• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

秀丽隐杆线虫转录因子序列特异性的映射与分析。

Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities.

作者信息

Narasimhan Kamesh, Lambert Samuel A, Yang Ally W H, Riddell Jeremy, Mnaimneh Sanie, Zheng Hong, Albu Mihai, Najafabadi Hamed S, Reece-Hoyes John S, Fuxman Bass Juan I, Walhout Albertha J M, Weirauch Matthew T, Hughes Timothy R

机构信息

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.

Department of Molecular Genetics, University of Toronto, Toronto, Canada.

出版信息

Elife. 2015 Apr 23;4:e06967. doi: 10.7554/eLife.06967.

DOI:10.7554/eLife.06967
PMID:25905672
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4434323/
Abstract

Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of regulatory elements has been limited, as DNA-binding motifs are known for only 71 of the estimated 763 sequence-specific transcription factors (TFs). To address this problem, we performed protein binding microarray experiments on representatives of canonical TF families in C. elegans, obtaining motifs for 129 TFs. Additionally, we predict motifs for many TFs that have DNA-binding domains similar to those already characterized, increasing coverage of binding specificities to 292 C. elegans TFs (∼40%). These data highlight the diversification of binding motifs for the nuclear hormone receptor and C2H2 zinc finger families and reveal unexpected diversity of motifs for T-box and DM families. Motif enrichment in promoters of functionally related genes is consistent with known biology and also identifies putative regulatory roles for unstudied TFs.

摘要

秀丽隐杆线虫是研究基因调控的强大模型，因为它具有紧凑的基因组和丰富的基因组工具。然而，调控元件的鉴定一直有限，因为在估计的763个序列特异性转录因子（TFs）中，只有71个的DNA结合基序是已知的。为了解决这个问题，我们对秀丽隐杆线虫中典型TF家族的代表进行了蛋白质结合微阵列实验，获得了129个TFs的基序。此外，我们预测了许多具有与已表征的DNA结合域相似的TFs的基序，将结合特异性的覆盖范围增加到292个秀丽隐杆线虫TFs（约40%）。这些数据突出了核激素受体和C2H2锌指家族结合基序的多样性，并揭示了T-box和DM家族基序的意外多样性。功能相关基因启动子中的基序富集与已知生物学一致，也确定了未研究TFs的假定调控作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/87ab72e37c57/elife06967f009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/aa9a300d728a/elife06967f001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/b45dd69bbcd7/elife06967fs001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/2ba04f41d1b9/elife06967f002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/8fa052fcc171/elife06967fs002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/aa9f3a359e24/elife06967fs003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/aa0a1e8b7e54/elife06967fs004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/bb0be665c823/elife06967fs005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/18b2269fa9ea/elife06967fs006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/f409709b8030/elife06967f003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/a00317f6ed54/elife06967f004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/de63030c006a/elife06967f005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/f0d329a68ec2/elife06967fs007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/a81acdfe9e28/elife06967f006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/dd2494a21275/elife06967fs008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/6b3204d6b8e3/elife06967f007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/097e65ca239b/elife06967fs009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/939eb54b509c/elife06967f008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/76931627fe20/elife06967fs010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/45614f1528ad/elife06967fs011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/459fd5e82479/elife06967fs012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/4584d946756c/elife06967fs013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/a5540481a6fa/elife06967fs014.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/87ab72e37c57/elife06967f009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/aa9a300d728a/elife06967f001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/b45dd69bbcd7/elife06967fs001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/2ba04f41d1b9/elife06967f002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/8fa052fcc171/elife06967fs002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/aa9f3a359e24/elife06967fs003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/aa0a1e8b7e54/elife06967fs004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/bb0be665c823/elife06967fs005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/18b2269fa9ea/elife06967fs006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/f409709b8030/elife06967f003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/a00317f6ed54/elife06967f004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/de63030c006a/elife06967f005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/f0d329a68ec2/elife06967fs007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/a81acdfe9e28/elife06967f006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/dd2494a21275/elife06967fs008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/6b3204d6b8e3/elife06967f007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/097e65ca239b/elife06967fs009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/939eb54b509c/elife06967f008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/76931627fe20/elife06967fs010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/45614f1528ad/elife06967fs011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/459fd5e82479/elife06967fs012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/4584d946756c/elife06967fs013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/a5540481a6fa/elife06967fs014.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/797c/4434323/87ab72e37c57/elife06967f009.jpg

