Topic Curation

WS241 Pilot Topic: Unfolded Protein Response (UPR)

UPR Papers

List of WBPaper IDs for candidate UPR papers:

WBPaper00003967 WBPaper00004394 WBPaper00005036 WBPaper00005044 WBPaper00005432 WBPaper00006537 WBPaper00013244 WBPaper00024210 WBPaper00024269 WBPaper00024285 WBPaper00025202 WBPaper00026830 WBPaper00026929 WBPaper00026939 WBPaper00027723 WBPaper00028479 WBPaper00030877 WBPaper00030999 WBPaper00031084 WBPaper00031456 WBPaper00031857 WBPaper00031951 WBPaper00031985 WBPaper00032003 WBPaper00032177 WBPaper00032192 WBPaper00032255 WBPaper00032443 WBPaper00032521 WBPaper00032977 WBPaper00033126 WBPaper00035154 WBPaper00035294 WBPaper00035302 WBPaper00035409 WBPaper00035580 WBPaper00035985 WBPaper00036008 WBPaper00036076 WBPaper00036115 WBPaper00036256 WBPaper00037064 WBPaper00037750 WBPaper00037991 WBPaper00038075 WBPaper00038219 WBPaper00038304 WBPaper00039930 WBPaper00039938 WBPaper00039975 WBPaper00040397 WBPaper00040453 WBPaper00040582 WBPaper00040692 WBPaper00040801 WBPaper00040821 WBPaper00041022 WBPaper00041065 WBPaper00041076 WBPaper00041159 WBPaper00041163 WBPaper00041212 WBPaper00041269 WBPaper00041295 WBPaper00041370 WBPaper00041512 WBPaper00041568 WBPaper00041851 WBPaper00041954 WBPaper00041961 WBPaper00042060 WBPaper00042074 WBPaper00042171 WBPaper00042217 WBPaper00042524

List of PMIDs for papers that do not yet (as of entry) have a WBPaper ID:

PMID: 23870130
PMID: 23872261 CG Added 11-1-2013

UPR Reviews:
WBPaper00013108
PMID: 23839579

UPR Genes & Gene Classes

Gene classes implicated in UPR

• upr (Unfolded Protein Response abnormal)
• abu (Activated in Blocked Unfolded protein response)
• hsp (Heat Shock Protein)

Genes Involved in Cytoplasmic UPR (Heat Shock Response)

• hsf-1
• hsp-1

Genes Involved in Endoplasmic Reticulum UPR

• abu-1
• atf-6
• atfs-1
• atm-1
• C14B9.2
• cdc-48.1
• cdc-48.2
• cnx-1
• crp-1
• crt-1
• cup-2
• dnj-7
• hsp-16.1
• hsp-16.11
• hsp-16.2
• hsp-16.41
• hsp-16.49
• hsp-3
• hsp-4
• hsp-6
• hsp-60
• hsp-70
• hut-1
• ire-1
• kgb-1
• pdi-2
• pdr-1
• pek-1
• R151.6
• R151.7
• sel-1
• shc-1
• T14G8.3
• uggt-1, uggt-2
• xbp-1

Genes Involved in Mitochondrial UPR

• atfs-1
• clpp-1
• dve-1
• haf-1
• hsp-6, hsp-60
• spg-7
• ubl-5

Other C. elegans genes implicated in UPR

• abu-2, abu-3, abu-4, abu-5, abu-6, abu-7, abu-8, abu-9, abu-10, abu-11, abu-12, abu-13, abu-14, abu-15
• apy-1
• ero-1
• rnf-121
• sca-1
• ufd-2
• upr-1

Hinxton

We will review the gene-models and naming of the genes in our non-core species (C.briggsae / C.remanei / C.brenneri / C.japonica / B.malayi).

Do you want the name of the genes for the Tier IIs, so you can add your GO-terms, etc?

UPR WikiPathways

Here are WikiPathways currently under development to represent the various branches of the UPR pathway:

Endoplasmic Reticulum UPR: http://www.wikipathways.org/index.php/Pathway:WP2578

Mitochondrial UPR: http://www.wikipathways.org/index.php/Pathway:WP525

UPR GO Terms & Associated Genes

GO branch: Biological process

• Term: UFP-specific transcription factor mRNA processing involved in endoplasmic reticulum unfolded protein response
  • GO ID: GO:0030969
  • Gene Associations: No associations in WB
  • Added: ire-1

• Term: positive regulation of gene-specific transcription involved in unfolded protein response
  • GO ID: GO:0006990
  • Gene Associations: pek-1

