Nature Genetics Nature Genetics is the primary research journal for the genetics community. With a reputation for quality global coverage, Nature Genetics delivers the latest research across the field, including human genetics and genomics, genomics in plant and animal breeding, epigenetics, cancer and genetic technology. With News and Views, Analysis, Perspectives, Letters, Articles and Technical Reports, Nature Genetics is consistently the most frequently cited primary research journal in the field of Genetics and Heredity. http://feeds.nature.com/ng/rss/current Nature Publishing Group en © 2024 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Nature Genetics © 2024 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. permissions@nature.com Nature Genetics https://www.nature.com/uploads/product/ng/rss.png http://feeds.nature.com/ng/rss/current <![CDATA[Protein-altering variants at copy number-variable regions influence diverse human phenotypes]]> https://www.nature.com/articles/s41588-024-01684-z Nature Genetics, Published online: 28 March 2024; doi:10.1038/s41588-024-01684-z

Incorporating protein-altering copy number variants ascertained from UK Biobank whole-exome sequencing data into analyses of rare predicted loss-of-function variants identifies complex trait associations not detectable using standard analysis methods.]]>
Margaux L. A. HujoelRobert E. HandsakerMaxwell A. ShermanNolan KamitakiAlison R. BartonRonen E. MukamelChikashi TeraoSteven A. McCarrollPo-Ru Loh doi:10.1038/s41588-024-01684-z Nature Genetics, Published online: 2024-03-28; | doi:10.1038/s41588-024-01684-z 2024-03-28 Nature Genetics 10.1038/s41588-024-01684-z https://www.nature.com/articles/s41588-024-01684-z
<![CDATA[Cell-type-specific and disease-associated expression quantitative trait loci in the human lung]]> https://www.nature.com/articles/s41588-024-01702-0 Nature Genetics, Published online: 28 March 2024; doi:10.1038/s41588-024-01702-0

Single-cell transcriptomics and expression quantitative trait locus mapping in 114 lung tissue samples, including 66 with interstitial lung disease, highlight the cell-type-specific functions of risk variants contributing to disease pathobiology.]]>
Heini M. NatriChristina B. Del AzodiLance PeterChase J. TaylorSagrika ChughRobert KendleMei-i ChungDavid K. FlahertyBrittany K. MatlockCarla L. CalviTimothy S. BlackwellLorraine B. WareMatthew BacchettaRajat WaliaCiara M. ShaverJonathan A. KropskiDavis J. McCarthyNicholas E. Banovich doi:10.1038/s41588-024-01702-0 Nature Genetics, Published online: 2024-03-28; | doi:10.1038/s41588-024-01702-0 2024-03-28 Nature Genetics 10.1038/s41588-024-01702-0 https://www.nature.com/articles/s41588-024-01702-0
<![CDATA[A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast]]> https://www.nature.com/articles/s41588-024-01688-9 Nature Genetics, Published online: 28 March 2024; doi:10.1038/s41588-024-01688-9

Single-cell RNA sequencing analysis of over 800,000 human adult breast cells from 55 female donors identifies 41 cell subtypes and highlights age- and parity-dependent effects. Samples from healthy women with germline mutations in BRCA1 or BRCA2 showed signs of T cell exhaustion.]]>
Austin D. ReedSara PensaAdi SteifJack StenningDaniel J. KunzLinsey J. PorterKui HuaPeng HeAlecia-Jane TwiggerAbigail J. Q. SiuKatarzyna KaniaRachel Barrow-McGeeIain GouldingJennifer J. GommValerie SpeirsJ Louise JonesJohn C. MarioniWalid T. Khaled doi:10.1038/s41588-024-01688-9 Nature Genetics, Published online: 2024-03-28; | doi:10.1038/s41588-024-01688-9 2024-03-28 Nature Genetics 10.1038/s41588-024-01688-9 https://www.nature.com/articles/s41588-024-01688-9
<![CDATA[Enhancer contacts during embryonic development show diverse interaction modes and modest yet significant increases upon gene activation]]> https://www.nature.com/articles/s41588-024-01700-2 Nature Genetics, Published online: 25 March 2024; doi:10.1038/s41588-024-01700-2

