Reference
Andersson, L., and Georges, M., 2004. Domestic-animal genomics:
deciphering the genetics of complex traits. Nat. Rev. Genet. 5, 202-212.
Barutcu, Rasim, A., Lajoie, Bryan, R., McCord, Rachel, P., Coralee, E.,
Hong, Deli, and Messier., 2015. Chromatin interaction analysis reveals
changes in small chromosome and telomere clustering between epithelial
and breast cancer cells. Genome Biol. 16, 214-217.
Battulin, N., Fishman, V. S., Mazur, A. M., Pomaznoy, M., Khabarova, A.
A., Afonnikov, D. A., Prokhortchouk, E. B., and Serov, O. L., 2016.
Comparison of the three-dimensional organization of sperm and fibroblast
genomes using the Hi-C approach. Genome Biol. 17, 6-7.
Beagrie, R. A., Scialdone, A., Schueler, M., Kraemer, D. C., Chotalia,
M., Xie, S. Q., Barbieri, M., de Santiago, I., Lavitas, L. M., Branco,
M. R., Fraser, J., Dostie, J., Game, L., Dillon, N., Edwards, P. A.,
Nicodemi, M., and Pombo, A., 2017. Complex multi-enhancer contacts
captured by genome architecture mapping. Nature 543, 519-524.
Bethany, D. S., Skibiel, A. L., Fabris, T. F., Zhang, Y., Dahl, G. E.,
Francisco, P., and Jimena, L., 2018. RNA-Seq reveals novel genes and
pathways involved in bovine mammary involution during the dry period and
under environmental heat stress. Sci. Rep. 8, 11096-11106.
Cardona, A., Pagani, L., Antao, T., Lawson, D. J., Eichstaedt, C. A.,
Yngvadottir, B., Shwe, M. T., Wee, J., Romero, I. G., Raj, S., Metspalu,
M., Villems, R., Willerslev, E., Tyler-Smith, C., Malyarchuk, B. A.,
Derenko, M. V., and Kivisild, T., 2014. Genome-wide analysis of cold
adaptation in indigenous Siberian populations. PLoS One 9, e98076.
Dixon, J. R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J.
E., Lee, A. Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., Diao, Y.,
Liang, J., Zhao, H., Lobanenkov, V. V., Ecker, J. R., Thomson, J. A.,
and Ren, B., 2015. Chromatin architecture reorganization during stem
cell differentiation. Nature 518, 331-336.
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M.,
Liu, J. S., and Ren, B., 2012. Topological domains in mammalian genomes
identified by analysis of chromatin interactions. Nature 485, 376-380.
Elbeltagy, A. R., Bertolini, F., Fleming, D. S., Goor, A. V., and
Rothschild, M. F., 2017. Evidence of Natural Selection Footprints Among
Some African Chicken Breeds and Village Ecotypes. Front Genet. 11.
Fleming, D. S., Weigend, S., Simianer, H., Weigend, A., Rothschild, M.,
Schmidt, C., Ashwell, C., Persia, M., Reecy, J., and Lamont, S. J.,
2017. Genomic Comparison of Indigenous African and Northern European
Chickens Reveals Putative Mechanisms of Stress Tolerance Related to
Environmental Selection Pressure. G3 (Bethesda) 7, 1525-1537.
Franke, M., Ibrahim, D. M., Andrey, G., Schwarzer, W., Heinrich, V.,
Schopflin, R., Kraft, K., Kempfer, R., Jerkovic, I., Chan, W. L.,
Spielmann, M., Timmermann, B., Wittler, L., Kurth, I., Cambiaso, P.,
Zuffardi, O., Houge, G., Lambie, L., Brancati, F., Pombo, A., Vingron,
M., Spitz, F., and Mundlos, S., 2016. Formation of new chromatin domains
determines pathogenicity of genomic duplications. Nature 538, 265-269.
Ishida, T., Hijioka, H., Kume, K., Miyawaki, A., and Nakamura, N.
(2013). Notch signaling induces EMT in OSCC cell lines in a hypoxic
environment. Oncol Lett 6, 1201-1206.
Jiang, S., An, H., Xu, F., and Zhang, X., 2020. Chromosome-level genome
assembly and annotation of the loquat (Eriobotrya japonica) genome.
Gigascience 9.