• Term: activation of signaling protein activity involved in unfolded protein response
  • GO ID: GO:0006987
  • Gene Associations: No associations in WB

• Term: endoplasmic reticulum unfolded protein response
  • GO ID: GO:0030968
  • Gene Associations: abu-1, atfs-1, C14B9.2, cdc-48.1, cdc-48.2, crp-1, crt-1, cup-2, hsp-16.1, hsp-16.11, hsp-16.2, hsp-16.41, hsp-16.49, hsp-3, hsp-4, hsp-6, hsp-60, hsp-70, ire-1, pdi-2, R151.6, R151.7, rnf-121, sca-1, spg-7, T14G8.3, uggt-1, uggt-2, xbp-1

• Term: mitochondrial unfolded protein response
  • GO ID: GO:0034514
  • Gene Associations: atfs-1, haf-1, hsp-6, hsp-60, ubl-5

• Term: response to unfolded protein
  • GO ID: GO:0006986
  • Gene Associations: No associations in WB

UPR Phenotypes & Associated Genes

Phenotype: "unfolded protein response variant" (WBPhenotype:0001719)

• Variations with this phenotype:
  • crt-1(jh101)
  • crp-1(ok685) [also affects ncRNA Y32F6B.5]
  • ufd-2(tm1380)
  • cdc-48.1(tm544) [also affects snoRNA C06A1.9]
  • ire-1(v33)
  • xbp-1(zc12)

• RNAi's with this phenotype:
  • WBRNAi00077405 (knocks down xbp-1)
  • WBRNAi00077406 (knocks down xbp-1)
  • WBRNAi00078673 (knocks down cdc-48.1, cdc-48.2)
  • WBRNAi00078678 (knocks down ire-1)
  • WBRNAi00078679 (knocks down xbp-1)
  • WBRNAi00080954 (knocks down cup-2)
  • WBRNAi00080960 (knocks down R151.6, R151.7)
  • WBRNAi00084583 (knocks down spg-7)
  • WBRNAi00084584 (knocks down spg-7)
  • WBRNAi00084585 (knocks down hsp-6)
  • WBRNAi00084587 (knocks down spg-7)
  • WBRNAi00084588 (knocks down spg-7)
  • WBRNAi00084604 (knocks down atfs-1)
  • WBRNAi00084605 (knocks down spg-7, atfs-1)
  • WBRNAi00084611 (knocks down hsp-60)
  • WBRNAi00084612 (knocks down hsp-60)
  • WBRNAi00084613 (knocks down spg-7)
  • WBRNAi00084614 (knocks down spg-7)
  • WBRNAi00084615 (knocks down hsp-60)
  • WBRNAi00084616 (knocks down hsp-60)
  • WBRNAi00084617 (knocks down hsp-60)
  • WBRNAi00084618 (knocks down spg-7)
  • WBRNAi00084619 (knocks down spg-7)
  • WBRNAi00084620 (knocks down spg-7)

• Genes implicated by Variation: crt-1, crp-1, ufd-2, cdc-48.1, ire-1, xbp-1

• Genes implicated by RNAi: xbp-1, cdc-48.1, cdc-48.2, ire-1, cup-2, R151.6, R151.7, spg-7, hsp-6, atfs-1, hsp-60

Phenotype: "ER stress response variant" (WBPhenotype:0001485)

• Variations with this phenotype:
  • crt-1(jh101)
  • cnx-1(nr2009)
  • hut-1(tm1435)

• RNAi's with this phenotype:
  • WBRNAi00084774 (knocks down xbp-1)
  • WBRNAi00084776 (knocks down xbp-1)

• Genes implicated by Variation: crt-1, cnx-1, hut-1

• Genes implicated by RNAi: xbp-1

Phenotype: "unfolded protein accumulation" (WBPhenotype:0001486)

• RNAi's with this phenotype:
  • WBRNAi00065521 (knocks down cup-2)
  • WBRNAi00065522 (knocks down cup-2)
  • WBRNAi00065523 (knocks down sel-1)
  • WBRNAi00065524 (knocks down ero-1)
  • WBRNAi00077072 (knocks down apy-1)
  • WBRNAi00077415 (knocks down dnj-7)
  • WBRNAi00077416 (knocks down dnj-7)

• Genes implicated by RNAi: cup-2, sel-1, ero-1, apy-1, dnj-7

Phenotype: "tunicamycin response variant" (WBPhenotype:0000359)

• Variations with this phenotype:
  • pdr-1(tm598)

