一半沽、 DAP-seq技術(shù)簡(jiǎn)介

DAP-seq（DNA親和純化測(cè)序）技術(shù)服務(wù)——高通量檢測(cè)轉(zhuǎn)錄因子或DNA結(jié)合蛋白在基因組上的結(jié)合位點(diǎn)。

在功能基因組學(xué)和表觀遺傳學(xué)研究中吴菠，轉(zhuǎn)錄因子結(jié)合位點(diǎn)（TFBS）的發(fā)掘一直是研究熱點(diǎn)者填。傳統(tǒng)的ChIP-seq（染色質(zhì)免疫共沉淀測(cè)序）方法，在抗體質(zhì)量很好的情況下能夠有效檢測(cè)到TFBS做葵。然而占哟，好的抗體可遇不可求，這限制了ChIP-seq更廣泛的應(yīng)用酿矢。

2016年榨乎，O'Malley RC等人在Cell上發(fā)表了使用DAP-seq技術(shù)，快速繪制轉(zhuǎn)錄因子調(diào)控靶向DNA區(qū)域圖譜的文章瘫筐。2017年蜜暑，Bartlett A等人在Nature Protocol上發(fā)表了 DAP-seq的實(shí)驗(yàn)方法。 DAP-seq技術(shù)的出現(xiàn)，使TFBS 的研究不再局限于物種察迟，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盲链。

二拙毫、 ChIP-seq和DAP-seq技術(shù)對(duì)比

三依许、DAP-seq技術(shù)流程：

藍(lán)景科信已發(fā)表文章列表：

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)

四、DAP-seq實(shí)驗(yàn)流程

五缀蹄、DAP-seq生信分析內(nèi)容

1.對(duì)原始數(shù)據(jù)進(jìn)行去除接頭峭跳、污染序列及低質(zhì)量 reads 的處理

2.數(shù)據(jù)產(chǎn)出統(tǒng)計(jì)

3.參考序列比對(duì)分析?

4.測(cè)序reads富集區(qū)域掃描（peak calling）

5.Peak長(zhǎng)度分布統(tǒng)計(jì)

6.Peak在基因功能元件上的分布統(tǒng)計(jì)

7.Peak序列模式發(fā)掘（motif search）

8.已知motif注釋

9.Peak相關(guān)基因鑒定

10.Peak相關(guān)基因的GO和KEGG富集分析

11.測(cè)序數(shù)據(jù)的差異分析（>=2個(gè)樣本）

12.測(cè)序數(shù)據(jù)的可視化分析