Study on the spatial distribution patterns of histone modifications in Hippo pathway genes

Wenxia Su; Dimeng Zhang; Qiang Zhang; Qianzhong Li

doi:10.52601/bpr.2021.200042

Volume 7 Issue 1

Feb. 2021

Turn off MathJax

Article Contents

Article Navigation > Biophysics Reports > 2021 > 7(1): 71-79

Wenxia Su, Dimeng Zhang, Qiang Zhang, Qianzhong Li. Study on the spatial distribution patterns of histone modifications in Hippo pathway genes[J]. Biophysics Reports, 2021, 7(1): 71-79. doi: 10.52601/bpr.2021.200042

Citation:

Wenxia Su, Dimeng Zhang, Qiang Zhang, Qianzhong Li. Study on the spatial distribution patterns of histone modifications in Hippo pathway genes[J]. Biophysics Reports, 2021, 7(1): 71-79. doi: 10.52601/bpr.2021.200042

Citation:

PDF (539 KB)

Study on the spatial distribution patterns of histone modifications in Hippo pathway genes

doi: 10.52601/bpr.2021.200042

Wenxia Su^{1
,
,},
Dimeng Zhang¹,
Qiang Zhang¹,
Qianzhong Li^{2, 3
,
,}

1.
College of Science, Inner Mongolia Agriculture University, Hohhot 010018, China
2.
Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
3.
The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010070, China

Funds: This work was supported by a grant from the Foundation for basic science research of Inner Mongolia Agricultural University (JC2017004), the Doctoral Initial Scientific Research Fund of Inner Mongolia Agricultural University (NDGCC2016-09), Scientific and Technological Research Project of Colleges and Universities in Inner Mongolia (NJZY21473) and the National Natural Science Foundation of China (31870838).

More Information

Corresponding author: swx@imau.edu.cn (W. Su); qzli@imu.edu.cn (Q. Li)
Received Date: 26 August 2020
Accepted Date: 13 December 2020

Available Online: 20 April 2021

Publish Date: 28 February 2021

Abstract

Abstract

Hippo pathway can regulate cell division, differentiation and apoptosis, and control the shape and size of organs. To study the distribution patterns of histone modifications of Hippo pathway genes in embryonic stem cells is helpful to understand the molecular regulation mechanism of histone modification and Hippo pathway on stem cell self-renewal. In this study, 19 genes of Hippo pathway including YAP, TAZ, LATS1/2, MST1 and SAV1, and eight histone modifications in embryonic stem cells were chosen to study the spatial distribution patterns of histone modifications. It was found that there were obvious type specificity and the location preference of target regions in the distributions of histone modifications, and H3K4me3 and H3K36me3 played the most important regulatory roles. Through the correlation analysis of histone modifications, a histone modification functional cluster composed of H3K4ac, H3K4me3, H3K9ac and H3K27ac was detected in YAP. In addition, the spatial distribution patterns of histone modifications in Hippo pathway genes were obtained, which provided a new theoretical reference for elucidating the mechanism of histone modifications regulating the gene expression of Hippo pathway, and for revealing the molecular regulatory mechanism of histone modifications affecting the self-renewal of embryonic stem cells by regulating the Hippo pathway.
- Embryonic stem cell,
- Hippo pathway,
- Histone modification,
- Spatial distribution pattern

FullText(HTML)

References(27)

