nucleotide motifs

Summary

Summary: Commonly observed BASE SEQUENCE or nucleotide structural components which can be represented by a CONSENSUS SEQUENCE or a SEQUENCE LOGO.

Top Publications

  1. Parvathaneni R, DeLeo V, Spiekerman J, Chakraborty D, Devos K. Parallel loss of introns in the ABCB1 gene in angiosperms. BMC Evol Biol. 2017;17:238 pubmed publisher
    ..In addition to size, the presence of regulatory motifs will make introns recalcitrant to loss. ..
  2. Park S, Kang K, Giannopoulou E, Qiao Y, Kang K, Kim G, et al. Type I interferons and the cytokine TNF cooperatively reprogram the macrophage epigenome to promote inflammatory activation. Nat Immunol. 2017;18:1104-1116 pubmed publisher
    ..Our findings reveal that signaling crosstalk between interferons and TNF is integrated at the level of chromatin to reprogram inflammatory responses, and identify previously unknown functions and mechanisms of action of these cytokines. ..
  3. Růzicka M, Kulhanek P, Radova L, Čechová A, Spackova N, Fajkusova L, et al. DNA mutation motifs in the genes associated with inherited diseases. PLoS ONE. 2017;12:e0182377 pubmed publisher
    ..We observed that the coldspots were inherently more flexible than the hotspots. We assume that this property might be critical for effective mismatch repair as DNA with a mutation recognized by MutS? protein is noticeably bent. ..
  4. Mironova V, Omelyanchuk N, Wiebe D, Levitsky V. Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome. BMC Genomics. 2014;15 Suppl 12:S4 pubmed publisher
    ..The specificity in location and orientation of the coupling elements suggests them as potential binding sites for ARFs partners. ..
  5. Asada R, Umeda M, Adachi A, Senmatsu S, Abe T, Iwasaki H, et al. Recruitment and delivery of the fission yeast Rst2 transcription factor via a local genome structure counteracts repression by Tup1-family corepressors. Nucleic Acids Res. 2017;45:9361-9371 pubmed publisher
  6. Majikes J, Ferraz L, Labean T. pH-Driven Actuation of DNA Origami via Parallel I-Motif Sequences in Solution and on Surfaces. Bioconjug Chem. 2017;28:1821-1825 pubmed publisher
    ..Here we characterize internal motion between DNA origami substructures via AFM and image analysis. Such parallel I-motif design and quantification of actuation provide a useful step toward more complex and effective molecular machines...
  7. Le T, Wagner A, Albers S. A conserved hexanucleotide motif is important in UV-inducible promoters in Sulfolobus acidocaldarius. Microbiology. 2017;163:778-788 pubmed publisher
    ..Given the fact that the identified motif is conserved among S. acidocaldarius and Sulfolobus tokodaii promoters, we speculate that a common regulatory mechanism is present in these two species in response to DNA-damaging conditions. ..
  8. Cereda M, Pozzoli U, Rot G, Juvan P, Schweitzer A, Clark T, et al. RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing. Genome Biol. 2014;15:R20 pubmed publisher
    ..RNAmotifs is available at https://bitbucket.org/rogrro/rna_motifs. ..
  9. Chen X, Yu B, Carriero N, Silva C, Bonneau R. Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility. Nucleic Acids Res. 2017;45:4315-4329 pubmed publisher
    ..Further, we describe a method for mapping new TFCT, for which no ChIP-seq data exists, onto our ensemble of classifiers and show that our cross-sample TFBS prediction method outperforms several previously described methods. ..

More Information

Publications86

  1. Benabou S, Aviñó A, Lyonnais S, Gonzalez C, Eritja R, de Juan A, et al. i-motif structures in long cytosine-rich sequences found upstream of the promoter region of the SMARCA4 gene. Biochimie. 2017;140:20-33 pubmed publisher
    ..This finding opens the door to the study of the interaction of these kind of i-motif structures with stabilizing ligands or proteins. ..
  2. Zheng Q, Hou J, Zhou Y, Li Z, Cao X. The RNA helicase DDX46 inhibits innate immunity by entrapping m6A-demethylated antiviral transcripts in the nucleus. Nat Immunol. 2017;18:1094-1103 pubmed publisher
    ..Thus, DDX46 inhibits antiviral innate responses by entrapping selected antiviral transcripts in the nucleus by erasing their m6A modification, a modification normally required for export from the nucleus and translation. ..
