LIVIVO - Das Suchportal für Lebenswissenschaften

switch to English language
Zurück zur letzten Suche Suchhistorie
Erweiterte Suche

Ihre letzten Suchen

  1. AU="Aracena, Katherine A"
  2. AU="Gainder, Shalini"
  3. AU="O'Brien, Catherine"
  4. AU="Lelieveld, Steven"
  5. AU="Kapusız, Ö"
  6. AU="Casey, W."
  7. AU="Knooihuizen, Remco"
  8. AU="Kashuk, Carl"
  9. AU="Räty, Silja"
  10. AU="Levasseur, Franck"
  11. AU="Arianna Rubin Means"
  12. AU="Murdan, Sudaxshina"
  13. AU=Kimberley Fiona C
  14. AU="Solís, José Gabriel"
  15. AU="Becker, Maximilian R"
  16. AU="Alasonati, Enrica"
  17. AU="Arribas, Silvia Magdalena"
  18. AU=Edry Efrat
  19. AU="James B. McCauley"
  20. AU="Offringa, Ite A"
  21. AU="Sakso, Salima Ahriz"
  22. AU="Huang, Zexiang"
  23. AU="Feleke, Sindew M"
  24. AU="van der Velden, Janielle"
  25. AU="Carmen Gonzalez"
  26. AU="Cheah, Jaime H"
  27. AU="Forte, Florence"
  28. AU="Anika Nier"
  29. AU="Bar, Adi"
  30. AU="Alvarado Pinedo, María F."
  31. AU="Scarlett, Garry"
  32. AU="Carlos G. Vanoye"
  33. AU=Lohrmann Jens
  34. AU="Petersen, Moritz"
  35. AU="Giovanni, L."
  36. AU="Liu, Xingzheng"
  37. AU="Głód, Mateusz"
  38. AU=Teo Kelvin Yi Chong
  39. AU="Khatmi, Aysan"
  40. AU="Erculiani, M"
  41. AU="Olivier Lortholary"
  42. AU="Lisnic, Vanda Juranic"
  43. AU="Seabloom, Eric W"
  44. AU="Odvina, Clarita V"
  45. AU="Singh, Inderbir"
  46. AU="Wonoh Lee"
  47. AU="Nelson, Warrick"
  48. AU="Douglas, David N"
  49. AU="King, Gary"
  50. AU="Barbera, Lauren"
  51. AU="Carlino, Antonio"
  52. AU="Shan, Qing-Hua"
  53. AU="Starko, S"
  54. AU="Lievre, Loïc"
  55. AU=Cammack N
  56. AU="Xia, Qin"
  57. AU="Ong, Ju Lynn"
  58. AU="Cullin, Christophe"
  59. AU="Georg K.S. Andersson"
  60. AU="Jeannel, Gaël-François"
  61. AU="Stuart Woods"
  62. AU="Shchegolev, A."
  63. AU="Nadeau, Pierre-Louis"
  64. AU="Gordon, David E A"
  65. AU="Shahid Mahmood"
  66. AU="Rosenblatt, Karin"
  67. AU="Dasgupta, Suvankar"
  68. AU=Nguyen Sylvain AU=Nguyen Sylvain

Suchergebnis

Treffer 1 - 8 von insgesamt 8

Suchoptionen

  1. Artikel ; Online: DNA methylation-environment interactions in the human genome.

    Johnston, Rachel A / Aracena, Katherine A / Barreiro, Luis B / Lea, Amanda J / Tung, Jenny

    eLife

    2024  Band 12

    Abstract: Previously, we showed that a massively parallel reporter assay, mSTARR-seq, could be used to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity for millions of loci in a single experiment (Lea et al., 2018) ...

    Abstract Previously, we showed that a massively parallel reporter assay, mSTARR-seq, could be used to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity for millions of loci in a single experiment (Lea et al., 2018). Here, we apply mSTARR-seq to query nearly the entire human genome, including almost all CpG sites profiled either on the commonly used Illumina Infinium MethylationEPIC array or via reduced representation bisulfite sequencing. We show that fragments containing these sites are enriched for regulatory capacity, and that methylation-dependent regulatory activity is in turn sensitive to the cellular environment. In particular, regulatory responses to interferon alpha (IFNA) stimulation are strongly attenuated by methyl marks, indicating widespread DNA methylation-environment interactions. In agreement, methylation-dependent responses to IFNA identified via mSTARR-seq predict methylation-dependent transcriptional responses to challenge with influenza virus in human macrophages. Our observations support the idea that pre-existing DNA methylation patterns can influence the response to subsequent environmental exposures-one of the tenets of biological embedding. However, we also find that, on average, sites previously associated with early life adversity are not more likely to functionally influence gene regulation than expected by chance.
    Mesh-Begriff(e) Humans ; DNA Methylation ; Gene-Environment Interaction ; Genome, Human ; Biological Assay ; Environmental Exposure ; Interferon-alpha
    Chemische Substanzen Interferon-alpha
    Sprache Englisch
    Erscheinungsdatum 2024-02-26
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.89371
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

    Zusatzmaterialien

    Kategorien

    Über subito bestellen

    Dieser Service ist kostenpflichtig (siehe Lieferbedingungen von subito). Bestellungen, die einen Artikel nebst Supplementary Material umfassen, werden grundsätzlich wie mehrfache Bestellungen bearbeitet. Gebühren fallen in diesen Fällen für jede einzelne Bestellung an.

