Опубликована: Март 31, 2025
Язык: Английский
Cell, Год журнала: 2024, Номер 187(5), С. 1223 - 1237.e16
Опубликована: Фев. 1, 2024
While CD4+ T cell depletion is key to disease progression in people living with HIV and SIV-infected macaques, the mechanisms underlying this remain incompletely understood, most death involving uninfected cells. In contrast, SIV infection of "natural" hosts such as sooty mangabeys does not cause AIDS despite high-level viremia. Here, we report that CARD8 inflammasome activated immediately after entry by viral protease encapsulated incoming virions. Sensing activity leads rapid pyroptosis quiescent cells without productive infection, while activation abolishes function increases permissiveness infection. humanized mice reconstituted CARD8-deficient cells, delayed high Finally, discovered loss-of-function mutations from "natural hosts," which may explain peculiarly non-pathogenic nature these infections. Our study suggests drives during pathogenic HIV/SIV
Язык: Английский
Процитировано
26
Cell, Год журнала: 2024, Номер 187(17), С. 4488 - 4519
Опубликована: Авг. 1, 2024
Язык: Английский
Процитировано
24
Nature, Год журнала: 2025, Номер unknown
Опубликована: Апрель 9, 2025
Abstract The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies 1–3 . Consequently, our understanding the evolution species is incomplete. Here we present haplotype-resolved reference analyses six species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) completely 215 gapless chromosomes telomere-to-telomere. resolve challenging regions, such as major histocompatibility complex immunoglobulin loci, to provide in-depth evolutionary insights. Comparative enabled investigations diversity previously uncharacterized or incompletely studied without bias mapping human genome. Such include newly minted gene families lineage-specific segmental duplications, centromeric DNA, acrocentric subterminal heterochromatin. This resource serves a comprehensive baseline for future humans closest living relatives.
Язык: Английский
Процитировано
2
Science, Год журнала: 2023, Номер 380(6648)
Опубликована: Июнь 1, 2023
Incomplete lineage sorting (ILS) causes the phylogeny of some parts genome to differ from species tree. In this work, we investigate frequencies and determinants ILS in 29 major ancestral nodes across entire primate phylogeny. We find up 64% affected by at individual nodes. exploit reconstruct speciation times population sizes. Estimated are much more recent than genomic divergence good agreement with fossil record. show extensive variation along genome, mainly driven recombination but also distance genes, highlighting a impact selection on genome. many nodes, is reduced X chromosome compared autosomes expected under neutrality, which suggests higher impacts natural chromosome. Finally, an excess genes immune functions deficit housekeeping genes. The primates discovered study provides insights into times, sizes, patterns that shape evolution.
Язык: Английский
Процитировано
40
Nature, Год журнала: 2023, Номер 625(7996), С. 735 - 742
Опубликована: Ноя. 29, 2023
Abstract Noncoding DNA is central to our understanding of human gene regulation and complex diseases 1,2 , measuring the evolutionary sequence constraint can establish functional relevance putative regulatory elements in genome 3–9 . Identifying genomic that have become constrained specifically primates has been hampered by faster evolution noncoding compared protein-coding 10 relatively short timescales separating primate species 11 previously limited availability whole-genome sequences 12 Here we construct a alignment 239 species, representing nearly half all extant order. Using this resource, identified are under selective across other mammals at 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites 267,410 transcription factor binding but not placental validate their cis -regulatory effects on expression. These enriched for genetic variants affect expression traits diseases. Our results highlight important role recent differentiating primates, including humans, from mammals.
Язык: Английский
Процитировано
38
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown
Опубликована: Июль 31, 2024
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran siamang. achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. resolve challenging regions, such as the major histocompatibility complex immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate evolution diversity regions previously uncharacterized or incompletely studied without bias from mapping human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, subterminal heterochromatin. resource should serve a definitive baseline for all future studies humans our closest living relatives.
Язык: Английский
Процитировано
14
Science, Год журнала: 2024, Номер 385(6712), С. 996 - 1003
Опубликована: Авг. 29, 2024
Humans, dolphins, and elephants are the only known species that vocally label their conspecifics. It remains unclear whether nonhuman primates share this ability. We recorded spontaneous "phee-call" dialogues between pairs of marmoset monkeys. discovered marmosets use these calls to Moreover, they respond more consistently correctly specifically directed at them. Analysis from multiple monkeys revealed family members similar acoustic features others perform vocal learning. These findings shed light on complexities social vocalizations among suggest may provide a model for understanding aspects human language, thereby offering new insights into evolution communication.
Язык: Английский
Процитировано
14
G3 Genes Genomes Genetics, Год журнала: 2024, Номер 14(10)
Опубликована: Авг. 7, 2024
The aye-aye (Daubentonia madagascariensis) is the only extant member of Daubentoniidae primate family. Although several reference genomes exist for this endangered strepsirrhine primate, predominant usage short-read sequencing has resulted in limited assembly contiguity and completeness, no protein-coding gene annotations have yet been released. Here, we present a novel, fully annotated, chromosome-level hybrid de novo species based on combination Oxford Nanopore Technologies long reads Illumina short scaffolded using genome-wide chromatin interaction data-a community resource that will improve future conservation efforts as well comparative analyses.
Язык: Английский
Процитировано
9
Опубликована: Ноя. 11, 2024
The aye-aye (
Язык: Английский
Процитировано
8
Genome Biology and Evolution, Год журнала: 2025, Номер 17(2)
Опубликована: Янв. 21, 2025
Ancient tooth enamel, and to some extent dentin bone, contain characteristic peptides that persist for long periods of time. In particular, from the enamel proteome (enamelome) have been used reconstruct phylogenetic relationships fossil taxa. However, enamelome is based on only about 10 genes, whose protein products undergo fragmentation in vivo post mortem. This raises question as whether alone provides enough information reliable inference. We address these considerations a selection enamel-associated proteins has computationally predicted genomic data 232 primate species. created multiple sequence alignments each estimated evolutionary rate site. examined which sites overlap with parts sequences are typically isolated fossils. Based this, we simulated ancient different degrees fragmentation, followed by analysis. compared trees reference species tree. Up degree similar samples 1 2 million years ago, placements most nodes at family level consistent tested analysis combinations found composition can influence deep splits phylogeny. With our methods, provide guidance researchers how evaluate potential paleoproteomics studies before sampling valuable specimens.
Язык: Английский
Процитировано
1