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a с STARR-seq construct ORF hkCP or dCP Enhancer ORF hkCP S2 STARR-seq 1,822 4,134 (32%) 3,586 pA site TCT TATA box MTE DPE Inr -AAAAA dCP S2 STARR-seq d dCP S2 STARR-seq enrichment (log₂) • NO b CG33936 CG33937-18473- Fold change .<2x hkCP and dCP 2x-4x hkCP.2x-4x dCP >4x hkCP >4x dCP hkCP S2 STARR-seq enrichment (log₂) Enr. rep2 (log₂) CG8129 Fps85D- Enr. rep2 (log₂) hkCP S2 STARR-seq hkCP S2 STARR-seq dCP S2 STARR-seq Enr. rep1 (log₂) dCP S2 STARR-seq Enr. rep1 (log,) e Per cent positive per tested 60 Luciferase construct hkCP luciferase 100121/24 80 40- 20- 1/24 LuciferasepA site---- Enhancer candidate hkCP enhancer Or85 CG9356 CG8132 2/12 CG34117 CG81354 RpL34b dop hkCP DCP 10/12 6/7 6/7 dCP luciferase enhancer Shared enhancer Figure 1 Distinct sets of enhancers activate transcription from the hkCP and dCP in S2 cells. a, STARR-seq set-up using the hkCP housekeeping (RpS12; purple) and dCP developmental core promoters (Drosophila synthetic core promoter (DSCP); brown) b, Genome browser screenshot depicting STARR-seq tracks for both core promoters. c, Overlap of hkCP and dCP enhancers. d, hkCP versus dCP STARR-seq enrichments at enhancers (insets show enrichment for replicates (Enr. rep) 1 versus 2 for hkCP and dCP; dCP data reanalysed from ref. 12). e, hkCP, dCP or shared enhancers that activate luciferase (>1.5-fold and P<0.05 (one-sided t-test); n = 3; Extended Data Figs 3 and 5) from hkCP (purple) or dCP (brown; numbers show positive/tested).

a с STARR-seq construct ORF hkCP or dCP Enhancer ORF hkCP S2 STARR-seq 1,822 4,134 (32%) 3,586 pA site TCT TATA box MTE DPE Inr -AAAAA dCP S2 STARR-seq d dCP S2 STARR-seq enrichment (log₂) • NO b CG33936 CG33937-18473- Fold change .<2x hkCP and dCP 2x-4x hkCP.2x-4x dCP >4x hkCP >4x dCP hkCP S2 STARR-seq enrichment (log₂) Enr. rep2 (log₂) CG8129 Fps85D- Enr. rep2 (log₂) hkCP S2 STARR-seq hkCP S2 STARR-seq dCP S2 STARR-seq Enr. rep1 (log₂) dCP S2 STARR-seq Enr. rep1 (log,) e Per cent positive per tested 60 Luciferase construct hkCP luciferase 100121/24 80 40- 20- 1/24 LuciferasepA site---- Enhancer candidate hkCP enhancer Or85 CG9356 CG8132 2/12 CG34117 CG81354 RpL34b dop hkCP DCP 10/12 6/7 6/7 dCP luciferase enhancer Shared enhancer Figure 1 Distinct sets of enhancers activate transcription from the hkCP and dCP in S2 cells. a, STARR-seq set-up using the hkCP housekeeping (RpS12; purple) and dCP developmental core promoters (Drosophila synthetic core promoter (DSCP); brown) b, Genome browser screenshot depicting STARR-seq tracks for both core promoters. c, Overlap of hkCP and dCP enhancers. d, hkCP versus dCP STARR-seq enrichments at enhancers (insets show enrichment for replicates (Enr. rep) 1 versus 2 for hkCP and dCP; dCP data reanalysed from ref. 12). e, hkCP, dCP or shared enhancers that activate luciferase (>1.5-fold and P<0.05 (one-sided t-test); n = 3; Extended Data Figs 3 and 5) from hkCP (purple) or dCP (brown; numbers show positive/tested).