  3. Shilo S, Tripathi P, Melamed Bessudo C, Tzfadia O, Muth T, Levy A. T-DNA-genome junctions form early after infection and are influenced by the chromatin state of the host genome. PLoS Genet. 2017;13:e1006875 pubmed publisher
    ..Such structures may play a role in capturing and silencing invading T-DNA. ..
  4. Brady L, Wang H, Radens C, Bi Y, Radovich M, Maity A, et al. Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation. PLoS Biol. 2017;15:e2002623 pubmed publisher
  5. Oh H, Grinberg Bleyer Y, Liao W, Maloney D, Wang P, Wu Z, et al. An NF-?B Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function. Immunity. 2017;47:450-465.e5 pubmed publisher
    ..These dual roles of canonical NF-?B in Tconv and Treg cells highlight the functional plasticity of the NF-?B signaling pathway and underscores the need for more selective strategies to therapeutically target NF-?B. ..
  6. Sethi I, Gluck C, Zhou H, Buck M, Sinha S. Evolutionary re-wiring of p63 and the epigenomic regulatory landscape in keratinocytes and its potential implications on species-specific gene expression and phenotypes. Nucleic Acids Res. 2017;45:8208-8224 pubmed publisher
  7. Ashoor H, Kleftogiannis D, Radovanovic A, Bajic V. DENdb: database of integrated human enhancers. Database (Oxford). 2015;2015: pubmed publisher
    ..DENdb is designed as a relational database that facilitates fast and efficient searching, browsing and visualization of information. Database URL: http://www.cbrc.kaust.edu.sa/dendb/. ..
  8. Guo Y, Wu H, Li X, Li Q, Zhao X, Duan X, et al. Identification and expression of GRAS family genes in maize (Zea mays L.). PLoS ONE. 2017;12:e0185418 pubmed publisher
    ..The data set expands our knowledge to understanding the function of GRAS genes in maize, an important crop plant in the world. ..
  9. Patel A, Zhang X, Blumenthal R, Cheng X. Structural basis of human PR/SET domain 9 (PRDM9) allele C-specific recognition of its cognate DNA sequence. J Biol Chem. 2017;292:15994-16002 pubmed publisher
    ..This Arg-Asp conformational switch allows identical ZF modules to recognize different sequences. Our findings illuminate the molecular mechanisms for flexible and conserved binding of human PRDM9 alleles to their cognate DNA sequences. ..
  10. Ye Z, Ma T, Kalmbach M, Dasari S, Kocher J, Wang L. CircularLogo: A lightweight web application to visualize intra-motif dependencies. BMC Bioinformatics. 2017;18:269 pubmed publisher
    ..logo is unable to display the intra-motif dependencies and therefore is insufficient to fully characterize nucleotide motifs. Many methods have been developed to quantify the intra-motif dependencies, but fewer tools are available ..
  11. Tarkkonen K, Hieta R, Kytölä V, Nykter M, Kiviranta R. Comparative analysis of osteoblast gene expression profiles and Runx2 genomic occupancy of mouse and human osteoblasts in vitro. Gene. 2017;626:119-131 pubmed publisher
  12. Ge S. Exploratory bioinformatics investigation reveals importance of "junk" DNA in early embryo development. BMC Genomics. 2017;18:200 pubmed publisher
    ..It also demonstrates that exploratory bioinformatics investigation can pinpoint developmental pathways for further study, and serve as a strategy to generate novel insights from big genomic data. ..
  13. Schimmer B, Parker K. Promoter elements of the mouse 21-hydroxylase (Cyp-21) gene involved in cell-selective and cAMP-dependent gene expression. J Steroid Biochem Mol Biol. 1992;43:937-50 pubmed publisher
    ..On the basis of these observations, we suggest that ACTH- and cAMP-dependent expression of Cyp-21 requires the combined actions of the element at -170, and the related elements at -140, -210 and -65. ..
  14. Shi L, Peng P, Du Y, Li T. Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device. Nucleic Acids Res. 2017;45:4306-4314 pubmed publisher
    ..The i-motif folding topology-programmed DNA nanoassembly may find more applications in the context of larger 2D/3D DNA nanostructures like lattices and polyhedra. ..
