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1.
Mol Cell ; 81(16): 3294-3309.e12, 2021 08 19.
Artigo em Inglês | MEDLINE | ID: mdl-34293321

RESUMO

Temperature is a variable component of the environment, and all organisms must deal with or adapt to temperature change. Acute temperature change activates cellular stress responses, resulting in refolding or removal of damaged proteins. However, how organisms adapt to long-term temperature change remains largely unexplored. Here we report that budding yeast responds to long-term high temperature challenge by switching from chaperone induction to reduction of temperature-sensitive proteins and re-localizing a portion of its proteome. Surprisingly, we also find that many proteins adopt an alternative conformation. Using Fet3p as an example, we find that the temperature-dependent conformational difference is accompanied by distinct thermostability, subcellular localization, and, importantly, cellular functions. We postulate that, in addition to the known mechanisms of adaptation, conformational plasticity allows some polypeptides to acquire new biophysical properties and functions when environmental change endures.


Assuntos
Adaptação Fisiológica/genética , Proteoma/genética , Estresse Fisiológico/genética , Transcriptoma/genética , Aclimatação/genética , Animais , Exposição Ambiental/efeitos adversos , Regulação Fúngica da Expressão Gênica/genética , Temperatura Alta/efeitos adversos , Saccharomycetales/genética
3.
Nature ; 583(7818): 744-751, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32728240

RESUMO

The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP-seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC-seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.


Assuntos
Cromatina/genética , Cromatina/metabolismo , Conjuntos de Dados como Assunto , Desenvolvimento Fetal/genética , Histonas/metabolismo , Anotação de Sequência Molecular , Sequências Reguladoras de Ácido Nucleico/genética , Animais , Cromatina/química , Sequenciamento de Cromatina por Imunoprecipitação , Doença/genética , Elementos Facilitadores Genéticos/genética , Feminino , Regulação da Expressão Gênica no Desenvolvimento/genética , Variação Genética , Histonas/química , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Especificidade de Órgãos/genética , Reprodutibilidade dos Testes , Transposases/metabolismo
4.
Brief Bioinform ; 24(5)2023 09 20.
Artigo em Inglês | MEDLINE | ID: mdl-37649383

RESUMO

Single-cell high-throughput chromatin conformation capture technologies (scHi-C) has been used to map chromatin spatial organization in complex tissues. However, computational tools to detect differential chromatin contacts (DCCs) from scHi-C datasets in development and through disease pathogenesis are still lacking. Here, we present SnapHiC-D, a computational pipeline to identify DCCs between two scHi-C datasets. Compared to methods designed for bulk Hi-C data, SnapHiC-D detects DCCs with high sensitivity and accuracy. We used SnapHiC-D to identify cell-type-specific chromatin contacts at 10 Kb resolution in mouse hippocampal and human prefrontal cortical tissues, demonstrating that DCCs detected in the hippocampal and cortical cell types are generally associated with cell-type-specific gene expression patterns and epigenomic features. SnapHiC-D is freely available at https://github.com/HuMingLab/SnapHiC-D.


Assuntos
Cromatina , Epigenômica , Humanos , Animais , Camundongos , Cromatina/genética , Hipocampo
5.
Nat Methods ; 18(3): 283-292, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33589836

RESUMO

Genome-wide profiling of histone modifications can reveal not only the location and activity state of regulatory elements, but also the regulatory mechanisms involved in cell-type-specific gene expression during development and disease pathology. Conventional assays to profile histone modifications in bulk tissues lack single-cell resolution. Here we describe an ultra-high-throughput method, Paired-Tag, for joint profiling of histone modifications and transcriptome in single cells to produce cell-type-resolved maps of chromatin state and transcriptome in complex tissues. We used this method to profile five histone modifications jointly with transcriptome in the adult mouse frontal cortex and hippocampus. Integrative analysis of the resulting maps identified distinct groups of genes subject to divergent epigenetic regulatory mechanisms. Our single-cell multiomics approach enables comprehensive analysis of chromatin state and gene regulation in complex tissues and characterization of gene regulatory programs in the constituent cell types.


