|Chromosome Yarns Organize Groups of Genes and Regulatory Elements|
|SciMed - Genetics & Genome|
|TS-Si News Service|
|Wednesday, 11 April 2012 08:00|
Worcester, MA, USA. A chromosome layer folds into contiguous yarns that harbor groups of genes and regulatory elements, enabling contact for coordinated development work.
This is a new layer in the complex organization of chromosomes, the molecular basis of genetic heredity. Even though chromosomes have remain largely enigmatic since biologist Walther Flemming discovered them in 1882, recent research has begun to unravel some of their mysteries.
The new research was led by the team of Edith Heard, PhD, from the Curie Institute, and Job Dekker, PhD, from the University of Massachusetts Medical School (UMMS). “We have known for decades that the DNA of individual genes is wrapped around nucleosomes to form the classical beads-on-a-string structure,” said Dekker, co-director of the UMMS Program in Systems Biology. “Our new study now shows that these beads-on-a-string subsequently fold up to form yarns-on-a-string, where each yarn is a group of genes. This domainal organization of chromosomes represents a previously unknown higher order level of folding that we believe is a fundamental organizing principle of genomes.” Findings appear in the journal Nature.
Click Pic for Details
Fractal Globule Organization
Previous researchers have found that the genome adopts a "fractal globule" organization, enabling the cell to pack DNA into an extremely tight package while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome.
A contiguous stretch of DNA chain inside a fractal globule packs into a compact, unknotted structure, making it easy to pack and unpack.
Image courtesy of X. Robert Bao, Leonid A. Mirn, and Maxim Imakaev.For review, chromosomes are relatively large molecules that can measure up to the length of an entire human arm when spread out. Despite their impressive size, chromosomes are confined within the small space of the cell nucleus -- which is just a few micrometers across. Not only that, each cell nucleus contains multiple chromosomes. In humans, for example, there are 23 pairs of chromosomes. In order to fit all this material into this small area, chromosomes are folded, compacted and mingled in the three-dimensional space of the nucleus.
A chromosome looks like a series of tiny yarns
So do chromosomes fill the nucleus just like spaghetti fills a plate? Elphège-Pierre Nora, PhD, is a post-doctoral fellow on the team of Dr. Heard, head of the Genetics and Developmental Biology Lab at the Curie Institute. The analogy to spaghetti is “Not quite” right, says Nora. “Chromosome folding follows a pattern, and this actually turns out to be important for ensuring their proper function.” In fact, a chromosome looks like a series of tiny globule-like yarns that span anywhere from a few hundred thousand to a million base pairs, explained Heard.
Job Dekker and colleagues developed Chromosome Conformation Capture (3C) to detect physical interactions between genomic elements (Dekker et al. Science, 2002).
His group later combined 3C, now widely used for genome regulation studies, with ultra-high-throughput DNA sequencing. This significanty increased the effective scale at which interactions between genomic loci can be studied.
The new 5C is essentially a high-throughput 3C version for large-scale mapping of chromatin interaction networks (Dostie et al. Genome Research 2006).
The team obtained detailed insights into the 3D arrangements of complete genomes at Kb resolution when they developed Hi-C technology.
It is a genome-wide and unbiased method that combines both 3C with deep sequencing (cf. Lieberman-Aiden, van Berkum et al. Science 2009).Base pairs (A, C, G and T) are the genome’s unit of measurement, and human DNA has over 3 billion of them. “The real surprise lies in how this spatial folding of chromosomes links up to their functional organization,” said Heard.
“This chromosome folding pattern brings together, into the same yarn, several genes, up to 10 of them, or even more.”
However, there are not just genes in these yarns. The network that regulates a cell consists, in part, of regulatory genomic elements that can control the activity of neighboring genes like switches. They too have been found clustered together with the genes in these same chromosomal yarns.
Thus, a group of genes belonging to the same yarn will therefore be likely to contact a similar set of regulatory elements, and this can result in the coordinated activity of these genes during development.
Unraveling genetic mysteries
These new observations shed some light on several long-standing mysteries of genetics, such as the reason why some DNA mutations can end up affecting genes that are located thousands or even a million base pairs away. The cell nucleus is packed with genes, Dekker notes, and the cell is faced with the challenge to turn on or off each one of them correctly. “By organizing groups of genes in isolated domains, or yarns that do not mingle or mix with other genes, the cell has solved the problem of how to regulate groups of genes coordinately and without interference from other genes.”
