Sex combs reduced (Scr) regulatory region of Drosophila revisited.
The Hox gene Sex combs reduced (Scr) is responsible for the differentiation of the labial and prothoracic segments in Drosophila. Scr is expressed in several specific tissues throughout embryonic development, following a complex path that must be coordinated by an equally complex regulatory region. Although some cis-regulatory modules (CRMs) have been identified in the Scr regulatory region (~75 kb), there has been no detailed and systematic study of the distinct regulatory elements present within this region. In this study, the Scr regulatory region was revisited with the aim of filling this gap. We focused on the identification of Initiator elements (IEs) that bind segmentation factors, Polycomb response elements (PREs) that are recognized by the Polycomb and Trithorax complexes, as well as insulators and tethering elements. To this end, we summarized all currently available information, mainly obtained from high throughput ChIP data projects. In addition, a bioinformatic analysis based on the evolutionary conservation of regulatory sequences using the software MOTEVO was performed to identify IE and PRE candidates in the Scr region. The results obtained by this combined strategy are largely consistent with the CRMs previously identified in the Scr region and help to: (i) delimit them more accurately, (ii) subdivide two of them into different independent elements, (iii) identify a new CRM, (iv) identify the composition of their binding sites and (v) better define some of their characteristics. These positive results indicate that an approach that integrates functional and bioinformatic data might be useful to characterize other regulatory regions.
Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
Juan M
JM
Calvo-Martín
Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
Montserrat
M
Papaceit
Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain. csegarra@ub.edu.
Carmen
http://orcid.org/0000-0002-3201-5405
C
Segarra
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D029721:Drosophila Proteins / Q000235:genetics*; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D063146:Polycomb-Group Proteins / Q000235:genetics; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics*
D029721:Drosophila Proteins; D063146:Polycomb-Group Proteins; C059627:Scr protein, Drosophila; D014157:Transcription Factors
Cis-regulatory modules; Drosophila; Initiator elements; Polycomb response elements; Sex combs reduced (Scr)