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We are analyzing https://link.springer.com/article/10.1186/s13059-016-1098-6.

Title:
Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans | Genome Biology
Description:
Background The 2’-5’ oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; yet, strong evidence of positive selection in the OAS region is still lacking. Results Here we used a broad array of selection tests in concert with neutral coalescent simulations to demonstrate a signal of adaptive introgression at the OAS locus. Furthermore, we characterized the functional consequences of the Neandertal haplotype in the transcriptional regulation of OAS genes at baseline and infected conditions. We found that cells from people with the Neandertal-like haplotype express lower levels of OAS3 upon infection, as well as distinct isoforms of OAS1 and OAS2. Conclusions We present evidence that a Neandertal haplotype at the OAS locus was subjected to positive selection in the human population. This haplotype is significantly associated with functional consequences at the level of transcriptional regulation of innate immune responses. Notably, we suggest that the Neandertal-introgressed haplotype likely reintroduced an ancestral splice variant of OAS1 encoding a more active protein, suggesting that adaptive introgression occurred as a means to resurrect adaptive variation that had been lost outside Africa.
Website Age:
28 years and 1 months (reg. 1997-05-29).

Matching Content Categories {📚}

  • Science
  • Education
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Content Management System {📝}

What CMS is link.springer.com built with?

Custom-built

No common CMS systems were detected on Link.springer.com, and no known web development framework was identified.

Traffic Estimate {📈}

What is the average monthly size of link.springer.com audience?

🌠 Phenomenal Traffic: 5M - 10M visitors per month


Based on our best estimate, this website will receive around 7,642,828 visitors per month in the current month.

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How Does Link.springer.com Make Money? {💸}

We can't see how the site brings in money.

Not all websites focus on profit; some are designed to educate, connect people, or share useful tools. People create websites for numerous reasons. And this could be one such example. Link.springer.com might have a hidden revenue stream, but it's not something we can detect.

Keywords {🔍}

oas, pubmed, neandertal, haplotype, article, google, scholar, allele, selection, additional, haplotypes, nls, data, frequency, cas, human, samples, introgression, file, central, snps, population, region, found, expression, adaptive, genes, genomes, european, levels, populations, individuals, fig, genome, locus, results, ancestral, genetic, sample, frequencies, table, expected, simulations, model, ancient, macrophages, genomewide, humans, calculated, positive,

Topics {✒️}

uk/impute/1000gp%20phase%203%20haplotypes%206%20october%202014 }_1=\frac{x_0}{x_0+\left tumor-necrosis-factor-alpha article download pdf quantitative real-time pcr rna-seq library preparation genome-wide statistical framework full size image high-coverage genome sequence mid-log phase prior central oas region comparable present-day frequencies gene-level expression estimates ]={\displaystyle \sum_i^{\left\{hg performing haplotype-based scans gene-level expression data genome-wide sequence data reach genome-wide significance fast model-based estimation present-day human populations 99th genome-wide percentiles present-day samples estimated long-term balancing selection unusually long-range ld transcript-level expression values present-day european samples uk/impute/1000gp_phase3 observed present-day frequency innate immune responses genome-wide genotype data present-day european populations neandertal-introgressed allele encodes similar present-day frequency genome-wide association studies privacy choices/manage cookies estimate genome-wide levels ihs calculated genome-wide wright–fisher neutral model type-ii interferon genes gene expression responses pickrell jk creative commons license single-pulse introgression model innate immune cells �genome-wide scan bi-allelic variants innate immune response empirical haplotype-based tests haplotype-based test statistic taqman gene assays

