المؤلفون: Noboru J. Sakabe, Ivy Aneas, Xin He, Carole Ober, Lindsey E. Montefiori, Amelia C Joslin, Jing Gu, Donna M. Lehman, Débora R. Sobreira, Marcelo A. Nobrega, Grace T Hansen, Kathryn M. Farris

المصدر: Nature Communications
Nature Communications, Vol 12, Iss 1, Pp 1-15 (2021)

مصطلحات موضوعية: Epigenomics, Heart Defects, Congenital, Science, Quantitative Trait Loci, Hypothalamus, General Physics and Astronomy, Genome-wide association study, Computational biology, MAP Kinase Kinase 5, Biology, Quantitative trait locus, Polymorphism, Single Nucleotide, Article, Gigantism, General Biochemistry, Genetics and Molecular Biology, Sarcoplasmic Reticulum Calcium-Transporting ATPases, Pleiotropy, Intellectual Disability, Adipocytes, Genetic Pleiotropy, Humans, Obesity, Enhancer, Gene, Genetic association, Neurons, Multidisciplinary, Functional genomics, Arrhythmias, Cardiac, Genetic Diseases, X-Linked, General Chemistry, Gene regulation, Enhancer Elements, Genetic, Transcriptome, Protein Kinases, Genome-Wide Association Study, Transcription Factors

الوصف: Genome-wide association studies (GWAS) have identified many disease-associated variants, yet mechanisms underlying these associations remain unclear. To understand obesity-associated variants, we generate gene regulatory annotations in adipocytes and hypothalamic neurons across cellular differentiation stages. We then test variants in 97 obesity-associated loci using a massively parallel reporter assay and identify putatively causal variants that display cell type specific or cross-tissue enhancer-modulating properties. Integrating these variants with gene regulatory information suggests genes that underlie obesity GWAS associations. We also investigate a complex genomic interval on 16p11.2 where two independent loci exhibit megabase-range, cross-locus chromatin interactions. We demonstrate that variants within these two loci regulate a shared gene set. Together, our data support a model where GWAS loci contain variants that alter enhancer activity across tissues, potentially with temporally restricted effects, to impact the expression of multiple genes. This complex model has broad implications for ongoing efforts to understand GWAS.
Many genetic loci have been linked to obesity, but knowledge of their functional mechanisms is limited. Here, the authors perform reporter assays and temporal functional genomics data generation to characterize obesity genetic loci and find that loci often harbor multiple functional variants.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3a38d28748fd50ff9893c210f86b5e26Test
https://doi.org/10.1038/s41467-021-25614-3Test

المؤلفون: James E. Gern, Christine Billstrand, Carole Ober, Marcelo A. Nobrega, Britney A Helling, Kaixuan Luo, Steven R. White, Grace T Hansen, Raluca Nicolae, Débora R. Sobreira, Dan L. Nicolae, Noboru J. Sakabe, Bharathi Laxman, Yury A. Bochkov

المصدر: Communications Biology, Vol 3, Iss 1, Pp 1-11 (2020)
Communications Biology

مصطلحات موضوعية: Adult, Epigenomics, 0301 basic medicine, Rhinovirus, Transcription, Genetic, Medicine (miscellaneous), Genome-wide association study, Respiratory Mucosa, Biology, medicine.disease_cause, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, immune system diseases, Gene expression, medicine, Humans, Genetic risk, lcsh:QH301-705.5, Gene, Cells, Cultured, Asthma, Epithelial Cells, Antimicrobial responses, respiratory system, medicine.disease, Chromatin, Gene regulation, respiratory tract diseases, 030104 developmental biology, lcsh:Biology (General), Apoptosis, 030220 oncology & carcinogenesis, Immunology, General Agricultural and Biological Sciences

