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Cai Z, He Y, Liu S, Xue Y, Quan H, Zhang L, Gao YQ. Hierarchical dinucleotide distribution in genome along evolution and its effect on chromatin packing. Life Sci Alliance 2021; 4:4/8/e202101028. [PMID: 34168075 PMCID: PMC8321668 DOI: 10.26508/lsa.202101028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 11/29/2022] Open
Abstract
It describes how hierarchical CpG distribution on the genomes of species change in the evolution and the correlation with the chromatin structure. Dinucleotide densities and their distribution patterns vary significantly among species. Previous studies revealed that CpG is susceptible to methylation, enriched at topologically associating domain boundaries and its distribution along the genome correlates with chromatin compartmentalization. However, the multi-scale organizations of CpG in the linear genome, their role in chromatin organization, and how they change along the evolution are only partially understood. By comparing the CpG distribution at different genomic length scales, we quantify the difference between the CpG distributions of different species and evaluate how the hierarchical uneven CpG distribution appears in evolution. The clustering of species based on the CpG distribution is consistent with the phylogenetic tree. Interestingly, we found the CpG distribution and chromatin structure to be correlated in many different length scales, especially for mammals and avians, consistent with the mosaic CpG distribution in the genomes of these species.
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Affiliation(s)
- Zhicheng Cai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Yueying He
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Sirui Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Yue Xue
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Hui Quan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Ling Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China .,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
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Effects of parity and serum prolactin levels on the incidence and regression of DMBA-induced tumors in OFA hr/hr rats. BIOMED RESEARCH INTERNATIONAL 2014; 2014:210424. [PMID: 25136563 PMCID: PMC4124788 DOI: 10.1155/2014/210424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/19/2014] [Accepted: 07/02/2014] [Indexed: 11/23/2022]
Abstract
Prolactin (PRL) is a key player in the development of mammary cancer. We studied the effects of parity or hyperprolactinemia on mammary carcinogenesis in OFA hr/hr treated with 7,12-dimethylbenzanthracene. They were divided into three groups: nulliparous (Null), primiparous (PL, after pregnancy and lactation), and hyperprolactinemic rats (I, implanted in the arcuate nucleus with 17β-estradiol). The tumor incidence was similar in the three groups. However, a higher percentage of regressing tumors was evident in the PL group. Serum PRL, mammary development, and mammary β-casein content were higher in I rats compared to Null. The expression of hormone receptors was similar in the different groups. However, mammary tissue from PL rats bearing tumors had increased expression of PRL and estrogen alpha receptors compared to rats free of tumors. Our results suggest that serum PRL levels do not have relevance on the incidence of tumors, probably because the low levels of PRL in OFA rats are not further decreased by PL like in other strains. However, supraphysiological levels of PRL affect carcinogenesis. PL induces regression of the tumors due to the differentiation produced on the mammary cells. Alterations in the expression of hormonal receptors may be involved in progression and regression of tumors.
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Benavides F, Oberyszyn TM, VanBuskirk AM, Reeve VE, Kusewitt DF. The hairless mouse in skin research. J Dermatol Sci 2008; 53:10-8. [PMID: 18938063 DOI: 10.1016/j.jdermsci.2008.08.012] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 07/21/2008] [Accepted: 08/19/2008] [Indexed: 01/07/2023]
Abstract
The hairless (Hr) gene encodes a transcriptional co-repressor highly expressed in the mammalian skin. In the mouse, several null and hypomorphic Hr alleles have been identified resulting in hairlessness in homozygous animals, characterized by alopecia developing after a single cycle of relatively normal hair growth. Mutations in the human ortholog have also been associated with congenital alopecia. Although a variety of hairless strains have been developed, outbred SKH1 mice are the most widely used in dermatologic research. These unpigmented and immunocompetent mice allow for ready manipulation of the skin, application of topical agents, and exposure to UVR, as well as easy visualization of the cutaneous response. Wound healing, acute photobiologic responses, and skin carcinogenesis have been extensively studied in SKH1 mice and are well characterized. In addition, tumors induced in these mice resemble, both at the morphologic and molecular levels, UVR-induced skin malignancies in man. Two limitations of the SKH1 mouse in dermatologic research are the relatively uncharacterized genetic background and its outbred status, which precludes inter-individual transplantation studies.
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Affiliation(s)
- Fernando Benavides
- Department of Carcinogenesis, Science Park Research Division, University of Texas, MD Anderson Cancer Center, Smithville, TX 78957, USA
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Valdez SR, Penissi AB, Deis RP, Jahn GA. Hormonal profile and reproductive performance in lactation deficient (OFA hr/hr) and normal (Sprague–Dawley) female rats. Reproduction 2007; 133:827-40. [PMID: 17504926 DOI: 10.1530/rep-06-0032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Lactation deficiency may have important consequences on infant health, particularly in populations of low socioeconomic status. The OFAhr/hr(OFA) strain of rats, derived from Sprague–Dawley (SD) rats, has deficient lactation and is a good model of lactation failure. We examined the reproductive performance and hormonal profiles in OFA and SD strains to determine the cause(s) of the lactation failure of the OFA strain. We measured hormonal (PRL, GH, gonadotropins, oxytocin, and progesterone) levels by RIA in cycling, pregnant, and lactating rats and in response to suckling. Dopaminergic metabolism was assessed by determination of mediobasal hypothalamic dopamine and dihydroxyphenylacetic acid (DOPAC) concentrations by HPLC and tyrosine hydroxylase expression by immunocytochemistry and western blot. OFA rats have normal fertility but 50% of the litters die of malnutrition on early lactation; only 6% of the mothers show normal lactation. The OFA rats showed lower circulating PRL during lactation, increased hypothalamic dopamine and DOPAC, and impaired milk ejection with decreased PRL and oxytocin response to suckling. Before parturition, PRL release and lactogenesis were normal, but dopaminergic metabolism was altered, suggesting activation of the dopaminergic system in OFA but not in SD rats. The number of arcuate and periventricular neurons expressing tyrosine hydroxylase was higher in SD rats, but hypothalamic expression of TH was higher in OFA rats at the end of pregnancy and early lactation. These results suggest that the OFA rats have impaired PRL release linked with an augmented dopaminergic tone which could be partially responsible for the lactational failure.
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MESH Headings
- 3,4-Dihydroxyphenylacetic Acid/analysis
- Animals
- Blotting, Western
- Caseins/analysis
- Chromatography, High Pressure Liquid
- Desmogleins/genetics
- Dopamine/analysis
- Female
- Hypothalamus, Middle/chemistry
- Lactation/physiology
- Lactose/analysis
- Mammary Glands, Animal/chemistry
- Mammary Glands, Animal/pathology
- Models, Animal
- Pregnancy
- Pregnancy, Animal/metabolism
- Proestrus/metabolism
- Prolactin/blood
- Rats
- Rats, Mutant Strains
- Rats, Sprague-Dawley
- Tyrosine 3-Monooxygenase/analysis
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Affiliation(s)
- Susana R Valdez
- Laboratorio de Reproducción y Lactancia, IMBECU, CRICYT-CONICET, Casilla de Correos 855, 5500 Mendoza, Argentina
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