However, damaging one of these chromosome yarns can lead to the misbehavior of all the genes it contains. The three-dimensional organization of chromosomes allows distal genomic elements to be brought together and to functionally interact with each other. "At certain points during development it is thus possible to precisely orchestrate the activity of genes that are far away from each other on the linear chromosome thread, but that are actually in contact physically, within a chromosome yarn,” said Nora. The down side of this organizational type is that a single mutation can alter the organization of the yarn and affect a whole group of genes.
3D folding provides shortcuts through the chromosome
“Together with Job Dekker, who has pioneered chromosome conformation capture technologies, we have discovered these principles by studying a critical region of the X chromosome, the X-inactivation center,” said Heard. “Thanks to a parallel study conducted by the team of Bing Ren, PhD, at the University of San Diego [published in the journal Nature alongside the Heard and Dekker study], we now know that the principles of chromosome folding we have seen on the X chromosome actually apply to the whole mouse and human genomes.”
These studies advance our fundamental understanding of chromosome biology, but also have other important implications. The work opens up new avenues for studying genetic disorders that are due to mutations in the DNA sequence which disrupt the proper activity of certain genes. Sometimes the mutation causing these defects is not directly in the gene, but affects one of its regulatory elements somewhere in its extended chromosomal neighborhood.
The degree of difficulty for finding such mutations along the chromosome has been quite high because scientists did not know which genes were partnered with which regulatory elements. The hunt for such mutations can now be directed first to the chromosomal region most likely to harbor the regulatory elements of the misbehaving gene – inside the chromosome yarn to which that gene belongs.
FundingGrants from the Ministère de l'enseignement supérieur et de la recherche and the ARC (to Elphège-Pierre Nora); a long term fellowship fom the Human Frontier Science Program (HFSP) to Edda G. Schulz. EU EpiGeneSys FP7 Network of Excellence.
The Fondation pour la recherche médicale en France (FRM), ANR, ERC Advanced Investigator award and EU FP7 SYBOSS grant to Edith Heard. Nynke L. van Berkum was supported by BMBF (FORSYS) and an EMBO fellowship.
Job Dekker, Bryan R. Lajoie. and Nynke L. van Berkum were supported by the National Institutes of health (NIH) and a W. M. Keck Foundation Distinguished Young Scholar Award.
ResourcesHigh-throughput data are deposited in the Gene Expression Omnibus (GEO) under accession number GSE35721 for all 5C experiments and GSE34243 for expression microarrays.
CitationSpatial partitioning of the regulatory landscape of the X-inactivation centre. Elphège-Pierre Nora, Bryan R. Lajoie, Edda G. Schulz, Luca Giorgetti, Ikuhiro Okamoto, Nicolas Servant, Tristan Piolot, Nynke L. van Berkum, Johannes Meisig, John Sedat, Joost Gribnau, Emmanuel Barillot, Nils Blüthgen, Job Dekker, and Edith Heard. Nature 2012. In press.
In eukaryotes transcriptional regulation often involves multiple long-range elements and is influenced by the genomic environment. A prime example of this concerns the mouse X-inactivation centre (Xic), which orchestrates the initiation of X-chromosome inactivation (XCI) by controlling the expression of the nonprotein-coding Xist transcript. The extent of Xic sequences required for the proper regulation of Xist remains unknown. Here we use chromosome conformation capture carbon-copy (5C)² and super-resolution microscopy to analyse the spatial organization of a 4.5-megabases (Mb) region including Xist. We discover a series of discrete 200-kilobase to 1Mb topologically associating domains (TADs), present both before and after cell differentiation and on the active and inactive X. TADs align with, but do not rely on, several domain-wide features of the epigenome, such as H3K27me3 or H3K9me2 blocks and lamina-associated domains.TADs also align with coordinately regulated gene clusters. Disruption of a TAD boundary causes ectopic chromosomal contacts and long-range transcriptional misregulation. The Xist/Tsix sense/antisense unit illustrates how TADs enable the spatial segregation of oppositely regulated chromosomal neighbourhoods, with the respective promoters of Xist and Tsix lying in adjacent TADs, each containing their known positive regulators. We identify a novel distal regulatory region of Tsix within its TAD, which produces a long intervening RNA, Linx. In addition to uncovering a new principle ofcis-regulatory architecture of mammalian chromosomes, our study sets the stage for the full genetic dissection of the X-inactivation centre.
|Last Updated on Wednesday, 11 April 2012 11:49|