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Journal articles on the topic 'Sequence motif'

Author: Grafiati

Published: 4 June 2021

Last updated: 20 February 2023

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1

Roebuck, K. A., D. P. Szeto, K. P. Green, Q. N. Fan, and W. E. Stumph. "Octamer and SPH motifs in the U1 enhancer cooperate to activate U1 RNA gene expression." Molecular and Cellular Biology 10, no. 1 (January 1990): 341–52. http://dx.doi.org/10.1128/mcb.10.1.341-352.1990.

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The transcriptional enhancer of a chicken U1 small nuclear RNA gene has been shown to extend over approximately 50 base pairs of DNA sequence located 180 to 230 base pairs upstream of the U1 transcription initiation site. It is composed of multiple functional motifs, including a GC box, an octamer motif, and a novel SPH motif. The contributions of these three distinct sequence motifs to enhancer function were studied with an oocyte expression assay. Under noncompetitive conditions in oocytes, the SPH motif is capable of stimulating U1 RNA transcription in the absence of the other functional mo

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Roebuck, K. A., D. P. Szeto, K. P. Green, Q. N. Fan, and W. E. Stumph. "Octamer and SPH motifs in the U1 enhancer cooperate to activate U1 RNA gene expression." Molecular and Cellular Biology 10, no. 1 (January 1990): 341–52. http://dx.doi.org/10.1128/mcb.10.1.341.

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The transcriptional enhancer of a chicken U1 small nuclear RNA gene has been shown to extend over approximately 50 base pairs of DNA sequence located 180 to 230 base pairs upstream of the U1 transcription initiation site. It is composed of multiple functional motifs, including a GC box, an octamer motif, and a novel SPH motif. The contributions of these three distinct sequence motifs to enhancer function were studied with an oocyte expression assay. Under noncompetitive conditions in oocytes, the SPH motif is capable of stimulating U1 RNA transcription in the absence of the other functional mo

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3

XING, ERIC P., WEI WU, MICHAEL I. JORDAN, and RICHARD M. KARP. "LOGOS: A MODULAR BAYESIAN MODEL FOR DE NOVO MOTIF DETECTION." Journal of Bioinformatics and Computational Biology 02, no. 01 (March 2004): 127–54. http://dx.doi.org/10.1142/s0219720004000508.

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The complexity of the global organization and internal structure of motifs in higher eukaryotic organisms raises significant challenges for motif detection techniques. To achieve successful de novo motif detection, it is necessary to model the complex dependencies within and among motifs and to incorporate biological prior knowledge. In this paper, we present LOGOS, an integrated LOcal and GlObal motif Sequence model for biopolymer sequences, which provides a principled framework for developing, modularizing, extending and computing expressive motif models for complex biopolymer sequence analy

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4

Zhai, Xiandun, and Adilai Tuerxun. "DNA Sequence Specificity Prediction Algorithm Based on Artificial Intelligence." Mathematical Problems in Engineering 2022 (October 3, 2022): 1–8. http://dx.doi.org/10.1155/2022/4150106.

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DNA sequence specificity refers to the ability of DNA sequences to bind specific proteins. These proteins play a central role in gene regulation such as transcription and alternative splicing. Obtaining DNA sequence specificity is very important for establishing the regulatory model of the biological system and identifying pathogenic variants. Motifs are sequence patterns shared by fragments of DNA sequences that bind to specific proteins. At present, some motif mining algorithms have been proposed, which perform well under the condition of given motif length. This research is based on deep le

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Wang, Mengchi, David Wang, Kai Zhang, Vu Ngo, Shicai Fan, and Wei Wang. "Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss." Genetics 216, no. 2 (August 19, 2020): 353–58. http://dx.doi.org/10.1534/genetics.120.303597.

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Sequence analysis frequently requires intuitive understanding and convenient representation of motifs. Typically, motifs are represented as position weight matrices (PWMs) and visualized using sequence logos. However, in many scenarios, in order to interpret the motif information or search for motif matches, it is compact and sufficient to represent motifs by wildcard-style consensus sequences (such as [GC][AT]GATAAG[GAC]). Based on mutual information theory and Jensen-Shannon divergence, we propose a mathematical framework to minimize the information loss in converting PWMs to consensus seque

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Wright, Elisé P., Mahmoud A. S. Abdelhamid, Michelle O. Ehiabor, Melanie C. Grigg, Kelly Irving, Nicole M. Smith, and Zoë A. E. Waller. "Epigenetic modification of cytosines fine tunes the stability of i-motif DNA." Nucleic Acids Research 48, no. 1 (November 28, 2019): 55–62. http://dx.doi.org/10.1093/nar/gkz1082.