  15. Liu Z, Wu C, Miao H, Wu H. RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. Database (Oxford). 2015;2015: pubmed publisher
    ..Database URL: http://www.regnetworkweb.org. ..
  16. Wu B, Xu J, Su S, Liu H, Gan J, Ma J. Structural insights into the specific recognition of DSR by the YTH domain containing protein Mmi1. Biochem Biophys Res Commun. 2017;491:310-316 pubmed publisher
    ..Moreover, different from other YTH domain family proteins, Mmi1-YTH domain has a distinctive RNA-binding properties although it has a similar fold as other ones. ..
  17. Wang J, Zhao S, He W, Wei Y, Zhang Y, Pegg H, et al. A transcription factor IIA-binding site differentially regulates RNA polymerase II-mediated transcription in a promoter context-dependent manner. J Biol Chem. 2017;292:11873-11885 pubmed publisher
    ..These findings extend our understanding of the role of TFIIA in transcription, and provide new insights into the regulatory mechanism of core promoter elements in gene transcription by pol II. ..
  18. Yu Q, Huo H, Chen X, Guo H, Vitter J, Huan J. An Efficient Algorithm for Discovering Motifs in Large DNA Data Sets. IEEE Trans Nanobioscience. 2015;14:535-44 pubmed publisher
    ..Also, the validity of MCES is tested on real data sets. MCES is freely available at http://sites.google.com/site/feqond/mces. ..
  19. Hom R, Wuttke D. Human CST Prefers G-Rich but Not Necessarily Telomeric Sequences. Biochemistry. 2017;56:4210-4218 pubmed publisher
    ..This biochemical activity is reminiscent of the yeast t-RPA and Tetrahymena thermophila CST complexes and is consistent with roles at G-rich sites throughout the genome...
  20. Zhang H, Zhao Q, Guo X, Guo M, Qi Z, Tang W, et al. Pleiotropic function of the putative zinc-finger protein MoMsn2 in Magnaporthe oryzae. Mol Plant Microbe Interact. 2014;27:446-60 pubmed publisher
  21. Takeda J, Masuda A, Ohno K. Six GU-rich (6GUR) FUS-binding motifs detected by normalization of CLIP-seq by Nascent-seq. Gene. 2017;618:57-64 pubmed publisher
    ..We propose that the 6GUR motifs predict FUS-binding sites more efficiently than previously reported individual motifs or 15 motifs in SpliceAid 2. ..
  22. Striedner Y, Schwarz T, Welte T, Futschik A, Rant U, Tiemann Boege I. The long zinc finger domain of PRDM9 forms a highly stable and long-lived complex with its DNA recognition sequence. Chromosome Res. 2017;25:155-172 pubmed publisher
  23. Reed B, Yakovleva L, Shuman S, Ghose R. Characterization of DNA Binding by the Isolated N-Terminal Domain of Vaccinia Virus DNA Topoisomerase IB. Biochemistry. 2017;56:3307-3317 pubmed publisher
    ..The importance of key N-terminal domain contacts in the context of full-length vTopIB is underscored by assessing the effects of double-alanine mutations on DNA transesterification and its sensitivity to ionic strength. ..
  24. Allevato M, Bolotin E, Grossman M, Mané Padrós D, Sladek F, Martinez E. Sequence-specific DNA binding by MYC/MAX to low-affinity non-E-box motifs. PLoS ONE. 2017;12:e0180147 pubmed publisher
    ..Hence, MYC binds diverse DNA motifs with a broad range of affinities in a sequence-specific and dose-dependent manner, suggesting that MYC overexpression has more selective effects on the tumor transcriptome than previously thought. ..
  25. Krishnan J, Athar F, Rani T, Mishra R. Simple sequence repeats showing 'length preference' have regulatory functions in humans. Gene. 2017;628:156-161 pubmed publisher
    ..sequence repeats (SSRs), simple tandem repeats (STRs) or microsatellites are short tandem repeats of 1-6 nucleotide motifs. They are twice as abundant as the protein coding DNA in the human genome and yet little is known about ..
  26. Kauffmann A, Kennedy S, Zhao J, Turner D. Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions. Biochemistry. 2017;56:3733-3744 pubmed publisher
    ..Hydrogen bonding patterns between base pairs in the loop, the all-atom root-mean-square deviation for the loop, and the deformation index were used to compare the structure to automated predictions by MC-sym, RNA FARFAR, and RNAComposer...
