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: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 including 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 as standard articles regarding availability of research materials and computational executables and/or source code, 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: email@example.com/) or Dr Georg Sczakiel (Email: firstname.lastname@example.org).
Surveys and Summaries. This section accommodates formal reviews relevant to nucleic acid chemistry and biology as well as other articles requiring more latitude in subject or format. Although many Surveys and Summaries are by invitation, the journal also welcomes unsolicited proposals. For unsolicited contributions, a presubmission enquiry should be sent to Dr William Dynan (Email: email@example.com). This should include a title, outline, proposed submission date, and a summary of the authors' qualifications, including citations to the authors' relevant publications in the topic area.
Database articles. In January of 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: firstname.lastname@example.org). 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 of 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: email@example.com). 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
The editors periodically review emerging scientific areas where the journal would like to attract more submissions. Currently these include:
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 cell 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 investigating transcriptional dynamics. We therefore encourage studies that measure single cell gene expression, using emerging (high throughput) technologies including sequencing, systems fluorescence/luminescence-based microscopy approaches and PCR-based methodologies.
Nuclear architecture and functional consequences
We welcome submissions describing experimental and theoretical studies that address the manner in which the architectural organization of genomes and RNomes determines and regulates biological function. Reciprocally, studies that uncover the mechanisms governing the establishment, maintenance and dynamic rearrangements of nuclear 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 are welcome.
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 or fusions 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 be considered only if the underlying biological question being studied is highly significant, novel and directly relevant to nucleic acid biology or chemistry. Such studies should provide 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.
Specific criteria apply in each subject category as outlined below:
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 nucleic acid based oligomers and polymers (i.e. nanotechnology and nanomaterial development), (ii) genome engineering, and/or (iii) the creation of novel genetic and cellular circuits or systems.
- Creation of new biological systems. Studies that reveal novel principles of rewriting and reconfiguring natural systems to understand the origins of life are also encouraged.
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 categories:
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. Incremental improvements or obvious modifications of existing algorithms will not be considered.
2. 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 insights pertaining directly to nucleic acids, or to 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 new 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
For consideration, papers should provide new insights into generally applicable principles or mechanisms that extend beyond a single gene, or present new information about the mechanisms underlying the regulation of genes involved in the synthesis, maturation, or degradation of nucleic acids. Findings must demonstrate relevance to the physiological or cellular context in which the process occurs.
The Journal specifically encourages manuscripts that:
- Identify novel structural or dynamic features of chromatin.
- Provide novel insights into the functions of elements or factors that mediate long-range interactions such as insulators and enhancers.
- Present new mechanisms underlying the functions of promoters,, terminators, silencers, RNA polymerases, transcription factors and other DNA binding proteins.
- Report significant new information about histone and DNA modifying enzymes and chromatin remodelling factors.
- Provide novel insights into mechanisms through which covalent modification of DNA or chromatin proteins impinge on gene expression.
- Probe the interfaces between transcription, chromatin and RNA processing.
- Provide mechanistic insights into how large or small non-coding RNAs influence chromatin structure and function and/or gene regulation.
- Use single cell approaches and mathematical modelling to reveal new gene regulatory mechanisms.
Papers that primarily report the application of genome-wide approaches to the analysis of gene expression or regulation should provide new biological or mechanistic insights with detailed follow-up investigation; otherwise, they may be more appropriate for the Data Resources and Analyses category.
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.
- Characterise 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 that:
- Report the DNA sequences of complete genomes, large chromosomes or extensive gene families accompanied by bioinformatic analyses that shed significant new light on basic questions of structural or functional interest. Papers should include complementary experimental data with relevance to genomic organisation, transcription, RNA processing, expression, genetic inheritance or other novel biology. These data would typically correspond to molecular, biochemical or other equally informative analyses that support sequence-based functional annotation. Exceptions to this requirement might be made for analyses of entire genomes or large/dynamic gene families that display unusual features or provide especially novel or significant insights, including comparative studies. 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. RNA sequencing/array and proteomic technologies, ChIP-Seq or computational methods). Such manuscripts must provide novel insights into a nucleic acid-based process and provide experimental evidence to validate hypotheses generated using genome-wide approaches. ChIP-seq studies should go beyond the analysis of a single factor associating with DNA/chromatin and basic downstream bioinformatic characterisation. Correlative studies or purely descriptive accounts of microarray or sequence data will not be considered. Extensive new sequence databases or comparative (data mining) studies that do not include experimental validation of biological relevance are more suitable for the Data Resources and Analyses category.
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 that report fundamental and general features that extend beyond individual cellular or viral 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 cellular processes;
- New insights into nucleic acid trafficking within and between 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 and RNA methyltransferases and other enzymes that act 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.
For consideration, papers should provide new insights into generally applicable principles that govern RNA metabolism or present new information about the mechanisms underlying the synthesis, maturation, or degradation of all classes of RNA in prokaryotes and eukaryotes. Findings must have implications that extend beyond a single transcript or RNA binding protein and include experimental evidence supporting biological and functional relevance such as mutational data.
The Journal specifically encourages manuscripts that:
- Describe novel aspects of the biogenesis, cellular roles or mechanisms underlying regulation of or by non-coding RNAs including microRNAs, small interfering RNAs, piwi-associated RNAs and long non-coding RNAs.
- Provide new insights into the molecular determinants of RNA half-lives, constitutive and regulated turnover mechanisms, and surveillance pathways that eliminate aberrant transcripts.
- Shed new light on the mechanisms and regulation of constitutive or alternative processing of pre-messenger RNAs including splicing, polyadenylation and editing.
- Report new insights into the structure, assembly, activity or regulation of ribosomes, snRNPs and other stable ribonucleoprotein particles.
- Provide new information about the structure and dynamics of RNA enzymes (ribozymes) or RNAs that contribute to catalysis such as spliceosomal snRNAs.
- Identify and elucidate the functional roles of novel RNA binding proteins or enzymes; studies that provide new insight into proteins that “write” or “read” RNA modifications are especially encouraged.
Papers that primarily report the application of transcriptome analyses or other genome-wide approaches to the identification and classification of RNAs may be more appropriate for the Data Resources and Analyses category.
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.
Submitted papers that describe the determination of new macromolecular structures (in this category or any other) must be accompanied by supplementary files for each structure (which will not be published but will be made available to editors and peer reviewers) corresponding to (i) final modeled coordinates, (ii) experimental data, and (iii) validation reports.
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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