• RNAi's with this phenotype:
  • WBRNAi00077192 (knocks down ire-1)
  • WBRNAi00077193 (knocks down xbp-1)
  • WBRNAi00077405 (knocks down xbp-1)
  • WBRNAi00077406 (knocks down xbp-1)
  • WBRNAi00078678 (knocks down ire-1)
  • WBRNAi00078679 (knocks down xbp-1)

• Genes implicated by Variation: pdr-1

• Genes implicated by RNAi: ire-1, xbp-1

Phenotype: "tunicamycin hypersensitive" (WBPhenotype:0001724)

• Variations with this phenotype:
  • atm-1(gk186)
  • crt-1(jh101)
  • kgb-1(km21)
  • cnx-1(nr2009)
  • crp-1(ok685) [also affects ncRNA Y32F6B.5]
  • shc-1(tm1729)
  • cdc-48.1(tm544) [also affects snoRNA C06A1.9]
  • ire-1(v33)

• RNAi's with this phenotype:
  • WBRNAi00077415 (knocks down dnj-7)
  • WBRNAi00077416 (knocks down dnj-7)

• Genes implicated by Variation: atm-1, crt-1, kgb-1, cnx-1, crp-1, shc-1, cdc-48.1, ire-1

• Genes implicated by RNAi: dnj-7

Biological Markers of UPR

NOTE: There is no tag for this connection in the Topic or Transgene model as of WS241. A model change will need to be requested for WS242. Thoughts are to add a tag to the Topic model and attach it to the Topic with no evidence.

Markers of Mitochondrial UPR:

• hsp-6::GFP
• hsp-60::GFP

Markers of ER UPR:

• hsp-4::GFP

Inducers of UPR

Chemicals/Molecules

• Tunicamycin (ER-stress inducing)
• Dithiothreitol [DTT] (ER-stress inducing)
• Ethidium Bromide (Mitochondrial UPR-stress inducing)

Gene Knockdowns

• spg-7 RNAi (Mitochondrial UPR-stress inducing)

WS242 Topic: non-coding RNAs?

Hinxton

We plan to add RFam based gene models for ncRNAs to our non-core species for WS242. We trialled it on B.malayi for WS241 and believe we ironed out most kinks. This in turn will allow us to test the RNA-GeneTree pipeline from Compara, as it depends on RFAM cross-references.

Conservation Matrix based on the Grishok paper and WS241 (3rd sheet).

Caltech

Plan to chose a specific type of ncRNA or a specific niche as general ncRNA is too broad.

Grishok, 2013 Review

List of genes mentioned (WBPaper00043989, PMID:23890211):

• adr-1
• adr-2
• ain-1
• ain-2
• akt-1
• alg-1
• alg-2
• alg-3
• alg-4
• cde-1
• cdh-3
• cdh-4
• cog-1
• csr-1
• cye-1
• daf-16
• dcr-1
• deps-1
• drh-1
• drh-3
• drsh-1
• ego-1
• ekl-1
• elo-2
• ergo-1
• eri-1
• eri-3
• eri-5
• eri-6
• eri-7
• eri-9
• fbf-1
• gfl-1
• gsk-3
• haf-6
• hbl-1
• henn-1
• hpl-2
• hrde-1=wago-9
• ksr-1
• let-7
• let-60
• lin-4
• lin-14
• lin-15a
• lin-15b
• lin-26
• lin-28
• lin-35
• lin-41
• lin-58
• lir-1
• lsy-6
• mef-2
• mes-4
• mir-1
• mir-34
• mir-35
• mir-36
• mir-37
• mir-38
• mir-39
• mir-40
• mir-41
• mir-42
• mir-51
• mir-52
• mir-53
• mir-54
• mir-55
• mir-56
• mir-57
• mir-58
• mir-61
• mir-71
• mir-80
• mir-81
• mir-82
• mir-84
• mir-124
• mir-238
• mir-239
• mir-240
• mir-241
• mir-243
• mir-246
• mir-786
• mut-2
• mut-7
• mut-14
• mut-15
• mut-16
• nob-1
• nrde-1
• nrde-2
• nrde-3
• nrde-4
• pash-1
• pdk-1
• pes-10
• prg-1
• prg-2
• rde-1
• rde-2
• rde-3
• rde-4
• rde-10
• rde-11
• rrf-1
• rrf-3
• rsd-2
• rsd-6
• set-25
• sid-1
• sid-2
• sid-3
• sid-5
• tbx-37
• tbx-38
• unc-22
• vav-1
• wago-1
• wago-2
• wago-3
• wago-4
• wago-5
• wago-6
• wago-7
• wago-8
• wago-10
• wago-11
• xrn-2
• zfp-1
• C04F12.1
• T23D8.7
• C14B1.7
• C06A1.4
• M03D4.6