الوصف: There is a life-long relationship between rhinovirus (RV) infection and the development and clinical manifestations of asthma. In this study we demonstrate that cultured primary bronchial epithelial cells from adults with asthma (n = 9) show different transcriptional and chromatin responses to RV infection compared to those without asthma (n = 9). Both the number and magnitude of transcriptional and chromatin responses to RV were muted in cells from asthma cases compared to controls. Pathway analysis of the transcriptionally responsive genes revealed enrichments of apoptotic pathways in controls but inflammatory pathways in asthma cases. Using promoter capture Hi-C we tethered regions of RV-responsive chromatin to RV-responsive genes and showed enrichment of these regions and genes at asthma GWAS loci. Taken together, our studies indicate a delayed or prolonged inflammatory state in cells from asthma cases and highlight genes that may contribute to genetic risk for asthma.
Britney Helling et al. report that cultured bronchial cells from adults with asthma show different gene expression and chromatin accessibility patterns when exposed to rhinovirus than do cells from individuals without asthma. Their data suggest that rhinovirus infection leads to a delayed or elongated activation of inflammatory genes in individuals with asthma compared to those without asthma.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ee35b336cab85a82108dfe6f4f1e811cTest
https://doi.org/10.1038/s42003-020-01411-4Test

المؤلفون: Marcelo A. Nobrega, Noboru J. Sakabe, Leelavati Narlikar, Alexander A. Blanski, Ivan Ovcharenko, Fabio Eiji Arimura, John M. Westlund

المصدر: Genome Research. 20:381-392

مصطلحات موضوعية: Mef2, Amino Acid Motifs, Computational biology, Regulatory Sequences, Nucleic Acid, Biology, Genome, Mice, Pregnancy, Methods, Genetics, Animals, Humans, Enhancer, Transcription factor, Gene, Zebrafish, Genetics (clinical), Mammals, Regulation of gene expression, Base Sequence, Reproducibility of Results, Heart, biology.organism_classification, Female, Classifier (UML), Protein Binding

الوصف: The various organogenic programs deployed during embryonic development rely on the precise expression of a multitude of genes in time and space. Identifying the cis-regulatory elements responsible for this tightly orchestrated regulation of gene expression is an essential step in understanding the genetic pathways involved in development. We describe a strategy to systematically identify tissue-specific cis-regulatory elements that share combinations of sequence motifs. Using heart development as an experimental framework, we employed a combination of Gibbs sampling and linear regression to build a classifier that identifies heart enhancers based on the presence and/or absence of various sequence features, including known and putative transcription factor (TF) binding specificities. In distinguishing heart enhancers from a large pool of random noncoding sequences, the performance of our classifier is vastly superior to four commonly used methods, with an accuracy reaching 92% in cross-validation. Furthermore, most of the binding specificities learned by our method resemble the specificities of TFs widely recognized as key players in heart development and differentiation, such as SRF, MEF2, ETS1, SMAD, and GATA. Using our classifier as a predictor, a genome-wide scan identified over 40,000 novel human heart enhancers. Although the classifier used no gene expression information, these novel enhancers are strongly associated with genes expressed in the heart. Finally, in vivo tests of our predictions in mouse and zebrafish achieved a validation rate of 62%, significantly higher than what is expected by chance. These results support the existence of underlying cis-regulatory codes dictating tissue-specific transcription in mammalian genomes and validate our enhancer classifier strategy as a method to uncover these regulatory codes.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1af2d52160f1ce4d3fdd05d29c968c54Test
https://doi.org/10.1101/gr.098657.109Test

المؤلفون: Nora F. Wasserman, Noboru J. Sakabe, Miguel Manzanares, Ivy Aneas, Niki Alizadeh Vakili, Davis Tam, José Luis Gómez-Skarmeta, Juan J. Tena, Kyoung-Han Kim, Eric R. Gamazon, Ju Hee Lee, Chi-chung Hui, Marcelo A. Nobrega, Joe Eun Son, Carlos Gómez-Marín, Flavia L. Credidio, Débora R. Sobreira, Scott Smemo, Rafael D. Acemel, Silvia Naranjo, Andras Nagy, Hoon Ki Sung, Vijitha Puviindran, Nancy J. Cox, Michael Shen

المساهمون: Junta de Andalucía, Canadian Institutes of Health Research, Heart and Stroke Foundation of Canada, National Institutes of Health (US), Ministerio de Economía y Competitividad (España)