Assuntos
Lobo Frontal/metabolismo , Regulação da Expressão Gênica/genética , Hipocampo/metabolismo , Código das Histonas/genética , Sequências Reguladoras de Ácido Nucleico/genética , Animais , Linhagem Celular Tumoral , Cromatina/metabolismo , Epigênese Genética/genética , Lobo Frontal/citologia , Perfilação da Expressão Gênica , Células HeLa , Hipocampo/citologia , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Processamento de Proteína Pós-Traducional , Análise de Célula Única , Transcriptoma/genética
6.
Nat Methods ; 18(9): 1056-1059, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34446921

RESUMO

Single-cell Hi-C (scHi-C) analysis has been increasingly used to map chromatin architecture in diverse tissue contexts, but computational tools to define chromatin loops at high resolution from scHi-C data are still lacking. Here, we describe Single-Nucleus Analysis Pipeline for Hi-C (SnapHiC), a method that can identify chromatin loops at high resolution and accuracy from scHi-C data. Using scHi-C data from 742 mouse embryonic stem cells, we benchmark SnapHiC against a number of computational tools developed for mapping chromatin loops and interactions from bulk Hi-C. We further demonstrate its use by analyzing single-nucleus methyl-3C-seq data from 2,869 human prefrontal cortical cells, which uncovers cell type-specific chromatin loops and predicts putative target genes for noncoding sequence variants associated with neuropsychiatric disorders. Our results indicate that SnapHiC could facilitate the analysis of cell type-specific chromatin architecture and gene regulatory programs in complex tissues.


Assuntos
Cromatina/química , Biologia Computacional/métodos , Análise de Célula Única/métodos , Algoritmos , Animais , Cromatina/genética , Sequenciamento de Cromatina por Imunoprecipitação , Visualização de Dados , Bases de Dados Factuais , Expressão Gênica , Humanos , Transtornos Mentais/genética , Camundongos , Células-Tronco Embrionárias Murinas/citologia , Células-Tronco Embrionárias Murinas/fisiologia , Polimorfismo de Nucleotídeo Único , Córtex Pré-Frontal/citologia , Reprodutibilidade dos Testes , Análise de Sequência de DNA/métodos
7.
Nat Methods ; 16(10): 991-993, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31384045

RESUMO

We report a molecular assay, Methyl-HiC, that can simultaneously capture the chromosome conformation and DNA methylome in a cell. Methyl-HiC reveals coordinated DNA methylation status between distal genomic segments that are in spatial proximity in the nucleus, and delineates heterogeneity of both the chromatin architecture and DNA methylome in a mixed population. It enables simultaneous characterization of cell-type-specific chromatin organization and epigenome in complex tissues.


Assuntos
Cromatina/metabolismo , Metilação de DNA , Análise de Célula Única/métodos , Animais , Ilhas de CpG , Conjuntos de Dados como Assunto , Humanos , Camundongos , Células-Tronco Embrionárias Murinas/citologia , Células-Tronco Embrionárias Murinas/metabolismo
9.
J Neurosci ; 39(43): 8457-8470, 2019 10 23.
Artigo em Inglês | MEDLINE | ID: mdl-31492772

RESUMO

The degeneration of injured axons involves a self-destruction pathway whose components and mechanism are not fully understood. Here, we report a new regulator of axonal resilience. The transmembrane protein Raw is cell autonomously required for the degeneration of injured axons, dendrites, and synapses in Drosophila melanogaster In both male and female raw hypomorphic mutant or knock-down larvae, the degeneration of injured axons, dendrites, and synapses from motoneurons and sensory neurons is strongly inhibited. This protection is insensitive to reduction in the levels of the NAD+ synthesis enzyme Nmnat (nicotinamide mononucleotide adenylyl transferase), but requires the c-Jun N-terminal kinase (JNK) mitogen-activated protein (MAP) kinase and the transcription factors Fos and Jun (AP-1). Although these factors were previously known to function in axonal injury signaling and regeneration, Raw's function can be genetically separated from other axonal injury responses: Raw does not modulate JNK-dependent axonal injury signaling and regenerative responses, but instead restrains a protective pathway that inhibits the degeneration of axons, dendrites, and synapses. Although protection in raw mutants requires JNK, Fos, and Jun, JNK also promotes axonal degeneration. These findings suggest the existence of multiple independent pathways that share modulation by JNK, Fos, and Jun that influence how axons respond to stress and injury.SIGNIFICANCE STATEMENT Axonal degeneration is a major feature of neuropathies and nerve injuries and occurs via a cell autonomous self-destruction pathway whose mechanism is poorly understood. This study reports the identification of a new regulator of axonal degeneration: the transmembrane protein Raw. Raw regulates a cell autonomous nuclear signaling pathway whose yet unknown downstream effectors protect injured axons, dendrites, and synapses from degenerating. These findings imply that the susceptibility of axons to degeneration is strongly regulated in neurons. Future understanding of the cellular pathway regulated by Raw, which engages the c-Jun N-terminal kinase (JNK) mitogen-activated protein (MAP) kinase and Fos and Jun transcription factors, may suggest new strategies to increase the resiliency of axons in debilitating neuropathies.