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Abstract i-Motifs are widely used in nanotechnology, play a part in gene regulation and have been detected in human nuclei. As these structures are composed of cytosine, they are potential sites for epigenetic modification. In addition to 5-methyl- and 5-hydroxymethylcytosine modifications, recent evidence has suggested biological roles for 5-formylcytosine and 5-carboxylcytosine. Herein the human telomeric i-motif sequence was used to examine how these four epigenetic modifications alter the thermal and pH stability of i-motifs. Changes in melting temperature and transitional pH depended on b

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MAURER-STROH, SEBASTIAN, HE GAO, HAO HAN, LIES BAETEN, JOOST SCHYMKOWITZ, FREDERIC ROUSSEAU, LOUXIN ZHANG, and FRANK EISENHABER. "MOTIF DISCOVERY WITH DATA MINING IN 3D PROTEIN STRUCTURE DATABASES: DISCOVERY, VALIDATION AND PREDICTION OF THE U-SHAPE ZINC BINDING ("HUF-ZINC") MOTIF." Journal of Bioinformatics and Computational Biology 11, no. 01 (February 2013): 1340008. http://dx.doi.org/10.1142/s0219720013400088.

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Data mining in protein databases, derivatives from more fundamental protein 3D structure and sequence databases, has considerable unearthed potential for the discovery of sequence motif—structural motif—function relationships as the finding of the U-shape (Huf-Zinc) motif, originally a small student's project, exemplifies. The metal ion zinc is critically involved in universal biological processes, ranging from protein-DNA complexes and transcription regulation to enzymatic catalysis and metabolic pathways. Proteins have evolved a series of motifs to specifically recognize and bind zinc ions.

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Liu, Xiang-Qin, and Jing Yang. "Bacterial Thymidylate Synthase with Intein, Group II Intron, and Distinctive ThyX Motifs." Journal of Bacteriology 186, no. 18 (September 15, 2004): 6316–19. http://dx.doi.org/10.1128/jb.186.18.6316-6319.2004.

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ABSTRACT The ThyX class of thymidylate synthases was previously characterized by a common ThyX motif, RHRX7S. We report bacterial ThyX sequences having distinctive ThyX motifs, suggesting a more general ThyX motif, R/THRX7-8S. One ThyX sequence has an intein in its ThyX motif that was shown to do protein splicing and a group II intron in its gene, suggesting a hot spot for these self-splicing mobile elements.

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Pal, Soumitra, Jan Hoinka, and Teresa M. Przytycka. "Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro." Nucleic Acids Research 47, no. 13 (June 21, 2019): 6632–41. http://dx.doi.org/10.1093/nar/gkz540.

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Abstract Understanding the principles of DNA binding by transcription factors (TFs) is of primary importance for studying gene regulation. Recently, several lines of evidence suggested that both DNA sequence and shape contribute to TF binding. However, the following compelling question is yet to be considered: in the absence of any sequence similarity to the binding motif, can DNA shape still increase binding probability? To address this challenge, we developed Co-SELECT, a computational approach to analyze the results of in vitro HT-SELEX experiments for TF–DNA binding. Specifically, Co-SELEC

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Gunawardana, D., V. A. Likic, and K. R. Gayler. "A Comprehensive Bioinformatics Analysis of the Nudix Superfamily inArabidopsis thaliana." Comparative and Functional Genomics 2009 (2009): 1–13. http://dx.doi.org/10.1155/2009/820381.

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Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by theArabidopsisgenome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs

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Motta-Mena, Laura B., Sarah A. Smith, Michael J. Mallory, Jason Jackson, Jiarong Wang, and Kristen W. Lynch. "A Disease-associated Polymorphism Alters Splicing of the Human CD45 Phosphatase Gene by Disrupting Combinatorial Repression by Heterogeneous Nuclear Ribonucleoproteins (hnRNPs)." Journal of Biological Chemistry 286, no. 22 (April 20, 2011): 20043–53. http://dx.doi.org/10.1074/jbc.m111.218727.

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Alternative splicing is typically controlled by complexes of regulatory proteins that bind to sequences within or flanking variable exons. The identification of regulatory sequence motifs and the characterization of sequence motifs bound by splicing regulatory proteins have been essential to predicting splicing regulation. The activation-responsive sequence (ARS) motif has previously been identified in several exons that undergo changes in splicing upon T cell activation. hnRNP L binds to this ARS motif and regulates ARS-containing exons; however, hnRNP L does not function alone. Interestingly

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Kumar, Vinod, Gopal Singh, A. K. Verma, and Sanjeev Agrawal. "In Silico Characterization of Histidine Acid Phytase Sequences." Enzyme Research 2012 (December 5, 2012): 1–8. http://dx.doi.org/10.1155/2012/845465.

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Histidine acid phytases (HAPhy) are widely distributed enzymes among bacteria, fungi, plants, and some animal tissues. They have a significant role as an animal feed enzyme and in the solubilization of insoluble phosphates and minerals present in the form of phytic acid complex. A set of 50 reference protein sequences representing HAPhy were retrieved from NCBI protein database and characterized for various biochemical properties, multiple sequence alignment (MSA), homology search, phylogenetic analysis, motifs, and superfamily search. MSA using MEGA5 revealed the presence of conserved sequenc

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FIGGE, JAMES, and TEMPLE F. SMITH. "Cell-division sequence motif." Nature 334, no. 6178 (July 1988): 109. http://dx.doi.org/10.1038/334109a0.

