SCOPE AND CRITERIA FOR CONSIDERATION
NAR provides rapid publication of papers on physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism and/or interactions. All manuscripts must present some novel development and meet the general criteria of originality, timeliness, significance and scientific excellence.
NAR is published online and in print. Methods, Database and Webserver papers only appear online.
The Journal publishes the following types of papers:
Standard papers. Standard papers are published both in print and online in the following subject categories:Emerging or specialized subject areas
Chemical Biology and Nucleic Acid Chemistry
Data Resources and Analyses
Gene Regulation, Chromatin and Epigenetics
Genome Integrity, Repair and Replication
Nucleic Acid Enzymes
Synthetic Biology and Bioengineering
Methods papers. Significant new methods can be published in two forms:
1. As Methods papers in NAR Methods Online: these papers are published online only but the titles of newly published Methods articles are included in the Table of Contents of the print edition. Methods papers are prepared in exactly the same format as Standard papers, and are counted for citation by ISI and Medline. They are searchable through all services, such as PubMed and the general NAR search page.
Papers should report novel techniques or significant advances in existing techniques that are relevant to NAR's core subject areas. These should be highly significant and useful, and contain an example of utility.
New applications of existing technologies (e.g. novel diagnostic applications of established techniques) are discouraged.
All Methods Online papers are subject to the same requirements regarding availability of research materials, and computational executables and/or source code as standard articles, as described for individual categories below and in 'Journal Policies'.
2. As part of Standard papers that primarily report novel findings relating to important biological and chemical problems. These papers are listed in the Table of Contents under one standard subject category, and titles are annotated with an M. The full text appears both online and in print.
All Methods papers are indexed in the NAR Methods special collection, which includes methods sub-categories (DNA characterisation, nucleic acid modification, microarray etc).
Queries regarding submission of methods papers may be directed to Dr Alan Kimmel
(Email: firstname.lastname@example.org/) or Dr Georg Sczakiel (Email: email@example.com).
Surveys and Summaries. This section, accommodates brief formal reviews relevant to nucleic acid chemistry and biology as well as other articles requiring more latitude in subject or format. Presubmission queries to Dr William Dynan are encouraged (Email: firstname.lastname@example.org) . Surveys and Summaries appear both online and in print.
Database articles. In January each year the journal devotes a special online issue to biological databases. For an article to be considered, a presubmission query must be sent to Dr Michael Galperin by July 1 of the preceding year (Email: email@example.com) Special Database issue submission instructions are available here. Papers appear online only but print copies of the Database issue are available for purchase.
Web Server articles. In July each year the Journal devotes an entire online issue to web-based software resources of value to the biological community. For an article to be considered, a presubmission query must be sent to Dr Gary Benson by January 1 of the publication year (Email: firstname.lastname@example.org) Special Web Server issue submission instructions are available here. Papers appear online only but print copies of the Web Server issue are available for purchase.
Criteria for Consideration
Specific criteria apply in each subject category as outlined below:
Emerging or specialized subject areas
Intercellular communication via RNA-containing vesicles
Although discovered in the 1980’s, interest in extracellular vesicles sometimes known as exosomes has increased with the recent discovery that they contain multiple classes of RNA and RNA binding proteins. The journal welcomes submissions that provide novel insights into nucleic acid-based mechanisms through which these vesicles convey information between cells. Reports should be based on experimental studies and include persuasive discussion of controls and a description of methods employed to accurately measure levels of nucleic acids. For consideration, papers should describe findings with implications that extend beyond a single cell type and demonstrate physiological or functional relevance of the vesicle contents. Studies that report sequencing or compositional data are acceptable only if they include follow-up experiments that shed new light on RNA-mediated mechanisms of intercellular communication.
Functional roles of RNA modification
Traditionally, studies of the mechanisms and consequences of base modification focused mainly on stable RNAs including tRNAs, rRNAs and snRNAs. These have gained importance in recent years through advances in understanding the roles of modified bases in translational decoding and pre-mRNA splicing, for example. In parallel, the development of more sensitive detection tools and the application of genome-wide approaches has paved the way for studies aimed at understanding the impact of base modification on the structure, function, and subcellular localization of mRNAs as well as both small and large noncoding RNAs. The journal welcomes submissions that describe experimental studies aimed at understanding the mechanisms through which RNA modification enzymes (“writer” proteins) select their target sites and downstream “reader” proteins recognize modified RNA molecules. Studies that report the results of sequencing RNA populations carrying a particular modification are acceptable only if they include follow-up experiments that provide mechanistic insight into the physiological or functional relevance of the modification.