Assuntos
Axônios/metabolismo , Proteínas do Citoesqueleto/metabolismo , Dendritos/metabolismo , Proteínas de Drosophila/metabolismo , Sistema de Sinalização das MAP Quinases/fisiologia , Degeneração Neural/metabolismo , Animais , Animais Geneticamente Modificados , Axônios/patologia , Proteínas do Citoesqueleto/genética , Dendritos/patologia , Proteínas de Drosophila/genética , Drosophila melanogaster , Feminino , Proteínas Quinases JNK Ativadas por Mitógeno/metabolismo , Masculino , Neurônios Motores/metabolismo , Neurônios Motores/patologia , Degeneração Neural/patologia , Sinapses/metabolismo
10.
PLoS Comput Biol ; 15(4): e1006982, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30986246

RESUMO

Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in the analysis of chromatin interactions from multiple PLAC-seq and HiChIP datasets centered on different transcriptional factors and histone marks. MAPS is freely available at https://github.com/ijuric/MAPS.


Assuntos
Montagem e Desmontagem da Cromatina/fisiologia , Mapeamento Cromossômico/métodos , Biologia Computacional/métodos , Cromatina/metabolismo , Cromatina/fisiologia , Imunoprecipitação da Cromatina/métodos , Simulação por Computador , Genoma , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Código das Histonas , Humanos , Análise de Sequência de DNA/métodos , Software
11.
J Paediatr Child Health ; 56(2): 231-236, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31408250

RESUMO

AIM: To examine the association of life-style factors, including second-hand smoke, with dental caries among 3-year-old children in Wuxi, China. METHODS: A multi-stage stratified random cluster sampling method was used, and 283 children were recruited. The prevalence of dental caries was 29.3% (83/283). RESULTS: Univariate analysis indicated that the possible related factors of dental caries included sleep duration, interest in snacks, candy, exposure to second-hand smoke and weight of birth (all P < 0.05). Meanwhile, multivariate logistic regression analysis suggested that children who had used fluoride were less susceptible to dental caries than those who had not used fluoride before (P < 0.05). Moreover, the risk of dental caries in children who were very interested in snacks was greater than those with little interest in snacks (P < 0.05). CONCLUSIONS: Life-style behaviours are crucial factors and should attract enough attention. There might be a potential negative effect of second-hand smoke on the deciduous caries, but it still requires further studies. A co-ordinated effort by health-care providers, policymakers and health institutions has successfully improved children's oral health and the awareness of hygiene knowledge among citizens in Wuxi city.


Assuntos
Cárie Dentária , Poluição por Fumaça de Tabaco , Pré-Escolar , China/epidemiologia , Estudos Transversais , Índice CPO , Cárie Dentária/epidemiologia , Cárie Dentária/etiologia , Humanos , Estilo de Vida , Prevalência , Fatores de Risco , Poluição por Fumaça de Tabaco/efeitos adversos
12.
J Biol Chem ; 291(37): 19274-86, 2016 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-27435678

RESUMO

A subset of thyroid carcinomas contains a t(2;3)(q13;p25) chromosomal translocation that fuses paired box gene 8 (PAX8) with the peroxisome proliferator-activated receptor γ gene (PPARG), resulting in expression of a PAX8-PPARγ fusion protein, PPFP. We previously generated a transgenic mouse model of PPFP thyroid carcinoma and showed that feeding the PPARγ agonist pioglitazone greatly decreased the size of the primary tumor and prevented metastatic disease in vivo The antitumor effect correlates with the fact that pioglitazone turns PPFP into a strongly PPARγ-like molecule, resulting in trans-differentiation of the thyroid cancer cells into adipocyte-like cells that lose malignant character as they become more differentiated. To further study this process, we performed cell culture experiments with thyrocytes from the PPFP mouse thyroid cancers. Our data show that pioglitazone induced cellular lipid accumulation and the expression of adipocyte marker genes in the cultured cells, and shRNA knockdown of PPFP eliminated this pioglitazone effect. In addition, we found that PPFP and thyroid transcription factor 1 (TTF-1) physically interact, and that these transcription factors bind near each other on numerous target genes. TTF-1 knockdown and overexpression studies showed that TTF-1 inhibits PPFP target gene expression and impairs adipogenic trans-differentiation. Surprisingly, pioglitazone repressed TTF-1 expression in PPFP-expressing thyrocytes. Our data indicate that TTF-1 interacts with PPFP to inhibit the pro-adipogenic response to pioglitazone, and that the ability of pioglitazone to decrease TTF-1 expression contributes to its pro-adipogenic action.