Schema {🗺️}

WebPage:
      mainEntity:
         headline:Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans
         description:The 2’-5’ oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; yet, strong evidence of positive selection in the OAS region is still lacking. Here we used a broad array of selection tests in concert with neutral coalescent simulations to demonstrate a signal of adaptive introgression at the OAS locus. Furthermore, we characterized the functional consequences of the Neandertal haplotype in the transcriptional regulation of OAS genes at baseline and infected conditions. We found that cells from people with the Neandertal-like haplotype express lower levels of OAS3 upon infection, as well as distinct isoforms of OAS1 and OAS2. We present evidence that a Neandertal haplotype at the OAS locus was subjected to positive selection in the human population. This haplotype is significantly associated with functional consequences at the level of transcriptional regulation of innate immune responses. Notably, we suggest that the Neandertal-introgressed haplotype likely reintroduced an ancestral splice variant of OAS1 encoding a more active protein, suggesting that adaptive introgression occurred as a means to resurrect adaptive variation that had been lost outside Africa.
         datePublished:2016-11-29T00:00:00Z
         dateModified:2016-11-29T00:00:00Z
         pageStart:1
         pageEnd:15
         license:http://creativecommons.org/publicdomain/zero/1.0/
         sameAs:https://doi.org/10.1186/s13059-016-1098-6
         keywords:
            Natural selection
            Introgression
            Innate immunity
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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                     address:
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                     address:
                        name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
                        type:PostalAddress
                     type:Organization
                     name:University of Montreal
                     address:
                        name:Department of Biochemistry, University of Montreal, Montreal, Canada
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               name:Vania Yotova
               affiliation:
                     name:Sainte-Justine Hospital Research Centre, University of Montreal
                     address:
                        name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
                        type:PostalAddress
                     type:Organization
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               name:Carolina Alfieri
               affiliation:
                     name:Sainte-Justine Hospital Research Centre, University of Montreal
                     address:
                        name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
                        type:PostalAddress
                     type:Organization
                     name:University of Montreal
                     address:
                        name:Department of Microbiology and Immunology, University of Montreal, Montreal, Canada
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Jerome E. Tanner
               affiliation:
                     name:Sainte-Justine Hospital Research Centre, University of Montreal
                     address:
                        name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
                        type:PostalAddress
                     type:Organization
               type:Person
               name:Philipp W. Messer
               affiliation:
                     name:Cornell University
                     address:
                        name:Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA
                        type:PostalAddress
                     type:Organization
               email:[email protected]
               type:Person
               name:Luis B. Barreiro
               affiliation:
                     name:Sainte-Justine Hospital Research Centre, University of Montreal
                     address:
                        name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
                        type:PostalAddress
                     type:Organization
                     name:University of Montreal
                     address:
                        name:Department of Pediatrics, University of Montreal, Montreal, Canada
                        type:PostalAddress
                     type:Organization
               email:[email protected]
               type:Person
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         type:ScholarlyArticle
      context:https://schema.org
ScholarlyArticle:
      headline:Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans
      description:The 2’-5’ oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; yet, strong evidence of positive selection in the OAS region is still lacking. Here we used a broad array of selection tests in concert with neutral coalescent simulations to demonstrate a signal of adaptive introgression at the OAS locus. Furthermore, we characterized the functional consequences of the Neandertal haplotype in the transcriptional regulation of OAS genes at baseline and infected conditions. We found that cells from people with the Neandertal-like haplotype express lower levels of OAS3 upon infection, as well as distinct isoforms of OAS1 and OAS2. We present evidence that a Neandertal haplotype at the OAS locus was subjected to positive selection in the human population. This haplotype is significantly associated with functional consequences at the level of transcriptional regulation of innate immune responses. Notably, we suggest that the Neandertal-introgressed haplotype likely reintroduced an ancestral splice variant of OAS1 encoding a more active protein, suggesting that adaptive introgression occurred as a means to resurrect adaptive variation that had been lost outside Africa.
      datePublished:2016-11-29T00:00:00Z
      dateModified:2016-11-29T00:00:00Z
      pageStart:1
      pageEnd:15
      license:http://creativecommons.org/publicdomain/zero/1.0/
      sameAs:https://doi.org/10.1186/s13059-016-1098-6
      keywords:
         Natural selection
         Introgression
         Innate immunity
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
      image:
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      isPartOf:
         name:Genome Biology
         issn:
            1474-760X
         volumeNumber:17
         type:
            Periodical
            PublicationVolume
      publisher:
         name:BioMed Central
         logo:
            url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
            type:ImageObject
         type:Organization
      author:
            name:Aaron J. Sams
            affiliation:
                  name:Cornell University
                  address:
                     name:Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA
                     type:PostalAddress
                  type:Organization
            email:[email protected]
            type:Person
            name:Anne Dumaine
            affiliation:
                  name:Sainte-Justine Hospital Research Centre, University of Montreal
                  address:
                     name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
                     type:PostalAddress
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            type:Person
            name:Yohann Nédélec
            affiliation:
                  name:Sainte-Justine Hospital Research Centre, University of Montreal
                  address:
                     name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
                     type:PostalAddress
                  type:Organization
                  name:University of Montreal
                  address:
                     name:Department of Biochemistry, University of Montreal, Montreal, Canada