Single cell gene regulation studies
While cel population based gene expression studies have proven invaluable in dissecting transcriptional networks, it is becoming increasingly recognised that single cell studies more accurately reflect the molecular events involved, particularly when transcriptional dynamics are investigated. We therefore encourage studies which measure single cell gene expression, involving emerging (high throughput) technologies including, sequencing, systems fluorescence/luminescence-based microscopy approaches and PCR-based methodologies.
Nuclear architecture and functional consequences
We welcome submissions that describe experimental and theoretical studies that address the manner in which the architectural organization of genomes and RNomes determines and regulates biological function. Studies are welcome that uncover the mechanisms governing the establishment, maintenance, and dynamic rearrangements of nucleic acid and nucleoprotein architectures, or the impact of these architectures on processes such as genome stability, DNA repair, transcription, or RNA processing, transport, translation and degradation.
We welcome submissions that describe new methods (computational and experimental) to address these questions on a cellular scale. Entirely computational studies that investigate or integrate information from published datasets should provide significant new biological insights into the phenomenon investigated.
Gene targeting and Genome Engineering
The journal encourages manuscripts that report novel approaches for the targeted insertion, disruption or modification of individual sites within biological genomes. Such papers might present completely novel strategies to engineer gene targeting scaffolds, or novel combinations orfusions of these scaffolds with functional or catalytic domains that enhance or alter their functions. Studies correlating the activity of such systems in living cells to clearly measured genetic outcomes (recombination, end-joining, mutagenesis, off-target activities) are also encouraged. We particularly welcome papers that describe novel strategies and applications to drive ex vivo or in vivo genome modifications in primary (patient-derived) cells and tissues for therapeutic purpose.
Papers describing extension of existing gene targeting approaches to alternative cell lines or additional model organisms are discouraged unless the underlying biological question being studied is highly significant, novel and directly relevant to nucleic acid biology or chemistry.
Molecular Machines and Complex Molecular Assemblages
Studies that elucidate novel features of the composition, structure or mechanism of molecular machines and higher order assemblages involved in nucleic acid biology are strongly encouraged. Topics of interest, which may be investigated using experimental and/or computational methods, include the manners in which molecular machines and systems are organized and dynamically remodeled.
We welcome submissions that describe new methods (computational and experimental) to address these questions. Studies that investigate or integrate information from published datasets will only be considered if the underlying biological question being studied is highly significant, novel and directly relevant to nucleic acid biology or chemistry. Such studies should provides significant new biological insights into the phenomenon investigated.
Single molecule studies of macromolecular function
Studies that use single molecule methods (optical and magnetic tweezers, atomic force microscopy, FRET pair analyses, etc) to study the function and mechanism of isolated biological macromolecules (either in conjunction with or separate from ensemble assays in solution) are strongly encouraged in the relevant biological category.
Chemical Biology and Nucleic Acid Chemistry
NAR encourages submission of papers describing the engineering, synthesis, delivery and application of novel nucleic acids, nucleic acid binding proteins, or their derivatives. Examples of such studies might include:
- Novel syntheses or modifications of nucleic acids or nucleic acid binding proteins that lead to a desired, beneficial effect in a biological application.
- Novel methods of delivery of nucleic acids or nucleic acid binding proteins, that involve new mechanisms or that demonstrate significantly improved effectiveness, especially in whole organisms.
- Cellular and in vivo targeting applications of nucleic acids or their derivatives (such as antisense, siRNA or aptamers) or nucleic acid binding proteins, where there is a strong emphasis on understanding their mechanism of action.
- Design or selection of nucleic acids, or nucleic acid binding proteins, that leads to a novel ligand binding or catalytic activity, a unique regulatory function, or the ability to selectively modify gene function. Studies that reveal novel principles of biomolecular engineering are particularly encouraged.
- Studies that facilitate (i) the creation of novel materials and devices via the manipulation of individual molecules nucleic acid based oligonucleotides and polymers (i.e. nanotechnology and nanomaterial development)
Chemical synthesis of novel nucleoside or nucleotide analogues will not be considered unless there is a significant and demonstrated useful application relating to oligonucleotide or nucleic acids structure or function. Papers that describe molecules that are primarily intended for use as in vitro sensors are more appropriate for the Methods category.