Assuntos
Adipogenia , Diferenciação Celular , Proteínas de Fusão Oncogênica/metabolismo , Fator de Transcrição PAX8/metabolismo , PPAR gama/metabolismo , Neoplasias da Glândula Tireoide/metabolismo , Animais , Linhagem Celular Tumoral , Camundongos , Proteínas Nucleares , Proteínas de Fusão Oncogênica/genética , Fator de Transcrição PAX8/genética , PPAR gama/genética , Ratos , Neoplasias da Glândula Tireoide/genética , Neoplasias da Glândula Tireoide/patologia , Fator Nuclear 1 de Tireoide , Fatores de Transcrição
13.
Bioinformatics ; 30(18): 2568-75, 2014 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-24894502

RESUMO

MOTIVATION: ChIP-Seq is the standard method to identify genome-wide DNA-binding sites for transcription factors (TFs) and histone modifications. There is a growing need to analyze experiments with biological replicates, especially for epigenomic experiments where variation among biological samples can be substantial. However, tools that can perform group comparisons are currently lacking. RESULTS: We present a peak-calling prioritization pipeline (PePr) for identifying consistent or differential binding sites in ChIP-Seq experiments with biological replicates. PePr models read counts across the genome among biological samples with a negative binomial distribution and uses a local variance estimation method, ranking consistent or differential binding sites more favorably than sites with greater variability. We compared PePr with commonly used and recently proposed approaches on eight TF datasets and show that PePr uniquely identifies consistent regions with enriched read counts, high motif occurrence rate and known characteristics of TF binding based on visual inspection. For histone modification data with broadly enriched regions, PePr identified differential regions that are consistent within groups and outperformed other methods in scaling False Discovery Rate (FDR) analysis. AVAILABILITY AND IMPLEMENTATION: http://code.google.com/p/pepr-chip-seq/.


Assuntos
Algoritmos , Imunoprecipitação da Cromatina/métodos , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Animais , Linhagem Celular Tumoral , Epigenômica , Camundongos , Motivos de Nucleotídeos , Análise de Sequência com Séries de Oligonucleotídeos , Análise de Sequência de DNA , Fatores de Transcrição/metabolismo
14.
Cell Rep ; 42(8): 112896, 2023 08 29.
Artigo em Inglês | MEDLINE | ID: mdl-37505983

RESUMO

The impact of chromosomal inversions on human brain morphology remains underexplored. We studied 35 common inversions classified from genotypes of 33,018 adults with European ancestry. The inversions at 2p22.3, 16p11.2, and 17q21.31 reach genome-wide significance, followed by 8p23.1 and 6p21.33, in their association with cortical and subcortical morphology. The 17q21.31, 8p23.1, and 16p11.2 regions comprise the LRRC37, OR7E, and NPIP duplicated gene families. We find the 17q21.31 MAPT inversion region, known for harboring neurological risk, to be the most salient locus among common variants for shaping and patterning the cortex. Overall, we observe the inverted orientations decreasing brain size, with the exception that the 2p22.3 inversion is associated with increased subcortical volume and the 8p23.1 inversion is associated with increased motor cortex. These significant inversions are in the genomic hotspots of neuropsychiatric loci. Our findings are generalizable to 3,472 children and demonstrate inversions as essential genetic variation to understand human brain phenotypes.


Assuntos
Inversão Cromossômica , Polimorfismo Genético , Adulto , Criança , Humanos , Inversão Cromossômica/genética , Encéfalo
15.
Commun Biol ; 6(1): 435, 2023 04 20.
Artigo em Inglês | MEDLINE | ID: mdl-37081156

RESUMO

Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1-3, but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11-80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.


Assuntos
Cromatina , Genoma , Animais , Camundongos , Cromatina/genética , Fenótipo
16.
Cell Res ; 32(11): 1008-1021, 2022 11.
Artigo em Inglês | MEDLINE | ID: mdl-36207411

RESUMO

Loss of heterochromatin has been implicated as a cause of pre-mature aging and age-associated decline in organ functions in mammals; however, the specific cell types and gene loci affected by this type of epigenetic change have remained unclear. To address this knowledge gap, we probed chromatin accessibility at single-cell resolution in the brains, hearts, skeletal muscles, and bone marrows from young, middle-aged, and old mice, and assessed age-associated changes at 353,126 candidate cis-regulatory elements (cCREs) across 32 major cell types. Unexpectedly, we detected increased chromatin accessibility within specific heterochromatin domains in old mouse excitatory neurons. The gain of chromatin accessibility at these genomic loci was accompanied by the cell-type-specific loss of heterochromatin and activation of LINE1 elements. Immunostaining further confirmed the loss of the heterochromatin mark H3K9me3 in the excitatory neurons but not in inhibitory neurons or glial cells. Our results reveal the cell-type-specific changes in chromatin landscapes in old mice and shed light on the scope of heterochromatin loss in mammalian aging.