The exact relationship between 3D chromatin interactions and enhancer function is unclear. By probing three-dimensional enhancer interactions in developing embryos, two studies now show nuanced dynamics in tissue-specific contexts and reveal how moderately increased enhancer–promoter interactions coincide with functionality.]]>
Daniel M. Ibrahim doi:10.1038/s41588-024-01700-2 Nature Genetics, Published online: 2024-03-25; | doi:10.1038/s41588-024-01700-2 2024-03-25 Nature Genetics 10.1038/s41588-024-01700-2 https://www.nature.com/articles/s41588-024-01700-2
<![CDATA[Exit from totipotency is controlled by DUXBL in mice]]> https://www.nature.com/articles/s41588-024-01690-1 Nature Genetics, Published online: 25 March 2024; doi:10.1038/s41588-024-01690-1

In mice, zygotic genome activation occurs at onset of the two-cell stage in embryonic development and coincides with the exit from totipotency. Our work shows that the transcription factor DUXBL participates in silencing part of the stage-specific two-cell-associated transcriptional program and is required for development to proceed.]]>
doi:10.1038/s41588-024-01690-1 Nature Genetics, Published online: 2024-03-25; | doi:10.1038/s41588-024-01690-1 2024-03-25 Nature Genetics 10.1038/s41588-024-01690-1 https://www.nature.com/articles/s41588-024-01690-1
<![CDATA[Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis]]> https://www.nature.com/articles/s41588-024-01689-8 Nature Genetics, Published online: 21 March 2024; doi:10.1038/s41588-024-01689-8

Single-cell ATAC + RNA linking (SCARlink) predicts gene expression by jointly modeling local tiled chromatin accessibility using regularized Poisson regression on multi-ome data. SCARlink predictions can be used to identify cell-type-specific enhancers and perform chromatin potential analysis.]]>
Sneha MitraRohan MalikWilfred WongAfsana RahmanAlexander J. HarteminkYuri PritykinKushal K. DeyChristina S. Leslie doi:10.1038/s41588-024-01689-8 Nature Genetics, Published online: 2024-03-21; | doi:10.1038/s41588-024-01689-8 2024-03-21 Nature Genetics 10.1038/s41588-024-01689-8 https://www.nature.com/articles/s41588-024-01689-8
<![CDATA[Cell subtype-specific effects of genetic variation in the Alzheimer’s disease brain]]> https://www.nature.com/articles/s41588-024-01685-y Nature Genetics, Published online: 21 March 2024; doi:10.1038/s41588-024-01685-y

Single-nucleus RNA sequencing from the dorsolateral prefrontal cortex of 424 aging individuals, and mapping the effect of genetic variation on gene expression, identified a large number of cis-expression quantitative trait loci at the level of cell types and cell subtypes.]]>
Masashi FujitaZongmei GaoLu ZengCristin McCabeCharles C. WhiteBernard NgGilad Sahar GreenOrit Rozenblatt-RosenDevan PhillipsLiat Amir-ZilbersteinHyo LeeRichard V. Pearse IIAtlas KhanBadri N. VardarajanKrzysztof KirylukChun Jimmie YeHans-Ulrich KleinGao WangAviv RegevNaomi HabibJulie A. SchneiderYanling WangTracy Young-PearseSara MostafaviDavid A. BennettVilas MenonPhilip L. De Jager doi:10.1038/s41588-024-01685-y Nature Genetics, Published online: 2024-03-21; | doi:10.1038/s41588-024-01685-y 2024-03-21 Nature Genetics 10.1038/s41588-024-01685-y https://www.nature.com/articles/s41588-024-01685-y
<![CDATA[Increased enhancer–promoter interactions during developmental enhancer activation in mammals]]> https://www.nature.com/articles/s41588-024-01681-2 Nature Genetics, Published online: 20 March 2024; doi:10.1038/s41588-024-01681-2

A catalog of enhancer–promoter (E–P) interactions across ten mouse embryonic tissues, supported by in vivo functional experiments, shows that E–P proximity increases upon enhancer activation during development.]]>
Zhuoxin ChenValentina SnetkovaGrace BowerSandra JacintoBenjamin ClockAtrin DizehchiIros BarozziBrandon J. MannionAna Alcaina-CaroJavier Lopez-RiosDiane E. DickelAxel ViselLen A. PennacchioEvgeny Z. Kvon doi:10.1038/s41588-024-01681-2 Nature Genetics, Published online: 2024-03-20; | doi:10.1038/s41588-024-01681-2 2024-03-20 Nature Genetics 10.1038/s41588-024-01681-2 https://www.nature.com/articles/s41588-024-01681-2