Biochemistry
Biochemistry
9th Edition
ISBN:9781319114671
Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Chapter1: Biochemistry: An Evolving Science
Section: Chapter Questions
Problem 1P
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Can you please explain this figure? Controls, experiments performed, conclusions and how the data supports them, theoretical basis for experiments etc... The figure is taken from the article https://www.nature.com/articles/nature13994 in case context is needed

a STARR-seq construct ORF hkCP or dCP Enhancer ORF hkCP S2 STARR-seq 1,822 4,134 (32%) 3,586 pA site TCT TATA box MTE DPE Inr dCP S2 STARR-seq AAAAA d dCP S2 STARR-seq enrichment (log₂) 6 b -2 CG33936 Fold change <2x hkCP and dCP 2x-4x hkCP.2x-4x dCP .>4x hkCP •>4x dCP 0 4 hkCP S2 STARR-seq enrichment (log₂) CG33937 2 6 Enr. rep2 (log₂) CG18473 CG8129 Enr. rep2 (log₂) Fps85D- hkCP S2 STARR-seq hkCP S2 STARR-seq dCP S2 STARR-seq Enr. rep1 (log₂) dCP S2 STARR-seq Enr. rep1 (log₂) e Per cent positive per tested 40 20 0 Luciferase-pA site hkCP luciferase 100 80 60 Luciferase construct 121/24 1/24 hkCP enhancer Or85f 2/12 dCP CG34117 CG8132 enhancer CG81354 CG9356 RpL34b Enhancer candidate dCP luciferase 10/12 6/7 6/7 ||| hkCP DCP or are Si Figure 1 Distinct sets of enhancers activate transcription from the hkCP and dCP in S2 cells. a, STARR-seq set-up using the hkCP housekeeping (RpS12; purple) and dCP developmental core promoters (Drosophila synthetic core promoter (DSCP)¹¹; brown) b, Genome browser screenshot depicting STARR-seq tracks for both core promoters. c, Overlap of hkCP and dCP enhancers. d, hkCP versus dCP STARR-seq enrichments at enhancers (insets show enrichment for replicates (Enr. rep) 1 versus 2 for hkCP and dCP; dCP data reanalysed from ref. 12). e, hkCP, dCP or shared enhancers that activate luciferase (>1.5-fold and P<0.05 (one-sided t-test); n = 3; Extended Data Figs 3 and 5) from hkCP (purple) or dCP (brown; numbers show positive/tested).
Transcribed Image Text:a STARR-seq construct ORF hkCP or dCP Enhancer ORF hkCP S2 STARR-seq 1,822 4,134 (32%) 3,586 pA site TCT TATA box MTE DPE Inr dCP S2 STARR-seq AAAAA d dCP S2 STARR-seq enrichment (log₂) 6 b -2 CG33936 Fold change <2x hkCP and dCP 2x-4x hkCP.2x-4x dCP .>4x hkCP •>4x dCP 0 4 hkCP S2 STARR-seq enrichment (log₂) CG33937 2 6 Enr. rep2 (log₂) CG18473 CG8129 Enr. rep2 (log₂) Fps85D- hkCP S2 STARR-seq hkCP S2 STARR-seq dCP S2 STARR-seq Enr. rep1 (log₂) dCP S2 STARR-seq Enr. rep1 (log₂) e Per cent positive per tested 40 20 0 Luciferase-pA site hkCP luciferase 100 80 60 Luciferase construct 121/24 1/24 hkCP enhancer Or85f 2/12 dCP CG34117 CG8132 enhancer CG81354 CG9356 RpL34b Enhancer candidate dCP luciferase 10/12 6/7 6/7 ||| hkCP DCP or are Si Figure 1 Distinct sets of enhancers activate transcription from the hkCP and dCP in S2 cells. a, STARR-seq set-up using the hkCP housekeeping (RpS12; purple) and dCP developmental core promoters (Drosophila synthetic core promoter (DSCP)¹¹; brown) b, Genome browser screenshot depicting STARR-seq tracks for both core promoters. c, Overlap of hkCP and dCP enhancers. d, hkCP versus dCP STARR-seq enrichments at enhancers (insets show enrichment for replicates (Enr. rep) 1 versus 2 for hkCP and dCP; dCP data reanalysed from ref. 12). e, hkCP, dCP or shared enhancers that activate luciferase (>1.5-fold and P<0.05 (one-sided t-test); n = 3; Extended Data Figs 3 and 5) from hkCP (purple) or dCP (brown; numbers show positive/tested).
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