{"id":8622,"date":"2025-05-03T16:06:45","date_gmt":"2025-05-03T07:06:45","guid":{"rendered":"http:\/\/dna.brc.riken.jp\/en\/?page_id=8622"},"modified":"2025-05-03T16:08:03","modified_gmt":"2025-05-03T07:08:03","slug":"autophagyen","status":"publish","type":"page","link":"http:\/\/dna.brc.riken.jp\/en\/biosensor01en\/autophagyen","title":{"rendered":"Research Tools of Autophagy"},"content":{"rendered":"<p><!-- js calling begin --><code><script type=\"text\/javascript\" src=\"\/en\/wp-content\/uploads\/js\/functions_list.js\"><\/script><\/code><!-- js calling end --><\/p>\n<p class=\"text02e\">The 2016 Nobel Prize in Physiology or Medicine was awarded to Dr. Yoshinori Ohsumi &#8220;for his discoveries of mechanisms for autophagy&#8221; [1]. Genetic resources for autophagy study are available. Looking forward to receiving your request.<\/p>\n<p><a name=\"research tool\"><\/a><\/p>\n<h3>Resarch Tools of Autophagy<\/h3>\n<p style=\"text-decoration: underline;\">A pulse-chasable reporter processing assay for mammalian autophagic flux with HaloTag.<\/p>\n<p>Yim, W.W., Yamamoto, H., Mizushima, N.<br \/>\nElife 11: e78923 (2022). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/35938926\">PubMed PMID 35938926<\/a>.<\/p>\n<table border=\"1\" width=\"100%\" cellspacing=\"0\" cellpadding=\"5\" bgcolor=\"#FFFFFF\">\n<tbody>\n<tr>\n<td><strong>Catalog no.<\/strong><\/td>\n<td><strong>Name of resource<\/strong><\/td>\n<td><strong>Description<\/strong><\/td>\n<\/tr>\n<tr>\n<td>RDB19962<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19962\">pMRX-IB-pSu9-HaloTag7-mGFP<\/a><\/td>\n<td>Retroviral vector for stable expression of pSu9-HaloTag7-mGFP to measure mitophagy activity.<\/td>\n<\/tr>\n<tr>\n<td>RDB19963<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19963\">pMRX-IB-HaloTag7-mGFP-KDEL<\/a><\/td>\n<td>Retroviral vector for stable expression of HaloTag7-mGFP-KDEL to measure ER-phagy activity. <\/td>\n<\/tr>\n<tr>\n<td>RDB19964<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19964\">pMRX-IB-HaloTag7-mGFP<\/a><\/td>\n<td>Retroviral vector for stable expression of HaloTag7-mGFP to measure autophagic flux.<\/td>\n<\/tr>\n<tr>\n<td>RDB19965<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19965\">pMRX-No-HaloTag7-mGFP-LC3-mRFP<\/a><\/td>\n<td>Retroviral vector for stable expression of HaloTag7-mGFP-LC3-mRFP to measure autophagic flux.<\/td>\n<\/tr>\n<tr>\n<td>RDB19966<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19966\">pMRX-No-HaloTag7-mGFP-LC3<\/a><\/td>\n<td>Retroviral vector for stable expression of HaloTag7-mGFP-LC3 to measure autophagic flux.<\/td>\n<\/tr>\n<tr>\n<td>RDB19967<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19967\">pMRX-No-HaloTag7-LC3<\/a><\/td>\n<td>Retroviral vector for stable expression of HaloTag7-LC3 to measure autophagic flux.<\/td>\n<\/tr>\n<tr>\n<td>RDB19968<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19968\">pMRX-IP-HaloTag7-LC3<\/a><\/td>\n<td>Retroviral vector for stable expression of HaloTag7-LC3 to measure autophagic flux.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr width=\"50%\" \/>\n<p style=\"text-decoration: underline;\"> Intrinsically Disordered Protein TEX264 Mediates ER-phagy. <\/p>\n<p>Chino, H., Hatta, T., Natsume, T., Mizushima, N.<br \/>\nMol. Cell 74 (5): 909-921.e6 (2019). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/31006538\">PubMed PMID 31006538<\/a>.