abstract：:Characterization of the epigenetic status of individual cells remains a challenge. Current sequencing approaches have limited coverage, and it is difficult to assign an epigenetic status to the transcription state of individual gene alleles in the same cell. To address these limitations, a targeted microscopy-based ep...

journal_title：Nucleic acids research

authors： Kint S,Van Criekinge W,Vandekerckhove L,De Vos WH,Bomsztyk K,Krause DS,Denisenko O

更新日期：2021-01-28 00:00:00

abstract：:Maintenance of stem-cell identity requires proper regulation of enhancer activity. Both transcription factors OCT4/SOX2/NANOG and histone methyltransferase complexes MLL/SET1 were shown to regulate enhancer activity, but how they are regulated in embryonic stem cells (ESCs) remains further studies. Here, we report a t...

journal_title：Nucleic acids research

authors： Niu C,Wang S,Guo J,Wei X,Jia M,Chen Z,Gong W,Qin Y,Wang X,Zhi X,Lu M,Chen S,Gu M,Zhang J,Han JJ,Lan F,Meng D

更新日期：2021-01-27 00:00:00

abstract：:Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia col...

journal_title：Nucleic acids research

authors： Wang T,Tague N,Whelan SA,Dunlop MJ

更新日期：2021-01-25 00:00:00

abstract：:Defects in the posttranscriptional modifications of mitochondrial tRNAs have been linked to human diseases, but their pathophysiology remains elusive. In this report, we investigated the molecular mechanism underlying a deafness-associated tRNAIle 4295A>G mutation affecting a highly conserved adenosine at position 37,...

journal_title：Nucleic acids research

authors： Meng F,Zhou M,Xiao Y,Mao X,Zheng J,Lin J,Lin T,Ye Z,Cang X,Fu Y,Wang M,Guan MX

更新日期：2021-01-25 00:00:00

abstract：:Modification of cytosine plays an important role in epigenetic regulation of gene expression and genome stability. Cytosine is converted to 5-methylcytosine (5mC) by DNA methyltransferase; in turn, 5mC may be oxidized to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation enzyme. The structural flexibility of D...

journal_title：Nucleic acids research

authors： Furukawa A,Walinda E,Arita K,Sugase K

更新日期：2021-01-25 00:00:00

abstract：:Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interact...

journal_title：Nucleic acids research

authors： Fuchs A,Riegler S,Ayatollahi Z,Cavallari N,Giono LE,Nimeth BA,Mutanwad KV,Schweighofer A,Lucyshyn D,Barta A,Petrillo E,Kalyna M

更新日期：2021-01-25 00:00:00

abstract：:Codon usage bias is a universal feature of all genomes. Although codon usage has been shown to regulate mRNA and protein levels by influencing mRNA decay and transcription in eukaryotes, little or no genome-wide correlations between codon usage and mRNA levels are detected in mammalian cells, raising doubt on the sign...

journal_title：Nucleic acids research

authors： Yang Q,Lyu X,Zhao F,Liu Y

更新日期：2021-01-25 00:00:00

abstract：:Chromosome stability is primarily determined by telomere length. TRF1 is the core subunit of shelterin that plays a critical role in telomere organization and replication. However, the dynamics of TRF1 in scenarios of telomere-processing activities remain elusive. Using single-molecule magnetic tweezers, we here inves...

journal_title：Nucleic acids research

authors： Li X,Wang M,Zheng W,Huang W,Wang Z,Jin K,Liu L,Yu Z

更新日期：2021-01-25 00:00:00

abstract：:Replication Protein A (RPA) is a critical complex that acts in replication and promotes homologous recombination by allowing recombinase recruitment to processed DSB ends. Most organisms possess three RPA subunits (RPA1, RPA2, RPA3) that form a trimeric complex critical for viability. The Caenorhabditis elegans genome...

journal_title：Nucleic acids research

authors： Hefel A,Honda M,Cronin N,Harrell K,Patel P,Spies M,Smolikove S

更新日期：2021-01-21 00:00:00

abstract：:The endonuclease activity within the influenza virus cap-snatching process is a proven therapeutic target. The anti-influenza drug baloxavir is highly effective, but is associated with resistance mutations that threaten its clinical efficacy. The endonuclease resides within the N-terminal domain of the PA subunit (PAN...