المصدر: Digital.CSIC. Repositorio Institucional del CSIC
instname

مصطلحات موضوعية: Regulation of gene expression, Genetics, Quantitative trait loci, Multidisciplinary, endocrine system diseases, Transcriptional regulatory elements, Intron, nutritional and metabolic diseases, Single-nucleotide polymorphism, Genome-wide association study, Biology, Phenotype, Gene regulation, Alpha-Ketoglutarate-Dependent Dioxygenase FTO, Obesity, Enhancer, Gene

الوصف: PMCID: PMC4113484.-- et al.
Genome-wide association studies (GWAS) have reproducibly associated variants within introns of FTO with increased risk for obesity and type 2 diabetes (T2D). Although the molecular mechanisms linking these noncoding variants with obesity are not immediately obvious, subsequent studies in mice demonstrated that FTO expression levels influence body mass and composition phenotypes. However, no direct connection between the obesity-associated variants and FTO expression or function has been made. Here we show that the obesity-associated noncoding sequences within FTO are functionally connected, at megabase distances, with the homeobox gene IRX3. The obesity-associated FTO region directly interacts with the promoters of IRX3 as well as FTO in the human, mouse and zebrafish genomes. Furthermore, long-range enhancers within this region recapitulate aspects of IRX3 expression, suggesting that the obesity-associated interval belongs to the regulatory landscape of IRX3. Consistent with this, obesity-associated single nucleotide polymorphisms are associated with expression of IRX3, but not FTO, in human brains. A direct link between IRX3 expression and regulation of body mass and composition is demonstrated by a reduction in body weight of 25 to 30% in Irx3-deficient mice, primarily through the loss of fat mass and increase in basal metabolic rate with browning of white adipose tissue. Finally, hypothalamic expression of a dominant-negative form of Irx3 reproduces the metabolic phenotypes of Irx3-deficient mice. Our data suggest that IRX3 is a functional long-range target of obesity-associated variants within FTO and represents a novel determinant of body mass and composition.
This work was funded by grants from the National Institutes of Health (DK093972, HL119967, HL114010 and DK020595) to M.A.N. and (MH101820, MH090937 and DK20595) to N.J.C. J.L.G.-S. was funded by grants from the Spanish Ministerio de Economía y Competitividad (BFU2010-14839, CSD2007-00008) and the Andalusian Government (CVI-3488). C.-C.H. was supported by a grant from the Canadian Institute of Health Research. K.-H.K. is supported by a fellowship from the Heart and Stroke Foundation of Canada. S.S. is supported by an NIH postdoctoral training grant (T32HL007381)

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bf45e804210869a3b19bebe1e65bfcd1Test
http://hdl.handle.net/10261/129403Test

المؤلفون: Marcelo A. Nobrega, Noboru J. Sakabe

المصدر: Wiley interdisciplinary reviews. Systems biology and medicine. 2(4)

مصطلحات موضوعية: Genetics, Regulation of gene expression, Chromatin Immunoprecipitation, Models, Genetic, Medicine (miscellaneous), Chromosome Mapping, Promoter, Computational biology, Genomics, Biology, Biochemistry, Genetics and Molecular Biology (miscellaneous), Genome, Trans-regulatory element, Chromatin, Humans, Computer Simulation, Regulatory Elements, Transcriptional, Chromatin immunoprecipitation, Gene, ChIA-PET

الوصف: Expression of eukaryotic genes with complex spatial-temporal regulation during development requires finer regulation than that of genes with simpler expression patterns. Given the high degree of conservation of the developmental gene set across distantly related phylogenetic taxa, it is argued that evolutionary variation has occurred by tweaking regulation of expression of developmental genes, rather than by changes in genes themselves. Complex regulation is often achieved through the coordinated action of transcription regulatory elements spread across the genome up to tens of kilobases from the promoters of their target genes. Disruption of regulatory elements has been implicated in several diseases and studies showing associations between disease traits and nonprotein coding variation hint for a role of regulatory elements as cause of diseases. Therefore, the identification and mapping of regulatory elements in genome scale is crucial to understand how gene expression is regulated, how organisms evolve, and to identify sequence variation causing diseases. Previously developed experimental techniques have been adapted to identify regulatory elements in genome scale and high-throughput, allowing a global view of their biological roles. We review methods as chromatin immunoprecipitation, DNase I hypersensitivity, and computational approaches and how they have been employed to generate maps of histone modifications, open chromatin, nucleosome positioning, and transcription factor binding regions in whole mammalian genomes. Given the importance of non-promoter elements in gene regulation and the recent explosion in the number of studies devoted to them, we focus on these elements and discuss the insights on gene regulation being obtained by these studies.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ed6c72f6a630b2c30bf0ad08a90f0803Test
https://pubmed.ncbi.nlm.nih.gov/20836039Test

