title: A de novo silencer causes elimination of MITF-M expression and profound hearing loss in pigs.
abstract: Genesis of novel gene regulatory modules is largely responsible for morphological and functional evolution. De novo generation of novel cis-regulatory elements (CREs) is much rarer than genomic events that alter existing CREs such as transposition, promoter switching or co-option. Only one case of de novo generation has been reported to date, in fish and without involvement of phenotype alteration. Yet, this event likely occurs in other animals and helps drive genetic/phenotypic variation.
  
  
  
  Using a porcine model of spontaneous hearing loss not previously characterized we performed gene mapping and mutation screening to determine the genetic foundation of the phenotype. We identified a mutation in the non-regulatory region of the melanocyte-specific promoter of microphthalmia-associated transcription factor (MITF) gene that generated a novel silencer. The consequent elimination of expression of the MITF-M isoform led to early degeneration of the intermediate cells of the cochlear stria vascularis and profound hearing loss, as well as depigmentation, all of which resemble the typical phenotype of Waardenburg syndrome in humans. The mutation exclusively affected MITF-M and no other isoforms. The essential function of Mitf-m in hearing development was further validated using a knock-out mouse model.
  
  
  
  Elimination of the MITF-M isoform alone is sufficient to cause deafness and depigmentation. To our knowledge, this study provides the first evidence of a de novo CRE in mammals that produces a systemic functional effect.
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.|Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Guo
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Ren
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
authors.forename: Mingyao
authors.initials: M
authors.lastname: Yang
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Yaofeng
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Zongyi
authors.initials: Z
authors.lastname: Guo
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Haijin
authors.initials: H
authors.lastname: Yi
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
authors.forename: Mingzhou
authors.initials: M
authors.lastname: Li
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Yiqing
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Xi
authors.initials: X
authors.lastname: Long
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
authors.forename: Boyuan
authors.initials: B
authors.lastname: Sun
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Jinxiu
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Suoqiang
authors.initials: S
authors.lastname: Zhai
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Tinghuan
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
authors.forename: Shilin
authors.initials: S
authors.lastname: Tian
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Qingyong
authors.initials: Q
authors.lastname: Meng
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Yu
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Zhu
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
authors.forename: Guoqing
authors.initials: G
authors.lastname: Tang
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
authors.forename: Qianzi
authors.initials: Q
authors.lastname: Tang
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Liming
authors.initials: L
authors.lastname: Ren
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Ke
authors.initials: K
authors.lastname: Liu
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Shihua
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, 625014, China.
authors.forename: Tiandong
authors.initials: T
authors.lastname: Che
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Zhengquan
authors.initials: Z
authors.lastname: Yu
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Wu
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Lan
authors.initials: L
authors.lastname: Jing
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Ran
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Cong
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Siqing
authors.initials: S
authors.lastname: Chen
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Yiqiang
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Bai
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Lidong
authors.initials: L
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Fengming
authors.initials: F
authors.lastname: Zhang
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Zhaohui
authors.initials: Z
authors.lastname: Hou
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Jiugang
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
authors.forename: Jianan
authors.initials: J
authors.lastname: Li
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Lijuan
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Communicative Disorders and Sciences, Center for Hearing and Deafness, State University of New York at Buffalo, Buffalo, New York, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Sun
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Xiangang
authors.initials: X
authors.lastname: Zou
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Wang
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Liangpeng
authors.initials: L
authors.lastname: Ge
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China.
authors.forename: Zuohua
authors.initials: Z
authors.lastname: Liu
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Xiaoxiang
authors.initials: X
authors.lastname: Hu
authors.affiliation: Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Science, Chongqing, 402460, China. kingyou@vip.sina.com.
authors.forename: Jingyong
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Otolaryngology, Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China. yangsm301@263.net.
authors.forename: Shiming
authors.initials: S
authors.lastname: Yang
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China. ninglcau@cau.edu.cn.
authors.forename: Ning
authors.initials: N
authors.lastname: Li
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D003051:Cochlea / Q000473:pathology / Q000503:physiopathology; D004195:Disease Models, Animal; D055724:Electrophysiological Phenomena; D005786:Gene Expression Regulation; D005820:Genetic Testing; D055106:Genome-Wide Association Study; D034381:Hearing Loss / Q000235:genetics* / Q000503:physiopathology; D051739:Microphthalmia-Associated Transcription Factor / Q000235:genetics* / Q000378:metabolism; D009154:Mutation / Q000235:genetics; D010641:Phenotype; D011401:Promoter Regions, Genetic; D020033:Protein Isoforms / Q000235:genetics; D037941:Silencer Elements, Transcriptional / Q000235:genetics*; D034421:Sus scrofa / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D051739:Microphthalmia-Associated Transcription Factor; D020033:Protein Isoforms
keywords: De novo silencer; Hearing loss; MITF-M; Pig; Waardenburg syndrome; cis-regulatory element