<\/p>\n<table border=\"1\" width=\"100%\" cellspacing=\"0\" cellpadding=\"5\" bgcolor=\"#FFFFFF\">\n<tbody>\n<tr>\n<td><strong>Catalog no.<\/strong><\/td>\n<td><strong>Name of resource<\/strong><\/td>\n<td><strong>Description<\/strong><\/td>\n<\/tr>\n<tr>\n<td>RDB19767<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19767\">pCW57-CMV-ssRFP-GFP-KDEL<\/a><\/td>\n<td>Lentiviral vector for inducible expression of ER-phagy marker ssRFP-GFP-KDEL.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr width=\"50%\" \/>\n<p style=\"text-decoration: underline;\">An Autophagic Flux Probe that Releases an Internal Control.<\/p>\n<p>Kaizuka, T., Morishita, H., Hama, Y., Tsukamoto, S., Matsui, T., Toyota, Y., Kodama, A., Ishihara, T., Mizushima, T., Mizushima, N.<br \/>\nMol. Cell 64 (4): 835-849 (2016). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/27818143\">PubMed PMID 27818143<\/a>.<\/p>\n<table border=\"1\" width=\"100%\" cellspacing=\"0\" cellpadding=\"5\" bgcolor=\"#FFFFFF\">\n<tbody>\n<tr>\n<td><strong>Catalog no.<\/strong><\/td>\n<td><strong>Name of resource<\/strong><\/td>\n<td><strong>Description<\/strong><\/td>\n<\/tr>\n<tr>\n<td>RDB14600<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB14600\">pMRX-IP-GFP-LC3-RFP-LC3 delta G<\/a><\/td>\n<td>Fluorescent probe to evaluate autophagic flux by the rat LC3 fused with GFP and RFP.<\/td>\n<\/tr>\n<tr>\n<td>RDB14601<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB14601\">pMRX-IP-GFP-LC3-RFP<\/a><\/td>\n<td>Fluorescent probe to evaluate autophagic flux by the rat LC3 fused with GFP and RFP.<\/td>\n<\/tr>\n<tr>\n<td>RDB19804<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19804\">pcDNA3-GFP-LC3-RFP-LC3 deltaG<\/a><\/td>\n<td>An autophagic flux probe, expression vector of GFP-rat LC3-RFP-rat LC3 deletion G.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<ul>\n<li>In order to visualize autophagosome and observe autophagy, MAP1LC3 (LC3) fused with fluorescent proteins as a probe are used. However, the fluorescence of the probe attenuates during autophagy progresses and it is not suitable for quantitative assay of autophagy. <\/li>\n<li>Dr. Noboru Mizushima and his colleagues at the University of Tokyo developed a new probe that can expresses GFP-LC3 and RFP-LC3 delta G (lacking glycine (G) at the LC 3 end) simultaneously at equimolar amounts. As autophagy progresses, the fluorescence of GFP-LC3 decays whereas that of RFP-LC3 delta G remains in the cytoplasm as an internal standard. Therefor, the activity of autophagy can be quantified evaluated by the fluorescence intensity ratio of GFP\/RFP.<br \/>\n<img decoding=\"async\" src=\"https:\/\/dnaconda.riken.jp\/images\/rdb14600_300.png\" alt=\"\" \/><\/li>\n<li>Using this probe, autophagic flux was measured in mouse and zebrafish embryos and tissues as well as cultured cells. This is also suitable for analysis of large number of samples.<\/li>\n<\/ul>\n<hr width=\"50%\" \/>\n<p style=\"text-decoration: underline;\">Establishment of a novel fluorescence-based method to evaluate chaperone-mediated autophagy in a single neuron.<\/p>\n<p>Seki, T., Yoshino, K.I., Tanaka, S., Dohi, E., Onji, T., Yamamoto, K., Hide, I., Paulson, H.L., Saito, N., Sakai, N.<br \/>\nPLoS One 7 (2): e31232 (2012). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/22363588\">PubMed PMID 22363588<\/a>.