  2. Artikel ; Online: Shaping immunity: The influence of natural selection on population immune diversity.

    Randolph, Haley E / Aracena, Katherine A / Lin, Yen-Lung / Mu, Zepeng / Barreiro, Luis B

    Immunological reviews

    2024  Band 323, Heft 1, Seite(n) 227–240

    Abstract: Humans exhibit considerable variability in their immune responses to the same immune challenges. Such variation is widespread and affects individual and population-level susceptibility to infectious diseases and immune disorders. Although the factors ... ...

    Abstract Humans exhibit considerable variability in their immune responses to the same immune challenges. Such variation is widespread and affects individual and population-level susceptibility to infectious diseases and immune disorders. Although the factors influencing immune response diversity are partially understood, what mechanisms lead to the wide range of immune traits in healthy individuals remain largely unexplained. Here, we discuss the role that natural selection has played in driving phenotypic differences in immune responses across populations and present-day susceptibility to immune-related disorders. Further, we touch on future directions in the field of immunogenomics, highlighting the value of expanding this work to human populations globally, the utility of modeling the immune response as a dynamic process, and the importance of considering the potential polygenic nature of natural selection. Identifying loci acted upon by evolution may further pinpoint variants critically involved in disease etiology, and designing studies to capture these effects will enrich our understanding of the genetic contributions to immunity and immune dysregulation.
    Mesh-Begriff(e) Humans ; Selection, Genetic ; Animals ; Genetic Predisposition to Disease ; Immunity/genetics ; Genetic Variation ; Genetics, Population ; Phenotype ; Disease Susceptibility/immunology
    Sprache Englisch
    Erscheinungsdatum 2024-04-05
    Erscheinungsland England
    Dokumenttyp Journal Article ; Review
    ZDB-ID 391796-4
    ISSN 1600-065X ; 0105-2896
    ISSN (online) 1600-065X
    ISSN 0105-2896
    DOI 10.1111/imr.13329
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

    Volltext online

    Zusatzmaterialien

    Kategorien

    Verfügbar in ZB MED Köln/Königswinter

    Se 160: Hefte anzeigen Standort:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Über subito bestellen

    Dieser Service ist kostenpflichtig (siehe Lieferbedingungen von subito). Bestellungen, die einen Artikel nebst Supplementary Material umfassen, werden grundsätzlich wie mehrfache Bestellungen bearbeitet. Gebühren fallen in diesen Fällen für jede einzelne Bestellung an.

  3. Artikel: DNA methylation-environment interactions in the human genome.

    Johnston, Rachel A / Aracena, Katherine A / Barreiro, Luis B / Lea, Amanda J / Tung, Jenny

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Previously we showed that a massively parallel reporter assay, mSTARR-seq, could be used to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity for millions of loci in a single experiment ( ... ...

    Abstract Previously we showed that a massively parallel reporter assay, mSTARR-seq, could be used to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity for millions of loci in a single experiment (Lea
    Sprache Englisch
    Erscheinungsdatum 2023-12-15
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.05.19.541437
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

    Zusatzmaterialien

    Kategorien

    Fernleihe an ZB MED

    Sie können sich den gewünschten Titel als lokale Nutzerin oder lokaler Nutzer von ZB MED direkt an den Standort Köln schicken lassen.

  4. Artikel ; Online: Genome graphs detect human polymorphisms in active epigenomic state during influenza infection.

    Groza, Cristian / Chen, Xun / Pacis, Alain / Simon, Marie-Michelle / Pramatarova, Albena / Aracena, Katherine A / Pastinen, Tomi / Barreiro, Luis B / Bourque, Guillaume

    Cell genomics

    2023  Band 3, Heft 5, Seite(n) 100294

    Abstract: Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that genome graphs, which encapsulate genetic diversity, could reveal missing epigenomic signals. To test this, we sequenced the epigenome of ...

