Genome-wide collections of Saccharomyces cerevisiae

Deletion

NA

A collection where each gene is precisely deleted and replaced with a kanMX4 (encoding G418 Resistance) selection marker. This deletion strategy combines molecular barcodes (UPTAG and DNTAG) flanking the marker, enabling high-throughput identification and quantification of each strain even in pooled cultures. The collection includes haploid (both mating types) and diploid versions, allowing for the assessment of both essential (as heterozygous diploids) and non-essential genes.

MATa MATα Diploid

(a) his3∆1 leu2∆0 met15∆0 ura3∆0 ∆xxx::UPTAG-G418R-DNTAG (α) his3∆1 leu2∆0 lys2Δ0 ura3∆0 ∆xxx::UPTAG-G418R-DNTAG (a/α) his3∆1/his3∆1 leu2∆0/leu2∆0 met15∆0/MET15 LYS2/lys2Δ0 ura3∆0/ura3∆0 ∆xxx::UPTAG-G418R-DNTAG /XXX

Winzeler et al. 1999

Full genome (5120 genes)

Giaever et al. 2002

C' GFP

C'

Each gene is altered such that the protein it encodes is fused at the C-terminus with a green fluorescent protein (GFP).

MATa

his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 XXX-GFP-HIS3

Huh et al. 2003

Full genome (5206 genes)

C' TAP-Tag

C'

Each gene is altered such that the protein it encodes is fused at the C-terminus with a Tandem Affinity Purification (TAP) tag. This tag allows for both immunodetection and purification of proteins using a single, high-affinity antibody.

MATa

his3∆1 leu2∆0 met15∆0 ura3∆0 XXX-TAP-HIS3

Ghaemmaghami et al. 2003

Full genome (4715 genes)

TEToff-Promoter

NA

The promoter of each essential gene is replaced with the tetracycline-repressible promoter (TetO7). This design allows for conditional repression of essential genes by the addition of doxycycline.

MATa

ura3∆0::URA3-CMV-tTA his3∆1 leu2∆0 met15∆0 G418R-TetO7pr-XXX

Mnaimneh et al. 2004

Essentials (892 genes)

mini ORFs

NA

Deletions of small open reading frames (sORFs, <100 amino acids), completing the deletion collection. Including molecular barcodes like those in the yeast deletion library. Built with the same selection markers and the same genotype as the yeast deletion library, so that they can be combined.

MATa MATα Diploid

(a) his3∆1 leu2∆0 met15∆0 ura3∆0 ∆xxx::G418R (α) his3∆1 leu2∆0 lys2Δ0 ura3∆0 ∆xxx::G418R (a/α) his3∆1/his3∆1 leu2∆0/leu2∆0 met15∆0/MET15 LYS2/lys2Δ0 ura3∆0/ura3∆0 ∆xxx::G418R/XXX

Kastenmayer et al. 2006

247 small genes

Temperature-sensitive (ts) 2008

NA

Essential Genes are represented by a temperature-sensitive (ts) allele. These ts alleles allow normal protein function at a permissive temperature (25°C) and impair function at a non-permissive temperature (37°C), enabling conditional analysis of essential genes. Each allele is flanked by UPTAG and DNTAG barcodes, enabling high-throughput identification and quantification of each strain even in pooled cultures.

MATa

ura3Δ0 leu2Δ0 his3Δ1 lys2Δ0 (or LYS2) met15Δ0 (or MET15) can1Δ::LEU2-MFA1pr-His3 UPTAG-XXX^ts-URA3-DNTAG

Ben-Aroya et al. 2008

Essentials (250 genes)

Temperature-sensitive (ts) 2011

NA

This collection complements the 2008 ts library by adding strains carrying at least one conditional ts allele.

MATa

his3∆1 leu2∆0 met15∆0 ura3∆0 XXX^ts-G418R

Li et al. 2011

Essentials (787 genes)

DAmP Hypomorphic Alleles

NA

The 3’ untranslated region (UTR) of each essential gene is deleted, altering mRNA stability, causing reduced abundance (two to ten-fold). Built with the same selection markers and genotype as the yeast deletion library, they can be combined.

MATa Diploid

(a) his3∆1 leu2∆0 met15∆0 ura3∆0 XXX-DAmP-G418R (a/α) his3∆1/his3∆1 leu2∆0/leu2∆0 met15∆0/met15∆0 ura3∆0/ura3∆0 XXX-DAmP-G418R/XXX

Breslow et al. 2008

Essentials (842 genes)

YETI

NA

The promoter of each gene is replaced with the β-estradiol-inducible Z3EV promoter. This system enables titratable gene induction/ repression. The collection covers essential genes in diploid form (YETI-E) and non-essential genes in haploid form (YETI-NE). Each strain is also barcoded.