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Das, Rahul K., Yongqi Huang, Aaron H. Phillips, Richard W. Kriwacki, and Rohit V. Pappu. "Cryptic sequence features within the disordered protein p27Kip1 regulate cell cycle signaling." Proceedings of the National Academy of Sciences 113, no. 20 (May 2, 2016): 5616–21. http://dx.doi.org/10.1073/pnas.1516277113.

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Peptide motifs embedded within intrinsically disordered regions (IDRs) of proteins are often the sites of posttranslational modifications that control cell-signaling pathways. How do IDR sequences modulate the functionalities of motifs? We answer this question using the polyampholytic C-terminal IDR of the cell cycle inhibitory protein p27Kip1 (p27). Phosphorylation of Thr-187 (T187) within the p27 IDR controls entry into S phase of the cell division cycle. Additionally, the conformational properties of polyampholytic sequences are predicted to be influenced by the linear patterning of opposit

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Hou, Benjun, Suping Feng, and Yaoting Wu. "Systemic Identification ofHevea brasiliensisEST-SSR Markers and Primer Screening." Journal of Nucleic Acids 2017 (2017): 1–9. http://dx.doi.org/10.1155/2017/6590902.

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This research aimed to systematically identify and preliminarily validate theHevea brasiliensisexpressed sequence tag (EST) information using Simple Sequence Repeat (SSR) and provide evidence for further development of SSR molecular marker. The definition of general SSR features ofHeveaEST splicing sequences and development of SSR primers founded the basis of diversity analysis and variety identification forHeveatree resource. 1134 SSR loci were identified in the EST splicing sequence and distributed in 840 Unigene. The occurrence rate of SSR loci was 23.9%, and the average distribution distan

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LIANG, S., M. P. SAMANTA, and B. A. BIEGEL. "cWINNOWER ALGORITHM FOR FINDING FUZZY DNA MOTIFS." Journal of Bioinformatics and Computational Biology 02, no. 01 (March 2004): 47–60. http://dx.doi.org/10.1142/s0219720004000466.

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The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich in proteinbinding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. The algorithm finds such motifs if a clique consisting of a suffciently large number of mutated copies of the motif (i.e., the signals) is present in the DNA sequence. The cWINNOWER algorithm substantially improves the sensitivity of the winnower method of Pevzner and Sze by imposing a consensus constraint, enabling it to detect much weaker signals. We studied the minimum detectable clique

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Hatstat, A. Katherine, Michael D. Pupi, and Dewey G. McCafferty. "Predicting PY motif-mediated protein-protein interactions in the Nedd4 family of ubiquitin ligases." PLOS ONE 16, no. 10 (October 12, 2021): e0258315. http://dx.doi.org/10.1371/journal.pone.0258315.

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The Nedd4 family contains several structurally related but functionally distinct HECT-type ubiquitin ligases. The members of the Nedd4 family are known to recognize substrates through their multiple WW domains, which recognize PY motifs (PPxY, LPxY) or phospho-threonine or phospho-serine residues. To better understand protein interactor recognition mechanisms across the Nedd4 family, we report the development and implementation of a python-based tool, PxYFinder, to identify PY motifs in the primary sequences of previously identified interactors of Nedd4 and related ligases. Using PxYFinder, we

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Yu, Qiang, Xiang Zhao, and Hongwei Huo. "A new algorithm for DNA motif discovery using multiple sample sequence sets." Journal of Bioinformatics and Computational Biology 17, no. 04 (August 2019): 1950021. http://dx.doi.org/10.1142/s0219720019500215.

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DNA motif discovery plays an important role in understanding the mechanisms of gene regulation. Most existing motif discovery algorithms can identify motifs in an efficient and effective manner when dealing with small datasets. However, large datasets generated by high-throughput sequencing technologies pose a huge challenge: it is too time-consuming to process the entire dataset, but if only a small sample sequence set is processed, it is difficult to identify infrequent motifs. In this paper, we propose a new DNA motif discovery algorithm: first divide the input dataset into multiple sample

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Bredesen, Bjørn André, and Marc Rehmsmeier. "DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements." Nucleic Acids Research 47, no. 15 (July 24, 2019): 7781–97. http://dx.doi.org/10.1093/nar/gkz617.