المؤلفون: Sandro J. de Souza, Noboru J. Sakabe

المصدر: BMC Genomics, Vol 8, Iss 1, p 59 (2007)
BMC Genomics

مصطلحات موضوعية: DNA, Complementary, lcsh:QH426-470, lcsh:Biotechnology, Biology, Mice, Exon, lcsh:TP248.13-248.65, Genetics, Animals, Humans, splice, Gene, Splice site mutation, Base Sequence, Alternative splicing, Intron, Group II intron, Introns, Alternative Splicing, lcsh:Genetics, Enhancer Elements, Genetic, RNA splicing, RNA Splice Sites, Research Article, Biotechnology

الوصف: Background One of the least common types of alternative splicing is the complete retention of an intron in a mature transcript. Intron retention (IR) is believed to be the result of intron, rather than exon, definition associated with failure of the recognition of weak splice sites flanking short introns. Although studies on individual retained introns have been published, few systematic surveys of large amounts of data have been conducted on the mechanisms that lead to IR. Results TTo understand how sequence features are associated with or control IR, and to produce a generalized model that could reveal previously unknown signals that regulate this type of alternative splicing, we partitioned intron retention events observed in human cDNAs into two groups based on the relative abundance of both isoforms and compared relevant features. We found that a higher frequency of IR in human is associated with individual introns that have weaker splice sites, genes with shorter intron lengths, higher expression levels and lower density of both a set of exon splicing silencers (ESSs) and the intronic splicing enhancer GGG. Both groups of retained introns presented events conserved in mouse, in which the retained introns were also short and presented weaker splice sites. Conclusion Although our results confirmed that weaker splice sites are associated with IR, they showed that this feature alone cannot explain a non-negligible fraction of events. Our analysis suggests that cis-regulatory elements are likely to play a crucial role in regulating IR and also reveals previously unknown features that seem to influence its occurrence. These results highlight the importance of considering the interplay among these features in the regulation of the relative frequency of IR.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6a318601a381ef40f924fc1f7170dd86Test
http://www.biomedcentral.com/1471-2164/8/59Test

المؤلفون: Noboru J. Sakabe, Marcelo A. Nobrega

المصدر: Philosophical Transactions of the Royal Society B: Biological Sciences. 368:20130022

مصطلحات موضوعية: Epigenomics, Genetics, Regulation of gene expression, Chromatin Immunoprecipitation, Genomics, Enhancer RNAs, Articles, Computational biology, Biology, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, Enhancer Elements, Genetic, Gene Expression Regulation, Databases, Genetic, General Agricultural and Biological Sciences, Enhancer, Chromatin immunoprecipitation, Gene, ChIA-PET, Transcription Factors

الوصف: The complex expression patterns observed for many genes are often regulated by distal transcription enhancers. Changes in the nucleotide sequences of enhancers may therefore lead to changes in gene expression, representing a central mechanism by which organisms evolve. With the development of the experimental technique of chromatin immunoprecipitation (ChIP), in which discrete regions of the genome bound by specific proteins can be identified, it is now possible to identify transcription factor binding events (putative cis -regulatory elements) in entire genomes. Comparing protein–DNA binding maps allows us, for the first time, to attempt to identify regulatory differences and infer global patterns of change in gene expression across species. Here, we review studies that used genome-wide ChIP to study the evolution of enhancers. The trend is one of high divergence of cis -regulatory elements between species, possibly compensated by extensive creation and loss of regulatory elements and rewiring of their target genes. We speculate on the meaning of the differences observed and discuss that although ChIP experiments identify the biochemical event of protein–DNA interaction, it cannot determine whether the event results in a biological function, and therefore more studies are required to establish the effect of divergence of binding events on species-specific gene expression.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::86f2c73f487dc9f0ad4ef725a3ea4f4fTest
https://doi.org/10.1098/rstb.2013.0022Test