    Abstract Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that genome graphs, which encapsulate genetic diversity, could reveal missing epigenomic signals. To test this, we sequenced the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after influenza infection, allowing us to investigate the role of MEIs in immunity. We characterized genetic variants and MEIs using linked reads and built a genome graph. Mapping epigenetic data revealed 2.3%-3% novel peaks for H3K4me1, H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq), and ATAC-seq. Additionally, the use of a genome graph modified some quantitative trait loci estimates and revealed 375 polymorphic MEIs in an active epigenomic state. Among these is an AluYh3 polymorphism whose chromatin state changed after infection and was associated with the expression of
    Sprache Englisch
    Erscheinungsdatum 2023-04-07
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 2666-979X
    ISSN (online) 2666-979X
    DOI 10.1016/j.xgen.2023.100294
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

    Zusatzmaterialien

    Kategorien

    Über subito bestellen

    Dieser Service ist kostenpflichtig (siehe Lieferbedingungen von subito). Bestellungen, die einen Artikel nebst Supplementary Material umfassen, werden grundsätzlich wie mehrfache Bestellungen bearbeitet. Gebühren fallen in diesen Fällen für jede einzelne Bestellung an.

    Fernleihe an ZB MED

    Sie können sich den gewünschten Titel als lokale Nutzerin oder lokaler Nutzer von ZB MED direkt an den Standort Köln schicken lassen.

  5. Artikel ; Online: EpiVar Browser: advanced exploration of epigenomics data under controlled access.

    Lougheed, David R / Liu, Hanshi / Aracena, Katherine A / Grégoire, Romain / Pacis, Alain / Pastinen, Tomi / Barreiro, Luis B / Joly, Yann / Bujold, David / Bourque, Guillaume

    Bioinformatics (Oxford, England)

    2024  Band 40, Heft 3

    Abstract: Motivation: Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, similarly to ... ...

    Abstract Motivation: Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, similarly to genetic data, most raw files generated by these consortia are stored in controlled-access databases. It is important to protect identifiable information, but this should not hinder secure sharing of these valuable datasets.
    Results: Guided by the Framework for responsible sharing of genomic and health-related data from the Global Alliance for Genomics and Health (GA4GH), we have developed an approach and a tool to facilitate the exploration of epigenomics datasets' aggregate results, while filtering out identifiable information. Specifically, the EpiVar Browser allows a user to navigate an epigenetic dataset from a cohort of individuals and enables direct exploration of genotype-chromatin phenotype relationships. Because individual genotypes and epigenetic signal tracks are not directly accessible, and rather aggregated in the portal output, no identifiable data is released, yet the interface allows for dynamic genotype-epigenome interrogation. This approach has the potential to accelerate analyses that would otherwise require a lengthy multi-step approval process and provides a generalizable strategy to facilitate responsible access to sensitive epigenomics data.
    Availability and implementation: Online portal: https://computationalgenomics.ca/tools/epivar; EpiVar Browser source code: https://github.com/c3g/epivar-browser; bw-merge-window tool source code: https://github.com/c3g/bw-merge-window.
    Mesh-Begriff(e) Humans ; Epigenomics/methods ; Software ; Genome ; Genomics ; Chromatin/genetics
    Chemische Substanzen Chromatin
    Sprache Englisch
    Erscheinungsdatum 2024-03-06
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btae136
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

    Zusatzmaterialien

    Kategorien

    Verfügbar in ZB MED Köln/Königswinter

    Zs.A 2374: Hefte anzeigen Standort:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Über subito bestellen

    Dieser Service ist kostenpflichtig (siehe Lieferbedingungen von subito). Bestellungen, die einen Artikel nebst Supplementary Material umfassen, werden grundsätzlich wie mehrfache Bestellungen bearbeitet. Gebühren fallen in diesen Fällen für jede einzelne Bestellung an.

  6. Artikel ; Online: Transposable elements are associated with the variable response to influenza infection.

    Chen, Xun / Pacis, Alain / Aracena, Katherine A / Gona, Saideep / Kwan, Tony / Groza, Cristian / Lin, Yen Lung / Sindeaux, Renata / Yotova, Vania / Pramatarova, Albena / Simon, Marie-Michelle / Pastinen, Tomi / Barreiro, Luis B / Bourque, Guillaume

    Cell genomics

    2023  Band 3, Heft 5, Seite(n) 100292

    Abstract: Influenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Here, we wanted to explore the potential contribution of transposable elements (TEs) to the variable human immune response. Transcriptome profiling in ... ...

