TY - JOUR
T1 - Cis-regulatory evolution of the recently expanded Ly49 gene family
AU - Fan, Changxu
AU - Xing, Xiaoyun
AU - Murphy, Samuel J.H.
AU - Poursine-Laurent, Jennifer
AU - Schmidt, Heather
AU - Parikh, Bijal A.
AU - Yoon, Jeesang
AU - Choudhary, Mayank N.K.
AU - Saligrama, Naresha
AU - Piersma, Sytse J.
AU - Yokoyama, Wayne M.
AU - Wang, Ting
N1 - Publisher Copyright:
© The Author(s) 2024.
PY - 2024/12
Y1 - 2024/12
N2 - Comparative genomics has revealed the rapid expansion of multiple gene families involved in immunity. Members within each gene family often evolved distinct roles in immunity. However, less is known about the evolution of their epigenome and cis-regulation. Here we systematically profile the epigenome of the recently expanded murine Ly49 gene family that mainly encode either inhibitory or activating surface receptors on natural killer cells. We identify a set of cis-regulatory elements (CREs) for activating Ly49 genes. In addition, we show that in mice, inhibitory and activating Ly49 genes are regulated by two separate sets of proximal CREs, likely resulting from lineage-specific losses of CRE activity. Furthermore, we find that some Ly49 genes are cross-regulated by the CREs of other Ly49 genes, suggesting that the Ly49 family has begun to evolve a concerted cis-regulatory mechanism. Collectively, we demonstrate the different modes of cis-regulatory evolution for a rapidly expanding gene family.
AB - Comparative genomics has revealed the rapid expansion of multiple gene families involved in immunity. Members within each gene family often evolved distinct roles in immunity. However, less is known about the evolution of their epigenome and cis-regulation. Here we systematically profile the epigenome of the recently expanded murine Ly49 gene family that mainly encode either inhibitory or activating surface receptors on natural killer cells. We identify a set of cis-regulatory elements (CREs) for activating Ly49 genes. In addition, we show that in mice, inhibitory and activating Ly49 genes are regulated by two separate sets of proximal CREs, likely resulting from lineage-specific losses of CRE activity. Furthermore, we find that some Ly49 genes are cross-regulated by the CREs of other Ly49 genes, suggesting that the Ly49 family has begun to evolve a concerted cis-regulatory mechanism. Collectively, we demonstrate the different modes of cis-regulatory evolution for a rapidly expanding gene family.
UR - http://www.scopus.com/inward/record.url?scp=85195439291&partnerID=8YFLogxK
U2 - 10.1038/s41467-024-48990-y
DO - 10.1038/s41467-024-48990-y
M3 - Article
C2 - 38844462
AN - SCOPUS:85195439291
SN - 2041-1723
VL - 15
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 4839
ER -