Evolutionary conservation of histone modifications in mammals
1Department of Ecology and Evolution, The University of Chicago, USA.
Molecular Biology and Evolution
|February 10, 2012
Summary
Stable histone modifications, like H3K4me3, H3K4me1, and H3K27ac, are conserved across cell types and species. This stability is linked to clustered transcription factor binding sites, aiding gene regulation.
Area of Science:
- Epigenetics and Genomics
- Evolutionary Biology
- Gene Regulation
Background:
- Histone modifications are crucial for eukaryotic gene regulation.
- Understanding the stable maintenance of histone marks amid changes is key in evolutionary biology.
Purpose of the Study:
- To investigate the stability and evolutionary conservation of histone modifications across cell types and species.
- To identify factors contributing to the maintenance of histone marks.
Main Methods:
- Genome-wide profiling of H3K4me3, H3K4me1, and H3K27ac in human and mouse cell types.
- Analysis of histone modification stability within species and conservation between species.
- Examination of genetic and epigenetic properties of conserved regions.
Main Results:
- Histone modifications stable across human cell types were also conserved between human and mouse.
- This stability was observed across promoter, intronic, and intergenic regions, irrespective of gene expression breadth.
- Regions with stable modifications exhibited clustered transcription factor binding sites (TFBSs), high GC content, and CTCF binding.
Conclusions:
- Clustering of TFBSs plays a significant role in stabilizing and conserving histone modifications.
- TFBS clustering promotes TFBS conservation, which in turn drives histone modification conservation.
- Mammalian genomes likely employ a common mechanism to maintain histone modifications against genetic and environmental changes.
Related Concept Videos
02:32Histone Modification
The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
02:32Histone Modification
The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
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...
02:38Heterochromatin
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
03:17Inheritance of Chromatin Structures
Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying DNA...
02:30Histone Variants at the Centromere
Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3 variants are also...