WormBase Model:Construct

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Model changes

WS251

Construct_for_disease	?DO_term	XREF	Associated_construct	#Evidence

Proposed model changes

Purpose: the technology of engineering mutations and gene replacement has been developed in C. elegans. With these new research tools, capture and display of the molecular information of these alleles needs to be updated. We propose a new class, Construct, to capture the specifics of the DNA tool used to perform the replacement or engineering, while the Variation model gets updated to record the engineering event itself and its impact on the genome. As a side benefit to the creation of the Construct model, we can use this new class to also capture the genomic arrays used create transgenes.

Variation

Proposed additions

?Variation
Variation_type 
    Engineered_allele 
Variation_summary ?Text//to house final engineered construct
Derived_from ?Construct XREF Engineered_variation
Corresponing_transgene Unique ?Transgene XREF Corresponding_variation
Method 
    Homologous_recombination //Homologous_recombination
    NHEJ //Non-homologous DNA end-joining, imprecise DNA repair
    MosSci
    TALENs
    CRISPR_Cas9
    ZFN-NHEJ repair //Zinc-finger nuclease
    ZFN-HR repair
Expr_pattern ?Expr_pattern XREF Variation #Evidence

notes on variation model changes

see discussion tab

WBPaper00045772 Paix et al., 2014
Discusses Homology directed repair (HDR) vs Nonhomologous end-joining (NHEJ). It would seem that distinguishing the method used to create engineered alleles is important. However, the tags should perhaps be modified to distinguish double stranded break method and repair method.

break_made_by
  Mos_excision
  CRISPR/Cas9
  TALENs
  Zinc_finger_endonuclease
  OTHER

repaired_by
  nonhomologous_end_joining_NHEJ
  homologous_direct_repair_HDR

repair_template
  Construct (note, ssODNs (single-strand oligonucleotides) should be added as a construct_type)



--Kyook (talk) 21:17, 16 October 2014 (UTC)

Construct (new)

Class itself is new

?Construct Evidence #Evidence
	   Curator_confirmed	?Person
	   Public_name ?Text
	   Other_name ?Text
	   Summary ?Text                      //genotype like [Pmyo-2::GFP]
	   Sequence_feature ?Feature XREF Associated_with_construct
	   Driven_by_gene ?Gene XREF Drives_construct #Evidence
	   Gene ?Gene XREF Construct_product #Evidence
	   3_UTR ?Gene #Evidence
	   Fusion_reporter ?Text              //fluorescent proteins GFP, RFP, mCherry, etc.
	   Other_reporter ?Text               //to add reporters, tags that aren�-F¢t included in model�-A
	   Purification_tag ?Text             //FLAG, HA, Myc, TAP, etc.
	   Recombination_site ?Text           //LoxP, FRT
	   Type_of_construct  Chimera
			      Domain_swap
			      Engineered_mutation
			      Fusion
			      Complex                    // complex changes
			      Transcriptional_fusion
			      Translational_fusion
			      Nterminal_translational_fusion
			      Cterminal_translational_fusion
			      Internal_coding_fusion
	   Selection_marker ?Text
	   Construction_summary  ?Text        // Backbone vector, mol bio
	   DNA_text Text                      // for mapping, can include entire construct sequence
	   Clone ?Clone XREF Construct
	   Used_for Transgene_construct ?Transgene XREF Construct
		    Transgene_coinjection ?Transgene XREF Coinjection
		    Engineered_variation ?Variation XREF Derived_from_construct
		    Topic_output_indicator ?WBProcess XREF Marker_construct
		    Expression_pattern ?Expr_pattern XREF Construct
		    Interactor ?Interaction
	   Reference ?Paper
	   Person ?Person
	   Laboratory ?Laboratory #Lab_Location
	   Historical_gene ?Gene #Evidence
	   Remark ?Text #Evidence

notes on construct model

see discussion tab

#Interactor_info

 Construct ?Construct XREF Interactor

Interaction

 Unaffiliated_construct   ?Construct
 Detection_method    Construct

Expression_pattern

proposed addition

Variation ?Variation XREF Expression_pattern
Construct ?Construct XREF Expression_pattern

Gene

proposed change

Drives_Transgene ?Transgene XREF Driven_by_gene
change to 
Drives_construct ?Construct XREF Driven_by_gene

Transgene

Proposed changes: Many of the transgene tags have been moved to the proposed ?Construct model, the remaining tags as well as some additions are shown below