相似文献

1
Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities.秀丽隐杆线虫转录因子序列特异性的映射与分析。
Elife. 2015 Apr 23;4:e06967. doi: 10.7554/eLife.06967.
2
A gene-centered C. elegans protein-DNA interaction network.一个以基因为中心的秀丽隐杆线虫蛋白质 - DNA 相互作用网络。
Cell. 2006 Jun 16;125(6):1193-205. doi: 10.1016/j.cell.2006.04.038.
3
The in vivo dissection of direct RFX-target gene promoters in C. elegans reveals a novel cis-regulatory element, the C-box.秀丽隐杆线虫体内 RFX 直接靶基因启动子的剖析揭示了一个新的顺式调控元件，C 盒。
Dev Biol. 2012 Aug 15;368(2):415-26. doi: 10.1016/j.ydbio.2012.05.033. Epub 2012 Jun 5.
4
Specificity of DNA-binding by the FAX-1 and NHR-67 nuclear receptors of Caenorhabditis elegans is partially mediated via a subclass-specific P-box residue.秀丽隐杆线虫的FAX-1和NHR-67核受体与DNA结合的特异性部分是通过一个亚类特异性的P盒残基介导的。
BMC Mol Biol. 2008 Jan 7;9:2. doi: 10.1186/1471-2199-9-2.
5
Chromatin immunoprecipitation and multiplex sequencing (ChIP-Seq) to identify global transcription factor binding sites in the nematode Caenorhabditis elegans.染色质免疫沉淀与多重测序（ChIP-Seq）用于鉴定线虫秀丽隐杆线虫中的全局转录因子结合位点。
Methods Enzymol. 2014;539:89-111. doi: 10.1016/B978-0-12-420120-0.00007-4.
6
Ectopic expression of a Haemonchus contortus GATA transcription factor in Caenorhabditis elegans reveals conserved function in spite of extensive sequence divergence.捻转血矛线虫GATA转录因子在秀丽隐杆线虫中的异位表达揭示了尽管序列存在广泛差异但仍具有保守功能。
Mol Biochem Parasitol. 2004 Feb;133(2):241-53. doi: 10.1016/j.molbiopara.2003.10.012.
7
The evolutionary duplication and probable demise of an endodermal GATA factor in Caenorhabditis elegans.秀丽隐杆线虫中一种内胚层GATA因子的进化复制及可能的消亡
Genetics. 2003 Oct;165(2):575-88. doi: 10.1093/genetics/165.2.575.
8
Zinc fingers in Caenorhabditis elegans: finding families and probing pathways.秀丽隐杆线虫中的锌指蛋白：寻找家族并探索途径
Science. 1998 Dec 11;282(5396):2018-22. doi: 10.1126/science.282.5396.2018.
9
Fine tuning of RFX/DAF-19-regulated target gene expression through binding to multiple sites in Caenorhabditis elegans.通过在秀丽隐杆线虫中结合多个位点来精细调节 RFX/DAF-19 调节的靶基因表达。
Nucleic Acids Res. 2012 Jan;40(1):53-64. doi: 10.1093/nar/gkr690. Epub 2011 Sep 8.
10
Exploring transcriptional regulatory networks in the worm.探索线虫中的转录调控网络。
Cell. 2006 Jun 16;125(6):1032-4. doi: 10.1016/j.cell.2006.06.002.

引用本文的文献

1
Caenorhabditis elegans LET-381 and DMD-4 control development of the mesodermal HMC endothelial cell.秀丽隐杆线虫的LET-381和DMD-4控制中胚层HMC内皮细胞的发育。
Development. 2025 Jul 15;152(14). doi: 10.1242/dev.204622. Epub 2025 Jul 29.
2
Lineage-resolved analysis of embryonic gene expression evolution in and .XX和XX中胚胎基因表达进化的谱系解析分析 。（你提供的原文不完整，缺少关键物种信息，这里只能给出大概的翻译框架，你可补充完整后再让我准确翻译）
Science. 2025 Jun 19;388(6753):eadu8249. doi: 10.1126/science.adu8249.
3
A GATA factor radiation in rewired the endoderm specification network.