journal_title：Nucleic acids research

authors： Kumar G,Cuypers M,Webby RR,Webb TR,White SW

更新日期：2021-01-19 00:00:00

abstract：:Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (l...

journal_title：Nucleic acids research

authors： Gerguri T,Fu X,Kakui Y,Khatri BS,Barrington C,Bates PA,Uhlmann F

更新日期：2021-01-12 00:00:00

abstract：:Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the...

journal_title：Nucleic acids research

authors： Jha V,Roy B,Jahagirdar D,McNutt ZA,Shatoff EA,Boleratz BL,Watkins DE,Bundschuh R,Basu K,Ortega J,Fredrick K

更新日期：2021-01-11 00:00:00

abstract：:The mammalian target of rapamycin (mTOR) is a critical regulator of cell growth, integrating multiple signalling cues and pathways. Key among the downstream activities of mTOR is the control of the protein synthesis machinery. This is achieved, in part, via the co-ordinated regulation of mRNAs that contain a terminal ...

journal_title：Nucleic acids research

authors： Smith EM,Benbahouche NEH,Morris K,Wilczynska A,Gillen S,Schmidt T,Meijer HA,Jukes-Jones R,Cain K,Jones C,Stoneley M,Waldron JA,Bell C,Fonseca BD,Blagden S,Willis AE,Bushell M

更新日期：2021-01-11 00:00:00

abstract：:Most mutations in cancer genomes occur in the non-coding regions with unknown impact on tumor development. Although the increase in the number of cancer whole-genome sequences has revealed numerous putative non-coding cancer drivers, their information is dispersed across multiple studies making it difficult to underst...

journal_title：Nucleic acids research

authors： Liu EM,Martinez-Fundichely A,Bollapragada R,Spiewack M,Khurana E

更新日期：2021-01-08 00:00:00

abstract：:The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. The Entrez system provides search and re...

journal_title：Nucleic acids research

authors： Sayers EW,Beck J,Bolton EE,Bourexis D,Brister JR,Canese K,Comeau DC,Funk K,Kim S,Klimke W,Marchler-Bauer A,Landrum M,Lathrop S,Lu Z,Madden TL,O'Leary N,Phan L,Rangwala SH,Schneider VA,Skripchenko Y,Wang J,Ye J,

更新日期：2021-01-08 00:00:00

abstract：:Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present...

journal_title：Nucleic acids research

authors： Liu F,Li Y,Yu H,Zhang L,Hu J,Bao Z,Wang S

更新日期：2021-01-08 00:00:00

abstract：:Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease...

journal_title：Nucleic acids research

authors： Bastian FB,Roux J,Niknejad A,Comte A,Fonseca Costa SS,de Farias TM,Moretti S,Parmentier G,de Laval VR,Rosikiewicz M,Wollbrett J,Echchiki A,Escoriza A,Gharib WH,Gonzales-Porta M,Jarosz Y,Laurenczy B,Moret P,Person E,

更新日期：2021-01-08 00:00:00

abstract：:Chewie Nomenclature Server (chewie-NS, https://chewbbaca.online/) allows users to share genome-based gene-by-gene typing schemas and to maintain a common nomenclature, simplifying the comparison of results. The combination between local analyses and a public repository of allelic data strikes a balance between potenti...

journal_title：Nucleic acids research

authors： Mamede R,Vila-Cerqueira P,Silva M,Carriço JA,Ramirez M

更新日期：2021-01-08 00:00:00

abstract：:The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), has for almost forty years continued in its mission to freely archive and present the world's public sequencing data for the benefit of the entire scie...

journal_title：Nucleic acids research

authors： Harrison PW,Ahamed A,Aslam R,Alako BTF,Burgin J,Buso N,Courtot M,Fan J,Gupta D,Haseeb M,Holt S,Ibrahim T,Ivanov E,Jayathilaka S,Balavenkataraman Kadhirvelu V,Kumar M,Lopez R,Kay S,Leinonen R,Liu X,O'Cathail C,Pa

更新日期：2021-01-08 00:00:00

abstract：:The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching...

journal_title：Nucleic acids research

authors： CNCB-NGDC Members and Partners.

