Simple expression domains are regulated by discrete CRMs during Drosophila oogenesis

Nicole T. Revaitis, Robert A. Marmion, Maira Farhat, Vesile Ekiz, Wei Wang, Nir Yakoby

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Eggshell patterning has been extensively studied in Drosophila melanogaster. However, the cis-regulatory modules (CRMs), which control spatiotemporal expression of these patterns, are vastly unexplored. The FlyLight collection contains >7000 intergenic and intronic DNA fragments that, if containing CRMs, can drive the transcription factor GAL4. We cross-listed the 84 genes known to be expressed during D. melanogaster oogenesis with the ~1200 listed genes of the FlyLight collection, and found 22 common genes that are represented by 281 FlyLight fly lines. Of these lines, 54 show expression patterns during oogenesis when crossed to an UAS-GFP reporter. Of the 54 lines, 16 recapitulate the full or partial pattern of the associated gene pattern. Interestingly, while the average DNA fragment size is ~3 kb in length, the vast majority of fragments show one type of spatiotemporal pattern in oogenesis. Mapping the distribution of all 54 lines, we found a significant enrichment of CRMs in the first intron of the associated genes' model. In addition, we demonstrate the use of different anteriorly active FlyLight lines as tools to disrupt eggshell patterning in a targeted manner. Our screen provides further evidence that complex gene patterns are assembled combinatorially by different CRMs controlling the expression of genes in simple domains.

Original languageEnglish (US)
Pages (from-to)2705-2718
Number of pages14
JournalG3: Genes, Genomes, Genetics
Volume7
Issue number8
DOIs
StatePublished - Jan 1 2017

Fingerprint

Oogenesis
Drosophila
Egg Shell
Genes
Drosophila melanogaster
Intergenic DNA
Diptera
Introns
Transcription Factors
Gene Expression
DNA

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Keywords

  • Eggshell patterning
  • GAL4
  • Gene regulation
  • Genetic tools

Cite this

Revaitis, Nicole T. ; Marmion, Robert A. ; Farhat, Maira ; Ekiz, Vesile ; Wang, Wei ; Yakoby, Nir. / Simple expression domains are regulated by discrete CRMs during Drosophila oogenesis. In: G3: Genes, Genomes, Genetics. 2017 ; Vol. 7, No. 8. pp. 2705-2718.
@article{4db628473dd84307857a8df401ef8d57,
title = "Simple expression domains are regulated by discrete CRMs during Drosophila oogenesis",
abstract = "Eggshell patterning has been extensively studied in Drosophila melanogaster. However, the cis-regulatory modules (CRMs), which control spatiotemporal expression of these patterns, are vastly unexplored. The FlyLight collection contains >7000 intergenic and intronic DNA fragments that, if containing CRMs, can drive the transcription factor GAL4. We cross-listed the 84 genes known to be expressed during D. melanogaster oogenesis with the ~1200 listed genes of the FlyLight collection, and found 22 common genes that are represented by 281 FlyLight fly lines. Of these lines, 54 show expression patterns during oogenesis when crossed to an UAS-GFP reporter. Of the 54 lines, 16 recapitulate the full or partial pattern of the associated gene pattern. Interestingly, while the average DNA fragment size is ~3 kb in length, the vast majority of fragments show one type of spatiotemporal pattern in oogenesis. Mapping the distribution of all 54 lines, we found a significant enrichment of CRMs in the first intron of the associated genes' model. In addition, we demonstrate the use of different anteriorly active FlyLight lines as tools to disrupt eggshell patterning in a targeted manner. Our screen provides further evidence that complex gene patterns are assembled combinatorially by different CRMs controlling the expression of genes in simple domains.",
keywords = "Eggshell patterning, GAL4, Gene regulation, Genetic tools",
author = "Revaitis, {Nicole T.} and Marmion, {Robert A.} and Maira Farhat and Vesile Ekiz and Wei Wang and Nir Yakoby",
year = "2017",
month = "1",
day = "1",
doi = "10.1534/g3.117.043810",
language = "English (US)",
volume = "7",
pages = "2705--2718",
journal = "G3: Genes, Genomes, Genetics",
issn = "2160-1836",
publisher = "Genetics Society of America",
number = "8",

}

Simple expression domains are regulated by discrete CRMs during Drosophila oogenesis. / Revaitis, Nicole T.; Marmion, Robert A.; Farhat, Maira; Ekiz, Vesile; Wang, Wei; Yakoby, Nir.