?Transgene      Evidence #Evidence
		Public_name UNIQUE ?Text
		Summary UNIQUE ?Text
		Synonym ?Text
		Corresponding_variation UNIQUE ?Variation XREF Corresponding_transgene //put in to unambiguously associate the allele/transgene
		Construction Construct   ?Construct XREF Transgene_construct
     			     Coinjection ?Construct XREF Transgene_coinjection
     			     Coinjection_other ?Text //for coinjection markers that are not specified as a construct
     			     Integration_method UNIQUE ?Text
     			     Integrated_from ?Transgene XREF Transgene_derivation
     			     Laboratory ?Laboratory #Lab_Location
     			     Author ?Author
		Construction_summary ?Text
		Genetic_information Extrachromosomal
				    Integrated
				    Map ?Map  #Map_position  //needed for transgenes with no granular mapping, e.g., just mapped to a LG
                                    Mapping_data 2_point ?2_point_data      //deleted for WS245, rolled back for WS246
				    Map_evidence #Evidence
				    Phenotype ?Phenotype XREF Transgene #Phenotype_info
				    Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info
		Used_for Transgene_derivation ?Transgene XREF Integrated_from
			 Expr_pattern ?Expr_pattern XREF Transgene
			 Marker_for   ?Text #Evidence
			 Interactor ?Interaction
		Associated_with Marked_rearrangement ?Rearrangement XREF By_transgene
				Strain ?Strain XREF Transgene
		Reference ?Paper XREF Transgene
		Species UNIQUE ?Species
		Remark ?Text #Evidence
                Historical_gene   ?Gene #Evidence

WBProcess

    Marker_construct ?Construct XREF Topic_output_indicator

Test data

Variation objects with constructs

LP132 nmy-2(cp7[nmy-2::gfp + LoxP unc-119(+) LoxP]) I; unc-119(ed3) I
Variation : "WBVar020000000"
Public_name "cp7"
Engineered_allele 
Variation_summary "[nmy-2::gfp + LoxP unc-119(+) LoxP]"
Derived_from "WBConstruct00000010"
Derived_from "WBConstruct00000011"
Homologous_recombination

Construct : "WBConstruct00000010"
Summary "[nmy-2::gfp]
Driven_by_gene "WBGene00003777"
Fusion_reporter "GFP"
N-terminal_translational_fusion

Construct : "WBConstruct00000011"
Summary "[LoxP unc-119(+) LoxP]
Recombination_site "LoxP"
Gene "WBGene00003777"

bus-50(e5000[T110E]) = An engineered missense mutation

bus-50(e5001[bus-50::gfp]) aka bus-50::gfp = 
 An engineered fusion of GFP to the C-terminus of BUS-50
Variation : "WBVar0200000001"
Public_name "e5001"
Engineered_allele 
Variation_summary "[bus-50::gfp]"
Derived_from "WBConstruct00000012"
CRISPR-Cas9

Construct : "WBConstruct00000012"
Summary "[bus-50::gfp]"
Gene "WBGene0020000001"
Fusion_reporter "GFP"
C-terminal_translational_fusion


bus-50(e5002[bus-50::gfp + loxP unc-119(+) loxP]) 
 An engineered insertion of GFP plus the unc-119(+) selectable marker, flanked by loxP sites.
Variation : "WBVar020000003"
Public_name "e5002"
Engineered_allele 
Variation_summary "[bus-50::gfp + loxP unc-119(+) loxP]"
Derived_from "WBConstruct00000012"
Derived_from "WBConstruct00000011"
HR

Construct : "WBConstruct00000012"
Summary "[bus-50::gfp]"
Gene "WBGene0020000001"
Fusion_reporter "GFP"
C-terminal_translational_fusion


Construct : "WBConstruct00000011"
Summary "[LoxP unc-119(+) LoxP]
Recombination_site "LoxP"
Gene "WBGene00003777"


bus-50(e5003[bus-50::gfp +loxP]) aka bus-50(e5003) = 
 bus-50(e5002) following Cre-mediated recombinase removal of unc-119(+) leaving a single loxP site
Variation : "WBVar020000004"
Public_name "e5003"
Engineered_allele 
Variation_summary "[bus-50::gfp + loxP]"
Derived_from "WBConstruct00000012"
Derived_from "WBConstruct00000011"
HR

Construct : "WBConstruct00000012"
Summary "[bus-50::gfp]"
Gene "WBGene0020000001"
Fusion_reporter "GFP"
C-terminal_translational_fusion

Construct : "WBConstruct00000011"
Summary "[LoxP unc-119(+) LoxP]
Recombination_site "LoxP"
Gene "WBGene00003777"