MATa Diploid

(a/α) barcode-URA3-Z3EVpr‐XXX hap1∆::NATR‐ACT1pr‐Z3EVTF‐ENO2term/ HAP1 ura3∆0/ura3∆0 can1∆::STE2pr‐spHIS5/CAN1 his3∆1/his3∆1 lyp1∆/LYP1 (a) barcode-URA3-Z3EVpr‐XXX hap1∆::NATR‐ACT1pr‐Z3EVTF‐ENO2term ura3∆0 can1∆::STE2pr‐spHIS5 his3∆1 lyp1∆

Arita et al. 2021

Full genome (4759 genes mat a, and 5811 genes in diploids)

C' AID-eGFP

C'

Based on the C’-SWAT parental collection (see section on Modular innovation), each gene is altered such that the protein it encodes is tagged at the C-terminus with a minimized auxin-inducible degron (AID*) followed by an enhanced GFP (eGFP). This design allows both visualization of protein localization and abundance (through the GFP tag) and rapid, conditional protein depletion (using the AID system). Each strain also contains the modified OsTIR1(F74G). adaptor for E3 ubiquitin ligases. Upon the addition of the modified auxin analog 5-Ph-IAA, the Tir1 adaptor targets the AID* fused protein for degradation via the ubiquitin-proteasome pathway.

MATα

his3∆1 leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI-STE2pr-spHIS5 lyp1∆::STE3pr-LEU2, NATR-TEF2pr-osTIR1(F74G), XXX-AID*-eGFP-G418R

Valenti et al. 2024

Genome-wide

C' AID-Monomeric Neon Green (mNG)

C'

Two libraries, all Based on the C’-SWAT parental collection (see section on Modular innovation), and on AID*. V1: Each gene is altered such that the protein it encodes is tagged with mNG-AID*-3myc and is represented as either containing or lacking the osTIR1 for control. V2: Each gene is altered such that the protein it encodes is fused to AID*-3myc, and the osTIR is regulated by the galactose inducible/glucose inhibited GAL1pr. These libraries offer versatile tools for conditional, proteome-wide protein depletion.

MATa

V1 (OsTIR1- set): lyp1Δ his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 can1Δ::STE3pr-LEU2-GAL1pr-NLS-I-SCEI XXX-mNG-AID*-3myc-HygroR V1 (OsTIR1+ set): his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 can1Δ::STE3pr-LEU2-GAL1pr-NLS-I-SCEI lyp1Δ::GAL1pr-osTIR1(F74G)-NATR XXX-mNG-AID*-3myc-HygroR V2 (OsTIR1+ set): his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 can1Δ::STE3pr-LEU2-GAL1pr-NLS-I-SCEI lyp1Δ::GAL1pr-osTIR1(F74G)-NATR XXX-AID*-3myc-HygroR

Gameiro et al. 2024

genome-wide

Sigma collection- Filamentous growth deletion

NA

Gene deletions were introduced into the filamentation-competent Σ1278b yeast strain background. The library includes both haploid and homozygous diploid deletions.

MATa

(a)can1Δ::STE2pr-Sp_his5 lyp1Δ::STE3pr-LEU2 his3::his3G leu2Δ ura3Δ ∆xxx::G418R (α)can1Δ::STE2pr-Sp_his5 lyp1Δ::STE3pr-LEU2 his3::his3G leu2Δ ura3Δ ∆xxx::G418R (a/α) can1Δ::STE2pr-Sp_his5 / CAN1 lyp1Δ::STE3pr-LEU2 / LYP1 his3::his3G / his3::his3G leu2Δ / leu2Δ ura3Δ / ura3Δ ∆xxx::G418R / ∆xxx::G418R

Ryan et al. 2012

Full genome (4028 genes in haploids and 3900 genes in homozygous diploid)

C' DHFR-PCA

C'

Two collections in which each gene is altered such that the protein it encodes is fused to complementary fragments of the methotrexate (MTX)-resistant dihydrofolate reductase (DHFR), one part in each mating type, and with different selections. Upon mating of strains from the complementing libraries and diploid selection, if proteins interact, their fused DHFR fragments would also reconstitute enzymatic activity. Upon addition of MTX, the endogenous, essential DHFR is inhibited, allowing strains to grow only if the reconstituted DHFR is active.