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Abstract Polycomb Response Elements (PREs) are cis-regulatory DNA elements that maintain gene transcription states through DNA replication and mitosis. PREs have little sequence similarity, but are enriched in a number of sequence motifs. Previous methods for modelling Drosophila melanogaster PRE sequences (PREdictor and EpiPredictor) have used a set of 7 motifs and a training set of 12 PREs and 16-23 non-PREs. Advances in experimental methods for mapping chromatin binding factors and modifications has led to the publication of several genome-wide sets of Polycomb targets. In addition to the s

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WU, CATHY H., HONGZHAN HUANG, and JERRY MCLARTY. "GENE FAMILY IDENTIFICATION NETWORK DESIGN FOR PROTEIN SEQUENCE ANALYSIS." International Journal on Artificial Intelligence Tools 08, no. 04 (December 1999): 419–32. http://dx.doi.org/10.1142/s0218213099000282.

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With the exponential accumulation of sequence data, continued progress in the Human Genome Project will depend increasingly on advanced computational tools to manage and analyze the data. Utilizing information embedded within families of homologous sequences, a gene family identification approach may facilitate the understanding of gene functions. We have developed a GeneFIND (Gene Family Identification Network Design) system for database searching against gene families. It provides rapid and accurate protein family identification by combining global and motif sequence similarities and incorpo

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Zhang, S., M. J. Ruiz-Echevarria, Y. Quan, and S. W. Peltz. "Identification and characterization of a sequence motif involved in nonsense-mediated mRNA decay." Molecular and Cellular Biology 15, no. 4 (April 1995): 2231–44. http://dx.doi.org/10.1128/mcb.15.4.2231.

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In both prokaryotes and eukaryotes, nonsense mutations in a gene can enhance the decay rate or reduce the abundance of the mRNA transcribed from that gene, and we call this process nonsense-mediated mRNA decay. We have been investigating the cis-acting sequences involved in this decay pathway. Previous experiments have demonstrated that, in addition to a nonsense codon, specific sequences 3' of a nonsense mutation, which have been defined as downstream elements, are required for mRNA destabilization. The results presented here identify a sequence motif (TGYYGATGYYYYY, where Y stands for either

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Sahu, Santosh Kumar, Himadri Gourav Behuria, Sangam Gupta, and Babita Sahoo. "Sequence Analysis of a Subset of Plasma Membrane Raft Proteome Containing CXXC Metal Binding Motifs." International Journal of Knowledge Discovery in Bioinformatics 5, no. 2 (July 2015): 1–15. http://dx.doi.org/10.4018/ijkdb.2015070101.

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In an attempt to identify the metal sensing proteins localized to mammalian plasma membrane, the authors screened a list of 300 raft associated proteins that are involved in cellular signaling mechanisms by searching the presence of metal thionin (CXXC) motifs. 50 proteins were found to possess CXXC motifs that could act as potential metal sensing proteins. The authors determined membrane topologies of the above CXXC motif containing proteins using TM-pred and analyzed the positions of their transmembrane (TM) domains using Bio-edit software. Based on the topology of CXXC domains, the authors

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Bostan, Hamed, Naomie Salim, Zeti Azura Hussein, Peter Klappa, and Mohd Shahir Shamsir. "CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures." Advances in Bioinformatics 2012 (October 10, 2012): 1–5. http://dx.doi.org/10.1155/2012/849830.

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Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD) is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We

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Ralton, J. E., X. Lu, A. M. Hutcheson, and R. A. Quinlan. "Identification of two N-terminal non-alpha-helical domain motifs important in the assembly of glial fibrillary acidic protein." Journal of Cell Science 107, no. 7 (July 1, 1994): 1935–48. http://dx.doi.org/10.1242/jcs.107.7.1935.

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The non-alpha-helical N-terminal domain of intermediate filament proteins plays a key role in filament assembly. Previous studies have identified a nonapeptide motif, SSYRRIFGG, in the non-alpha-helical N-terminal domain of vimentin that is required for assembly. This motif is also found in desmin, peripherin and the type IV intermediate filament proteins. GFAP is the only type III intermediate filament protein in which this motif is not readily identified. This study has identified two motifs in the non-alpha-helical N-terminal domain of mouse GFAP that play important roles in GFAP assembly.

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Li, Xiang, Linna Ma, Xinyue Mei, Yixiang Liu, and Huichuan Huang. "ggmotif: An R Package for the extraction and visualization of motifs from MEME software." PLOS ONE 17, no. 11 (November 3, 2022): e0276979. http://dx.doi.org/10.1371/journal.pone.0276979.

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MEME (Multiple Em for Motif Elicitation) is the most commonly used tool to identify motifs within deoxyribonucleic acid (DNA) or protein sequences. However, the results generated by the MEMEare saved using file formats .xml and .txt, which are difficult to read, visualize, or integrate with other widely used phylogenetic tree packages, such as ggtree. To overcome this problem, we developed the ggmotif R package, which provides two easy-to-use functions that can facilitate the extraction and visualization of motifs from the results files generated by the MEME. ggmotif can extract the informatio

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Blum, Christopher F., and Markus Kollmann. "Neural networks with circular filters enable data efficient inference of sequence motifs." Bioinformatics 35, no. 20 (March 27, 2019): 3937–43. http://dx.doi.org/10.1093/bioinformatics/btz194.