Kim, J. W., Han, K. R., Kim, W., Jung, H. Y., Nam, S. M., Yoo, D. Y.,
Hwang, I. K., Seong, J. K., and Yoon, Y. S., 2019. Adult Hippocampal
Neurogenesis Can Be Enhanced by Cold Challenge Independently From
Beigeing Effects. Front. Neurosci. 13, 92.
Larson, G., and Fuller, D. Q., 2014. The Evolution of Animal
Domestication. Annu. Rev. Ecol. Evol. S. 45, 115-136.
Lawal, R. A., Al-Atiyat, R. M., Aljumaah, R. S., Pradeepa, S., Mwacharo,
J. M., and Olivier, H., 2018. Whole-Genome Resequencing of Red
Junglefowl and Indigenous Village Chicken Reveal New Insights on the
Genome Dynamics of the Species. Front. Genet. 9, 264-280.
Li, M., Sun, C., Xu, N., Bian, P., Tian, X., Wang, X., Wang, Y., Jia,
X., Heller, R., Wang, M., Wang, F., Dai, X., Luo, R., Guo, Y., Wang, X.,
Yang, P., Hu, D., Liu, Z., Fu, W., Zhang, S., Li, X., Wen, C., Lan, F.,
Siddiki, A. Z., Suwannapoom, C., Zhao, X., Nie, Q., Hu, X., Jiang, Y.,
and Yang, N., 2022. De Novo Assembly of 20 Chicken Genomes Reveals the
Undetectable Phenomenon for Thousands of Core Genes on Microchromosomes
and Subtelomeric Regions. Mol. Biol. Evol. 39, msac066.
Lieberman-Aiden, E., Berkum, N. V., Williams, L., Imakaev, M., Ragoczy,
T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., and Dorschner, M.
O., 2009. Comprehensive Mapping of Long-Range Interactions Reveals
Folding Principles of the Human Genome. Science 326, 289-293.
Lindsey, B. W., and Tropepe, V., 2014. Changes in the social environment
induce neurogenic plasticity predominantly in niches residing in sensory
structures of the zebrafish brain independently of cortisol levels. Dev.
Neurobiol. 74, 1053-1077.
Liu, Y., Su, H., Li, R., Li, X., Xu, Y., Dai, X., Zhou, Y., and Wang,
H., 2017. Comparative transcriptome analysis of Glyphodes pyloalis
Walker (Lepidoptera: Pyralidae) reveals novel insights into heat stress
tolerance in insects. Bmc Genomics 18, 974-986.
Luger, D., Shinder, D., Wolfenson, D., and Yahav, S., 2003.
Erythropoiesis regulation during the development of ascites syndrome in
broiler chickens: a possible role of corticosterone. J. Anim. Sci. 81,
784-790.
Miao, Y. W., Peng, M. S., Wu, G. S., Ouyang, Y. N., Yang, Z. Y., Yu, N.,
Liang, J. P., Pianchou, G., Beja-Pereira, A., Mitra, B., Palanichamy, M.
G., Baig, M., Chaudhuri, T. K., Shen, Y. Y., Kong, Q. P., Murphy, R. W.,
Yao, Y. G., and Zhang, Y. P., 2013. Chicken domestication: an updated
perspective based on mitochondrial genomes. Heredity (Edinb) 110,
277-282.
Pasha, M. Q., Pandey, P., Mohammad, G., and Singh, Y., 2015. ROCK2 and
MYLK variants under hypobaric hypoxic environment of high altitude
associate with high altitude pulmonary edema and adaptation. Application
of Clinical Genetics 8, 257-267.
Rafique, S., Thomas, J. S., Sproul, D., and Bickmore, W. A., 2015.
Estrogen-induced chromatin decondensation and nuclear re-organization
linked to regional epigenetic regulation in breast cancer. Genome biol.
16, 145-163.
Rao, S. S., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I.
D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., and
Lander, E. S., 2014. A 3D map of the human genome at kilobase resolution
reveals principles of chromatin looping. Cell 159, 1665-1680.
Shi, S., Shao, D., Yang, L., Liang, Q., Han, W., Xue, Q., Qu, L., Leng,
L., Li, Y., Zhao, X., Dong, P., Walugembe, M., Kayang, B. B., Muhairwa,
A. P., Zhou, H., and Tong, H., 2022. Whole genome analyses reveal novel
genes associated with chicken adaptation to tropical and frigid
environments. J. Adv. Res.
Steven, W., Philip, E., Mayra, F. M., Takashi, N., Stefan, S., Peter,
F., and Simon, A.. 2015. HiCUP: pipeline for mapping and processing Hi-C
data. F1000res 4, 1310.
