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Genetic engineering articles within Nature Genetics
Review Article | 12 November 2024
Engineering structural variants to interrogate genome function
Structural variations (SVs) impact gene expression, genome stability and disease susceptibility. This Review discusses recent advances in genome-engineering tools that enable precise SV generation and highlights the challenges that remain.
- Jonas Koeppel
- , Juliane Weller
- & Leopold Parts
Article | 11 November 2024
Brca1 haploinsufficiency promotes early tumor onset and epigenetic alterations in a mouse model of hereditary breast cancer
A second hit to Brca1 in heterozygous mice leads to accelerated tumor development compared to wild-type mice in which both alleles are simultaneously deleted. This is because of an epigenetic state associated with Brca1 haploinsufficiency that impacts AP-1 and Wnt10a .
- Carman Man-Chung Li
- , Alyssa Cordes
- & Joan S. Brugge
Research Highlight | 13 June 2024
RNA editing with CRISPR
- Petra Gross
Research Briefing | 20 May 2024
Chromatin modifications integrate cis genomic context to instruct transcriptional outputs
By developing a modular system for precision epigenome editing, we were able to delineate the causal and quantitative role of chromatin modifications in transcription regulation. The precise effect of chromatin modifications is influenced by multiple contextual factors, including the underlying DNA sequence, transcription factor occupancy and genomic positioning.
Article | 24 April 2024
Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification
BEAN is a Bayesian approach for analyzing base editing screens with improved effect size quantification and variant classification. Applied to low-density lipoprotein (LDL)-associated common variants and saturation base editing of LDLR , BEAN identifies new LDL uptake genes and offers insights into variant structure–pathogenicity mechanisms.
- Jayoung Ryu
- , Sam Barkal
- & Luca Pinello
Article | 03 July 2023
Potent and uniform fetal hemoglobin induction via base editing
A comparison of fetal hemoglobin gene editing strategies using human sickle cell disease donor cells and in vivo transplantation finds that adenine base editing of the –175A>G site in the γ-globin gene promoters results in durable and potent expression.
- Thiyagaraj Mayuranathan
- , Gregory A. Newby
- & Jonathan S. Yen
Article 06 April 2023 | Open Access
Precise modulation of transcription factor levels identifies features underlying dosage sensitivity
SOX9 titration in neural crest cells identifies regulatory elements and genes with sensitive or buffered responses. Sensitive genes are enriched for craniofacial disorder genes phenocopying SOX9, suggesting differential sensitivity contributes to phenotypic specificity.
- Sahin Naqvi
- , Seungsoo Kim
- & Joanna Wysocka
Article | 23 March 2023
Thymidine nucleotide metabolism controls human telomere length
Genome-wide CRISPR screening identifies thymidine nucleotide metabolism as a key regulator of human telomere length. Thymidine supplementation promotes telomere elongation in cells derived from patients with telomere biology disorders.
- William Mannherz
- & Suneet Agarwal
Research Highlight | 13 March 2023
Engineering epigenetic inheritance
- Tiago Faial
Genome-scale characterization of transcription factors
- Michael Fletcher
Comment | 11 July 2022
30 years of progress from positional cloning to precision genome editing
Thirty years ago, I had the privilege of launching Nature Genetics , the first spin-off journal bearing the famous Nature logo. Spurred on by the Human Genome Project, there were high hopes for the new journal and indeed the future of human genetics. But there was little expectation that we would launch a science publishing franchise of more than 30 sister journals — or be able to therapeutically rewrite the faulty genomes of patients. Here, I reflect on the humble beginnings of Nature Genetics and 30 years of progress in genetics.
- Kevin Davies
Research Highlight | 07 September 2021
RNA demethylation for increased crop yields
Research Highlight | 06 August 2021
Sickle-cell anemia gene therapy
Hybrid potato genetics.
Article | 02 August 2021
Activation of γ-globin gene expression by GATA1 and NF-Y in hereditary persistence of fetal hemoglobin
Introduction of hereditary persistence of fetal hemoglobin variants into the γ-globin promoter by using CRISPR mutagenesis and editing provides insights into transcription factor interplay, with implications for gene therapies targeting this element.
- Phillip A. Doerfler
- , Ruopeng Feng
- & Mitchell J. Weiss
Perspective | 06 May 2021
Engineering three-dimensional genome folding
Recent technologies allow experimental manipulation of chromatin conformation. This Perspective discusses the insights obtained from gain-of-function studies that engineer the three-dimensional genome.
- , Jessica Lam
- & Gerd A. Blobel
Comment | 08 April 2021
A resource of targeted mutant mouse lines for 5,061 genes
The International Mouse Phenotyping Consortium reports the generation of new mouse mutant strains for more than 5,000 genes, including 2,850 novel null, 2,987 novel conditional-ready and 4,433 novel reporter alleles.
- Marie-Christine Birling
- , Atsushi Yoshiki
- & Stephen A. Murray
News & Views | 30 September 2020
Setting new boundaries with transcription and CTCF
How do boundary elements divide chromosomes into domains? A new study uses random genomic insertions to show how small genomic fragments can shape chromatin folding through the interplay of loop extrusion and compartmentalization. Spoiler: context matters.
- Erika C. Anderson
- & Elphège P. Nora
Article | 31 August 2020
Alteration of genome folding via contact domain boundary insertion
Insertion of a tissue-invariant chromatin domain boundary into 16 ectopic loci leads to various structural phenotypes, which depend on local chromatin features, CTCF binding and transcriptional status.
- , Peng Huang
Article | 01 June 2020
Selective Mediator dependence of cell-type-specifying transcription
Analysis with alleles encoding pharmacologically degradable Mediator subunits shows that Mediator acts as a global coactivator that facilitates transcription globally but is acutely required for cell-type-specific gene regulatory circuits.
- Martin G. Jaeger
- , Björn Schwalb
- & Georg E. Winter
Editorial | 28 February 2019
Brave new dialogue
The development of CRISPR–Cas technology and its applications in biomedical research have generated much excitement. If fully realized, this technology has the potential to help treat or prevent severe diseases. However, these tools also carry considerable risk if improperly used. The scientific community must promote constructive dialogue among its members and within society at large to ensure that research on genome editing is conducted responsibly.
Article | 27 July 2018
CRISPR–Cas9 genome editing in human cells occurs via the Fanconi anemia pathway
A coupled knockdown-editing screen shows that CRISPR–Cas9 editing in human cells requires the Fanconi anemia pathway, which acts by diverting double-strand break repair away from non-homologous end joining toward single-strand template repair.
- Chris D. Richardson
- , Katelynn R. Kazane
- & Jacob E. Corn
Editorial | 27 January 2016
Where genome editing is needed
The journal endorses the principle of transparency in the production of genome-edited crops and livestock as a precondition for the registration of a breed or cultivar, with no further need for regulation or distinction of these goods from the products of traditional breeding.
Research Highlights | 29 January 2014
A CRISPR method for genome-wide screening
- Brooke LaFlamme
Synthetic modeling of developmental enhancers
- Emily Niemitz
Research Highlights | 27 December 2013
ELABELA, a peptide hormone for heart development
Technical Report | 20 March 2011
Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor
Francois Spitz and colleagues report GROMIT, a Sleeping Beauty transposon–based system for mapping genetic regulatory architecture in mouse. GROMIT is a regulatory sensor that responds to the activity of nearby enhancers.
- , Orsolya Symmons
- & François Spitz
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