Manuscripts may be considered if they fall into one of two descriptions:
1. Description of a new algorithm that represents a substantial improvement over current methodology, and that has direct biological relevance. It should be bench-marked on gold-standard datasets and ideally, be supported by experimental validation where applicable. The performance of such algorithms must be compared with current methods and the relevant statistics (e.g., sensitivity, selectivity, etc) of the performance must be indicated. Limitations of the method and general directions for future improvement should be reported. Small improvements or obvious modifications of existing algorithms will not be considered.
2. Manuscripts that primarily describe the use of existing computational methods to generate significant, novel biological information and insight. Limitations of the approach and issues that may affect the conclusions drawn must be explicitly stated. Purely descriptive 'data mining' studies, (e.g., those that computationally predict biomarkers from disease expression datasets or those that simply compile or catalogue microRNAs from published datasets without providing significant biological or mechanistic insight) are discouraged.
In either case, the manuscript must be written so as to be understandable to biologists. It should ideally report research performed on information pertaining to, or cellular processes that involve, nucleic acids. Extensive use of equations should be avoided in the main text and any detailed mathematics should be presented as supplementary material.
Availability of algorithms and code: If the manuscript describes new software tools or the implementation of novel algorithms the software must be freely available to users at the time of submission (either as executable versions for multiple, common platforms or as source code). Availability must be clearly stated in the article. Authors must ensure that the software is available for a full TWO YEARS following publication, preferably through a download link on a stable URL. Authors are strongly encouraged to make their source code available through an open source license (see www.opensource.org for examples).
Manuscripts that describe computational methods that primarily focus on protein multi-sequence alignment algorithms, prediction of protein folds or structures, or prediction of protein-protein binding sites or affinities will not be considered by NAR (with the possible exception of papers prepared specifically for the annual NAR special issues on WebServers or Databases, as described above).
Manuscripts describing results from molecular dynamics simulations will be considered only if they provide valuable insights into biological questions related to nucleic acids. Theoretical results must be put into perspective with available structural and/or biological data, although it is not always essential for them to be accompanied by experimentation. However, theoretical interpretations or speculative ideas should be experimentally testable and, if not backed up by experimental results, should constitute only a small part of the manuscript. Constraints or limitations of the simulation method or theoretical approach used should be identified and discussed. Manuscripts must be written so as to be intelligible to as wide an audience as possible and should avoid jargon and undefined terms.
Data Resources and Analyses
The Data Resource and Analyses category is designed to highlight papers documenting and interpreting substantive amounts of new biological data. Typically, these manuscripts will not only report a major informational database but also should provide new biological insights that can be derived from an analysis of the dataset(s). Comprehensive experimental and/or theoretical validation must be provided. Examples of such resources might be collections of ChIP-seq data accompanying changes in cell fate, substantive functional genomics screens, and sequencing derived data from the genomes or transcriptomes of multiple samples. Comprehensive meta analyses of existing datasets might be considered in this category. Papers proposing biomarkers will not be considered. Data Resources can be made available via web services or as standalone repositories to be downloaded for local use.
Gene regulation, Chromatin and Epigenetics
The Journal encourages manuscripts that:
- detail promoters, enhancers, terminators, silencers, insulators, RNA polymerases, transcription factors and regulators, constitutive and alternative splicing, polyadenylation, editing and RNA turnover.
- identify novel structural or dynamic features of chromatin.
- provide new and general insights into mechanisms that modulate covalent modification of DNA or chromatin proteins.
- report significant and new information about DNA modifying enzymes and nucleic acid binding proteins.
For consideration, papers should provide new or generally applicable insights, with implications that extend beyond a single gene or new information about the regulation of genes involved in the synthesis, maturation, or degradation of nucleic acids. Findings must demonstrate physiological or cellular relevance to the context in which the process occurs.
Genome Integrity, Repair and Replication
The Journal encourages manuscripts focusing on systems for maintenance of genome integrity. In particular we encourage manuscripts that:
- report novel mechanisms for sensing and responding to DNA damage.
- characterize the structural biology of DNA damage sensors and repair enzymes.
- use novel experimental approaches or models.
Manuscripts dealing with DNA replication should provide significant new information about proteins that act by directly contacting the template.
Papers may use physical, genetic, developmental, biochemical, or cell biological approaches.
