title: Regulatory Divergence among Beta-Keratin Genes during Bird Evolution.
abstract: Feathers, which are mainly composed of α- and β-keratins, are highly diversified, largely owing to duplication and diversification of β-keratin genes during bird evolution. However, little is known about the regulatory changes that contributed to the expressional diversification of β-keratin genes. To address this issue, we studied transcriptomes from five different parts of chicken contour and flight feathers. From these transcriptomes we inferred β-keratin enriched co-expression modules of genes and predicted transcription factors (TFs) of β-keratin genes. In total, we predicted 262 TF-target gene relationships in which 56 TFs regulate 91 β-keratin genes; we validated 14 of them by in vitro tests. A dual criterion of TF enrichment and "TF-target gene" expression correlation identified 26 TFs as the major regulators of β-keratin genes. According to our predictions, the ancestral scale and claw β-keratin genes have common and unique regulators, whereas most feather β-keratin genes show chromosome-wise regulation, distinct from scale and claw β-keratin genes. Thus, after expansion from the β-keratin gene on Chr7 to other chromosomes, which still shares a TF with scale and claw β-keratin genes, most feather β-keratin genes have recruited distinct or chromosome-specific regulators. Moreover, our data showed correlated gene expression profiles, positive or negative, between predicted TFs and their target genes over the five studied feather regions. Therefore, regulatory divergences among feather β-keratin genes have contributed to structural differences among different parts of feathers. Our study sheds light on how feather β-keratin genes have diverged in regulation from scale and claw β-keratin genes and among themselves.
authors: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
authors: Maloyjo Joyraj
authors: MJ
authors: Bhattacharjee
authors: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
authors: Chun-Ping
authors: CP
authors: Yu
authors: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Sciences, Academia Sinica, Nankang, Taipei, Taiwan Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan.
authors: Jinn-Jy
authors: JJ
authors: Lin
authors: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan.
authors: Chen Siang
authors: CS
authors: Ng
authors: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
authors: Tzi-Yuan
authors: TY
authors: Wang
authors: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
authors: Hsin-Hung
authors: HH
authors: Lin
authors: Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, Taiwan Department of Ecology and Evolution, University of Chicago, Chicago, Illinois whli@sinica.edu.tw.
authors: Wen-Hsiung
authors: WH
authors: Li
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002645:Chickens / Q000235:genetics*; D019143:Evolution, Molecular; D005241:Feathers / Q000378:metabolism / Q000502:physiology*; D005786:Gene Expression Regulation / Q000235:genetics*; D014644:Genetic Variation; D005810:Multigene Family; D017422:Sequence Analysis, DNA / Q000379:methods; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome; D053800:beta-Keratins / Q000235:genetics* / Q000378:metabolism
chemical_list: D014157:Transcription Factors; D053800:beta-Keratins
keywords: cis elements; feather evolution; keratin genes; regulatory evolution