairpin in the biogenesis of functional Hfq-binding sRNAs. RNA. 2017;23:1419-1431 pubmed publisher..i> We constructed variant sRNA genes in which the GC-rich inverted repeat sequences are extended to stabilize the terminator hairpins...
- Pendleton K, Chen B, Liu K, Hunter O, Xie Y, Tu B, et al. The U6 snRNA m6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention. Cell. 2017;169:824-835.e14 pubmed publisher..These observations suggest that the conserved U6 snRNA methyltransferase evolved an additional function in vertebrates to regulate SAM homeostasis. ..
- Tateishi Karimata H, Ohyama T, Muraoka T, Podbevsek P, Wawro A, Tanaka S, et al. Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH-? interactions. Nucleic Acids Res. 2017;45:7021-7030 pubmed publisher..The results suggest that numerous cellular co-solutes likely affect DNA function through these CH-? and lone pair-? interactions. ..
- Choi Y, Gibala K, Ayele T, Deventer K, Resendiz M. Biophysical properties, thermal stability and functional impact of 8-oxo-7,8-dihydroguanine on oligonucleotides of RNA-a study of duplex, hairpins and the aptamer for preQ1 as models. Nucleic Acids Res. 2017;45:2099-2111 pubmed publisher..These studies show the capability of 8-oxoG to affect structure and function of RNA, resulting in distinct outcomes as a function of number and position of the lesion. ..
- Montavon T, Kwon Y, Zimmermann A, Hammann P, Vincent T, Cognat V, et al. A specific dsRNA-binding protein complex selectively sequesters endogenous inverted-repeat siRNA precursors and inhibits their processing. Nucleic Acids Res. 2017;45:1330-1344 pubmed publisher..The existence of such a complex and its implication regarding the still elusive biological function of plant endoIR-siRNA will be discussed. ..
- Ebert M, Schweyen P, Bröring M, Laass S, Härtig E, Jahn D. Heme and nitric oxide binding by the transcriptional regulator DnrF from the marine bacterium Dinoroseobacter shibae increases napD promoter affinity. J Biol Chem. 2017;292:15468-15480 pubmed publisher..On the basis of these results, we propose a model for the DnrF-mediated NO stress response of this marine bacterium. ..
- Lee H, Jung S, Hwang H, Kang D, De S, Dudekula D, et al. WIG1 is crucial for AGO2-mediated ACOT7 mRNA silencing via miRNA-dependent and -independent mechanisms. Nucleic Acids Res. 2017;45:6894-6910 pubmed publisher..Altogether, our data indicate that WIG1 governs the miRNA-dependent and the miRNA-independent recruitment of AGO2 to lower the stability of and suppress the translation of ACOT7 mRNA. ..
- Kiliszek A, Blaszczyk L, Kierzek R, Rypniewski W. Stabilization of RNA hairpins using non-nucleotide linkers and circularization. Nucleic Acids Res. 2017;45:e92 pubmed publisher..Another method uses click chemistry to stitch the RNA ends with a triazole linker. Both techniques are efficient and easy to perform. They should be useful in making stable, biologically relevant RNA constructs for structural studies. ..