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Abstract Motivation Nucleic acids and proteins often have localized sequence motifs that enable highly specific interactions. Due to the biological relevance of sequence motifs, numerous inference methods have been developed. Recently, convolutional neural networks (CNNs) have achieved state of the art performance. These methods were able to learn transcription factor binding sites from ChIP-seq data, resulting in accurate predictions on test data. However, CNNs typically distribute learned motifs across multiple filters, making them difficult to interpret. Furthermore, networks trained on sma

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Hong, Jian, Ying C. Q. Zang, Maria V. Tejada-Simon, Milena Kozovska, Sufang Li, Rana A. K. Singh, Deye Yang, Victor M. Rivera, James K. Killian та Jingwu Z. Zhang. "A Common TCR V-D-J Sequence in Vβ13.1 T Cells Recognizing an Immunodominant Peptide of Myelin Basic Protein in Multiple Sclerosis". Journal of Immunology 163, № 6 (15 вересня 1999): 3530–38. http://dx.doi.org/10.4049/jimmunol.163.6.3530.

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Abstract T cell responses to the immunodominant peptide (residues 83–99) of myelin basic protein are potentially associated with multiple sclerosis (MS). This study was undertaken to examine whether a common sequence motif(s) exists within the TCR complementarity-determining region (CDR)-3 of T cells recognizing the MBP83–99 peptide. Twenty MBP83–99-reactive T cell clones derived from patients with MS were analyzed for CDR3 sequences, which revealed several shared motifs. Some Vβ13.1 T cell clones derived from different patients with MS were found to contain an identical CDR3 motif, Vβ13.1-LGR

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Wohlschlegel, James A., Brian T. Dwyer, David Y. Takeda, and Anindya Dutta. "Mutational Analysis of the Cy Motif from p21 Reveals Sequence Degeneracy and Specificity for Different Cyclin-Dependent Kinases." Molecular and Cellular Biology 21, no. 15 (August 1, 2001): 4868–74. http://dx.doi.org/10.1128/mcb.21.15.4868-4874.2001.

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ABSTRACT Inhibitors, activators, and substrates of cyclin-dependent kinases (cdks) utilize a cyclin-binding sequence, known as a Cy or RXL motif, to bind directly to the cyclin subunit. Alanine scanning mutagenesis of the Cy motif of the cdk inhibitor p21 revealed that the conserved arginine or leucine (constituting the conserved RXL sequence) was important for p21's ability to inhibit cyclin E-cdk2 activity. Further analysis of mutant Cy motifs showed, however, that RXL was neither necessary nor sufficient for a functional cyclin-binding motif. Replacement of either of these two residues with

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Magandhi, Mahat, Sobir, Yudiwanti W. E. Kusumo, Sudarmono, and Deden Derajat Matra. "Development and characterization of Simple Sequence Repeats (SSRs) markers in durian kura-kura (Durio testudinarius Becc.) using NGS data." IOP Conference Series: Earth and Environmental Science 948, no. 1 (December 1, 2021): 012082. http://dx.doi.org/10.1088/1755-1315/948/1/012082.

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Abstract Durian Kura-kura (Durio testudinarius Becc.) belongs to the Malvaceae family and is an endemic species of Borneo. Recently, genomic-based next-generation sequencing (NGS) approaches have been carried out for germplasm conservation and plant breeding programs. The NGS technologies allow plant genomes to be sequenced quickly and inexpensively and enable the efficient development of SSR markers through the in-silico approaches. This study aimed to develop and characterize simple sequence repeats (SSRs) from the assembled genome. The 1203929 scaffolds of the assembled genome were produced

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Liu, Jiao, Wen Rui Xia, Yan Ping Hu, Yuan Yao, Shao Ping Fu, Rui Jun Duan, Rui Mei Li, and Jian Chun Guo. "Cloning and Analysis of MeCWINV6 Promoter from Biofuel Plant Cassava (Manihot esculenta Crantz)." Advanced Materials Research 986-987 (July 2014): 25–29. http://dx.doi.org/10.4028/www.scientific.net/amr.986-987.25.

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In order to gain insight into the specific function of the cassava cell wall invertase 6 (MeCWINV6), the promoter sequence of MeCWINV6 gene was cloned using the PCR amplification approach. 118 bp CDS sequence and 1042 bp potential promoter sequence of MeCWINV6 gene were obtained. PlantCARE analyzed the putative cis-elements in silico revealed that these elements can be grouped into five classes: basic transcription elements (CAAT box and TATA box), light responsive elements (ACE, AE-box, ATCT-motif, AT1-motif, Box 4, GAG-motif, GT1-motif and Sp1), phytohormone responsive motifs (GARE-motif, TA

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Bielecka, Patrycja, Anna Dembska, and Bernard Juskowiak. "Monitoring of pH Using an i-Motif-Forming Sequence Containing a Fluorescent Cytosine Analogue, tC." Molecules 24, no. 5 (March 8, 2019): 952. http://dx.doi.org/10.3390/molecules24050952.

