Genome Biology最新文献

We present iNOMe-seq, a novel method for in vivo simultaneous profiling of chromatin accessibility, nucleosome occupancy, DNA-binding protein sites, and DNA methylation in living tissues. iNOMe-seq utilizes an ^m5C methyltransferase to mark accessible cytosines in a GpC context, bypassing nucleosome-restricted regions. Using Arabidopsis thaliana, we demonstrate that iNOMe-seq improves chromatin accessibility quantification compared to existing methods. Furthermore, it allows for the spatial and temporal analysis of chromatin dynamics, transcription factor binding, and DNA methylation, offering insight into the role of epigenetic components in transcriptional regulation across tissues and genetic variations in natural populations.

Developing glycosylase-based base editors (gBEs) to broaden the editing scope is highly desirable for biomedical research and agricultural applications. However, the off-target effects and applicability of gBEs need further investigation. We employ GOTI to detect rare DNA off-target events in mouse embryos injected with N-methylpurine glycosylase-based AYBE and gGBE. Transcriptome-wide RNA analysis reveals that TadA8e-V106W, derived from AYBE, induces low-frequency RNA off-target editing. Both base editors efficiently induce A/G-to-Y editing in mouse and sheep embryos, and in newborn lambs. The robust efficiency and specificity of AYBE and gGBE underscore their potential for clinical applications and genetic improvement in livestock.

Background: Transposable elements (TEs) represent a threat to genome integrity due to their proliferative capacity. Eukaryotic cells silence TEs through different molecular mechanisms, including the deposition of repressive histone marks. Previous studies have shown that TE repressive marks can spread to neighboring sequences. However, evidence for this spreading leading to nearby gene silencing remains limited. Similarly, whether TEs induce changes in the enrichment of active histone marks genome-wide, and the potential impact on gene expression have not been widely studied.

Results: In this work, we perform a comprehensive study of the epigenetic effects of 2235 TEs and their potential effects on nearby gene expression on Drosophila melanogaster head, gut, and ovary. While most TEs (816) induce the enrichment of the H3K9me3 repressive mark, with stronger epigenetic effects in the ovary, a substantial number (345 TEs) induce the enrichment of the H3K27ac active mark, particularly in the gut. We find that 70% of the H3K9me3 enriched TEs associated with expression changes downregulate the nearby gene, and 50% of the H3K27ac enriched TEs associated with expression changes lead to gene upregulation. These changes in expression affect specific regulatory networks only in the head. Furthermore, TE epigenetic effects on gene expression are genomic context dependent. Finally, we find that 221 TEs also affect gene expression by disrupting regions enriched for histone marks.  CONCLUSIONS: Overall, our results show that TEs contribute to the generation of regulatory novelty through epigenetic changes, with these epigenetic effects not restricted to gene silencing and being genomic context dependent.

Background: Recent ancient DNA studies uncovering large-scale demographic events in Iberia have presented very limited data for Portugal, a country located at the westernmost edge of continental Eurasia. Here, we present the most comprehensive collection of Portuguese ancient genome-wide data, from 67 individuals spanning 5000 years of human history, from the Neolithic to the nineteenth century.

Results: We identify early admixture between local hunter-gatherers and Anatolian-related farmers in Neolithic Portugal, with a northeastern-southwestern gradient of increasing Magdalenian-associated ancestry persistence in Iberia. This profile continues into the Chalcolithic, though Bell Beaker-associated sites reveal Portugal's first evidence of Steppe-related ancestry. Such ancestry has a broader demographic impact during the Bronze Age, despite continuity of local Chalcolithic genetic ancestry and limited Mediterranean connections. The village of Idanha-a-Velha emerges in the Roman period as a site of significant migration and interaction, presenting a notably diverse genetic profile that includes North African and Eastern Mediterranean ancestries. The Early Medieval period is marked by the arrival of Central European genetic diversity, likely linked to migrations of Germanic tribes, adding to coeval local, African, and Mediterranean influences. The Islamic and Christian Conquest periods show strong genetic continuity in northern Portugal and significant additional African admixture in the south. The latter remains stable during the post-Islamic period, suggesting enduring African influences.

Conclusions: We reveal dynamic patterns of migration in line with cultural exchange across millennia, but also the persistence of local ancestries. Our findings integrate genetic information with historical and archeological data, enhancing our understanding of Iberia's biological and cultural heritage.

Species from diverse animal lineages have conserved groups of orthologous genes together on the same chromosome for over half a billion years since the last common ancestor of bilaterians. Although notable exceptions exist, the stability of chromosome-scale gene linkages has been proposed to be the norm among animals. Here we test this hypothesis across species from 52 bilaterian classes representing 15 different phyla. Contrary to expectations, we find that cases of genome structure conservation are rare, taxonomically restricted and unrepresentative of the general state of bilaterian genomes. Genome restructuring correlates with increased rates of protein sequence evolution and may be an underappreciated factor driving animal adaptation and diversification.

