title: Progressive Loss of Function in a Limb Enhancer during Snake Evolution.
abstract: The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP.
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Evgeny Z
authors: EZ
authors: Kvon
authors: Department of Biology, Stanford University, Stanford, CA 94305, USA.
authors: Olga K
authors: OK
authors: Kamneva
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Uirá S
authors: US
authors: Melo
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Iros
authors: I
authors: Barozzi
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Marco
authors: M
authors: Osterwalder
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Brandon J
authors: BJ
authors: Mannion
authors: Department of Biomedicine, University of Basel, 4058 Basel, Switzerland.
authors: Virginie
authors: V
authors: Tissières
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Catherine S
authors: CS
authors: Pickle
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Ingrid
authors: I
authors: Plajzer-Frick
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Elizabeth A
authors: EA
authors: Lee
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Momoe
authors: M
authors: Kato
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Tyler H
authors: TH
authors: Garvin
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Jennifer A
authors: JA
authors: Akiyama
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Veena
authors: V
authors: Afzal
authors: Department of Biomedicine, University of Basel, 4058 Basel, Switzerland.
authors: Javier
authors: J
authors: Lopez-Rios
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors: Edward M
authors: EM
authors: Rubin
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Diane E
authors: DE
authors: Dickel
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA. Electronic address: lapennacchio@lbl.gov.
authors: Len A
authors: LA
authors: Pennacchio
authors: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95343, USA. Electronic address: avisel@lbl.gov.
authors: Axel
authors: A
authors: Visel
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D004742:Enhancer Elements, Genetic; D019143:Evolution, Molecular; D005121:Extremities / Q000254:growth & development*; D055879:Gene Knock-In Techniques; D053823:Hedgehog Proteins / Q000235:genetics*; D051379:Mice; D008822:Mice, Transgenic; D009154:Mutation; D010802:Phylogeny; D012911:Snakes / Q000145:classification / Q000235:genetics*
chemical_list: D053823:Hedgehog Proteins
keywords: CRISPR/Cas9; Sonic hedgehog (Shh); ZRS; cis-regulatory element; enhancer; evo-devo; genome editing; limb development; morphological evolution; snakes