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The i-motif is a four-stranded DNA structure formed from the cytosine (C)-rich ssDNA sequence, which is stabilized in slightly acidic pH. Additionally, labeling of a cytosine-rich sequence with a fluorescent molecule may constitute a way to construct a pH-sensitive biosensor. In this paper, we report tC-modified fluorescent probes that contain RET-related sequence C4GC4GC4GC4A. Results of the UV absorption melting experiments, circular dichroism (CD) spectra, and steady-state fluorescence measurements of tC-modified i-motifs are presented and discussed here. Efficient fluorescence quenching of

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Speckmann, Wayne, Aarthi Narayanan, Rebecca Terns, and Michael P. Terns. "Nuclear Retention Elements of U3 Small Nucleolar RNA." Molecular and Cellular Biology 19, no. 12 (December 1, 1999): 8412–21. http://dx.doi.org/10.1128/mcb.19.12.8412.

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ABSTRACT The processing and methylation of precursor rRNA is mediated by the box C/D small nucleolar RNAs (snoRNAs). These snoRNAs differ from most cellular RNAs in that they are not exported to the cytoplasm. Instead, these RNAs are actively retained in the nucleus where they assemble with proteins into mature small nucleolar ribonucleoprotein particles and are targeted to their intranuclear site of action, the nucleolus. In this study, we have identified the cis-acting sequences responsible for the nuclear retention of U3 box C/D snoRNA by analyzing the nucleocytoplasmic distributions of an

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Adams, Peter D., Xiaotong Li, William R. Sellers, Kayla B. Baker, Xiaohong Leng, J. Wade Harper, Yoichi Taya, and William G. Kaelin. "Retinoblastoma Protein Contains a C-terminal Motif That Targets It for Phosphorylation by Cyclin-cdk Complexes." Molecular and Cellular Biology 19, no. 2 (February 1, 1999): 1068–80. http://dx.doi.org/10.1128/mcb.19.2.1068.

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ABSTRACT Stable association of certain proteins, such as E2F1 and p21, with cyclin-cdk2 complexes is dependent upon a conserved cyclin-cdk2 binding motif that contains the core sequence ZRXL, where Z and X are usually basic. In vitro phosphorylation of the retinoblastoma tumor suppressor protein, pRB, by cyclin A-cdk2 and cyclin E-cdk2 was inhibited by a short peptide spanning the cyclin-cdk2 binding motif present in E2F1. Examination of the pRB C terminus revealed that it contained sequence elements related to ZRXL. Site-directed mutagenesis of one of these sequences, beginning at residue 870

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Su, J., R. A. Bapat, G. Visakan, and J. Moradian-Oldak. "An Evolutionarily Conserved Helix Mediates Ameloblastin-Cell Interaction." Journal of Dental Research 99, no. 9 (May 13, 2020): 1072–81. http://dx.doi.org/10.1177/0022034520918521.

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Ameloblastin (Ambn) has the potential to regulate cell-matrix adhesion through familiar cell-binding domains, but the proposed sequence motifs are not highly conserved across species. Here, we report that Ambn binds to ameloblast-like cell membranes through a highly evolutionary conserved amphipathic helix-forming (AH) motif encoded by exon 5. We applied high-resolution confocal microscopy to show colocalization of Ambn with ameloblast membrane surfaces in developing mouse incisors. Using a series of Ambn-derived peptides and Ambn variants, we showed that Ambn binds to cell membranes through a

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Andersson, Samuel A., and Jens Lagergren. "Motif Yggdrasil: Sampling Sequence Motifs from a Tree Mixture Model." Journal of Computational Biology 14, no. 5 (June 2007): 682–97. http://dx.doi.org/10.1089/cmb.2007.r010.

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TAYLOR, WILLIAM R. "Motif-Biased Protein Sequence Alignment." Journal of Computational Biology 1, no. 4 (January 1994): 297–310. http://dx.doi.org/10.1089/cmb.1994.1.297.

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Shaw, Gerry. "A neurofilament-specific sequence motif." Trends in Biochemical Sciences 17, no. 9 (September 1992): 345. http://dx.doi.org/10.1016/0968-0004(92)90309-w.

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Colombo, Nicoló, and Nikos Vlassis. "FastMotif: spectral sequence motif discovery." Bioinformatics 31, no. 16 (April 16, 2015): 2623–31. http://dx.doi.org/10.1093/bioinformatics/btv208.

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Martyanov, Viktor, and Robert H. Gross. "Transcriptional Regulation in the G1-S Cell Cycle Stage in Fungi: Insights through Computational Analysis." Open Bioinformatics Journal 6, no. 1 (September 7, 2012): 43–54. http://dx.doi.org/10.2174/1875036201206010043.