  27. Kumagai Y, Vandenbon A, Teraguchi S, Akira S, Suzuki Y. Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs. BMC Genomics. 2016;17:1032 pubmed publisher
    ..Identification of novel motif candidates implied post-transcriptional controls different from that by known pairs of RNA-binding protein and RNA motif. ..
  28. 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...
  29. Schiller B, Chodankar R, Watson L, Stallcup M, Yamamoto K. Glucocorticoid receptor binds half sites as a monomer and regulates specific target genes. Genome Biol. 2014;15:418 pubmed publisher
    ..This approach may contribute to predictive models for GR activity and therapy. ..
  30. Islam S, Ge P, Zhang S. CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures. Nucleic Acids Res. 2017;45:e136 pubmed publisher
    ..We have achieved different levels of improvements for various methods and datasets, including an example of significant sensitivity and precision enhancement from 28 to 57% and from 53 to 82%, respectively. ..
  31. Li S, Dong F, Wu Y, Zhang S, Zhang C, Liu X, et al. A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data. Nucleic Acids Res. 2017;45:e129 pubmed publisher
    ..The source code of DeBooster can be downloaded from http://github.com/dongfanghong/deepboost. ..
  32. Chu H, Cifuentes Rojas C, Kesner B, Aeby E, Lee H, Wei C, et al. TERRA RNA Antagonizes ATRX and Protects Telomeres. Cell. 2017;170:86-101.e16 pubmed publisher
    ..We conclude that TERRA functions as an epigenomic modulator in trans and as an essential regulator of telomeres in cis. ..
  33. Hendershot J, O Brien P. Search for DNA damage by human alkyladenine DNA glycosylase involves early intercalation by an aromatic residue. J Biol Chem. 2017;292:16070-16080 pubmed publisher
  34. Omidi S, Zavolan M, Pachkov M, Breda J, Berger S, van Nimwegen E. Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Comput Biol. 2017;13:e1005176 pubmed publisher
    ..unibas.ch, that allow users to automatically perform 'motif finding', i.e. the inference of DWT motifs from a set of sequences, binding site prediction with DWTs, and visualization of DWT 'dilogo' motifs. ..
  35. Crocker J, Stern D. Functional regulatory evolution outside of the minimal even-skipped stripe 2 enhancer. Development. 2017;144:3095-3101 pubmed publisher
    ..Our results illustrate how sequences outside of minimal enhancer regions can evolve functionally through mechanisms other than changes in transcription factor-binding sites that drive patterning. ..
  36. Hill J, Demarest B, Gorsi B, Smith M, Yost H. Heart morphogenesis gene regulatory networks revealed by temporal expression analysis. Development. 2017;144:3487-3498 pubmed publisher
    ..This dataset provides an essential resource for future studies on the genetic/epigenetic pathways implicated in congenital heart defects and the mechanisms of cardiac transcriptional regulation. ..
  37. Vo Ngoc L, Wang Y, Kassavetis G, Kadonaga J. The punctilious RNA polymerase II core promoter. Genes Dev. 2017;31:1289-1301 pubmed publisher
    ..This model may eventually lead to a more unified conceptual understanding of the core promoter. ..
  38. Ahmed W, Sala C, Hegde S, Jha R, Cole S, Nagaraja V. Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase. PLoS Genet. 2017;13:e1006754 pubmed publisher
    ..Importantly, the occupancy of DNA gyrase, sole type II topoisomerase in Mtb, near the Ter domain of the Mtb chromosome validates its function as a decatenase. ..
  39. Beltrán Anaya F, Poblete T, Román Román A, Reyes S, de Sampedro J, Peralta Zaragoza O, et al. The EPIYA-ABCC motif pattern in CagA of Helicobacter pylori is associated with peptic ulcer and gastric cancer in Mexican population. BMC Gastroenterol. 2014;14:223 pubmed publisher
    ..cagA-positive H. pylori is highly prevalent in southern Mexico, and all CagA variants were of the western type. The cagA alleles that code for EPIYA-ABCC motif patterns are associated with peptic ulcers and gastric cancer. ..
