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1.
Nature ; 630(8017): 596-608, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38898293

RESUMO

The evolution of the modern human brain was accompanied by distinct molecular and cellular specializations, which underpin our diverse cognitive abilities but also increase our susceptibility to neurological diseases. These features, some specific to humans and others shared with related species, manifest during different stages of brain development. In this multi-stage process, neural stem cells proliferate to produce a large and diverse progenitor pool, giving rise to excitatory or inhibitory neurons that integrate into circuits during further maturation. This process unfolds over varying time scales across species and has progressively become slower in the human lineage, with differences in tempo correlating with differences in brain size, cell number and diversity, and connectivity. Here we introduce the terms 'bradychrony' and 'tachycrony' to describe slowed and accelerated developmental tempos, respectively. We review how recent technical advances across disciplines, including advanced engineering of in vitro models, functional comparative genetics and high-throughput single-cell profiling, are leading to a deeper understanding of how specializations of the human brain arise during bradychronic neurodevelopment. Emerging insights point to a central role for genetics, gene-regulatory networks, cellular innovations and developmental tempo, which together contribute to the establishment of human specializations during various stages of neurodevelopment and at different points in evolution.


Assuntos
Evolução Biológica , Encéfalo , Humanos , Encéfalo/citologia , Encéfalo/fisiologia , Encéfalo/crescimento & desenvolvimento , Animais , Células-Tronco Neurais/citologia , Células-Tronco Neurais/metabolismo , Neurogênese , Fatores de Tempo , Neurônios/citologia , Neurônios/fisiologia , Análise de Célula Única , Redes Reguladoras de Genes
2.
Bioinformatics ; 40(6)2024 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-38796686

RESUMO

SUMMARY: The increasing development of sequence-based machine learning models has raised the demand for manipulating sequences for this application. However, existing approaches to edit and evaluate genome sequences using models have limitations, such as incompatibility with structural variants, challenges in identifying responsible sequence perturbations, and the need for vcf file inputs and phased data. To address these bottlenecks, we present Sequence Mutator for Predictive Models (SuPreMo), a scalable and comprehensive tool for performing and supporting in silico mutagenesis experiments. We then demonstrate how pairs of reference and perturbed sequences can be used with machine learning models to prioritize pathogenic variants or discover new functional sequences. AVAILABILITY AND IMPLEMENTATION: SuPreMo was written in Python, and can be run using only one line of code to generate both sequences and 3D genome disruption scores. The codebase, instructions for installation and use, and tutorials are on the GitHub page: https://github.com/ketringjoni/SuPreMo.


Assuntos
Aprendizado de Máquina , Software , Simulação por Computador , Biologia Computacional/métodos , Humanos , Mutagênese
3.
Brain ; 2024 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-38940350

RESUMO

In frontotemporal lobar degeneration (FTLD), pathological protein aggregation in specific brain regions is associated with declines in human-specialized social-emotional and language functions. In most patients, disease protein aggregates contain either TDP-43 (FTLD-TDP) or tau (FTLD-tau). Here, we explored whether FTLD-associated regional degeneration patterns relate to regional gene expression of human accelerated regions (HARs), conserved sequences that have undergone positive selection during recent human evolution. To this end, we used structural neuroimaging from patients with FTLD and human brain regional transcriptomic data from controls to identify genes expressed in FTLD-targeted brain regions. We then integrated primate comparative genomic data to test our hypothesis that FTLD targets brain regions linked to expression levels of recently evolved genes. In addition, we asked whether genes whose expression correlates with FTLD atrophy are enriched for genes that undergo cryptic splicing when TDP-43 function is impaired. We found that FTLD-TDP and FTLD-tau subtypes target brain regions with overlapping and distinct gene expression correlates, highlighting many genes linked to neuromodulatory functions. FTLD atrophy-correlated genes were strongly enriched for HARs. Atrophy-correlated genes in FTLD-TDP showed greater overlap with TDP-43 cryptic splicing genes and genes with more numerous TDP-43 binding sites compared with atrophy-correlated genes in FTLD-tau. Cryptic splicing genes were enriched for HAR genes, and vice versa, but this effect was due to the confounding influence of gene length. Analyses performed at the individual-patient level revealed that the expression of HAR genes and cryptically spliced genes within putative regions of disease onset differed across FTLD-TDP subtypes.