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The transcription factor complexes Mlu1-box binding factor (MBF) and Swi4/6 cell cycle box binding factor (SBF) regulate the cell cycle in Saccharomyces cerevisiae. They activate hundreds of genes and are responsible for nor-mal cell cycle progression from G1 to S phase. We investigated the conservation of MBF and SBF binding sites during fungal evolution. Orthologs of S. cerevisiae targets of these transcription factors were identified in 37 fungal species and their upstream regions were analyzed for putative transcription factor binding sites. Both groups displayed enrichment in specific put

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Weiner, Benjamin G., Andrew G. T. Pyo, Yigal Meir, and Ned S. Wingreen. "Motif-pattern dependence of biomolecular phase separation driven by specific interactions." PLOS Computational Biology 17, no. 12 (December 29, 2021): e1009748. http://dx.doi.org/10.1371/journal.pcbi.1009748.

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Eukaryotic cells partition a wide variety of important materials and processes into biomolecular condensates—phase-separated droplets that lack a membrane. In addition to nonspecific electrostatic or hydrophobic interactions, phase separation also depends on specific binding motifs that link together constituent molecules. Nevertheless, few rules have been established for how these ubiquitous specific, saturating, motif-motif interactions drive phase separation. By integrating Monte Carlo simulations of lattice-polymers with mean-field theory, we show that the sequence of heterotypic binding m

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Peng, He. "CFSP: a collaborative frequent sequence pattern discovery algorithm for nucleic acid sequence classification." PeerJ 8 (April 20, 2020): e8965. http://dx.doi.org/10.7717/peerj.8965.

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Background Conserved nucleic acid sequences play an essential role in transcriptional regulation. The motifs/templates derived from nucleic acid sequence datasets are usually used as biomarkers to predict biochemical properties such as protein binding sites or to identify specific non-coding RNAs. In many cases, template-based nucleic acid sequence classification performs better than some feature extraction methods, such as N-gram and k-spaced pairs classification. The availability of large-scale experimental data provides an unprecedented opportunity to improve motif extraction methods. The p

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Uchiumi, F., K. Semba, Y. Yamanashi, J. Fujisawa, M. Yoshida, K. Inoue, K. Toyoshima, and T. Yamamoto. "Characterization of the promoter region of the src family gene lyn and its trans activation by human T-cell leukemia virus type I-encoded p40tax." Molecular and Cellular Biology 12, no. 9 (September 1992): 3784–95. http://dx.doi.org/10.1128/mcb.12.9.3784-3795.1992.

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The src family gene lyn is expressed preferentially in B lymphocytes but very little in normal T lymphocytes. Transcription of the lyn gene in T lymphocytes was shown to be induced by the p40tax protein encoded by human T-cell lymphotropic virus type I. For determination of the mechanism of p40tax-mediated trans activation, the transcriptional promoter region of the lyn gene was characterized. By endonuclease S1 mapping, the transcriptional initiation sites were identified within the 770-bp EcoRI-SacI fragment of the 5'-terminal portion of the human lyn gene. This fragment showed promoter acti

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Uchiumi, F., K. Semba, Y. Yamanashi, J. Fujisawa, M. Yoshida, K. Inoue, K. Toyoshima, and T. Yamamoto. "Characterization of the promoter region of the src family gene lyn and its trans activation by human T-cell leukemia virus type I-encoded p40tax." Molecular and Cellular Biology 12, no. 9 (September 1992): 3784–95. http://dx.doi.org/10.1128/mcb.12.9.3784.

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The src family gene lyn is expressed preferentially in B lymphocytes but very little in normal T lymphocytes. Transcription of the lyn gene in T lymphocytes was shown to be induced by the p40tax protein encoded by human T-cell lymphotropic virus type I. For determination of the mechanism of p40tax-mediated trans activation, the transcriptional promoter region of the lyn gene was characterized. By endonuclease S1 mapping, the transcriptional initiation sites were identified within the 770-bp EcoRI-SacI fragment of the 5'-terminal portion of the human lyn gene. This fragment showed promoter acti

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Mohanty, Satarupa, Prasant Kumar Pattnaik, Ahmed Abdulhakim Al-Absi, and Dae-Ki Kang. "A Review on Planted (l, d) Motif Discovery Algorithms for Medical Diagnose." Sensors 22, no. 3 (February 5, 2022): 1204. http://dx.doi.org/10.3390/s22031204.

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Personalized diagnosis of chronic disease requires capturing the continual pattern across the biological sequence. This repeating pattern in medical science is called “Motif”. Motifs are the short, recurring patterns of biological sequences that are supposed signify some health disorder. They identify the binding sites for transcription factors that modulate and synchronize the gene expression. These motifs are important for the analysis and interpretation of various health issues like human disease, gene function, drug design, patient’s conditions, etc. Searching for these patterns is an impo

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Shen, Zeyang, Marten A. Hoeksema, Zhengyu Ouyang, Christopher Benner, and Christopher K. Glass. "MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function." Bioinformatics 36, Supplement_1 (July 1, 2020): i84—i92. http://dx.doi.org/10.1093/bioinformatics/btaa476.