  40. Yano M, Kato Y. Using hidden Markov models to investigate G-quadruplex motifs in genomic sequences. BMC Genomics. 2014;15 Suppl 9:S15 pubmed publisher
    ..The C++ and Perl programs are available at http://tcs.cira.kyoto-u.ac.jp/~ykato/program/g4hmm/. ..
  41. Liao V, Chen M. Efficient mining gapped sequential patterns for motifs in biological sequences. BMC Syst Biol. 2013;7 Suppl 4:S7 pubmed publisher
    ..GenPrefixSpan is an approach built on PrefixSpan with gap constraints, and therefore we compare DFSG with GenPrefixSpan. In the experimental results, DFSG mines biological sequences much faster than GenPrefixSpan. ..
  42. Woodcock C, Yakubov A, Reich N. Caulobacter crescentus Cell Cycle-Regulated DNA Methyltransferase Uses a Novel Mechanism for Substrate Recognition. Biochemistry. 2017;56:3913-3922 pubmed publisher
    ..Collectively, the data provide evidence that CcrM and other DNA-modifying enzymes may use a new mechanism to recognize DNA in a key epigenetic process...
  43. Schmitt F, Freund I, Weigand M, Helm M, Dalpke A, Eigenbrod T. Identification of an optimized 2'-O-methylated trinucleotide RNA motif inhibiting Toll-like receptors 7 and 8. RNA. 2017;23:1344-1351 pubmed publisher
    ..Given the growing interest in the development of inhibitors of nucleic acid-sensing TLRs for therapeutic purposes, these results will facilitate the rational design of such antagonists in the future. ..
  44. Podsiadło A, Wrzesień M, Paja W, Rudnicki W, Wilczynski B. Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data. BMC Syst Biol. 2013;7 Suppl 6:S16 pubmed publisher
  45. Esaki S, Evich M, Erlitzki N, Germann M, Poon G. Multiple DNA-binding modes for the ETS family transcription factor PU.1. J Biol Chem. 2017;292:16044-16054 pubmed publisher
    ..As sequential dimerization did not occur with the ETS domain of Ets-1, a close structural homolog of PU.1, 2:1 complex formation may represent an alternative autoinhibitory mechanism in the ETS family at the protein-DNA level. ..
  46. Zinshteyn B, Rojas Duran M, Gilbert W. Translation initiation factor eIF4G1 preferentially binds yeast transcript leaders containing conserved oligo-uridine motifs. RNA. 2017;23:1365-1375 pubmed publisher
    ..Taken together, our results demonstrate RNA sequence preferences for a general initiation factor, which cells potentially exploit for translational control of specific mRNAs. ..
  47. Zhang S, Zhou X, Du C, Su Z. SPIC: a novel similarity metric for comparing transcription factor binding site motifs based on information contents. BMC Syst Biol. 2013;7 Suppl 2:S14 pubmed publisher
  48. Habara A, Shaikho E, Steinberg M. Fetal hemoglobin in sickle cell anemia: The Arab-Indian haplotype and new therapeutic agents. Am J Hematol. 2017;92:1233-1242 pubmed publisher
    ..We review the genetic basis of HbF regulation focusing on sickle cell anemia in Saudi Arabia and discuss new drugs that can induce increased levels of HbF. ..
  49. Zamanighomi M, Lin Z, Wang Y, Jiang R, Wong W. Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data. Nucleic Acids Res. 2017;45:5666-5677 pubmed publisher
    ..Our analysis resulted in the assignment of motifs to 200 TFs with no SELEX-derived motifs, roughly a 50% increase compared to the existing coverage. ..
  50. Park S, Phukan P, Zeeb M, Martinez Yamout M, Dyson H, Wright P. Structural Basis for Interaction of the Tandem Zinc Finger Domains of Human Muscleblind with Cognate RNA from Human Cardiac Troponin T. Biochemistry. 2017;56:4154-4168 pubmed publisher
    ..Binding of the MBNL zinc fingers to cardiac troponin T pre-mRNA is specific and relatively simple, unlike the complex multiple dimer-trimer stoichiometries postulated in some previous studies. ..
  51. Ibryashkina E, Solonin A, Zakharova M. Protein NCRII-18: the role of gene fusion in the molecular evolution of restriction endonucleases. FEBS Lett. 2017;591:1702-1711 pubmed publisher
  52. Liu Y, Walavalkar N, Dozmorov M, Rich S, Civelek M, Guertin M. Identification of breast cancer associated variants that modulate transcription factor binding. PLoS Genet. 2017;13:e1006761 pubmed publisher
    ..This integrative analysis pipeline is a general framework to identify candidate causal variants within regulatory regions and TF binding sites that confer phenotypic variation and disease risk. ..
