TY - JOUR
T1 - Selective sweep for an enhancer involucrin allele identifies skin barrier adaptation out of Africa
AU - Mathyer, Mary Elizabeth
AU - Brettmann, Erin A.
AU - Schmidt, Alina D.
AU - Goodwin, Zane A.
AU - Oh, Inez Y.
AU - Quiggle, Ashley M.
AU - Tycksen, Eric
AU - Ramakrishnan, Natasha
AU - Matkovich, Scot J.
AU - Guttman-Yassky, Emma
AU - Edwards, John R.
AU - de Guzman Strong, Cristina
N1 - Funding Information:
We thank Renate Lewis at the Hope Center for the design and targeting of the gRNAs, Mia Wallace at the Mouse Core facility for the mice, Toni Sinnwell at the Washington University Genome Technology Access Center for the preparations of the RNA-seq libraries and Illumina sequencing, and Justin Fay and Don Conrad for helpful early discussions. The work cited in this publication was performed in a facility partially supported by NCI Cancer Center Support Grant P30CA91842 to the Siteman Cancer Center and by ICTS/CTSA UL1TR002345 and C06RR015502 from National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), NIH Roadmap for Medical Research, Society of Investigative Dermatology/Sun Pharma Research Innovation Fellowship (E.A.B., M.E.M.), NHGRI T32HG000045 (Z.A.G., A.D. S. [2020–to date]), T32GM007067 (M.E.M.), R25GM103757 (A.D.S. [2017–2019]), and by NIAMS R01AR065523 and R56075427 (C.dG.S.). This content is solely the responsibility of the authors and does not necessarily represent the official views of NCRR or NIH.
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12/1
Y1 - 2021/12/1
N2 - The genetic modules that contribute to human evolution are poorly understood. Here we investigate positive selection in the Epidermal Differentiation Complex locus for skin barrier adaptation in diverse HapMap human populations (CEU, JPT/CHB, and YRI). Using Composite of Multiple Signals and iSAFE, we identify selective sweeps for LCE1A-SMCP and involucrin (IVL) haplotypes associated with human migration out-of-Africa, reaching near fixation in European populations. CEU-IVL is associated with increased IVL expression and a known epidermis-specific enhancer. CRISPR/Cas9 deletion of the orthologous mouse enhancer in vivo reveals a functional requirement for the enhancer to regulate Ivl expression in cis. Reporter assays confirm increased regulatory and additive enhancer effects of CEU-specific polymorphisms identified at predicted IRF1 and NFIC binding sites in the IVL enhancer (rs4845327) and its promoter (rs1854779). Together, our results identify a selective sweep for a cis regulatory module for CEU-IVL, highlighting human skin barrier evolution for increased IVL expression out-of-Africa.
AB - The genetic modules that contribute to human evolution are poorly understood. Here we investigate positive selection in the Epidermal Differentiation Complex locus for skin barrier adaptation in diverse HapMap human populations (CEU, JPT/CHB, and YRI). Using Composite of Multiple Signals and iSAFE, we identify selective sweeps for LCE1A-SMCP and involucrin (IVL) haplotypes associated with human migration out-of-Africa, reaching near fixation in European populations. CEU-IVL is associated with increased IVL expression and a known epidermis-specific enhancer. CRISPR/Cas9 deletion of the orthologous mouse enhancer in vivo reveals a functional requirement for the enhancer to regulate Ivl expression in cis. Reporter assays confirm increased regulatory and additive enhancer effects of CEU-specific polymorphisms identified at predicted IRF1 and NFIC binding sites in the IVL enhancer (rs4845327) and its promoter (rs1854779). Together, our results identify a selective sweep for a cis regulatory module for CEU-IVL, highlighting human skin barrier evolution for increased IVL expression out-of-Africa.
UR - http://www.scopus.com/inward/record.url?scp=85105451459&partnerID=8YFLogxK
U2 - 10.1038/s41467-021-22821-w
DO - 10.1038/s41467-021-22821-w
M3 - Article
C2 - 33963188
AN - SCOPUS:85105451459
SN - 2041-1723
VL - 12
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 2557
ER -