<\/p>\n<table border=\"1\" width=\"100%\" cellspacing=\"0\" cellpadding=\"5\" bgcolor=\"#FFFFFF\">\n<tbody>\n<tr>\n<td><strong>Catalog no.<\/strong><\/td>\n<td><strong>Name of resource<\/strong><\/td>\n<td><strong>Description<\/strong><\/td>\n<\/tr>\n<tr>\n<td>RDB15088<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB15088\">pcDNA5-GAPDH-HaloTag<\/a><\/td>\n<td>Expression vector for the visualization of chaperone-mediated autophagy (CMA).<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<ul>\n<li>The GAPDH-HT indicator is a chaperone-mediated autophagy (CMA) marker consisting of HaloTag and GAPDH which is a typical substrate of CMA. The CMA activity in the cells can be evaluated by using GAPDH-HT indicator and an appropriate under the fluorescent-labeled HaloTag ligand.<\/li>\n<\/ul>\n<p>References and Related Articles:<\/p>\n<ul>\n<li>Sato, M. et al. Fluorescent-based evaluation of chaperone-mediated autophagy and microautophagy activities in cultured cells. Genes Cells 21 (8): 861-873, 2016. PubMed PMID: 27377049<\/li>\n<\/ul>\n<hr width=\"50%\" \/>\n<p style=\"text-decoration: underline;\">A conditional proteomics approach to identify proteins involved in zinc homeostasis.<\/p>\n<p>Miki, T., Awa, M., Nishikawa, Y., Kiyonaka, S., Wakabayashi, M., Ishihama, Y., Hamachi, I.<br \/>\nNat. Methods 13 (11): 931-937 (2016). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/27617391\">PubMed PMID 27617391<\/a>.<\/p>\n<table border=\"1\" width=\"100%\" cellspacing=\"0\" cellpadding=\"5\" bgcolor=\"#FFFFFF\">\n<tbody>\n<tr>\n<td><strong>Catalog no.<\/strong><\/td>\n<td><strong>Name of resource<\/strong><\/td>\n<td><strong>Description<\/strong><\/td>\n<\/tr>\n<tr>\n<td>RDB15159<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB15159\">mCherry-LC3B<\/a><\/td>\n<td>Autophagosome marker. Expression vector of rat Microtubule-associated proteins 1A\/1B light chain 3B (LC3B), mCherry tag.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr width=\"50%\" \/>\n<p style=\"text-decoration: underline;\">The nucleolar protein nucleophosmin is essential for autophagy induced by inhibiting Pol I transcription.<\/p>\n<p>Katagiri, N., Kuroda, T., Kishimoto, H., Hayashi, Y., Kumazawa, T., Kimura, K.<br \/>\nSci. Rep. 5: 8903 (2015). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25754892\">PubMed PMID 25754892<\/a>.<\/p>\n<table border=\"1\" width=\"100%\" cellspacing=\"0\" cellpadding=\"5\" bgcolor=\"#FFFFFF\">\n<tbody>\n<tr>\n<td><strong>Catalog no.<\/strong><\/td>\n<td><strong>Name of resource<\/strong><\/td>\n<td><strong>Description<\/strong><\/td>\n<\/tr>\n<tr>\n<td>RDB13435<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB13435\">pEGFP-C1-hLC3B<\/a><\/td>\n<td>Indicator of autophagy. Expression clone of human LC3B in mammalian cells.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr width=\"50%\" \/>\n<p style=\"text-decoration: underline;\">Parkin mediates proteasome-dependent protein degradation and rupture of the outer mitochondrial membrane.<\/p>\n<p>Yoshii, S.R., Kishi, C., Ishihara, N., Mizushima, N. J. Biol. Chem. 286 (22): 19630-19640 (2011). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21454557\">PubMed PMID 21454557<\/a>.<\/p>\n<table border=\"1\" width=\"100%\" cellspacing=\"0\" cellpadding=\"5\" bgcolor=\"#FFFFFF\">\n<tbody>\n<tr>\n<td><strong>Catalog no.