4.
Nat Commun ; 15(1): 6373, 2024 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-39075082

RESUMO

Recent studies have highlighted the impact of both transcription and transcripts on 3D genome organization, particularly its dynamics. Here, we propose a deep learning framework, called AkitaR, that leverages both genome sequences and genome-wide RNA-DNA interactions to investigate the roles of chromatin-associated RNAs (caRNAs) on genome folding in HFFc6 cells. In order to disentangle the cis- and trans-regulatory roles of caRNAs, we have compared models with nascent transcripts, trans-located caRNAs, open chromatin data, or DNA sequence alone. Both nascent transcripts and trans-located caRNAs improve the models' predictions, especially at cell-type-specific genomic regions. Analyses of feature importance scores reveal the contribution of caRNAs at TAD boundaries, chromatin loops and nuclear sub-structures such as nuclear speckles and nucleoli to the models' predictions. Furthermore, we identify non-coding RNAs (ncRNAs) known to regulate chromatin structures, such as MALAT1 and NEAT1, as well as several new RNAs, RNY5, RPPH1, POLG-DT and THBS1-IT1, that might modulate chromatin architecture through trans-interactions in HFFc6. Our modeling also suggests that transcripts from Alus and other repetitive elements may facilitate chromatin interactions through trans R-loop formation. Our findings provide insights and generate testable hypotheses about the roles of caRNAs in shaping chromatin organization.


Assuntos
Cromatina , Aprendizado Profundo , Cromatina/metabolismo , Cromatina/genética , Humanos , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , Linhagem Celular , RNA/metabolismo , RNA/genética , DNA/metabolismo , DNA/genética
5.
bioRxiv ; 2024 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-38798605

RESUMO

CellWalker2 is a graph diffusion-based method for single-cell genomics data integration. It extends the CellWalker model by incorporating hierarchical relationships between cell types, providing estimates of statistical significance, and adding data structures for analyzing multi-omics data so that gene expression and open chromatin can be jointly modeled. Our open-source software enables users to annotate cells using existing ontologies and to probabilistically match cell types between two or more contexts, including across species. CellWalker2 can also map genomic regions to cell ontologies, enabling precise annotation of elements derived from bulk data, such as enhancers, genetic variants, and sequence motifs. Through simulation studies, we show that CellWalker2 performs better than existing methods in cell type annotation and mapping. We then use data from the brain and immune system to demonstrate CellWalker2's ability to discover cell type-specific regulatory programs and both conserved and divergent cell type relationships in complex tissues.

6.
mSystems ; 9(6): e0032124, 2024 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-38742892

RESUMO

Ticks are increasingly important vectors of human and agricultural diseases. While many studies have focused on tick-borne bacteria, far less is known about tick-associated viruses and their roles in public health or tick physiology. To address this, we investigated patterns of bacterial and viral communities across two field populations of western black-legged ticks (Ixodes pacificus). Through metatranscriptomic analysis of 100 individual ticks, we quantified taxon prevalence, abundance, and co-occurrence with other members of the tick microbiome. In addition to commonly found tick-associated microbes, we assembled 11 novel RNA virus genomes from Rhabdoviridae, Chuviridae, Picornaviridae, Phenuiviridae, Reoviridae, Solemovidiae, Narnaviridae and two highly divergent RNA virus genomes lacking sequence similarity to any known viral families. We experimentally verified the presence of these in I. pacificus ticks across several life stages. We also unexpectedly identified numerous virus-like transcripts that are likely encoded by tick genomic DNA, and which are distinct from known endogenous viral element-mediated immunity pathways in invertebrates. Taken together, our work reveals that I. pacificus ticks carry a greater diversity of viruses than previously appreciated, in some cases resulting in evolutionarily acquired virus-like transcripts. Our findings highlight how pervasive and intimate tick-virus interactions are, with major implications for both the fundamental biology and vectorial capacity of I. pacificus ticks. IMPORTANCE: Ticks are increasingly important vectors of disease, particularly in the United States where expanding tick ranges and intrusion into previously wild areas has resulted in increasing human exposure to ticks. Emerging human pathogens have been identified in ticks at an increasing rate, and yet little is known about the full community of microbes circulating in various tick species, a crucial first step to understanding how they interact with each and their tick host, as well as their ability to cause disease in humans. We investigated the bacterial and viral communities of the Western blacklegged tick in California and found 11 previously uncharacterized viruses circulating in this population.


