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natrevgenet.nature.com
Nature Reviews Genetics
@natrevgenet.nature.com
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Publishing reviews and commentaries across the fields of genetics and genomics. Part of Springer Nature and Nature Portfolio.

https://www.nature.com/nrg/
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natrevgenet.nature.com
Want to know about using machine learning for alternative splicing predictions? Read our recent Review: From computational models of the splicing code to regulatory mechanisms and therapeutic implications go.nature.com/4oYCL8N
(free to read here: rdcu.be/dVNV4)
November 24, 2025 at 3:15 PM
natrevgenet.nature.com
Our December 2025 issue is now live: go.nature.com/3Lx0PB0
Topics include: the evolution of transcriptional regulatory mechanisms in animals; cell-type deconvolution methods for spatial transcriptomics; fine-mapping of candidate causal variants; and genomics of psychiatric disorders
November 14, 2025 at 9:02 AM
natrevgenet.nature.com
DNA and RNA modification mapping methods based on next-generation sequencing and long-read sequencing technologies
go.nature.com/47yAbPc
a, Next-generation sequencing (NGS)-based methods require pretreatment or pre-labelling of the nucleic acid with antibodies (left), restriction enzymes or endonucleases (middle), or chemicals (right) before sequencing, so that modified and unmodified bases can be distinguished during NGS sequencing. b, Long-read sequencing (LRS)-based methods can directly detect modified bases. In single-molecule, real-time (SMRT) sequencing (left), a DNA polymerase (or reverse transcriptase for RNA) is bound within the zero-mode waveguide (ZMW). When a dNTP is incorporated at the polymerase active site, it will emit a fluorescent pulse in the corresponding colour channel. The order of pulses provides the read sequence and inter-pulse duration (IPD) between base incorporation events indicates the presence of a covalent modification in the DNA or RNA template. Nanopore sequencing (right) relies on engineered biological nanopores embedded in a lipid membrane to sequence single-stranded DNA (ssDNA) or RNA. The ionic current measured as DNA or RNA gets ratcheted through the nanopore depends on the precise set of nucleotides occupying the constriction point. Modified nucleotides in the ssDNA or RNA introduce distinct current patterns, making it possible to detect the existence of modified bases relative to non-modified nucleotides.
October 31, 2025 at 3:03 PM
natrevgenet.nature.com
Our November 2025 issue is now live: go.nature.com/4hlXnVx
Topics include: the impact of structural variation on the 3D genome in disease; single-cell DNA sequencing of somatic mutations; the role of transcription compartments in gene regulation; synonymous mutations and their consequences
October 15, 2025 at 11:54 AM
natrevgenet.nature.com
The authors discuss challenges, opportunities and promising examples in advancing spatial technologies to clinical applications, including the increasing importance of artificial intelligence, and explore possible avenues for a more comprehensive, multidimensional assessment of tissues
October 9, 2025 at 8:41 AM
natrevgenet.nature.com
This Review examines spatially resolved pathological molecular alterations in a wide range of disease processes, such as developmental disorders, tumorigenesis, fibrosis and injury responses, neurodegeneration, infection and inflammation, through the lens of universal biological frameworks
October 9, 2025 at 8:41 AM
natrevgenet.nature.com
Spatial analysis empowers the discovery of developmental and disease-associated molecular signatures, cell states and multicellular niches, as well as the evaluation of disease heterogeneity within and across organs
October 9, 2025 at 8:41 AM
natrevgenet.nature.com
Recent advances in high-throughput spatial omics technologies have enabled the investigation of this complexity in stunning detail, providing groundbreaking insights into how spatial molecular organization shapes health and disease
October 9, 2025 at 8:41 AM
natrevgenet.nature.com
Tissue architecture is a product of a multilayered molecular landscape, where even subtle disruptions in the spatial context can initiate or reflect disease processes
October 9, 2025 at 8:41 AM
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Happy 25th anniversary to us! We're celebrating the journal's birthday with a bumper issue: go.nature.com/3VSbPdW
Read more in our editorial "Making sense of the regulatory genome": go.nature.com/3IbWP7F
And don't miss our new collection on "Long-read sequencing": go.nature.com/41Yy1Xs
September 16, 2025 at 3:15 PM
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Happy #InternationalDogDay! To commemorate, here is one of our favourite NRG covers of all time, based on a review by Elaine A. Ostrander, Robert K. Wayne, Adam H. Freedman & Brian W. Davis on the canine genome go.nature.com/3JP9CNw
August 26, 2025 at 1:52 PM
natrevgenet.nature.com
Our September 2025 issue is now live: go.nature.com/47FpUCu
Topics include: epigenome dynamics during early mammalian development; the genetics of human height; long-read computational analysis of DNA methylation; methodological approaches to promote equity in genomics
August 18, 2025 at 9:27 AM
natrevgenet.nature.com
Primary cilia as dynamic and diverse signalling hubs in development and disease go.nature.com/4fBBalv
#Review by Pleasantine Mill @cilialab.bsky.social, ‪@sorentc.bsky.social‬ & @lottepedersen.bsky.social
Schematic of a generic primary cilium showing the main ciliary subcompartments