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Abstract Motivation Genetic variation in regulatory elements can alter transcription factor (TF) binding by mutating a TF binding motif, which in turn may affect the activity of the regulatory elements. However, it is unclear which motifs are prone to impact transcriptional regulation if mutated. Current motif analysis tools either prioritize TFs based on motif enrichment without linking to a function or are limited in their applications due to the assumption of linearity between motifs and their functional effects. Results We present MAGGIE (Motif Alteration Genome-wide to Globally Investigat

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Kong, Qing, Perng-Kuang Chang, Chunjuan Li, Zhaorong Hu, Mei Zheng, Quanxi Sun, and Shihua Shan. "Identification of AflR Binding Sites in the Genome of Aspergillus flavus by ChIP-Seq." Journal of Fungi 6, no. 2 (April 21, 2020): 52. http://dx.doi.org/10.3390/jof6020052.

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We report here the AflR binding motif of Aspergillus flavus for the first time with the aid of ChIP-seq analysis. Of the 540 peak sequences associated with AflR binding events, 66.8% were located within 2 kb upstream (promoter region) of translational start sites. The identified 18-bp binding motif was a perfect palindromic sequence, 5′-CSSGGGWTCGAWCCCSSG’3′ with S representing G or C and W representing A or T. On closer examination, we hypothesized that the 18-bp motif sequence identified contained two identical parts (here called motif A and motif B). Motif A was in positions 8–18 on the upp

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Brylinski, Michał, Leszek Konieczny, Patryk Czerwonko, Wiktor Jurkowski, and Irena Roterman. "Early-Stage Folding in Proteins(In Silico)Sequence-to-Structure Relation." Journal of Biomedicine and Biotechnology 2005, no. 2 (2005): 65–79. http://dx.doi.org/10.1155/jbb.2005.65.

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A sequence-to-structure library has been created based on the complete PDB database. The tetrapeptide was selected as a unit representing a well-defined structural motif. Seven structural forms were introduced for structure classification. The early-stage folding conformations were used as the objects for structure analysis and classification. The degree of determinability was estimated for the sequence-to-structure and structure-to-sequence relations. Probability calculus and informational entropy were applied for quantitative estimation of the mutual relation between them. The structural mot

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Jia, Hui, and Jinming Li. "Finding Transcription Factor Binding Motifs for Coregulated Genes by Combining Sequence Overrepresentation with Cross-Species Conservation." Journal of Probability and Statistics 2012 (2012): 1–18. http://dx.doi.org/10.1155/2012/830575.

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Novel computational methods for finding transcription factor binding motifs have long been sought due to tedious work of experimentally identifying them. However, the current prevailing methods yield a large number of false positive predictions due to the short, variable nature of transcriptional factor binding sites (TFBSs). We proposed here a method that combines sequence overrepresentation and cross-species sequence conservation to detect TFBSs in upstream regions of a given set of coregulated genes. We applied the method to 35S. cerevisiaetranscriptional factors with known DNA binding moti

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Sasso, E. H., K. Willems van Dijk, A. Bull, S. M. van der Maarel, and E. C. Milner. "VH genes in tandem array comprise a repeated germline motif." Journal of Immunology 149, no. 4 (August 15, 1992): 1230–36. http://dx.doi.org/10.4049/jimmunol.149.4.1230.

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Abstract In a study of human VH gene heterogeneity, we have previously used sequence-specific oligonucleotide probes to demonstrate polymorphism of 56pl and three highly homologous VH3 germline elements. We now extend these findings with VH nucleotide sequences obtained from a person who possesses restriction fragments corresponding to each of these four VH3 genes. From a lambda-phage library of genomic DNA, distinct phage clones containing putative 56pl, hv3005, 1.9III, and hv3019b9 genes were selected by screening with oligonucleotide probes. PCR amplification, subcloning, and sequencing fro

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Håland, Else Marie, Astrid Salte Wiig, Lars Magnus Hvattum, and Magnus Stålhane. "Evaluating the effectiveness of different network flow motifs in association football." Journal of Quantitative Analysis in Sports 16, no. 4 (November 18, 2020): 311–23. http://dx.doi.org/10.1515/jqas-2019-0097.

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AbstractIn association football, a network flow motif describes how distinct players from a team are involved in a passing sequence. The flow motif encodes whether the same players appear several times in a passing sequence, and in which order the players make passes. This information has previously been used to classify the passing style of different teams. In this work, flow motifs are analyzed in terms of their effectiveness in terms of generating shots. Data from four seasons of the Norwegian top division are analyzed, using flow motifs representing subsequences of three passes. The analys

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