更新日期：2021-01-08 00:00:00

abstract：:Computational analysis of biosynthetic gene clusters (BGCs) has revolutionized natural product discovery by enabling the rapid investigation of secondary metabolic potential within microbial genome sequences. Grouping homologous BGCs into Gene Cluster Families (GCFs) facilitates mapping their architectural and taxonom...

journal_title：Nucleic acids research

authors： Kautsar SA,Blin K,Shaw S,Weber T,Medema MH

更新日期：2021-01-08 00:00:00

abstract：:Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis...

journal_title：Nucleic acids research

authors： Grigoriev IV,Hayes RD,Calhoun S,Kamel B,Wang A,Ahrendt S,Dusheyko S,Nikitin R,Mondo SJ,Salamov A,Shabalov I,Kuo A

更新日期：2021-01-08 00:00:00

abstract：:The FlyRNAi database at the Drosophila RNAi Screening Center and Transgenic RNAi Project (DRSC/TRiP) provides a suite of online resources that facilitate functional genomics studies with a special emphasis on Drosophila melanogaster. Currently, the database provides: gene-centric resources that facilitate ortholog map...

journal_title：Nucleic acids research

authors： Hu Y,Comjean A,Rodiger J,Liu Y,Gao Y,Chung V,Zirin J,Perrimon N,Mohr SE

更新日期：2021-01-08 00:00:00

abstract：:The recent outbreak of COVID-19 has generated an enormous amount of Big Data. To date, the COVID-19 Open Research Dataset (CORD-19), lists ∼130,000 articles from the WHO COVID-19 database, PubMed Central, medRxiv, and bioRxiv, as collected by Semantic Scholar. According to LitCovid (11 August 2020), ∼40,300 COVID19-re...

journal_title：Nucleic acids research

authors： Tworowski D,Gorohovski A,Mukherjee S,Carmi G,Levy E,Detroja R,Mukherjee SB,Frenkel-Morgenstern M

更新日期：2021-01-08 00:00:00

abstract：:PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem...

journal_title：Nucleic acids research

authors： Kim S,Chen J,Cheng T,Gindulyte A,He J,He S,Li Q,Shoemaker BA,Thiessen PA,Yu B,Zaslavsky L,Zhang J,Bolton EE

更新日期：2021-01-08 00:00:00

abstract：:GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 9.9 trillion base pairs from over 2.1 billion nucleotide sequences for 478 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverag...

journal_title：Nucleic acids research

authors： Sayers EW,Cavanaugh M,Clark K,Pruitt KD,Schoch CL,Sherry ST,Karsch-Mizrachi I

更新日期：2021-01-08 00:00:00

abstract：:The BRENDA enzyme database (https://www.brenda-enzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data. In 2018, BRENDA was selected as an ELIXIR Core Data Resource. BRENDA provides reliable data, continuous curation and updates of classified enzymes, and the in...

journal_title：Nucleic acids research

authors： Chang A,Jeske L,Ulbrich S,Hofmann J,Koblitz J,Schomburg I,Neumann-Schaal M,Jahn D,Schomburg D

更新日期：2021-01-08 00:00:00

abstract：:The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problema...

journal_title：Nucleic acids research

authors： Tweedie S,Braschi B,Gray K,Jones TEM,Seal RL,Yates B,Bruford EA

更新日期：2021-01-08 00:00:00

abstract：:The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our int...

journal_title：Nucleic acids research

authors： Howe KL,Achuthan P,Allen J,Allen J,Alvarez-Jarreta J,Amode MR,Armean IM,Azov AG,Bennett R,Bhai J,Billis K,Boddu S,Charkhchi M,Cummins C,Da Rin Fioretto L,Davidson C,Dodiya K,El Houdaigui B,Fatima R,Gall A,Garcia G

更新日期：2021-01-08 00:00:00

abstract：:The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes,...

journal_title：Nucleic acids research

authors： Howe DG,Ramachandran S,Bradford YM,Fashena D,Toro S,Eagle A,Frazer K,Kalita P,Mani P,Martin R,Moxon ST,Paddock H,Pich C,Ruzicka L,Schaper K,Shao X,Singer A,Van Slyke CE,Westerfield M

更新日期：2021-01-08 00:00:00

abstract：:Various in vivo mutagenesis methods have been developed to facilitate fast and efficient continuous evolution of proteins in cells. However, they either modify the DNA region that does not match the target gene, or suffer from low mutation rates. Here, we report a mutator, eMutaT7 (enhanced MutaT7), with very fast in ...