The Journal encourages the submission of manuscripts which:
- report analysis of complete chromosomes or genomes, including comparative studies. Papers should contain complementary experimental data with relevance to genomic organisation, transcription, RNA processing, expression, genetic analysis or other novel biology. These data would typically correspond to biochemical assays or equally informative analyses that support sequence-based functional annotation. Exceptions to this requirement might be made for descriptions of either whole genome sequences, or characterization of gene families, which display exceptional novelty or significance. Reported sequences must shed significant new light on basic questions of structural or functional interest. Reports that merely summarize information from DNA sequence database annotations, or that focus primarily on topics outside of NAR's core subject areas, are discouraged.
- report application of whole genomic approaches to the analysis of gene regulation (e.g. array and proteomic technologies, or computational methods). Such manuscripts must provide novel insights into biological problems and provide evidence to corroborate and validate hypotheses which have been generated using whole genomic approaches. Purely descriptive accounts of microarray data or sequence characterizations (data mining) that do not lead to a testable hypothesis, or experimentally tested prediction of biological function will not be considered (see also massively parallel (Deep) sequencing section below for guidance on ChIP-seq studies).
Nucleic acid sequences must be deposited in a databank with a release date no later than the date of publication (see General Policies).
The Journal encourages the submission of manuscripts that relate to physical, chemical, biochemical, or biological characteristics of nucleic acids. Examples of such papers include:
- Novel studies of nucleic acid processing and packaging which report fundamental and general features that extend beyond individual viral or cellular systems.
- Characterization of nucleic acid folding or nucleic acid binding interactions, including studies that report the thermodynamic and/or kinetic basis for folding or binding events, where there is a clear and important question or hypothesis relevant to biological processes in cells.
- New insights into nucleic acid trafficking in cells, including nuclear or organellar transport, and/or nucleic acid intracellular modification.
- Novel aspects of molecular recognition between DNA and RNA sequences and small molecules where such studies have clear biological relevance. This may include sequence-dependent binding, base recognition and novel recognition motifs. Descriptions of in vitro aptamer selection experiments and resulting constructs will generally not be considered.
Nucleic Acid Enzymes
The Journal encourages manuscripts that report detailed enzymological studies of DNA and RNA polymerases, restriction enzymes and other nucleases, DNA methyltransferases and other enzymes that work directly on DNA or RNA substrates. Papers that describe restriction and modification methyltransferases with novel recognition sequences, but do not provide detailed enzymological characterization will be considered for the Methods category.
The Journal welcomes manuscripts that:
- report the structure, assembly, mechanisms of action or regulation of ribonucleoprotein complexes;
- report the structure, biogenesis, cellular roles or regulation of non-coding RNAs including microRNAs, small interfering RNAs, piwi-associated RNAs, and long non-coding RNAs. Studies suitable for NAR should stress mechanistic insights that can be generalized to other systems. Manuscripts that focus on the impact of an RNA through a known mechanism on a specific physiologic process may be more suitable for a journal with a different specialization. Rigorous controls are required to support the conclusion that observations are likely not due to off-target effects;
- provide new information about the structure or biochemistry of nucleic acid binding proteins or enzymes that function in RNA metabolism, particularly if these involve new motifs.
Papers should provide novel structural or functional insights, preferably with implications extending beyond a single gene or organism. Papers that report natural RNA transcripts (e.g. antisense RNA, miRNA) must provide evidence for their functional significance. This might include mutational data, information about differential control, or other convincing evidence of biological relevance.
The Journal encourages manuscripts that report significant, biologically relevant structural features or principles as determined by X-ray crystallographic or NMR studies. Reports on minor variants of well-established structures are generally not suitable unless significant new insights are obtained. Manuscripts that utilise database and bioinformatics approaches must be firmly related to experimental observations. Papers that describe new biophysical and structural methods, but do not contain novel findings relating to an important biological problem, are more appropriate for the Methods category.
Synthetic Biology and Bioengineering
NAR encourages submission of papers describing the modification and/or redesign of genomic information in living cells and organisms, deliberate genetic recoding of biological pathways and decision points to alter biological behaviors and responses, or the generation of organisms harboring dramatically altered or synthetic genomes. Examples of such studies might include:
- Development and application of tools and methods for site-specific genome engineering.
- The creation of novel genetic circuits or pathways in living cells.
- The creation of new biological systems and synthetic organisms. Studies that reveal novel principles of rewriting and rebuilding the natural systems to understand the origins of life are encouraged.
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