Variation object with transgene

eIs2002 = eIs2002[unc-119::gfp] = eIs2002[unc-119::gfp, III:2992500]  
 Engineered insertions in apparent intergenic region with optional 
 descriptors (nature of the insertion or position in the genome)
Variation : "WBVar020000005"
Public_name "eIs2002"
Engineered_allele 
Variation_summary "[unc-119::gfp]"
Derived_from "WBConstruct00000013"
Identical_transgene "WBTransgene00024514"
MosSci

Construct : "WBConstruct00000013"
Summary "[unc-119::gfp]"
Gene "WBGene0020000001"
Fusion_reporter "GFP"
Translational_fusion

Transgene : "WBTransgene00024514"
Public_name "eIs2002"
Summary "[unc-119::GFP]"
Construct "WBConstruct00000013"


ozIs909, or ozIs909[unc-119::mCherry *eIs2002] = 
  Engineered changes to existing Is (or Si) insertions, which should 
  receive new Is numbers using originating lab’s prefix. The original 
  Is insertion is indicated in brackets with a preceding asterisk (*), 
  in order to allow searches for all derivatives from a given insertion. 
  In this case, an engineered change from GFP to mCherry in eIs2002
Variation : "WBVar020000006"
Public_name "ozIs909"
Engineered_allele 
Variation_summary "[unc-119::mCherry *eIs2002]"
Derived_from "WBConstruct00000015"
Identical_transgene "WBTransgene00024515"
MosSci

Construct : "WBConstruct00000015"
Summary "[unc-119::mCherry]"
Gene "WBGene0020000001"
Fusion_reporter "mCherry"
Translational_fusion

Transgene : "WBTransgene00024515"
Public_name "ozIs909"
Summary "[unc-119::mCherry]
Construct "WBConstruct00000015"

Transgene with construct

The following depicts how current transgenes would be redistributed into the proposed Construct and Transgene models

(Original)Transgene : "WBTransgene00000001"
Public_name	"adEx1256"
Summary	"[egl-19::sGFP-NLS + lin-15(+)]"
Reporter_product	"GFP"
Driven_by_gene	"WBGene00001187"
Strain	"DA1256"
Reference	"WBPaper00029359"
Reporter_type	"Transcriptional fusion"
Synonym	"[C48A7.1::gfp]"


(New)Transgene : "WBTransgene00000001"
Public_name	"adEx1256"
Summary	"[egl-19::sGFP-NLS + lin-15(+)]"
Construct "WBConstruct00000001"
Coinjection_other "lin-15(+)"
Extrachromosomal
Strain	"DA1256"
Reference	"WBPaper00029359"

(New)Construct : WBConstruct00000001
Public_name	"adEx1256"
Other_name	"[C48A7.1::gfp]"
Summary	"[egl-19::sGFP-NLS]"
Fusion_reporter	"GFP"
Driven_by_gene	"WBGene00001187"
Reference	"WBPaper00029359"
Transcriptional_fusion


(Original)Transgene : "WBTransgene00000011"
Public_name	"adIs1240"
Summary	"[lin-15(+) eat-4::sGFP]"
Reporter_product	"GFP"
Driven_by_gene	"WBGene00001135"
Strain	"DA1240"
Strain	"DA1243"
Map	"X"
Map_evidence	Paper_evidence	"WBPaper00038205"
Reference	"WBPaper00030960"
Reference	"WBPaper00032252"
Reference	"WBPaper00035265"
Reference	"WBPaper00036277"
Reference	"WBPaper00036704"
Reference	"WBPaper00037626"
Reference	"WBPaper00038205"
Reference	"WBPaper00044482"
Synonym	"[eat-4::gfp]"

(New)Transgene : "WBTransgene00000011"
Public_name	"adIs1240"
Summary	"[lin-15(+) eat-4::sGFP]"
Strain	"DA1240"
Strain	"DA1243"
Map	"X"
Map_evidence	Paper_evidence	"WBPaper00038205"
Coninjection_other "lin-15(+)"
Reference	"WBPaper00030960"
Reference	"WBPaper00032252"
Reference	"WBPaper00035265"
Reference	"WBPaper00036277"
Reference	"WBPaper00036704"
Reference	"WBPaper00037626"
Reference	"WBPaper00038205"
Reference	"WBPaper00044482"

(New)Construct : "WBConstruct00000011"
Public_name	"adIs1240"
Other_name	"[eat-4::gfp]"
Summary	"[eat-4::sGFP]"
Fusion_reporter	"GFP"
Driven_by_gene	"WBGene00001135"
Reference	"WBPaper00030960"