Taberlay, P. C., Achinger-Kawecka, J., Lun, A., Buske, F. A., Sabir, K.,
Gould, C. M., Zotenko, E., Bert, S. A., Giles, K. A., and Bauer, D. C.,
2016. Three-dimensional disorganization of the cancer genome occurs
coincident with long-range genetic and epigenetic alterations. Genome
Res. 26.719-731.
Takashima, S., 2009. Phosphorylation of myosin regulatory light chain by
myosin light chain kinase, and muscle contraction. Circ. J. 73, 208-213.
Tian, S., Zhou, X., Zhang, D., Ning, C., Li, D., and Zhao, H., 2020.
Genomic Analyses Reveal Genetic Adaptations to Tropical Climates in
Chickens. iScience 23, 101644-101658.
Tjong, H., Li, W., Kalhor, R., Dai, C., Hao, S., Gong, K., Zhou, Y., Li,
H., Zhou, X. J., Le Gros, M. A., Larabell, C. A., Chen, L., and Alber,
F., 2016. Population-based 3D genome structure analysis reveals driving
forces in spatial genome organization. Proc. Natl. Acad. Sci. U. S. A.
113, E1663-E1672.
Veniamin, Fishman, Nariman, Battulin, Miroslav, Nuriddinov, Antonina,
Maslova, Anna, and Zlotina., 2018. 3D organization of chicken genome
demonstrates evolutionary conservation of topologically associated
domains and highlights unique architecture of erythrocytes’ chromatin.
Nucleic Acids Res. 47, 648-665.
Walsh, M. P., 1994. Calmodulin and the regulation of smooth muscle
contraction. Mol. Cell. Biochem. 135, 21-41.
Wang, M., Wang, P., Lin, M., Ye, Z., Li, G., Tu, L., Shen, C., Li, J.,
Yang, Q., and Zhang, X., 2018. Evolutionary dynamics of 3D genome
architecture following polyploidization in cotton. Nature Plants. 4,
90-97.
Wang, M. S., Li, Y., Peng, M. S., Zhong, L., Wang, Z. J., Li, Q. Y., Tu,
X. L., Dong, Y., Zhu, C. L., Wang, L., Yang, M. M., Wu, S. F., Miao, Y.
W., Liu, J. P., Irwin, D. M., Wang, W., Wu, D. D., and Zhang, Y. P.,
2015. Genomic Analyses Reveal Potential Independent Adaptation to High
Altitude in Tibetan Chickens. Mol. Biol. Evol. 32, 1880-1889.
Wang, M. S., Thakur, M., Peng, M. S., Jiang, Y., and Zhang, Y. P., 2020.
Author Correction: 863 genomes reveal the origin and domestication of
chicken. Cell Res. 30, 693-701.
Wang, Y., Guo, F., Pan, C., Lou, Y., Zhang, P., Guo, S., Yin, J., and
Deng, Z., 2012. Effects of low temperatures on proliferation-related
signaling pathways in the hippocampus after traumatic brain injury. Exp.
Biol. Med. 237, 1424-1432.
Wu, P., Li, T., Li, R., Jia, L., Zhu, P., Liu, Y., Chen, Q., Tang, D.,
Yu, Y., and Li, C., 2017. 3D genome of multiple myeloma reveals spatial
genome disorganization associated with copy number variations. Nat.
Commun. 8, 1937.
Ying, S. U., Long, Y., Liao, X., Huashui, A. I., Zhang, Z., Yang, B.,
Xiao, S., Tang, J., Xin, W., and Huang, L., 2015. Detection of genomic
signatures for pig hairlessness using high-density SNP data. Front. Agr.
Sci. Engi. 1, 307-313.
Zhang, W., Jiao, L., Liu, R., Zhang, Y., Ji, Q., Zhang, H., Gao, X., Ma,
Y., and Shi, H. N., 2018a. The effect of exposure to high altitude and
low oxygen on intestinal microbial communities in mice. PLoS One 13,
e0203701.
Zhang, Z., Du, H., Bai, L., Yang, C., Li, Q., Li, X., Qiu, M., Yu, C.,
Jiang, Z., Jiang, X., Liu, L., Hu, C., Xia, B., Xiong, X., Song, X., and
Jiang, X., 2018b. Whole genome bisulfite sequencing reveals unique
adaptations to high-altitude environments in Tibetan chickens. PLoS One
13, e0193597.