  53. Chen J, VanEtten D, Fountain M, Yildirim I, Disney M. Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1. Biochemistry. 2017;56:3463-3474 pubmed publisher
    ..The results will be useful for understanding the dynamic trajectory of these RNA repeats but also may aid in the development of therapeutics. ..
  54. Stewart J, Subramanian H, Franco E. Self-assembly of multi-stranded RNA motifs into lattices and tubular structures. Nucleic Acids Res. 2017;45:5449-5457 pubmed publisher
    ..These large assemblies could be potentially integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for colocalization of cellular components. ..
  55. Lannes L, Young P, Richter C, Morgner N, Schwalbe H. Interaction of the N-Terminal Tandem Domains of hnRNP LL with the BCL2 Promoter i-Motif DNA Sequence. Chembiochem. 2017;18:2033-2044 pubmed publisher
    ..It is observed that RRM12 binds to Py39wt regardless of the DNA conformation. We propose that RRM12 recognises a single-stranded CTCCC element present in loop 1 of the i-motif and in the apical loop of the hairpin conformation. ..
  56. Weinberg Z, Lünse C, Corbino K, Ames T, Nelson J, Roth A, et al. Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. Nucleic Acids Res. 2017;45:10811-10823 pubmed publisher
    ..We expect that further research on these newly found RNA classes will reveal additional aspects of novel biology, and allow for greater insights into the biochemistry performed by ncRNAs...
  57. Yang Y, Fan X, Mao M, Song X, Wu P, Zhang Y, et al. Extensive translation of circular RNAs driven by N6-methyladenosine. Cell Res. 2017;27:626-641 pubmed publisher
    ..Our study expands the coding landscape of human transcriptome, and suggests a role of circRNA-derived proteins in cellular responses to environmental stress. ..
  58. Rao C, Chin D, Ensminger A. Priming in a permissive type I-C CRISPR-Cas system reveals distinct dynamics of spacer acquisition and loss. RNA. 2017;23:1525-1538 pubmed publisher
    ..Based on these observations, we propose that the Legionella pneumophila type I-C system represents a powerful model to study primed adaptation and the interplay between CRISPR interference and adaptation. ..
  59. 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. ..
  60. Grey C, Clément J, Buard J, Leblanc B, Gut I, Gut M, et al. In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites. Genome Res. 2017;27:580-590 pubmed publisher
    ..We propose that these DSB-independent sites result from interactions between hotspot-bound PRDM9 and genomic sequences located on the chromosome axis. ..
  61. Röll S, Härtle S, Lütteke T, Kaspers B, Härtle S. Tissue and time specific expression pattern of interferon regulated genes in the chicken. BMC Genomics. 2017;18:264 pubmed publisher
    ..We confirmed many known IRGs and established a multitude of so far undescribed ones, thus providing a large database for future research on antiviral mechanisms and additional IFN functions in non-mammalian species. ..
  62. Zhang J, Le T, Liu L, Li J. Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer. BMC Bioinformatics. 2017;18:243 pubmed publisher
    ..Taken together, the results demonstrate that miRSCoPPI is a promising tool for inferring BRCA-related miRNA sponge co-regulation of PPIs and it can help with the understanding of the co-regulation roles of miRNA sponges on the PPIs. ..
  63. López Y, Patil A, Nakai K. Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana. BMC Syst Biol. 2013;7 Suppl 3:S10 pubmed publisher
    ..thaliana structures from background genomic promoters. Our method can be used to predict novel motifs and decipher a similar promoter architecture for genes co-expressed in A. thaliana under different conditions. ..
  64. Petrov A, Zirbel C, Leontis N. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas. RNA. 2013;19:1327-40 pubmed publisher
    ..bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. ..
  65. Skowron P, Anton B, Czajkowska E, Zebrowska J, Sulecka E, Krefft D, et al. The third restriction-modification system from Thermus aquaticus YT-1: solving the riddle of two TaqII specificities. Nucleic Acids Res. 2017;45:9005-9018 pubmed publisher
    ..Putative positions and aa that specify DNA recognition were identified and recognition motifs for 6 uncharacterized Thermus-family enzymes were predicted. ..