(Original) Transgene : "WBTransgene00000017"
Public_name	"ajIs1"
Summary	"[pgp-5::gfp]"
Coinjection_marker	"pRF4[rol-6(su1006)]"
Construction_summary	"Integrated from BC10030 sEx864."
Reporter_product	"GFP"
Driven_by_gene	"WBGene00003999"
Driven_by_gene	"WBGene00006767"
Integration_method	"Gamma_ray"
Integrated
Reference	"WBPaper00002968"
Reference	"WBPaper00031023"

(New) Transgene : "WBTransgene00000017"
Public_name	"ajIs1"
Integration_method	"Gamma_ray"
Integrated
Reference	"WBPaper00002968"
Reference	"WBPaper00031023"
Integrated_from "WBTransgene00002030"
Construction_summary	"Integrated from BC10030 sEx864."

(New) Transgene : "WBTransgene00002030"
Public_name "sEx864"
Synonym "[pgp-5::gfp]"
Synonym	"[C05A9.1::gfp]"
Summary "[rCesC05A9.1::GFP + pCeh361]"
Extrachromosomal
Construct "WBConstruct00000017"
Construct "WBConstruct00000018"
Construct "WBConstruct00000002"

(New) Construct : "WBConstruct00000018"
Public_name "pRF4"
Summary "[rol-6(su1006)]"
Gene "WBGene00004397"

(New) Construct : "WBConstruct00000017"
Public_name "[pgp-5::gfp]"
Summary	"[rCesC05A9.1::GFP]"
Reporter_product	"GFP"
Transcriptional_fusion
Driven_by_gene	"WBGene00003999"

(New) Construct : "WBConstruct00000002"
Public_name "pCeh361"
Summary "[pCeh::DPY-5]"
Clone "pGEM-5
Construction_summary "A 3.3-kb Nco I fragment containing a predicted cuticle 
  collagen gene was isolated from the cosmid F27C1, and cloned into the Nco I 
  site of pGEM-5 to generate the clone pCeh361"
Reference	"WBPaper00027361"

(New) Transgene : "WBTransgene00000600"
Public_name	"hIs2"
Summary	"[DPY-5::GFP + rol-6(su1006) + pBluescript]
Construct  "WBConstruct00000003"//pCeh358
Coinjection "WBConstruct00000004"//PCes1943
Coinjection "WBConstruct00000005"//pBluescript KS
Construction_summary	"Transgenic animals were generated by microinjection of 
  pCeh358 (5 ng/ul) and pBluescript KS (100 ng/ul), or in combination with 50 ng/ul 
  pCes1943, which carries a dominant rol-6 mutation [rol-6(su1006)] used as a 
  morphological marker for successful transformation"

(New) Construct : "WBConstruct00000003"
Public_name	"pCeh358"
Summary	"[dpy-5::gfp]"
Driven_by_gene	"WBGene00001067"
Gene	"WBGene00001067"
Clone "pPD95.69"
Translational_fusion
Construction_summary	"The dpy-5::gfp reporter construct pCeh358 was 
  generated by insertion of a 750 bp Sph I fragment from pCeh361 into the 
  Sph I site of the gfp expression vector pPD95.69 (kindly provided by A. Fire). 
  This fragment contains 5' sequences from an Sph I site in the polylinker of 
  pCeh361 to a site 30 bp downstream from the predicted DPY-5 initiator methionine, 
  resulting in an in-frame fusion of the first 12 codons of dpy-5 with gfp."
Reference	"WBPaper00027361"

(New) Construct : "WBConstruct00000004"
Public_name	"pCes1943"
Summary "[rol-6(su1006)]

(New) Construct : "WBConstruct00000005"
Public_name	"pBluescript KS"


Expression objects with construct

Examples of two expression objects pertaining to sequence feature


Example 1:

Expr_pattern : "Expr11377"
Anatomy_term	"WBbt:0005813" Certain
Anatomy_term	"WBbt:0008588" Certain
Anatomy_term	"WBbt:0008589" Certain
Gene	"WBGene00001948"
Life_stage	"WBls:0000003"
Life_stage	"WBls:0000041"
Pattern	"enh-1 was preferentially active in the posterior C and D lineages 
 in the embryo and in body wall musculature in the adult."
Reference	"WBPaper00032967"
Reporter_gene
Construct	"WBConstruct00000020"
Associated_feature "WBsf047531"