References

[1]	Bhanu NV, Sidoli S, Garcia BA (2016) Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation. Proteomics 16: 448−458 doi: 10.1002/pmic.201500231
[2]	Camargo FD, Gokhale S, Johnnidis JB, Fu D, Bell GW, Jaenisch R, Brummelkamp TR (2007) YAP1 increases organ size and expands undifferentiated progenitor cells. Curr Biol 17: 2054−2060 doi: 10.1016/j.cub.2007.10.039
[3]	Chen YA, Lu CY, Cheng TY, Pan SH, Chen HF, Chang NS (2019) WW domain-containing proteins YAP and TAZ in the Hippo pathway as key regulators in stemness maintenance, tissue homeostasis, and tumorigenesis. Front Oncol 9: 60. https://doi.org/10.3389/fonc.2019.00060
[4]	Darr H, Benvenisty N (2006) Human embryonic stem cells: the battle between self-renewal and differentiation. Regen Med 3: 317−325
[5]	Evans, M. (2011) Discovering pluripotency: 30 years of mouse embryonic stem cells. Nat Rev Mol Cell Biol 12: 680−686 doi: 10.1038/nrm3190
[6]	Fischle W, Wang Y, Allis CD (2003) Histone and chromatin cross-talk. Curr Opin Cell Biol 15: 172−183 doi: 10.1016/S0955-0674(03)00013-9
[7]	Feng ZX, Li QZ, Meng JJ (2019) Modeling the relationship of diverse genomic signatures to gene expression levels with the regulation of long-range enhancer-promoter interactions. Biophys Rep 5: 123−132 doi: 10.1007/s41048-019-0089-z
[8]	Fu V, Plouﬀe, Steven W, Guan KL (2017) The Hippo pathway in organ development, homeostasis, and regeneration. Curr Opin Cell Biol 49: 99−107 doi: 10.1016/j.ceb.2017.12.012
[9]	Huang J, Wu S, Barrera J, Matthews K, Pan D (2005) The Hippo signaling pathway coordinately regulates cell proliferation and apoptosis by inactivating Yorkie, the Drosophila homolog of YAP. Cell 122: 421−434 doi: 10.1016/j.cell.2005.06.007
[10]	Kim N, Koh E (2011) E-cadherin mediates contact inhibition of proliferation through Hippo signaling-pathway components. Proc Natl Acad Sci USA 2011: 11930−11935
[11]	Lee KK, Yonehara S (2012) Identification of mechanism that couples multisite phosphorylation of Yes-associated protein (YAP) with transcriptional coactivation and regulation of apoptosis. J Biol Chem 287: 9568−9578 doi: 10.1074/jbc.M111.296954
[12]	Lei QY, Zhang H, Zhao B, Zha ZY, Bai F, Pei XH, Zhao S, Xiong Y, Guan KL (2008) TAZ promotes cell proliferation and epithelial mesenchymal transition and is inhibited by the hippo pathway. Mol Cell Biol 28: 2426−2436 doi: 10.1128/MCB.01874-07
[13]	Li S, Yang D, Gao L, Wang YX, Peng Q (2020) Epigenetic regulation and mechanobiology. Biophys Rep 6: 33−48 doi: 10.1007/s41048-020-00106-x
[14]	Mo JS, Park HW, Guan KL (2014) The Hippo signaling pathway in stem cell biology and cancer. EMBO Rep 15: 642−656 doi: 10.15252/embr.201438638
[15]	Mori M, Triboulet R, Mohseni M, Schlegelmilch K, Shrestha K, Camargo FD, Gregory RI (2014) Hippo signaling regulates microprocessor and links cell-density-dependent miRNA biogenesis to cancer. Cell 156: 893−906 doi: 10.1016/j.cell.2013.12.043
[16]	Pan D (2010) The hippo signaling pathway in development and cancer. Dev Cell 19: 491−505 doi: 10.1016/j.devcel.2010.09.011
[17]	Qin H, Blaschke K, Wei G, Ohi Y, Blouin L, Qi ZX, Yu JW, Yeh RF, Hebrok M, Miguel RS (2012) Transcriptional analysis of pluripotency reveals the Hippo pathway as a barrier to reprogramming. Hum Mol Genet 21: 2054−2067 doi: 10.1093/hmg/dds023
[18]	Ramos A, Camargo FD (2012) The Hippo signaling pathway and stem cell biology. Trends Cell Biol 22: 339−346 doi: 10.1016/j.tcb.2012.04.006
[19]	Su WX, Li QZ, Zuo YC, Zhang LQ (2016a) Association analysis between the distributions of histone modifications and gene expression in the human embryonic stem cell. Gene 575: 90−100 doi: 10.1016/j.gene.2015.08.041
[20]	Su WX, Li QZ, Zhang LQ, Fan GL, Wu CY, Yan ZH, Zuo YC (2016b) Gene expression classification using epigenetic features and DNA sequence composition in the human embryonic stem cell line H1. Gene 592: 227−234 doi: 10.1016/j.gene.2016.07.059
[21]	Su WX, Li QZ (2015) The relationship between CG content and histone modifications of promoters in human embryonic stem cell. Biophys Rep 31: 263−271
[22]	Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663−676 doi: 10.1016/j.cell.2006.07.024
[23]	Ucar D, Hu Q, Tan K (2011) Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering. Nucleic Acids Res 39: 4063−4075 doi: 10.1093/nar/gkr016
[24]	Wang Y, Yu A, Yu FX (2017) The Hippo pathway in tissue homeostasis and regeneration. Protein Cell 8: 349−359 doi: 10.1007/s13238-017-0371-0
[25]	Xiao L, Yuan X, Sharkis SJ (2006) Activin A maintains self-renewal and regulates fibroblast growth factor, Wnt, and bone morphogenic protein pathways in human embryonic stem cells. Stem Cells 24: 1476−1486 doi: 10.1634/stemcells.2005-0299
[26]	Yu FX, Guan KL (2013) The Hippo pathway: regulators and regulations. Genes Dev 27: 355−371 doi: 10.1101/gad.210773.112
[27]	Zhao B, Wei X, Li W, Udan RS, Yang Q, Kim J, Xie J, Ikenoue T, Yu J, Li L, Zheng P, Ye K, Chinnaiyan A, Halder G, Lai Z-C, Guan K-L (2007) Inactivation of YAP oncoprotein by the Hippo pathway is involved in cell contact inhibition and tissue growth control. Genes Dev 21: 2747−2761 doi: 10.1101/gad.1602907