The false discovery rate (FDR) controlling method by Benjamini and Hochberg (BH) is a popular choice in the omics fields. Here, we demonstrate that in datasets with a large degree of dependencies between features, FDR correction methods like BH can sometimes counter-intuitively report very high numbers of false positives, potentially misleading researchers. We call the attention of researchers to use suited multiple testing strategies and approaches like synthetic null data (negative control) to identify and minimize caveats related to false discoveries, as in the cases where false findings do occur, they may be numerous.

We present direct sequencing methodologies, scTAPS for 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) and scCAPS + specifically for 5hmC, enabling quantitative detection of 5mC and 5hmC at single-base resolution and single-cell level. Achieving approximately 90% mapping efficiency, our plate-based methods accurately recover 5mC and 5hmC profiles in CD8 + T and mouse embryonic stem cells. Notably, scCAPS + reveals a global increase in 5hmC across neuronal and non-neuronal cells in the hippocampus of aging mice. Our methods offer strong potential for seamless integration into high-throughput single-cell multi-omics, facilitating future investigations of epigenomic dynamics in specific biological processes.

Background: Efforts to characterize regulatory elements in plant genomes traditionally rely on evolutionary conservation and chromatin accessibility. Recently, intergenic bi-directional nascent transcript has emerged as a putative hallmark of active enhancers. Here, we integrate these approaches to better define the cis-regulatory landscape of the rice genome.

Results: In juvenile leaf tissues of the Azucena rice variety, we analyze conserved noncoding sequences, intergenic bi-directional transcripts, and regions of open chromatin. These three features highlight distinct classes of regulatory targets, each exhibiting complexity and regulatory roles. Conserved noncoding sequences are associated with more complex regulatory interactions, while regions marked by chromatin accessibility or bi-directional nascent transcription tend to promote more stable regulatory activity. Some transcribed regulatory sites harbor elements linked to transposable element silencing, whereas others correlate with increased expression of nearby genes, pointing to candidate transcribed regulatory elements. We further identified molecular interactions between genic regions and intergenic transcribed regulatory elements using 3-dimensional chromatin contact data, we identify physical interactions between transcribed intergenic regions and genic regions. These interactions often co-localize with expression quantitative trait loci and coincide with increased transcription, further supporting a regulatory role.

Conclusions: Our integrative analysis reveals multiple distinct classes of regulatory elements in the rice genome, with overlapping but non-identical targets and signatures. Many candidate elements share features consistent with transcriptional enhancement, though the specific criteria for defining active enhancers in plants require further characterization. These findings underscore the importance of using complementary genomic signals to discover and characterize functionally diverse regulatory elements in plant genomes.

Standard protocols for meta-analysis of association studies are inadequate for microbiome data due to their complex compositional structure, leading to inaccurate and unstable microbial signature selection. To address this issue, we introduce Melody, a framework that generates, harmonizes, and combines study-specific summary association statistics to powerfully and robustly identify microbial signatures in meta-analysis. Comprehensive and realistic simulations demonstrate that Melody substantially outperforms existing approaches in prioritizing true signatures. In the meta-analyses of five studies on colorectal cancer and eight studies on the gut metabolome, we showcase the superior stability, reliability, and predictive performance of Melody-identified signatures.

Background: Genome-wide association studies (GWAS) have identified thousands of loci for disease-related human traits in cross-sectional data. However, the impact of age on genetic effects is underacknowledged. Also, identifying genetic effects on longitudinal trait change has been hampered by small sample sizes for longitudinal data. Such effects on deteriorating trait levels over time or disease progression can be clinically relevant.

Results: Under certain assumptions, we demonstrate analytically that genetic-by-age interaction observed in cross-sectional data can be indicative of genetic association on longitudinal trait change. We propose a 2-stage approach with genome-wide pre-screening for genetic-by-age interaction in cross-sectional data and testing identified variants for longitudinal change in independent longitudinal data. Within UK Biobank cross-sectional data, we analyze 8 complex traits (up to 370,000 individuals). We identify 44 genetic-by-age interactions (7 loci for obesity traits, 26 for pulse pressure, few to none for lipids). Our cross-trait view reveals trait-specificity regarding the proportion of loci with age-modulated effects, which is particularly high for pulse pressure. Testing the 44 variants in longitudinal data (up to 50,000 individuals), we observe significant effects on change for obesity traits (near APOE, TMEM18, TFAP2B) and pulse pressure (near FBN1, IGFBP3; known for implication in arterial stiffness processes).

Conclusions: We provide analytical and empirical evidence that cross-sectional genetic-by-age interaction can help pinpoint longitudinal-change effects, when cross-sectional data surpasses longitudinal sample size. Our findings shed light on the distinction between traits that are impacted by age-dependent genetic effects and those that are not.