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Relating enhancer g...
Relating enhancer genetic variation across mammals to complex phenotypes using machine learning
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- Kaplow, Irene M. (author)
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.;Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA.
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- Lawler, Alyssa J. (author)
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA.;Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA.
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- Schäffer, Daniel E. (author)
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.
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- Srinivasan, Chaitanya (author)
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.
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- Sestili, Heather H. (author)
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.
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- Wirthlin, Morgan E. (author)
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.;Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA.
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- Phan, BaDoi N. (author)
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.;Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA.;Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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- Prasad, Kavya (author)
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.
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- Brown, Ashley R. (author)
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.
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- Zhang, Xiaomeng (author)
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.
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- Foley, Kathleen (author)
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
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- Genereux, Diane P. (author)
- Broad Institute, Cambridge, MA, USA.;Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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- Karlsson, Elinor K. (author)
- Broad Institute, Cambridge, MA, USA.;Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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- Lindblad-Toh, Kerstin (author)
- Uppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi,Science for Life Laboratory, SciLifeLab,Broad Institute, Cambridge, MA, USA.
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- Meyer, Wynn K. (author)
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA.
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- Pfenning, Andreas R. (author)
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA.;Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA.;Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA.
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Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA;Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA. Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA.;Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA. (creator_code:org_t)
- American Association for the Advancement of Science (AAAS), 2023
- 2023
- English.
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6643
- Related links:
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
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- Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
Subject headings
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Kaplow, Irene M.
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Lawler, Alyssa J ...
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Schäffer, Daniel ...
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Srinivasan, Chai ...
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Sestili, Heather ...
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Wirthlin, Morgan ...
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show more...
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Phan, BaDoi N.
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Prasad, Kavya
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Brown, Ashley R.
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Zhang, Xiaomeng
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Foley, Kathleen
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Genereux, Diane ...
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Karlsson, Elinor ...
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Lindblad-Toh, Ke ...
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Meyer, Wynn K.
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Pfenning, Andrea ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Genetics
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Science
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Uppsala University