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Vania Yotova
            affiliation:
                  name:Sainte-Justine Hospital Research Centre, University of Montreal
                  address:
                     name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Carolina Alfieri
            affiliation:
                  name:Sainte-Justine Hospital Research Centre, University of Montreal
                  address:
                     name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
                     type:PostalAddress
                  type:Organization
                  name:University of Montreal
                  address:
                     name:Department of Microbiology and Immunology, University of Montreal, Montreal, Canada
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Jerome E. Tanner
            affiliation:
                  name:Sainte-Justine Hospital Research Centre, University of Montreal
                  address:
                     name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
                     type:PostalAddress
                  type:Organization
            type:Person
            name:Philipp W. Messer
            affiliation:
                  name:Cornell University
                  address:
                     name:Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA
                     type:PostalAddress
                  type:Organization
            email:[email protected]
            type:Person
            name:Luis B. Barreiro
            affiliation:
                  name:Sainte-Justine Hospital Research Centre, University of Montreal
                  address:
                     name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
                     type:PostalAddress
                  type:Organization
                  name:University of Montreal
                  address:
                     name:Department of Pediatrics, University of Montreal, Montreal, Canada
                     type:PostalAddress
                  type:Organization
            email:[email protected]
            type:Person
      isAccessibleForFree:1
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      name:Genome Biology
      issn:
         1474-760X
      volumeNumber:17
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      name:BioMed Central
      logo:
         url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
         type:ImageObject
      name:Cornell University
      address:
         name:Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA
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      address:
         name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
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      name:Sainte-Justine Hospital Research Centre, University of Montreal
      address:
         name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
         type:PostalAddress
      name:University of Montreal
      address:
         name:Department of Biochemistry, University of Montreal, Montreal, Canada
         type:PostalAddress
      name:Sainte-Justine Hospital Research Centre, University of Montreal
      address:
         name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
         type:PostalAddress
      name:Sainte-Justine Hospital Research Centre, University of Montreal
      address:
         name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
         type:PostalAddress
      name:University of Montreal
      address:
         name:Department of Microbiology and Immunology, University of Montreal, Montreal, Canada
         type:PostalAddress
      name:Sainte-Justine Hospital Research Centre, University of Montreal
      address:
         name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
         type:PostalAddress
      name:Cornell University
      address:
         name:Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA
         type:PostalAddress
      name:Sainte-Justine Hospital Research Centre, University of Montreal
      address:
         name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
         type:PostalAddress
      name:University of Montreal
      address:
         name:Department of Pediatrics, University of Montreal, Montreal, Canada
         type:PostalAddress
ImageObject:
      url:https://www.springernature.com/app-sn/public/images/logo-springernature.png
Person:
      name:Aaron J. Sams
      affiliation:
            name:Cornell University
            address:
               name:Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA
               type:PostalAddress
            type:Organization
      email:[email protected]
      name:Anne Dumaine
      affiliation:
            name:Sainte-Justine Hospital Research Centre, University of Montreal
            address:
               name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
               type:PostalAddress
            type:Organization
      name:Yohann Nédélec
      affiliation:
            name:Sainte-Justine Hospital Research Centre, University of Montreal
            address:
               name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
               type:PostalAddress
            type:Organization
            name:University of Montreal
            address:
               name:Department of Biochemistry, University of Montreal, Montreal, Canada
               type:PostalAddress
            type:Organization
      name:Vania Yotova
      affiliation:
            name:Sainte-Justine Hospital Research Centre, University of Montreal
            address:
               name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
               type:PostalAddress
            type:Organization
      name:Carolina Alfieri
      affiliation:
            name:Sainte-Justine Hospital Research Centre, University of Montreal
            address:
               name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
               type:PostalAddress
            type:Organization
            name:University of Montreal
            address:
               name:Department of Microbiology and Immunology, University of Montreal, Montreal, Canada
               type:PostalAddress
            type:Organization
      name:Jerome E. Tanner
      affiliation:
            name:Sainte-Justine Hospital Research Centre, University of Montreal
            address:
               name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
               type:PostalAddress
            type:Organization
      name:Philipp W. Messer
      affiliation:
            name:Cornell University
            address:
               name:Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA
               type:PostalAddress
            type:Organization
      email:[email protected]
      name:Luis B. Barreiro
      affiliation:
            name:Sainte-Justine Hospital Research Centre, University of Montreal
            address:
               name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
               type:PostalAddress
            type:Organization
            name:University of Montreal
            address:
               name:Department of Pediatrics, University of Montreal, Montreal, Canada
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA
      name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
      name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
      name:Department of Biochemistry, University of Montreal, Montreal, Canada
      name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
      name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
      name:Department of Microbiology and Immunology, University of Montreal, Montreal, Canada
      name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
      name:Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, USA
      name:Department of Genetics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
      name:Department of Pediatrics, University of Montreal, Montreal, Canada

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