MATa MATα

(a) his3∆1 leu2∆0 met15∆0 ura3∆0 XXX-DHFR1,2-NATR (α) his3∆1 leu2∆0 lys2Δ0 ura3∆0 XXX-DHFR3-HygroR

Tarassov et al. 2008

Full genome (4320 genes in MATa and 4470 genes in MATα)

C' Split Venus

C'

Derived from the TAP library by manual replacement of the TAP cassette, each gene is altered such that the protein it encodes is C-terminally tagged with split fragments of the Venus fluorescent protein: VN (N-terminal part) and VC (C-terminal part).

MATa

his3∆1 leu2∆0 met15∆0 ura3∆0 XXX-VC-LEU2 or his3∆1 leu2∆0 met15∆0 ura3∆0 XXX-VN-LEU2

Kim et al. 2019

Full genome VC (5956 genes)

Sung et al. 2013

Full genome VN (5671 genes)

Tandem Fluorescent Protein Timer (tFT)

C'

Each gene is altered such that the protein it encodes is seamlessly C-terminally tagged with a tandem fluorescent timer (mCherry–sfGFP) for measuring protein age by a simple fluorescent readout.

MATα

YMaM344-2 XXX-mCherry-sfGFP-NATIVEter

Khmelinskii et al. 2014

Full genome VN (4044 genes)

N’-SWAT parental

N'

Each gene is altered such that the protein it encodes is N-terminally tagged with GFP and expressed under the constitutive NOP1 promoter, flanked by the SWAp-Tag (SWAT) sequences to enable cassette swapping. To ensure proper targeting, proteins containing a Mitochondrial Targeting Signal (MTS) or a Signal Peptide (SP) also have a synthetic MTS/SP before the GFP tag, respectively.

MATa

his3∆1 leu2∆0 met15∆0 ura3∆0 Hygro∆N'-URA3-spNOP1pr-sfGFP-XXX

Weill et al. 2018

Full genome (5457 genes)

Yofe et al. 2016

1759 genes

N' SWAT NATIVEpr-GFP

N'

Derived from the parental N’-SWAT collection, each gene is altered such that the protein it encodes is N-terminally tagged with GFP without altering the native sequence of the promoter and N-terminal targeting signals (MTS or SP).

MATα

his3∆1 leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI-STE2pr-spHIS5 lyp1∆::STE3pr-LEU2 XXXpr-sfGFP-XXX

Weill et al. 2018

Genome-wide

N' SWAT TEF2pr-mCherry

N'

Derived from the parental N’-SWAT collection, each gene is altered such that the protein it encodes is N-terminally tagged with mCherry and expressed under the strong, constitutive TEF2 promoter.

MATα

his3∆1 leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI-STE2pr-spHIS5 lyp1∆::STE3pr-LEU2 NATR-TEF2pr-mCherry-XXX

Weill et al. 2018

Genome-wide

C'-SWAT parental

NA

Each gene is capped by a CYC1 terminator flanked by the SWAT sequences to enable high-throughput modification of the 3’ of the gene.

MATa

his3∆1 leu2∆0 met15∆0 ura3∆0 XXX-CYC1term-scURA3-HygroRΔN'-ALG9term

Meurer et al. 2018

Full genome (5661 genes)

C'-SWAT mNG

C'

Based on the C’-SWAT parental collection, each gene is altered such that the protein it encodes is tagged at the C-terminus with the bright fluorescent protein mNG.

MATa

his3∆1 met15∆0 ura3∆0 leu2∆0::GAL1pr-NLS-SceI-NATR can1∆::STE2pr-spHIS5 lyp1∆::STE3pr-LEU2 XXX-mNG-ADH1term-HygroR or XXX-mNG

Meurer et al. 2018

Genome-wide

C'-SWAT mScarlet-I

C'

Based on the C’-SWAT parental collection, each gene is altered such that the protein it encodes is tagged at the C-terminus with the bright fluorescent protein mScarlet-I.

MATa

his3∆1 met15∆0 ura3∆0 leu2∆0::GAL1pr-NLS-SceI-NATR can1∆::STE2pr-spHIS5 lyp1∆::STE3pr-LEU2 XXX-mScarlet-I-ADH1term-HygroR

Meurer et al. 2018

Genome-wide

N' SWAT split-DHFR

N’

Derived from the parental N’-SWAT collection, this library employs the split DHFR approach (See above) by seamless tagging. Mating of strains from opposite mating types is enabled by selection cassettes at a distal, inert locus.