  66. Vo T, Wang S, Poon G, Wilson W. Electrostatic control of DNA intersegmental translocation by the ETS transcription factor ETV6. J Biol Chem. 2017;292:13187-13196 pubmed publisher
    ..Our findings establish biosensors as a general technique for directly and specifically measuring target site search by DNA-binding proteins via intersegmental translocation. ..
  67. Yang L, Wang C, Li F, Zhang J, Nayab A, Wu J, et al. The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity. J Biol Chem. 2017;292:16221-16234 pubmed publisher
    ..The binding motif identified here will provide valuable information for future investigations of the functional pathways controlled by human MEX-3C and for predicting potential mRNAs regulated by this enzyme. ..
  68. Kleinman C, Sycz G, Bonomi H, Rodríguez R, Zorreguieta A, Sieira R. ChIP-seq analysis of the LuxR-type regulator VjbR reveals novel insights into the Brucella virulence gene expression network. Nucleic Acids Res. 2017;45:5757-5769 pubmed publisher
    ..Taken together, our results bring new insights into the extent and functionality of LuxR-type-related transcriptional networks. ..
  69. Kim D, Xi Y, Sung S. Modular function of long noncoding RNA, COLDAIR, in the vernalization response. PLoS Genet. 2017;13:e1006939 pubmed publisher
    ..Our study reveals the molecular framework in which COLDAIR lncRNA mediates the PRC2-mediated repression of FLC during vernalization. ..
  70. Panopoulos A, Smith E, ARIAS A, Shepard P, Hishida Y, Modesto V, et al. Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics. Cell Stem Cell. 2017;20:505-517.e6 pubmed publisher
    ..Our results argue that a non-genetic biological mechanism underlies aberrant methylation in iPSCs and that it is likely based on a probabilistic process involving MYC that takes place during or shortly after reprogramming. ..
  71. Kamenskaya D, Pankova M, Atopkin D, Brykov V. [Divergence of paralogous growth-hormone-encoding genes and their promoters in Salmonidae]. Mol Biol (Mosk). 2017;51:314-323 pubmed publisher
    ..The observed differences in the rates of accumulation of changes in growth hormone encoding paralogs could be explained by differences in the intensity of selection. ..
  72. Jung C, Hawkins J, Jones S, Xiao Y, Rybarski J, Dillard K, et al. Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips. Cell. 2017;170:35-47.e13 pubmed publisher
    ..CHAMP provides a framework for high-throughput, quantitative analysis of protein-DNA interactions on synthetic and genomic DNA. PAPERCLIP. ..
  73. Li J, Dantas Machado A, Guo M, Sagendorf J, Zhou Z, Jiang L, et al. Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site. Biochemistry. 2017;56:3745-3753 pubmed publisher
    ..Our findings provide the structural basis for FOXA2 protein binding to a consensus forkhead site and elucidate how members of the forkhead protein family bind different DNA sites. ..
  74. Basha Gutierrez J, Nakai K. A study on the application of topic models to motif finding algorithms. BMC Bioinformatics. 2016;17:502 pubmed publisher
  75. Jung I, Ahn H, Shin S, Kim J, Kwon H, Jung W, et al. Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice. BMC Syst Biol. 2016;10:115 pubmed publisher
    ..In summary, we show that siRNAs are important respondents to drought stress and regulate genes related to the drought tolerance in water deficit conditions. ..
  76. Rihan K, Antoine E, Maurin T, Bardoni B, Bordonné R, Soret J, et al. A new cis-acting motif is required for the axonal SMN-dependent Anxa2 mRNA localization. RNA. 2017;23:899-909 pubmed publisher
    ..Altogether, our studies show that this G-motif represents a novel and essential determinant for axonal localization of the Anxa2 mRNA mediated by the SMN complex. ..
  77. Liu Y, Chen Y, Gong Q, Lai J, Du J, Deng X. Paternity assignment in the polyploid Acipenser dabryanus based on a novel microsatellite marker system. PLoS ONE. 2017;12:e0185280 pubmed publisher
    ..dabryanus, and the 20 SSRs developed in this study can be applied to the future breeding program to avoid inbreeding for this stock or other related species of Acipenseriformes. ..