August 14, 2025 at 5:09 PM
natrevgenet.nature.com
Our August 2025 issue is now live: go.nature.com/4kIXzOI
Topics include: systems biology in the single-cell era; ADAR1-mediated RNA editing; retrotransposable element reactivation and its biological impact; transcriptional condensates as temporal signal integrators; X-linked competition
July 18, 2025 at 8:05 AM
natrevgenet.nature.com
Evolution of splicing model architectures go.nature.com/4eweliE
Figure from our recent Review: From computational models of the splicing code to regulatory mechanisms and therapeutic implications (free to read here: rdcu.be/dVNV4)
a, Early models built sequence motifs to describe the consensus sequences of individual core splicing elements, such as splice sites (SSs) and intronic and/or exonic enhancers and silencers. Statistical and machine-learning models were built to output the probability of a novel sequence acting as a core splicing element. The sequence logos shown for 5′SS and 3′SS were generated from Human hg38 RefSeq annotations (code available at https://www.github.com/ulelab/splicelogos). b, As our understanding of splicing mechanisms progressed, expert-selected features were extracted from sequences and used to train integrative models to predict splicing outcomes. c, With the advent of deep-learning, models could jointly learn features directly from raw sequence input. Although theoretically, sequence context could be as large as shown in part d, in practice smaller windows of up to 30 kb have been used. d, Supervised models with convolutional and transformer layers produce multimodal genome-wide data. These models use a much larger sequence context and can predict genome-wide data including RNA sequencing coverage, which can be further processed to evaluate splicing. e, By learning how to reconstruct partially masked genomic sequences across multiple species, self-supervised masked language models capture evolutionarily conserved sequence elements and their functional context in a very generic and flexible fashion. The informative numerical representations obtained by large language models can be used for splicing prediction tasks. Here 3′SS within different sequence contexts from multiple species are shown aligned for easier interpretation, but in practice sequences do not have to be aligned. Current masked language models with application to splicing use variable context windows from 1,000 to 1 million base pairs; however, it is currently unclear whether larger context windows confer better performance
July 2, 2025 at 10:21 AM
natrevgenet.nature.com
Our July 2025 issue is now live: go.nature.com/3ZzmXyQ
Topics include: structural variation in the human genome; cytoplasmic mRNA decay; the mammalian segmentation clock; genetic models and genomic studies of cancer metastasis
June 19, 2025 at 1:06 PM
natrevgenet.nature.com
The somatic DNA methylation landscape
Figure from our #Review by Zachary D. Smith, Sara Hetzel & Alexander Meissner: DNA methylation in mammalian development and disease go.nature.com/3DlswZn
Free to read here: rdcu.be/dQEND
Magnified view of partially methylated domains or highly methylated domains over CpG islands and DNA methylation valleys (DMVs)
May 28, 2025 at 11:25 AM
natrevgenet.nature.com
Our June issue is live and includes an editorial on RNA splicing (go.nature.com/3SdWVgk) that acts as a foreword for a new joint collection by @natrevgenet.nature.com‬ and ‪@natrevmcb.nature.com‬ on this topic (go.nature.com/3H0vEvp)
RNA ribbon that is being cut and re-stitched together, representing pre-mRNA splicing of introns and exon ligation
May 21, 2025 at 2:51 PM
natrevgenet.nature.com
In this Review, the authors discuss the principles of these models, the types of training data sets that are available and the strengths and limitations of different approaches
May 14, 2025 at 7:41 AM
natrevgenet.nature.com
S2E models also show great promise in predicting the effects of non-coding variants, in uncovering detailed molecular mechanisms of gene regulation and designing synthetic regulatory elements for biotechnology
May 14, 2025 at 7:41 AM
natrevgenet.nature.com
Sequence-to-expression (S2E) models enable predictions of gene expression levels from DNA sequence alone and capture the regulatory grammar with remarkable accuracy
May 14, 2025 at 7:41 AM
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Recent advances in deep learning techniques applied to data from epigenome mapping and high-throughput reporter assays have made substantial progress towards addressing this complexity
May 14, 2025 at 7:41 AM
natrevgenet.nature.com
Transcription is regulated by DNA elements such as promoters and enhancers, the activity of which is controlled by many transcription factors. Given the highly complex combinatorial logic involved, it has been difficult to construct computational models that predict gene activity from DNA sequence
May 14, 2025 at 7:41 AM
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Resharing our January issue featured article for #EMBLChromatin:
DNA methylation in mammalian development and disease go.nature.com/3X14Ali #Review by Zachary D. Smith @yaleschoolofmed.bsky.social, Sara Hetzel & Alexander Meissner @molgen.mpg.de
Free to read here: rdcu.be/dQEND
A landscape of red and transparent lollipops (reminiscent of typical DNA methylation schematics that show a filled or empty circle to denote methylated and unmethylated cytosines, respectively)
May 13, 2025 at 1:21 PM
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A great start to #EMBLChromatin 🤩
May 13, 2025 at 12:13 PM