轉(zhuǎn)錄因子結(jié)合位點方法

轉(zhuǎn)錄因子結(jié)合位點方法

高通量檢測轉(zhuǎn)錄因子或DNA結(jié)合蛋白在基因組上的結(jié)合位點

在功能基因組學(xué)和表觀遺傳學(xué)研究中，轉(zhuǎn)錄因子結(jié)合位點(TFBS)的發(fā)掘一直是研究熱點。傳統(tǒng)的ChlP-seq(染色質(zhì)免疫共沉淀測序)方法，在抗體質(zhì)量很好的情況下能夠有效檢測到TFBS。

然而,好的抗體可遇不可求，

這限制了ChlP-seq更廣泛的應(yīng)用。

DAP-seq技術(shù)的出現(xiàn),

使TFBS的研究不再局限于物種，

不再受抗體質(zhì)量的限制,

為生命科學(xué)和醫(yī)學(xué)領(lǐng)域轉(zhuǎn)錄因子的研究提供了新的有效工具。

生信分析

1

對原始數(shù)據(jù)進行去除接頭、污染序列及低

Peak序列模式發(fā)掘(motif search)

質(zhì)量reads的處理

已知motif注釋

數(shù)據(jù)產(chǎn)出統(tǒng)計

Peak相關(guān)基因鑒定

3參考序列比對分析

1Peak相關(guān)基因的GO和KEGG富集分析

測序reads富集區(qū)域掃描(peak calling)

Peak長度分布統(tǒng)計

1

測序數(shù)據(jù)的差異分析(>=2個樣本)

Peak在基因功能元件上的分布統(tǒng)計

1測序數(shù)據(jù)的可視化分析

項目可行性分析

本地保存成功

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開展項目之前,我們會根據(jù)您具體的轉(zhuǎn)錄因子做可行性分析報告,供您參考,從多個方面進行可行性分析,包括轉(zhuǎn)錄因子分子量,亞細(xì)胞定位預(yù)測,跨膜區(qū)預(yù)測,蛋白質(zhì)結(jié)構(gòu)域預(yù)測、翻譯后修飾預(yù)測,并且根據(jù)文獻報道和我們的經(jīng)驗來進行可行性分析。

轉(zhuǎn)錄因子結(jié)合位點方法

合作案例：

Zhang SL, Wang L, Yao J, Wu N, Ahmad B, Nocker S, Wu JY, Abudureheman R, Li Z, Wang XP. Control of ovule development in Vitis vinifera by VvMADS28 and interacting genes. Horticulture Research. 2023. doi: 10.1093/hr/uhad070. (IF=7.291) 

Wang L, Tian T, Liang J, Li R, Xin X, Qi Y, Zhou Y, Fan Q, Ning G, Becana M, Duanmu D. A transcription factor of the NAC family regulates nitrate-induced legume nodule senescence. New Phytol. 2023 Mar 22. doi: 10.1111/nph.18896. (IF=10.323)

Sun Y, Han Y, Sheng K, Yang P, Cao Y, Li H, Zhu QH, Chen J, Zhu S, Zhao T. Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii. Mol Plant. 2023. doi: 10.1016/j.molp.2023.02.005. (IF=21.949) 

Liu Y, Liu Q, Li X, Zhang Z, Ai S, Liu C, Ma F, Li C. MdERF114 enhances the resistance of apple roots to Fusarium solani by regulating the transcription of MdPRX63. Plant Physiol. 2023. doi: 10.1093/plphys/kiad057. (IF=8.005) 

Liu YN, Wu FY, Tian RY, Shi YX, Xu ZQ, Liu JY, Huang J, Xue FF, Liu BY, Liu GQ. The bHLH-zip transcription factor SREBP regulates triterpenoid and lipid metabolisms in the medicinal fungus Ganoderma lingzhi. Commun Biol. 2023. doi: 10.1038/s42003-022-04154-6. (IF=6.548)

Liu L, Chen G, Li S, Gu Y, Lu L, Qanmber G, Mendu V, Liu Z, Li F, Yang Z. A brassinosteroid transcriptional regulatory network participates in regulating fiber elongation in cotton. Plant Physiol. 2022. doi: 10.1093/plphys/kiac590. (IF=8.005)

Li M, Hou L, Zhang C, Yang W, Liu X, Zhao H, Pang X, Li Y. Genome-Wide Identification of Direct Targets of ZjVND7 Reveals the Putative Roles of Whole-Genome Duplication in Sour Jujube in Regulating Xylem Vessel Differentiation and Drought Tolerance. Front Plant Sci. 2022 Feb 4;13:829765. doi: 10.3389/fpls.2022.829765. (IF=6.627)

Bi Y, Wang H, Yuan X, Yan Y, Li D, Song F. The NAC transcription factor ONAC083 negatively regulates rice immunity against Magnaporthe oryzae by directly activating transcription of the RING-H2 gene OsRFPH2-6. J Integr Plant Biol. 2022. doi: 10.1111/jipb.13399. (IF=9.106)

