Biology subjects

Adami, A.

Publications and source records attributed to Adami, A..

8 recordsLinked to original sources

bioRxiv2025

Loss of H3K9me3 maintenance in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons

Heterochromatin is characterised by an inaccessibility to the transcriptional machinery and is associated with the histone mark H3K9me3. However, studying the functional consequences of heterochromatin loss in human cells has been challenging. Here, we used CRISPRi-mediated silencing of the histone methyltransferase SETDB1 to remove H3K9me3 heterochromatin in human neural progenitor cells. Despite a major loss of H3K9me3 peaks resulting in genome-wide reorganization of heterochromatin domains, silencing of SETDB1 had a limited effect on cell viability. Cells remained proliferative and expressed appropriate marker genes. We found that a key event following the loss of SETDB1-mediated H3K9me3 was the expression of evolutionarily young L1 retrotransposons. Derepression of L1s was associated with a loss of CpG DNA methylation at their promoters, suggesting that deposition of H3K9me3 at the L1 promoter is required to maintain DNA methylation. In conclusion, these results demonstrate that loss of H3K9me3 in human neural somatic cells transcriptionally activates evolutionary young L1 retrotransposons.

molecular biology↗

bioRxiv2025

Human brain cell-type-specific aging clocks based on single-nuclei transcriptomics

Aging is the primary risk factor for most neurodegenerative diseases, yet the cell-type-specific progression of brain aging remains poorly understood. Here, we developed human cell-type-specific transcriptomic aging clocks using high-quality single-nucleus RNA sequencing data from post mortem human prefrontal cortex tissue of 31 donors aged 18 - 94 years, encompassing 73,941 high-quality nuclei. We observed distinct transcriptomic changes across major cell types, including upregulation of inflammatory response genes in microglia from older samples. Aging clocks trained on each major cell type accurately predicted chronological age and remained robust in independent single-nucleus RNA-sequencing datasets, underscoring their broad applicability. These findings demonstrate the feasibility of cell-type-specific transcriptomic clocks to measure biological aging in the human brain and highlight potential mechanisms of selective vulnerability in neurodegenerative diseases. We anticipate these clocks will serve as a basis for further studies in other brain regions and more diverse populations, ultimately advancing our understanding of age-related neurodegenerative processes at the single-cell level.

neuroscience↗

bioRxiv2025

LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development

Long interspersed nuclear element 1 (L1) retrotransposons represent a vast source of divergent genetic information. However, mechanistic analysis of whether and how L1s contribute to human developmental programs is lacking, in part due to the challenges associated with specific profiling and manipulation of human L1 expression. Here we show that thousands of hominoid-specific L1 integrants are expressed in human induced pluripotent stem cells and cerebral organoids. The activity of individual L1 promoters is surprisingly divergent and correlates with an active epigenetic state. Efficient on-target CRISPRi silencing of L1s revealed nearly a hundred co-opted L1-derived chimeric transcripts and L1 silencing resulted in changes in neural differentiation programs and reduced cerebral organoid size. Together, these data implicate L1s and L1-derived transcripts in hominoid-specific CNS developmental processes.

developmental biology↗

bioRxiv2023

Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease

SVA retrotransposons remain active in humans and contribute to individual genetic variation. Polymorphic SVA alleles harbor gene-regulatory potential and can cause genetic disease. However, how SVA insertions are controlled and functionally impact human disease is unknown. Here, we dissect the epigenetic regulation and influence of SVAs in cellular models of X-linked dystonia-parkinsonism (XDP), a neurodegenerative disorder caused by an SVA insertion at the TAF1 locus. We demonstrate that the KRAB zinc finger protein ZNF91 establishes H3K9me3 and DNA methylation over SVAs, including polymorphic alleles, in human neural progenitor cells. The resulting mini-heterochromatin domains attenuate the cis-regulatory impact of SVAs. This is critical for XDP pathology; removal of local heterochromatin severely aggravates the XDP molecular phenotype, resulting in increased TAF1 intron retention and reduced expression. Our results provide unique mechanistic insights into how human polymorphic transposon insertions are recognized, and their regulatory impact constrained by an innate epigenetic defense system.

neuroscience↗

bioRxiv2023

DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor

The human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. However, how HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains poorly understood. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1. Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding. Simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric -satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the independent epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development.

molecular biology↗

bioRxiv2023

L1 retrotransposons drive human neuronal transcriptome complexity and functional diversification

The genetic mechanisms underlying the expansion in size and complexity of the human brain remains poorly understood. L1 retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution is largely unknown. Using multi-omic profiling we here demonstrate that L1-promoters are dynamically active in the developing and adult human brain. L1s generate hundreds of developmentally regulated and cell-type specific transcripts, many which are co-opted as chimeric transcripts or regulatory RNAs. One L1-derived lncRNA, LINC01876, is a human-specific transcript expressed exclusively during brain development. CRISPRi-silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. In summary, our results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain.

neuroscience↗

bioRxiv2022

Pseudogenes limit the identification of novel common transcripts generated by their parent genes

The human genome contains numerous duplicated regions, such as parent-pseudogene pairs, causing sequencing reads to align equally well to either gene. The extent to which this ambiguity complicates transcriptomic analyses is currently unknown. This is concerning as many parent genes have been linked to disease, including GBA1, causally linked to both Parkinsons and Gaucher disease. We find that most of the short sequencing reads that map to GBA1, also map to its pseudogene, GBAP1. Using long-read RNA-sequencing in human brain, where all reads mapped uniquely, we demonstrate significant differences in expression compared to short-read data. We identify novel transcripts from both GBA1 and GBAP1, including protein-coding transcripts that are translated in vitro and detected in proteomic data, but that lack GCase activity. By combining long-read with single-nuclear RNA-sequencing to analyse brain-relevant cell types we demonstrate that transcript expression varies by brain region with cell-type-selectivity. Taken together, these results suggest a non-lysosomal function for both GBA1 and GBAP1 in brain. Finally, we demonstrate that inaccuracies in annotation are widespread among parent genes, with implications for many human diseases.

genetics↗

bioRxiv2019

Relationship between maximal incremental and high-intensity interval exercise performance in elite athletes

It remains unclear whether the number of total bouts to limitation (Blim) in high-intensity interval testing (HIIT) differs among individuals, no matter if performed at the same relative intensity. This study aimed to explore the physiologic factors determining tolerance to effort during a HIIT. Forty-seven female participants (15-28 years old) were included: 23 athletes from Taiwan national or national reserve teams, and 24 moderately-active female. Each participant underwent maximal incremental (INC; modified-Bruce protocol) cardiopulmonary exercise testing and HIIT on treadmill, on separate days. HIIT protocol alternated a 1-min effort at 120% of the maximal speed and the same slope reached at the end of INC, with a 1-min rest, until volitional exhaustion. Gas-exchanges, and muscle oxygenation at right vastus lateralis by near-infrared spectroscopy, were continuously recorded. Additionally, bioelectrical impedance was utilized for body composition analysis. The result showed that Blim differed greatly (range: 2.6 to 12) among participants. Stepwise regression revealed that Blim was determined primarily by oxygen consumption (VO2) and heart rate (HR) at second-minute recovery; and, muscle tissue saturation index at peak of INC (R=0.644). Also, age and percent body fat were linearly correlated with Blim (adjusted R=-0.475, -0.371, p<0.05). Therefore, HIIT performance is determined by fast recovery of VO2 and HR, rather than maximal VO2 or muscle oxygenation recovery. Moreover, capacity to sustain a HIIT declines with age since as early as late adolescent. Further investigations on which factors should be manipulated to further improve athletes performance are warrant.

physiology↗