journal_title：Nucleic acids research

authors： Park H,Kim S

更新日期：2021-01-06 00:00:00

abstract：:The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. RdRPs are essential in virus life cycle due to their central role in viral genome replication/transcription processes. However, their contribution in host adaption has not been well documented. By sol...

journal_title：Nucleic acids research

authors： Yang J,Jing X,Yi W,Li XD,Yao C,Zhang B,Zheng Z,Wang H,Gong P

更新日期：2021-01-06 00:00:00

abstract：:Optogenetic control of CRISPR-Cas9 systems has significantly improved our ability to perform genome perturbations in living cells with high precision in time and space. As new Cas orthologues with advantageous properties are rapidly being discovered and engineered, the need for straightforward strategies to control th...

journal_title：Nucleic acids research

authors： Hoffmann MD,Mathony J,Upmeier Zu Belzen J,Harteveld Z,Aschenbrenner S,Stengl C,Grimm D,Correia BE,Eils R,Niopek D

更新日期：2020-12-16 00:00:00

abstract：:Ribonucleoprotein (RNP) granules are membraneless organelles (MLOs), which majorly consist of RNA and RNA-binding proteins and are formed via liquid-liquid phase separation (LLPS). Experimental studies investigating the drivers of LLPS have shown that intrinsically disordered proteins (IDPs) and nucleic acids like RNA...

journal_title：Nucleic acids research

authors： Regy RM,Dignon GL,Zheng W,Kim YC,Mittal J

更新日期：2020-12-16 00:00:00

abstract：:Telomeres at the ends of eukaryotic chromosomes are essential for genome integrality and stability. In order to identify genes that sustain telomere maintenance independently of telomerase recruitment, we have exploited the phenotype of over-long telomeres in the cells that express Cdc13-Est2 fusion protein, and exami...

journal_title：Nucleic acids research

authors： Liu JC,Li QJ,He MH,Hu C,Dai P,Meng FL,Zhou BO,Zhou JQ

更新日期：2020-12-16 00:00:00

abstract：:The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The s...

journal_title：Nucleic acids research

authors： Wacker A,Weigand JE,Akabayov SR,Altincekic N,Bains JK,Banijamali E,Binas O,Castillo-Martinez J,Cetiner E,Ceylan B,Chiu LY,Davila-Calderon J,Dhamotharan K,Duchardt-Ferner E,Ferner J,Frydman L,Fürtig B,Gallego J,Grün JT

更新日期：2020-12-16 00:00:00

abstract：:Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline ...

journal_title：Nucleic acids research

authors： Mestre MR,González-Delgado A,Gutiérrez-Rus LI,Martínez-Abarca F,Toro N

更新日期：2020-12-16 00:00:00

abstract：:Sensitive detection of microsatellite instability (MSI) in tissue or liquid biopsies using next generation sequencing (NGS) has growing prognostic and predictive applications in cancer. However, the complexities of NGS make it cumbersome as compared to established multiplex-PCR detection of MSI. We present a new appro...

journal_title：Nucleic acids research

authors： Yu F,Leong KW,Makrigiorgos A,Adalsteinsson VA,Ladas I,Ng K,Mamon H,Makrigiorgos GM

更新日期：2020-12-08 00:00:00

abstract：:Proper cytokine gene expression is essential in development, homeostasis and immune responses. Studies on the transcriptional control of cytokine genes have mostly focused on highly researched transcription factors (TFs) and cytokines, resulting in an incomplete portrait of cytokine gene regulation. Here, we used enha...

journal_title：Nucleic acids research

authors： Santoso CS,Li Z,Lal S,Yuan S,Gan KA,Agosto LM,Liu X,Pro SC,Sewell JA,Henderson A,Atianand MK,Fuxman Bass JI

更新日期：2020-12-02 00:00:00

abstract：:Riboswitches are important gene regulatory elements frequently encountered in bacterial mRNAs. The recently discovered nadA riboswitch contains two similar, tandemly arrayed aptamer domains, with the first domain possessing high affinity for nicotinamide adenine dinucleotide (NAD+). The second domain which comprises t...

journal_title：Nucleic acids research

authors： Chen H,Egger M,Xu X,Flemmich L,Krasheninina O,Sun A,Micura R,Ren A

更新日期：2020-12-02 00:00:00