Guo X, Yu X, Xu Z, Zhao P, Zou L, Li W, Geng M, Zhang P, Peng M, Ruan M. CC-type glutaredoxin, MeGRXC3, associates with catalases and negatively regulates drought tolerance in cassava (Manihot esculenta Crantz). Plant Biotechnol J. 2022. doi: 10.1111/pbi.13920. (IF=13.263)

Chai Z, Fang J, Huang C, Huang R, Tan X, Chen B, Yao W, Zhang M. A novel transcription factor, ScAIL1, modulates plant defense responses by targeting DELLA and regulating gibberellin and jasmonic acid signaling in sugarcane. J Exp Bot. 2022. 73: 6727-6743. doi: 10.1093/jxb/erac339. (IF=7.298)

Li R, Zheng W, Yang R, Hu Q, Ma L, Zhang H. OsSGT1 promotes melatonin-ameliorated seed tolerance to chromium stress by affecting the OsABI5-OsAPX1 transcriptional module in rice. Plant J. 2022. 112: 151-171. doi: 10.1111/tpj.15937. (IF=5.726)

Li Q, Zhou L, Chen Y, Xiao N, Zhang D, Zhang M, Wang W, Zhang C, Zhang A, Li H, Chen J, Gao Y. Phytochrome interacting factor regulates stomatal aperture by coordinating red light and abscisic acid. Plant Cell. 2022. 34: 4293-4312. doi: 10.1093/plcell/koac244. (IF=12.085)

Luo M, Lu B, Shi Y, Zhao Y, Wei Z, Zhang C, Wang Y, Liu H, Shi Y, Yang J, Song W, Lu X, Fan Y, Xu L, Wang R, Zhao J. A newly characterized allele of ZmR1 increases anthocyanin content in whole maize plant and the regulation mechanism of different ZmR1 alleles. Theor Appl Genet. 2022. 135: 3039-3055. doi: 10.1007/s00122-022-04166-0. (IF=5.574)

Wei H, Xu H, Su C, Wang X, Wang L. Rice CIRCADIAN CLOCK ASSOCIATED 1 transcriptionally regulates ABA signaling to confer multiple abiotic stress tolerance. Plant Physiol. 2022. 190: 1057-1073. doi: 10.1093/plphys/kiac196. (IF=8.005)

Tang N, Cao Z, Yang C, Ran D, Wu P, Gao H, He N, Liu G, Chen Z. A R2R3-MYB transcriptional activator LmMYB15 regulates chlorogenic acid biosynthesis and phenylpropanoid metabolism in Lonicera macranthoides. Plant Sci. 2021. 308: 110924. doi: 10.1016/j.plantsci.2021.110924. (IF=5.363)

Liang S, Gao X, Wang Y, Zhang H, Yin K, Chen S, Zhang M, Zhao R. Phytochrome-interacting factors regulate seedling growth through ABA signaling. Biochem Biophys Res Commun. 2020. 526: 1100-1105. doi: 10.1016/j.bbrc.2020.04.011. (IF=3.322)

Yao J, Shen Z, Zhang Y, Wu X, Wang J, Sa G, Zhang Y, Zhang H, Deng C, Liu J, Hou S, Zhang Y, Zhang Y, Zhao N, Deng S, Lin S, Zhao R, Chen S. Populus euphratica WRKY1 binds the promoter of H+-ATPase gene to enhance gene expression and salt tolerance. J Exp Bot. 2020. 71: 1527-1539. doi: 10.1093/jxb/erz493. (IF=5.36)

相關(guān)服務(wù)：

1、 凝膠阻滯實驗（EMSA）：DAP-seq后續(xù)驗證服務(wù)。

2、 酵母單雜交：DAP-seq后續(xù)驗證服務(wù)

3、 ChIP-seq：高效檢測重組蛋白、轉(zhuǎn)錄因子在基因組的結(jié)合位點

4、 DAP-seq與RNA-seq聯(lián)合分析： 分析轉(zhuǎn)錄因子的靶基因在RNA-seq數(shù)據(jù)中的表達變化，深入挖掘DAP-seq和RNA-seq測序數(shù)據(jù)，增加轉(zhuǎn)錄組測序的分析深度。

5、 DNA-pull down：鑒定與DNA結(jié)合的蛋白。

6、 精美的論文圖片設(shè)計與制作：專業(yè)設(shè)計師，設(shè)計精美論文插圖，提升論文的嚴(yán)謹(jǐn)性和美觀度。

DAP-seq是基于DNA親和純化，通過體外表達轉(zhuǎn)錄因子鑒定TFBS的技術(shù)，具有不受抗體和物種限制，且高通量的優(yōu)勢，自該技術(shù)問世以來，已被廣泛應(yīng)用于轉(zhuǎn)錄調(diào)控和表觀組學(xué)的研究。能幫助您快速找到轉(zhuǎn)錄因子的結(jié)合位點，尋找轉(zhuǎn)錄因子調(diào)控的靶基因。