Related Experiment Video
Updated: Jun 22, 2026
07:18
Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling
Published on: May 21, 2020
Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation
Xi Wang1, Georg Haberer, Klaus F X Mayer
1MIPS/IBIS Institute of Bioinformatics and System Biology, Helmholtz Center Munich, Neuherberg, Germany. xi.wang@helmholtz-muenchen.de
BMC Genomics
|June 30, 2009
Summary
Researchers identified thousands of conserved cis-elements in rice and sorghum promoters using comparative genomics. These findings advance our understanding of gene regulation in important grass species.
Area of Science:
- Plant genomics
- Gene regulation
- Comparative bioinformatics
Background:
- Spatiotemporal gene expression relies on cis-regulatory elements within promoters.
- Knowledge of transcription factor binding sites and networks in grasses is limited.
- Comparative promoter analysis offers genome-scale cis-element detection.
Purpose of the Study:
- To identify conserved cis-elements in rice and sorghum promoters.
- To explore the role of cis-elements in gene regulation within grasses.
Main Methods:
- Identified phylogenetic footprints conserved in orthologous rice and sorghum upstream regions.
- Utilized co-expression data from three rice expression datasets to support findings.
- Discovered cis-motifs through conserved co-occurrence in syntenic promoter pairs.
Main Results:
- Discovered thousands of conserved phylogenetic footprints between rice and sorghum.
- Sequence conservation and known plant motifs validated identified cis-elements.
- Shared motifs correlate with expression similarity, indicating functional importance in gene regulation.
Conclusions:
- Generated the first large-scale collection of cis-elements for rice and sorghum.
- Provides a foundational resource for studying cis-elements in grasses.
- Establishes comparative genomics as a powerful approach for cis-element discovery.
Related Concept Videos
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
02:13Overview of Transposition and Recombination
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
02:31Homologous Recombination
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...