Assuntos
Ixodes , Animais , Ixodes/virologia , Ixodes/microbiologia , Transcriptoma , RNA Mensageiro/genética , Microbiota/genética , Genoma Viral/genética , Vírus de RNA/genética , Vírus de RNA/isolamento & purificação , Bactérias/genética , Bactérias/virologia , Bactérias/isolamento & purificação
7.
Science ; 384(6698): eadh0559, 2024 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-38781390

RESUMO

Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated the cis-regulatory activity of 102,767 open chromatin regions, including thousands of sequences with cell type-specific accessibility and variants associated with brain gene regulation. In primary cells, we identified 46,802 active enhancer sequences and 164 variants that alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development.


Assuntos
Córtex Cerebral , Neurogênese , Organoides , Humanos , Córtex Cerebral/embriologia , Córtex Cerebral/metabolismo , Cromatina/metabolismo , Cromatina/genética , Aprendizado Profundo , Elementos Facilitadores Genéticos , Regulação da Expressão Gênica no Desenvolvimento , Neurogênese/genética , Neurônios/metabolismo , Organoides/metabolismo , Sequências Reguladoras de Ácido Nucleico , Regiões Promotoras Genéticas , Elementos Reguladores de Transcrição
8.
Sci Rep ; 14(1): 18558, 2024 08 09.
Artigo em Inglês | MEDLINE | ID: mdl-39122767

RESUMO

Fecal microbial transplantation (FMT) offers promise for treating ulcerative colitis (UC), though the mechanisms underlying treatment failure are unknown. This study harnessed longitudinally collected colonic biopsies (n = 38) and fecal samples (n = 179) from 19 adults with mild-to-moderate UC undergoing serial FMT in which antimicrobial pre-treatment and delivery mode (capsules versus enema) were assessed for clinical response (≥ 3 points decrease from the pre-treatment Mayo score). Colonic biopsies underwent dual RNA-Seq; fecal samples underwent parallel 16S rRNA and shotgun metagenomic sequencing as well as untargeted metabolomic analyses. Pre-FMT, the colonic mucosa of non-responsive (NR) patients harbored an increased burden of bacteria, including Bacteroides, that expressed more antimicrobial resistance genes compared to responsive (R) patients. NR patients also exhibited muted mucosal expression of innate immune antimicrobial response genes. Post-FMT, NR and R fecal microbiomes and metabolomes exhibited significant divergence. NR metabolomes had elevated concentrations of immunostimulatory compounds including sphingomyelins, lysophospholipids and taurine. NR fecal microbiomes were enriched for Bacteroides fragilis and Bacteroides salyersiae strains that encoded genes capable of taurine production. These findings suggest that both effective mucosal microbial clearance and reintroduction of bacteria that reshape luminal metabolism associate with FMT success and that persistent mucosal and fecal colonization by antimicrobial-resistant Bacteroides species may contribute to FMT failure.


Assuntos
Bacteroides , Colite Ulcerativa , Transplante de Microbiota Fecal , Fezes , Mucosa Intestinal , Humanos , Colite Ulcerativa/microbiologia , Colite Ulcerativa/terapia , Colite Ulcerativa/metabolismo , Masculino , Feminino , Fezes/microbiologia , Bacteroides/genética , Adulto , Mucosa Intestinal/microbiologia , Mucosa Intestinal/metabolismo , Pessoa de Meia-Idade , Microbioma Gastrointestinal , Falha de Tratamento , RNA Ribossômico 16S/genética , Metaboloma
9.
Nat Genet ; 56(6): 1156-1167, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38811842