<\/strong><\/td>\n<td><strong>Name of resource<\/strong><\/td>\n<td><strong>Description<\/strong><\/td>\n<\/tr>\n<tr>\n<td>RDB19786<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19786\">pMXs-IP-GFP-Omp25<\/a><\/td>\n<td>Retroviral vector for stable expression of rat Omp25 with N-terminal EGFP.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr width=\"50%\" \/>\n<p style=\"text-decoration: underline;\">Characterization of autophagosome formation site by a hierarchical analysis of mammalian Atg proteins.<\/p>\n<p>Itakura, E., Mizushima, N. Autophagy 6 (6): 764-776 (2010). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/20639694\">PubMed PMID 20639694<\/a>.<\/p>\n<table border=\"1\" width=\"100%\" cellspacing=\"0\" cellpadding=\"5\" bgcolor=\"#FFFFFF\">\n<tbody>\n<tr>\n<td><strong>Catalog no.<\/strong><\/td>\n<td><strong>Name of resource<\/strong><\/td>\n<td><strong>Description<\/strong><\/td>\n<\/tr>\n<tr>\n<td>RDB19630<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19630\">pMXs-IP-GFP-WIPI1<\/a><\/td>\n<td>Retroviral vector for stable expression of human WIPI1 with N-terminal EGFP.<\/td>\n<\/tr>\n<tr>\n<td>RDB19768<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19768\">pMXs-IP spGFP-ERGIC53<\/a><\/td>\n<td>Retroviral vector for stable expression of human ERGIC-53 with N-terminal GFP.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr width=\"50%\" \/>\n<p style=\"text-decoration: underline;\">FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells.<\/p>\n<p>Hara, T., Takamura, A., Kishi, C., Iemura, S., Natsume, T., Guan, J.L., Mizushima, N. J. Cell Biol.  181 (3): 497-510 (2008). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/18443221\">PubMed PMID 18443221<\/a>.<\/p>\n<table border=\"1\" width=\"100%\" cellspacing=\"0\" cellpadding=\"5\" bgcolor=\"#FFFFFF\">\n<tbody>\n<tr>\n<td><strong>Catalog no.<\/strong><\/td>\n<td><strong>Name of resource<\/strong><\/td>\n<td><strong>Description<\/strong><\/td>\n<\/tr>\n<tr>\n<td>RDB19634<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19634\">pMXs-IP-EGFP-mAtg5<\/a><\/td>\n<td>Retroviral vector for stable expression of mouse Atg5 with C-terminal EGFP.<\/td>\n<\/tr>\n<tr>\n<td>RDB19798<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19798\">pMXs-IP-EGFP-LC3<\/a><\/td>\n<td>Retroviral vector for stable expression of rat LC3 with N-terminal EGFP.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr \/>\n<h3>Related article<\/h3>\n<ul style=\"line-height: 1.5em;\">\n<li><a href=\"https:\/\/brc.riken.jp\/dna\/GSB0021e#gene resource\">Genes involved in the autophagy pathway (GSB0021e)<\/a><\/li>\n<li>Other Resources in Riken BRC<\/a>\n<ul style=\"line-height: 1.5em;\">\n<li><a href=\"http:\/\/mus.brc.riken.jp\/en\/info20161004\">Mouse resources (Experimental Animal Division) [link]<\/a><\/li>\n<li><a href=\"http:\/\/cell.brc.riken.jp\/en\/nobel_prize_2016\">Cell lines (Cell Engineering Division) [link]<\/a><\/li>\n<\/ul>\n<\/li>\n<li>Mitophagy\n<ul style=\"line-height: 1.5em;\">\n<li><a href=\"\/en\/biosensoren\/mitophagyen\">Resarch Tools of Mitophagy<\/a><\/li>\n<li><a href=\"https:\/\/brc.riken.jp\/dna\/GSB0051e\">Genes involved in the mitophagy pathway (GSB0051e)<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<hr \/>\n<p style=\"text-align:left;\">2025.05.03 (T.M.)