Assuntos
Epigenoma , Heterocromatina , Camundongos , Animais , Cromatina , Neurônios , Encéfalo , Mamíferos/genética
17.
Nat Cardiovasc Res ; 1(9): 830-843, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-36817700

RESUMO

The heart, a vital organ which is first to develop, has adapted its size, structure and function in order to accommodate the circulatory demands for a broad range of animals. Although heart development is controlled by a relatively conserved network of transcriptional/chromatin regulators, how the human heart has evolved species-specific features to maintain adequate cardiac output and function remains to be defined. Here, we show through comparative epigenomic analysis the identification of enhancers and promoters that have gained activity in humans during cardiogenesis. These cis-regulatory elements (CREs) are associated with genes involved in heart development and function, and may account for species-specific differences between human and mouse hearts. Supporting these findings, genetic variants that are associated with human cardiac phenotypic/disease traits, particularly those differing between human and mouse, are enriched in human-gained CREs. During early stages of human cardiogenesis, these CREs are also gained within genomic loci of transcriptional regulators, potentially expanding their role in human heart development. In particular, we discovered that gained enhancers in the locus of the early human developmental regulator ZIC3 are selectively accessible within a subpopulation of mesoderm cells which exhibits cardiogenic potential, thus possibly extending the function of ZIC3 beyond its conserved left-right asymmetry role. Genetic deletion of these enhancers identified a human gained enhancer that was required for not only ZIC3 and early cardiac gene expression at the mesoderm stage but also cardiomyocyte differentiation. Overall, our results illuminate how human gained CREs may contribute to human-specific cardiac attributes, and provide insight into how transcriptional regulators may gain cardiac developmental roles through the evolutionary acquisition of enhancers.

18.
Nat Genet ; 53(7): 1064-1074, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34002095

RESUMO

Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here we explore the sequence requirements of CTCF-mediated transcriptional insulation using a sensitive insulator reporter in mouse embryonic stem cells. We find that insulation potency depends on the number of CTCF-binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on upstream flanking sequences at its binding sites. CTCF-binding sites at topologically associating domain boundaries are more likely to function as insulators than those outside topologically associating domain boundaries, independently of binding strength. We demonstrate that insulators form local chromatin domain boundaries and weaken enhancer-promoter contacts. Taken together, our results provide genetic, molecular and structural evidence connecting chromatin topology to the action of insulators in the mammalian genome.


Assuntos
Fator de Ligação a CCCTC/genética , Fator de Ligação a CCCTC/metabolismo , Cromatina/genética , Cromatina/metabolismo , Regulação da Expressão Gênica , Transcrição Gênica , Animais , Sítios de Ligação , Fator de Ligação a CCCTC/química , Elementos Facilitadores Genéticos , Humanos , Elementos Isolantes , Camundongos , Células-Tronco Embrionárias Murinas/metabolismo , Regiões Promotoras Genéticas , Ligação Proteica
19.
Sci Adv ; 7(20)2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33990324

RESUMO

Misregulated gene expression in human hearts can result in cardiovascular diseases that are leading causes of mortality worldwide. However, the limited information on the genomic location of candidate cis-regulatory elements (cCREs) such as enhancers and promoters in distinct cardiac cell types has restricted the understanding of these diseases. Here, we defined >287,000 cCREs in the four chambers of the human heart at single-cell resolution, which revealed cCREs and candidate transcription factors associated with cardiac cell types in a region-dependent manner and during heart failure. We further found cardiovascular disease-associated genetic variants enriched within these cCREs including 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Additional functional studies revealed that two of these variants affect a cCRE controlling KCNH2/HERG expression and action potential repolarization. Overall, this atlas of human cardiac cCREs provides the foundation for illuminating cell type-specific gene regulation in human hearts during health and disease.


Assuntos
Coração , Sequências Reguladoras de Ácido Nucleico , Humanos , Regiões Promotoras Genéticas , Sequências Reguladoras de Ácido Nucleico/genética , Fatores de Transcrição/metabolismo
20.
Nat Commun ; 12(1): 1337, 2021 02 26.
Artigo em Inglês | MEDLINE | ID: mdl-33637727

RESUMO

Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals ~370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.


Assuntos
Sequenciamento de Cromatina por Imunoprecipitação/métodos , Análise de Célula Única/métodos , Animais , Cromatina , Biologia Computacional , Epigenômica , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Córtex Motor , Análise de Sequência de DNA/métodos
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