本文引用的文献

1
C2H2 zinc finger proteins greatly expand the human regulatory lexicon.C2H2 锌指蛋白极大地扩展了人类调控词汇。
Nat Biotechnol. 2015 May;33(5):555-62. doi: 10.1038/nbt.3128. Epub 2015 Feb 18.
2
Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module.转录因子家族中DNA特异性的进化产生了一个新的基因调控模块。
Cell. 2014 Sep 25;159(1):58-68. doi: 10.1016/j.cell.2014.09.003.
3
Determination and inference of eukaryotic transcription factor sequence specificity.真核转录因子序列特异性的测定和推断。
一种GATA因子辐射重新连接了内胚层特化网络。
bioRxiv. 2025 May 12:2022.05.20.492851. doi: 10.1101/2022.05.20.492851.
4
CelEst: a unified gene regulatory network for estimating transcription factor activities in C. elegans.CelEst：用于估计秀丽隐杆线虫中转录因子活性的统一基因调控网络。
Genetics. 2025 Mar 17;229(3). doi: 10.1093/genetics/iyae189.
5
Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors.密码本的视角：未表征的人类转录因子的序列特异性
bioRxiv. 2024 Nov 12:2024.11.11.622097. doi: 10.1101/2024.11.11.622097.
6
Binding profiles for 961 and transcription factors reveal tissue-specific regulatory relationships.961与转录因子的结合图谱揭示了组织特异性调控关系。
Genome Res. 2024 Dec 23;34(12):2319-2334. doi: 10.1101/gr.279037.124.
7
Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function.疫霉属真菌（Phytophthora infestans）转录因子结合特异性反映了保守和分歧的进化模式，并可预测其功能。
BMC Genomics. 2024 Jul 23;25(1):710. doi: 10.1186/s12864-024-10630-6.
8
LET-381/FoxF and its target UNC-30/Pitx2 specify and maintain the molecular identity of C. elegans mesodermal glia that regulate motor behavior.LET-381/FoxF 和其靶基因 UNC-30/Pitx2 决定并维持线虫中调控运动行为的中胚层胶质细胞的分子特性。
EMBO J. 2024 Mar;43(6):956-992. doi: 10.1038/s44318-024-00049-w. Epub 2024 Feb 15.
9
Binding profiles for 954 Drosophila and transcription factors reveal tissue specific regulatory relationships.954种果蝇和转录因子的结合图谱揭示了组织特异性调控关系。
bioRxiv. 2024 Jan 20:2024.01.18.576242. doi: 10.1101/2024.01.18.576242.
10
Gene regulatory patterning codes in early cell fate specification of the embryo.胚胎早期细胞命运特化中的基因调控模式。
Elife. 2024 Jan 29;12:RP87099. doi: 10.7554/eLife.87099.
Cell. 2014 Sep 11;158(6):1431-1443. doi: 10.1016/j.cell.2014.08.009.
4
Comparative analysis of regulatory information and circuits across distant species.不同物种间调控信息与调控回路的比较分析
Nature. 2014 Aug 28;512(7515):453-6. doi: 10.1038/nature13668.
5
Regulatory analysis of the C. elegans genome with spatiotemporal resolution.对秀丽隐杆线虫基因组进行具有时空分辨率的调控分析。
Nature. 2014 Aug 28;512(7515):400-5. doi: 10.1038/nature13497.
6
Diversification of transcription factor paralogs via noncanonical modularity in C2H2 zinc finger DNA binding.通过 C2H2 锌指 DNA 结合中非典型模块性转录因子的基因复制多样化。
Mol Cell. 2014 Aug 21;55(4):640-8. doi: 10.1016/j.molcel.2014.06.019. Epub 2014 Jul 17.
7
Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape.通过建模 DNase 图谱幅度和形状发现有向和无向先驱转录因子。
Nat Biotechnol. 2014 Feb;32(2):171-178. doi: 10.1038/nbt.2798. Epub 2014 Jan 19.
8
CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.CCAT：转录调控的组合编码分析工具。
Nucleic Acids Res. 2014 Mar;42(5):2833-47. doi: 10.1093/nar/gkt1302. Epub 2013 Dec 23.
9
Data, information, knowledge and principle: back to metabolism in KEGG.数据、信息、知识和原理：回到 KEGG 的代谢途径中。
Nucleic Acids Res. 2014 Jan;42(Database issue):D199-205. doi: 10.1093/nar/gkt1076. Epub 2013 Nov 7.
10
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.JASPAR 2014：一个广泛扩展和更新的转录因子结合谱公开访问数据库。
Nucleic Acids Res. 2014 Jan;42(Database issue):D142-7. doi: 10.1093/nar/gkt997. Epub 2013 Nov 4.