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The 2016 Nobel Prize in Physiology or Medicine was awarded to Dr. Yoshinori Ohsumi &#8220;for his discoveries of mechanisms for autophagy&#8221; [1]. Genetic resources for autophagy study are available. Looking forward to receiving your request. Resarch Tools of Autophagy A pulse-chasable reporter processing assay for mammalian autophagic flux with HaloTag. Yim, W.W., Yamamoto, H., Mizushima, N. Elife 11: e78923 (2022). PubMed PMID 35938926. Catalog no. Name of resource Description RDB19962 pMRX-IB-pSu9-HaloTag7-mGFP Retroviral vector for stable expression of pSu9-HaloTag7-mGFP to measure mitophagy activity. RDB19963 pMRX-IB-HaloTag7-mGFP-KDEL Retroviral vector for stable expression of HaloTag7-mGFP-KDEL to measure ER-phagy activity. RDB19964 pMRX-IB-HaloTag7-mGFP Retroviral vector for stable expression of HaloTag7-mGFP to measure autophagic flux. RDB19965 pMRX-No-HaloTag7-mGFP-LC3-mRFP Retroviral vector for stable expression of HaloTag7-mGFP-LC3-mRFP to measure autophagic flux. RDB19966 pMRX-No-HaloTag7-mGFP-LC3 Retroviral vector for stable expression of HaloTag7-mGFP-LC3 to measure autophagic flux. RDB19967 pMRX-No-HaloTag7-LC3 Retroviral vector for stable expression of HaloTag7-LC3 to measure autophagic flux. RDB19968 pMRX-IP-HaloTag7-LC3 Retroviral vector for stable expression of HaloTag7-LC3 to measure autophagic flux. Intrinsically Disordered Protein TEX264 Mediates ER-phagy. Chino, H., Hatta, T., Natsume, T., Mizushima, N. Mol. Cell 74 (5): 909-921.e6 (2019). PubMed PMID 31006538. Catalog no. Name of resource Description RDB19767 pCW57-CMV-ssRFP-GFP-KDEL Lentiviral vector for inducible expression of ER-phagy marker ssRFP-GFP-KDEL. [&hellip;]<\/p>\n","protected":false},"author":13,"featured_media":0,"parent":8590,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","_seopress_robots_follow":"","_seopress_robots_imageindex":"","_seopress_robots_snippet":"","_seopress_robots_primary_cat":"","_seopress_robots_breadcrumbs":"","_seopress_robots_freeze_modified_date":"","_seopress_robots_custom_modified_date":"","_seopress_robots_canonical":"","_seopress_social_fb_title":"","_seopress_social_fb_desc":"","_seopress_social_fb_img":"","_seopress_social_fb_img_attachment_id":0,"_seopress_social_fb_img_width":0,"_seopress_social_fb_img_height":0,"_seopress_social_twitter_title":"","_seopress_social_twitter_desc":"","_seopress_social_twitter_img":"","_seopress_social_twitter_img_attachment_id":0,"_seopress_social_twitter_img_width":0,"_seopress_social_twitter_img_height":0,"_seopress_redirections_value":"","_seopress_redirections_enabled":"","_seopress_redirections_enabled_regex":"","_seopress_redirections_logged_status":"both","_seopress_redirections_param":"","_seopress_redirections_type":301,"_seopress_analysis_target_kw":"","footnotes":"","_wp_rev_ctl_limit":""},"class_list":["post-8622","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8622","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/users\/13"}],"replies":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/comments?post=8622"}],"version-history":[{"count":3,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8622\/revisions"}],"predecessor-version":[{"id":8627,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8622\/revisions\/8627"}],"up":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8590"}],"wp:attachment":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/media?parent=8622"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}