MATa MATα

(a) his3∆1 leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI::STE2pr-SpHIS5 lyp1∆::STE3pr-LEU2 chrV VCAJ1-TPA1::NATR NATIVEpr- DHFR[1,2]-XXX (α) his3∆1 leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI::STE2pr-SpHIS5 lyp1∆::STE3pr-LEU2 chrV VCAJ1-TPA1::HygroR NATIVEpr-DHFR[3]-XXX

Weill et al. 2018

Genome-wide

N' SWAT split-Venus

N’

Derived from the parental N’-SWAT collection, this library builds on the split Venus approach (See above).

MATa MATα

his3∆1 leu2∆0 met15∆0 ura3∆0 HygroR-TEF2pr-VC-XXX or G418R::CET1pr-VN-XXX can1∆::GAL1pr-SceI::STE2pr-SpHIS5 lyp1∆::STE3pr-LEU2

Weill et al. 2018

Genome-wide

C'-SWAT split-β-galactosidase

C'

Based on the C’-SWAT parental collection, each gene is altered such that the protein it encodes is fused to the alpha subunit of β-galactosidase at its C-terminus.

MATα

his3∆1 leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI-NLS-STE2pr-spHIS5 lyp1∆::STE3pr-LEU2 XXX-alpha-ADH1ter-HygroR

Mark et al. 2023

Genome-wide

C'-SWAT Split-GFP

C'

Based on the C’-SWAT parental collection, each gene is altered such that the protein it encodes is C-terminally tagged with three repeats of the small subunit of a split GFP (3×GFP11). The library also expresses MTS-mCherry as a mitochondrial marker. The library can be mated with a strain harboring the big subunit of the split GFP (GFP1–10) for visualizing reconstitution of the complete GFP signal.

MATα

his3∆1 leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI::STE2pr-SpHIS5 lyp1∆::STE3pr-LEU2 XXX-3xGFP11-ADH1ter-HygroR

Bykov et al. 2024

Genome-wide

C'-SWAT SmBiT

C'

Based on the C’-SWAT parental collection, A pair of libraries in which each gene is altered such that the protein it encodes is C-terminally tagged with either SmBiT (Small BiT, MATa) or LgBiT (Large BiT, MATα) fragments of NanoLuc luciferase.

MATa

his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 XXX-SmBiT-NATR fcy1Δ::STE2pr-spHIS5-GAL1pr-NLS-SceI

Le Boulch et al., 2020

Genome-wide

C'-SWAT LgBiT

C'

MATα

his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 XXX-LgBiT-10HIS-HygroR can1Δ::STE3pr-LEU2-GAL1pr-NLS-SceI lyp1Δ

Lazarewicz et al. 2024

Genome-wide

C'-SWAT NanoLuc

C'

Based on the C’-SWAT parental collection, each gene is C-terminally tagged with full-length NanoLuc luciferase.

MATα

his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 XXX-NanoLuc-HygroR can1Δ::STE3pr-LEU2-GAL1pr-NLS-SceI lyp1Δ

Lazarewicz et al. 2024

Genome-wide

N'-SWAT BioID-HA tag

N'

Derived from the parental N’-SWAT collection, each gene is altered such that the protein it encodes is tagged at the N-terminus with a BioID2-HA tag under the control of the CYC1 promoter. The BioID2 provides the capacity to nonspecifically biotinylate proximal proteins at 37 ° Celsius.

MATα

his3∆1 leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI-STE2pr-spHIS5 lyp1∆::STE3pr-LEU2 HygroR-CYC1pr-BioID-HA-XXX

Fenech et al. 2023

Genome-wide

N'-SWAT BirA/ ABOLISH

N'

Derived from the parental N’-SWAT collection, each gene is altered such that the protein it encodes is fused to BirA at their N-terminus under their native promoters. BirA has the capacity to biotinylate proteins carrying a specific AviTag. This library integrates the ABOLISH system, where the endogenous biotin ligase Bpl1 is fused to an AID* tag on the background of the Tir1 adaptor, allowing for controlled degradation of Bpl1 to reduce background biotinylation.