Construct : "WBConstruct00000020"
Public_name "enh-1 reporter"  
Summary	"[hlh-1.enh-1::pPD107.94]"  
Clone "pPD107.94"                     //added clone back to the construct model
Sequence_feature "WBsf047531"
Gene	"WBGene00001948"
Fusion_reporter	"GFP"
Construction_summary "Enhancer region enh-1 for hlh-1 cloned into the 
 (del)Pes-10 basal promoter vector pPD107.94"
Reference	"WBPaper00032967"



Example 2:

Expr_pattern : "Expr11284"
Anatomy_term	"WBbt:0006894"
Gene	"WBGene00001185"
Pattern	"The distal enhancer activity was observed in P6.p and its 
 descendants from the two-cell stage and increased with time. Distal 
 enhancer activity persisted into much later stages than the proximal 
 enhancer did."
Reference	"WBPaper00005841"
Reporter_gene
Construct	"WBConstruct00000021"
Associated_feature "WBsf919543"


Construct : "WBConstruct00000021"
Public_name "[Distal egl-17 enhancer reporter]" 
Summary	"[egl-17.distal::pPD122.53]" 
Clone "pPD122.53"                        //added clone back into model
Sequence_feature "WBsf919543"
Gene	"WBGene00001185"
Fusion_reporter	"GFP"
Construction_summary "Distal egl-17 enhancer inserted into the pPD122.53 vector."
Reference	"WBPaper00005841"



Expression objects described with reporter fusions that do not have a classical Ex transgene designation


Expr_pattern : "Expr11598"
Anatomy_term	"WBbt:0003681" Certain
Anatomy_term	"WBbt:0005772" Certain
Anatomy_term	"WBbt:0006749" Certain
Gene	"WBGene00001753"
Life_stage	"WBls:0000023"
Life_stage	"WBls:0000041"
Pattern	"gst-5 was expressed in intestine, pharynx, and circumpharyngeal neurons. 
 Expression is seen from L1 to adult stages."
Reference	"WBPaper00037704"
Reporter_gene	 
Construct	"WBConstruct00000021"


Construct : "WBConstruct00000021"  
Public_name	"Expr11598_Ex"  
Summary	"[GST-5::GFP]"
Driven_by_gene	"WBGene00001753"
Gene	"WBGene00001753"
Fusion_reporter	"GFP"
Translational_fusion
Reference	"WBPaper00037704"

Interaction/Regulation objects pertaining to construct

Interaction/Regulation object contains sequence feature. I am not sure shall we add construct tag in our model? --Xiaodong


Interaction : "WBInteraction000502404"
Change_of_expression_level
Interactor_overlapping_gene      "WBGene00004077" Trans_regulator
Interactor_overlapping_gene      "WBGene00004077" Variation "WBVar00241166"
Interactor_overlapping_gene      "WBGene00009560" Trans_regulated
Interactor_overlapping_gene      "WBGene00009560" Expr_pattern "Expr4287"
Feature_interactor       "WBsf034247" Cis_regulator
Interaction_summary      "psa-3 expression was induced in T.p after the T cell division, and it accumulated in the posterior granddaughters. psa-3 expression in the T.p lineage was much lower in a pop-1 hypomorphic allele, q645."
Reporter_gene    "[psa-3::gfp], translational fusion"  //This information seems like it can be captured by transgene or construct now, I am missing why this tag is needed. 
//Xiaodong's comments: this tag has been in the model from the beginning. it's just curator's simple notes on reporter construct. if you notice, I don't even have the precise reporter description. 
//We can leave as it is now, and let user have a rough idea of what reporter looks like. if they want, they can go to check construct for detailed info.
//If the construct model goes in, the webteam can port the construct summary to this interaction page, likewise with the transgene summary info. But I leave it to you.
Construct       "WBConstruct00000021"
Transcriptional 
Positive_regulate        Anatomy_term "WBbt:0006996"
Positive_regulate        Anatomy_term "WBbt:0006997"
Positive_regulate        Anatomy_term "WBbt:0007000"
Positive_regulate        Anatomy_term "WBbt:0007007"
Positive_regulate        Anatomy_term "WBbt:0007012"
Positive_regulate        Anatomy_term "WBbt:0007016"
Paper    "WBPaper00027741"Remark   "POP-1 function is known to be required in T.p to determine the neural fate. POP-1 regulates psa-3 expression in T.p through the POP-1 binding site."


Construct : "WBConstruct00000021"
Public_name "osEx113"
Summary	"[Ppsa-3::psa-3::gfp]"
Construction_summary	"psa-3 promoter and the entire coding region."
Reporter_product	"GFP"
Driven_by_gene	"WBGene00009560"
Gene	"WBGene00009560"
Translational_fusion
Reference	"WBPaper00040473"
Reference	"WBPaper00027741"