In: G3: Genes, Genomes, Genetics, Vol. 7, No. 8, 01.01.2017, p. 2705-2718.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Simple expression domains are regulated by discrete CRMs during Drosophila oogenesis

AU - Revaitis, Nicole T.

AU - Marmion, Robert A.

AU - Farhat, Maira

AU - Ekiz, Vesile

AU - Wang, Wei

AU - Yakoby, Nir

PY - 2017/1/1

Y1 - 2017/1/1

N2 - Eggshell patterning has been extensively studied in Drosophila melanogaster. However, the cis-regulatory modules (CRMs), which control spatiotemporal expression of these patterns, are vastly unexplored. The FlyLight collection contains >7000 intergenic and intronic DNA fragments that, if containing CRMs, can drive the transcription factor GAL4. We cross-listed the 84 genes known to be expressed during D. melanogaster oogenesis with the ~1200 listed genes of the FlyLight collection, and found 22 common genes that are represented by 281 FlyLight fly lines. Of these lines, 54 show expression patterns during oogenesis when crossed to an UAS-GFP reporter. Of the 54 lines, 16 recapitulate the full or partial pattern of the associated gene pattern. Interestingly, while the average DNA fragment size is ~3 kb in length, the vast majority of fragments show one type of spatiotemporal pattern in oogenesis. Mapping the distribution of all 54 lines, we found a significant enrichment of CRMs in the first intron of the associated genes' model. In addition, we demonstrate the use of different anteriorly active FlyLight lines as tools to disrupt eggshell patterning in a targeted manner. Our screen provides further evidence that complex gene patterns are assembled combinatorially by different CRMs controlling the expression of genes in simple domains.

AB - Eggshell patterning has been extensively studied in Drosophila melanogaster. However, the cis-regulatory modules (CRMs), which control spatiotemporal expression of these patterns, are vastly unexplored. The FlyLight collection contains >7000 intergenic and intronic DNA fragments that, if containing CRMs, can drive the transcription factor GAL4. We cross-listed the 84 genes known to be expressed during D. melanogaster oogenesis with the ~1200 listed genes of the FlyLight collection, and found 22 common genes that are represented by 281 FlyLight fly lines. Of these lines, 54 show expression patterns during oogenesis when crossed to an UAS-GFP reporter. Of the 54 lines, 16 recapitulate the full or partial pattern of the associated gene pattern. Interestingly, while the average DNA fragment size is ~3 kb in length, the vast majority of fragments show one type of spatiotemporal pattern in oogenesis. Mapping the distribution of all 54 lines, we found a significant enrichment of CRMs in the first intron of the associated genes' model. In addition, we demonstrate the use of different anteriorly active FlyLight lines as tools to disrupt eggshell patterning in a targeted manner. Our screen provides further evidence that complex gene patterns are assembled combinatorially by different CRMs controlling the expression of genes in simple domains.

KW - Eggshell patterning

KW - GAL4

KW - Gene regulation

KW - Genetic tools

UR - http://www.scopus.com/inward/record.url?scp=85027284768&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85027284768&partnerID=8YFLogxK

U2 - 10.1534/g3.117.043810

DO - 10.1534/g3.117.043810

M3 - Article

C2 - 28634244

AN - SCOPUS:85027284768

VL - 7

SP - 2705

EP - 2718

JO - G3: Genes, Genomes, Genetics

JF - G3: Genes, Genomes, Genetics

SN - 2160-1836

IS - 8

ER -