RESUMO

Cis-regulatory elements (CREs) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of the adjacent costimulatory genes CD28, CTLA4 and ICOS, encoding regulators of T cell-mediated immunity. Tiling CRISPR interference (CRISPRi) screens in primary human T cells, both conventional and regulatory subsets, uncovered gene-, cell subset- and stimulation-specific CREs. Integration with CRISPR knockout screens and assay for transposase-accessible chromatin with sequencing (ATAC-seq) profiling identified trans regulators influencing chromatin states at specific CRISPRi-responsive elements to control costimulatory gene expression. We then discovered a critical CCCTC-binding factor (CTCF) boundary that reinforces CRE interaction with CTLA4 while also preventing promiscuous activation of CD28. By systematically mapping CREs and associated trans regulators directly in primary human T cell subsets, this work overcomes longstanding experimental limitations to decode context-dependent gene regulatory programs in a complex, multi-gene locus critical to immune homeostasis.


Assuntos
Antígenos CD28 , Antígeno CTLA-4 , Cromatina , Regulação da Expressão Gênica , Humanos , Antígeno CTLA-4/genética , Antígenos CD28/genética , Cromatina/genética , Cromatina/metabolismo , Linfócitos T/imunologia , Linfócitos T/metabolismo , Proteína Coestimuladora de Linfócitos T Induzíveis/genética , Proteína Coestimuladora de Linfócitos T Induzíveis/metabolismo , Fator de Ligação a CCCTC/metabolismo , Fator de Ligação a CCCTC/genética , Sistemas CRISPR-Cas
10.
Science ; 384(6698): eadh0829, 2024 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-38781368

RESUMO

Neuropsychiatric genome-wide association studies (GWASs), including those for autism spectrum disorder and schizophrenia, show strong enrichment for regulatory elements in the developing brain. However, prioritizing risk genes and mechanisms is challenging without a unified regulatory atlas. Across 672 diverse developing human brains, we identified 15,752 genes harboring gene, isoform, and/or splicing quantitative trait loci, mapping 3739 to cellular contexts. Gene expression heritability drops during development, likely reflecting both increasing cellular heterogeneity and the intrinsic properties of neuronal maturation. Isoform-level regulation, particularly in the second trimester, mediated the largest proportion of GWAS heritability. Through colocalization, we prioritized mechanisms for about 60% of GWAS loci across five disorders, exceeding adult brain findings. Finally, we contextualized results within gene and isoform coexpression networks, revealing the comprehensive landscape of transcriptome regulation in development and disease.


Assuntos
Processamento Alternativo , Encéfalo , Regulação da Expressão Gênica no Desenvolvimento , Transtornos Mentais , Humanos , Atlas como Assunto , Transtorno do Espectro Autista/genética , Encéfalo/metabolismo , Encéfalo/crescimento & desenvolvimento , Encéfalo/embriologia , Redes Reguladoras de Genes , Estudo de Associação Genômica Ampla , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Locos de Características Quantitativas , Esquizofrenia/genética , Transcriptoma , Transtornos Mentais/genética
11.
bioRxiv ; 2023 Dec 23.
Artigo em Inglês | MEDLINE | ID: mdl-38187606

RESUMO

Understanding variation in chromatin contact patterns across human populations is critical for interpreting non-coding variants and their ultimate effects on gene expression and phenotypes. However, experimental determination of chromatin contacts at a population-scale is prohibitively expensive. To overcome this challenge, we develop and validate a machine learning method to quantify the diversity 3D chromatin contacts at 2 kilobase resolution from genome sequence alone. We then apply this approach to thousands of diverse modern humans and the inferred human-archaic hominin ancestral genome. While patterns of 3D contact divergence genome-wide are qualitatively similar to patterns of sequence divergence, we find that 3D divergence in local 1-megabase genomic windows does not follow sequence divergence. In particular, we identify 392 windows with significantly greater 3D divergence than expected from sequence. Moreover, 26% of genomic windows have rare 3D contact variation observed in a small number of individuals. Using in silico mutagenesis we find that most sequence changes to do not result in changes to 3D chromatin contacts. However in windows with substantial 3D divergence, just one or a few variants can lead to divergent 3D chromatin contacts without the individuals carrying those variants having high sequence divergence. In summary, inferring 3D chromatin contact maps across human populations reveals diverse contact patterns. We anticipate that these genetically diverse maps of 3D chromatin contact will provide a reference for future work on the function and evolution of 3D chromatin contact variation across human populations.

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