    Abstract Influenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Here, we wanted to explore the potential contribution of transposable elements (TEs) to the variable human immune response. Transcriptome profiling in monocyte-derived macrophages from 39 individuals following IAV infection revealed significant inter-individual variation in viral load post-infection. Using transposase-accessible chromatin using sequencing (ATAC-seq), we identified a set of TE families with either enhanced or reduced accessibility upon infection. Of the enhanced families, 15 showed high variability between individuals and had distinct epigenetic profiles. Motif analysis showed an association with known immune regulators (e.g., BATFs, FOSs/JUNs, IRFs, STATs, NFkBs, NFYs, and RELs) in stably enriched families and with other factors in variable families, including KRAB-ZNFs. We showed that TEs and host factors regulating TEs were predictive of viral load post-infection. Our findings shed light on the role TEs and KRAB-ZNFs may play in inter-individual variation in immunity.
    Sprache Englisch
    Erscheinungsdatum 2023-04-07
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 2666-979X
    ISSN (online) 2666-979X
    DOI 10.1016/j.xgen.2023.100292
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

    Zusatzmaterialien

    Kategorien

    Über subito bestellen

    Dieser Service ist kostenpflichtig (siehe Lieferbedingungen von subito). Bestellungen, die einen Artikel nebst Supplementary Material umfassen, werden grundsätzlich wie mehrfache Bestellungen bearbeitet. Gebühren fallen in diesen Fällen für jede einzelne Bestellung an.

    Fernleihe an ZB MED

    Sie können sich den gewünschten Titel als lokale Nutzerin oder lokaler Nutzer von ZB MED direkt an den Standort Köln schicken lassen.

  7. Artikel: EpiVar Browser: advanced exploration of epigenomics data under controlled access.

    Lougheed, David R / Liu, Hanshi / Aracena, Katherine A / Grégoire, Romain / Pacis, Alain / Pastinen, Tomi / Barreiro, Luis B / Joly, Yann / Bujold, David / Bourque, Guillaume

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Motivation: Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, similarly to ... ...

    Abstract Motivation: Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, similarly to genetic data, most raw files generated by these consortia are stored in controlled-access databases. It is important to protect identifiable information, but this should not hinder secure sharing of these valuable datasets.
    Results: Guided by the
    Availability and implementation: Online portal instance: https://computationalgenomics.ca/tools/epivarSource code: https://github.com/c3g/epivar-browser.
    Sprache Englisch
    Erscheinungsdatum 2023-08-05
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.08.03.551309
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

    Zusatzmaterialien

    Kategorien

    Fernleihe an ZB MED

    Sie können sich den gewünschten Titel als lokale Nutzerin oder lokaler Nutzer von ZB MED direkt an den Standort Köln schicken lassen.

  8. Artikel ; Online: Epigenetic variation impacts individual differences in the transcriptional response to influenza infection.

    Aracena, Katherine A / Lin, Yen-Lung / Luo, Kaixuan / Pacis, Alain / Gona, Saideep / Mu, Zepeng / Yotova, Vania / Sindeaux, Renata / Pramatarova, Albena / Simon, Marie-Michelle / Chen, Xun / Groza, Cristian / Lougheed, David / Gregoire, Romain / Brownlee, David / Boye, Carly / Pique-Regi, Roger / Li, Yang / He, Xin /
    Bujold, David / Pastinen, Tomi / Bourque, Guillaume / Barreiro, Luis B

    Nature genetics

    2024  Band 56, Heft 3, Seite(n) 408–419

    Abstract: Humans display remarkable interindividual variation in their immune response to identical challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such variation remains limited. Here we performed in-depth genetic, ... ...

    Abstract Humans display remarkable interindividual variation in their immune response to identical challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such variation remains limited. Here we performed in-depth genetic, epigenetic and transcriptional profiling on primary macrophages derived from individuals of European and African ancestry before and after infection with influenza A virus. We show that baseline epigenetic profiles are strongly predictive of the transcriptional response to influenza A virus across individuals. Quantitative trait locus (QTL) mapping revealed highly coordinated genetic effects on gene regulation, with many cis-acting genetic variants impacting concomitantly gene expression and multiple epigenetic marks. These data reveal that ancestry-associated differences in the epigenetic landscape can be genetically controlled, even more than gene expression. Lastly, among QTL variants that colocalized with immune-disease loci, only 7% were gene expression QTL, while the remaining genetic variants impact epigenetic marks, stressing the importance of considering molecular phenotypes beyond gene expression in disease-focused studies.
    Mesh-Begriff(e) Humans ; Influenza, Human/genetics ; Individuality ; Quantitative Trait Loci/genetics ; Chromosome Mapping ; Epigenesis, Genetic
    Sprache Englisch
    Erscheinungsdatum 2024-02-29
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-024-01668-z
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

    Zusatzmaterialien

    Kategorien

    Verfügbar in ZB MED Köln/Königswinter

    Zs.A 3613: Hefte anzeigen Standort:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 46: Hefte anzeigen

    Über subito bestellen

    Dieser Service ist kostenpflichtig (siehe Lieferbedingungen von subito). Bestellungen, die einen Artikel nebst Supplementary Material umfassen, werden grundsätzlich wie mehrfache Bestellungen bearbeitet. Gebühren fallen in diesen Fällen für jede einzelne Bestellung an.

Zum Seitenanfang