MATa

his3∆1 leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI-STE2pr-spHIS5 lyp1∆::STE3pr-LEU2 BPL1-AID*-9myc-NATR Nativepr-BirA-XXX

Fenech et al. 2023

Genome-wide

N'-SWAT AviTag/ ABOLISH

N'

Derived from the parental N’-SWAT collection, each gene is altered such that the protein it encodes has N-terminal AviTag fusions seamlessly integrated, allowing native promoter regulation. This library should be used in combination with the BirA library, and they are created in opposite mating types. The library also incorporates the ABOLISH system.

MATα

leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI-STE2pr-spHIS5 lyp1∆::STE3pr-LEU2 BPL1-AID*-6HA-HygroR his3∆1::Tir1-HIS3 Nativepr-AviTag-XXX

Fenech et al. 2023

Genome-wide

N'-SWAT TurboID-HA tag

N'

Derived from the parental N’-SWAT collection, each gene is altered such that the protein it encodes is tagged at the N-terminus with TurboID-HA under the control of the CYC1 promoter. TurboID is a highly active biotin ligase capable of rapidly biotinylating proximal proteins non specifically.

MATα

his∆1 leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI-STE2pr-spHIS5 lyp1∆::STE3pr-LEU2 HygroR-CYC1pr-TurboID-HA-XXX

Fenech et al. 2023

Genome-wide

N'-SWAT TurboID-HA tag/ ABOLISH

N'

Derived from the parental N’-SWAT collection, this library enhances the TurboID-HA N’ library by incorporating the ABOLISH system.

MATα

leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI-STE2pr-spHIS5 lyp1∆::STE3pr-LEU2 HygroR-CYC1pr-TurboID-HA-XXX, BPL1-AID*-9myc-G418R his3∆1::osTIR1-HIS3

Fenech et al. 2023

Genome-wide

C'-SWAT Myc-HRV-Flag tag

C'

Based on the C’-SWAT parental collection, each gene is altered such that the protein it encodes is tagged with a C-terminal myc epitope followed by a human rhinovirus (HRV) 3C protease cleavage site, and a 3xFLAG tag for efficient protein purification.

MATa

his3∆1 leu2∆0 met15∆0 ura3∆0 can1∆::GAL1pr-SceI-NLS-STE2pr-spHIS5 lyp1∆::STE3pr-LEU2 XXX-myc-HRV-3xFlag-ADH1term-G418R

Reinhard et al. 2022

Genome-wide

N'-SWAT HaloTag

N'

Derived from the parental N’ and C’-SWAT collections, each gene is altered such that the protein it encodes is fused with the Halo tag, either at its N- or C-terminus (respectively).

MATa

his3Δ1 ura3Δ0 met15Δ0 lyp1Δ can1Δ::STE3pr-LEU2-GAL1pr-NLS-I-SCEI leu2Δ::NATR-TEF1pr-mNeonGreen-CYC1term pdr5Δ::HygroR NATIVEpr-HaloTag-3myc-XXX

Gameiro et al. 2024

Genome-wide

C'-SWAT HaloTag

C'

MATa

his3Δ1 ura3Δ0 met15Δ0 lyp1Δ can1Δ::STE3pr-LEU2-GAL1pr-NLS-I-SCEI leu2Δ::NATR-TEF1pr-mCherry-CYC1term pdr5Δ::HygroR XXX-HaloTag-3myc-NATIVEterm

Gameiro et al. 2024

Genome-wide

C'-SWAT H2O2 biosensor

C'

Based on the C’-SWAT parental collection, each gene is altered such that the protein it encodes is C-terminally tagged with the hydrogen peroxide (H₂O₂) sensor HyPer7, enabling the detection of local redox changes at the level of individual proteins. A corresponding control library using a redox-insensitive mutant of the sensor (SypHer7) allows precise mapping of nanoscale redox microenvironments.

MATa

can1Δ::STE2pr-SpHIS5 lyp1Δ::STE3pr-LEU2 his3Δ1 ura3Δ0 leu2Δ0::GAL1pr-NLS-I-SCEI-natNT2 XXX-HyPer7-ADH1term-HygroR or XXX-SypHer7-ADH1term-HygroR

Kritsiligkou et al. 2023

Genome-wide

N'-SWAT HA tag

N'

Derived from the parental N’-SWAT collection, each gene is altered such that the protein it encodes is N-terminally tagged with a 3xHA epitope under the regulation of the TEF1 promoter.

MATa

his3∆1 leu2∆0 met15∆0 ura3∆0 TEF1pr-3HA-XXX-NATR can1∆::GAL1pr-SceI-STE2pr-spHIS5 lyp1∆::STE3pr-LEU2

Baruch et al. 2025

Genome-wide