We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

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Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Flavonoids are nearly ubiquitous in plants and are recognized as the pigments responsible for the colors of leaves, especially in autumn. They are rich in seeds, citrus fruits, olive oil, tea, and red wine. They are low molecular weight compounds composed of a three-ring structure with various substitutions. This basic structure is shared by tocopherols (vitamin E). Flavonoids can be subdivided according to the presence of an oxy group at position 4, a double bond between carbon atoms 2 and 3, or a hydroxyl group in position 3 of the C (middle) ring. These characteristics appear to also be required for best activity, especially antioxidant and antiproliferative, in the systems studied. The particular hydroxylation pattern of the B ring of the flavonoles increases their activities, especially in inhibition of mast cell secretion. Certain plants and spices containing flavonoids have been used for thousands of years in traditional Eastern medicine. In spite of the voluminous literature available, however, Western medicine has not yet used flavonoids therapeutically, even though their safety record is exceptional. Suggestions are made where such possibilities may be worth pursuing.

The Effects of Plant Flavonoids on Mammalian Cells:Implications for Inflammation, Heart Disease, and Cancer

Between the 1960s and 1980s, most life scientists focused their attention on studies of nucleic acids and the translation of the coded information. Protein degradation was a neglected area, conside...

The Ubiquitin-Proteasome Proteolytic Pathway: Destruction for the Sake of Construction

Heterochromatin protein 1 (HP1) is localized at heterochromatin sites where it mediates gene silencing. The chromo domain of HP1 is necessary for both targeting and transcriptional repression. In the fission yeast Schizosaccharomyces pombe, the correct localization of Swi6 (the HP1 equivalent) depends on Clr4, a homologue of the mammalian SUV39H1 histone methylase. Both Clr4 and SUV39H1 methylate specifically lysine 9 of histone H3 (ref. 6). Here we show that HP1 can bind with high affinity to histone H3 methylated at lysine 9 but not at lysine 4. The chromo domain of HP1 is identified as its methyl-lysine-binding domain. A point mutation in the chromo domain, which destroys the gene silencing activity of HP1 in Drosophila, abolishes methyl-lysine-binding activity. Genetic and biochemical analysis in S. pombe shows that the methylase activity of Clr4 is necessary for the correct localization of Swi6 at centromeric heterochromatin and for gene silencing. These results provide a stepwise model for the formation of a transcriptionally silent heterochromatin: SUV39H1 places a 'methyl marker' on histone H3, which is then recognized by HP1 through its chromo domain. This model may also explain the stable inheritance of the heterochromatic state.

Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain.

IF human lymphocytes1 or Chinese hamster2 cells are treated with the base analogue 5-bromodeoxyuridine (BrdU) in the latter part of the S period, Giemsa stained chromosomes exhibit a pattern of condensed and extended segments along their length. This phenomenon has been attributed to a delay in the spiralisation pattern of the late replicating regions along the chromosomes. Other experiments3 with Chinese hamster ovary (CHO) cells have shown that after two rounds of replication in the presence of BrdU or IdU, sister chromatids stain differentially with Giemsa, allowing the identification of the two chromatids, and the observation of sister chromatid exchanges (SCEs) without recourse to autoradiography. The chromatid with the bifilarly substituted DNA (BrdU substituted in both strands of DNA) is less condensed and stains more weakly with Giemsa than the unifilarly substituted sister chromatid. The yield of SCEs is approximately that observed by autoradiography.

New Giemsa method for the differential staining of sister chromatids

A staining technique that detects sister chromatid exchanges (SCEs) has been used to examine the response of chromosomes in cultured Chinese hamster cells to a wide variety of mutagens-carcinogens. The test gives a very sensitive and rapid method for detecting chromosome mutagenicity of chemical agents and provides a powerful new method for detecting environmental mutagens.

Cytological detection of mutagen-carcinogen exposure by sister chromatid exchange.

Current techniques for three-dimensional (3D) optical microscopy (deconvolution, confocal microscopy, and optical coherence tomography) generate 3D data by "optically sectioning" the specimen. This places severe constraints on the maximum thickness of a specimen that can be imaged. We have developed a microscopy technique that uses optical projection tomography (OPT) to produce high-resolution 3D images of both fluorescent and nonfluorescent biological specimens with a thickness of up to 15 millimeters. OPT microscopy allows the rapid mapping of the tissue distribution of RNA and protein expression in intact embryos or organ systems and can therefore be instrumental in studies of developmental biology or gene function.

https://science.sciencemag.org/content/sci/296/5567/541.full.pdf

Optical Projection Tomography as a Tool for 3D Microscopy and Gene Expression Studies

Using fluorescence in situ hybridization we show striking differences in nuclear position, chromosome morphology, and interactions with nuclear substructure for human chromosomes 18 and 19. Human chromosome 19 is shown to adopt a more internal position in the nucleus than chromosome 18 and to be more extensively associated with the nuclear matrix. The more peripheral localization of chromosome 18 is established early in the cell cycle and is maintained thereafter. We show that the preferential localization of chromosomes 18 and 19 in the nucleus is reflected in the orientation of translocation chromosomes in the nucleus. Lastly, we show that the inhibition of transcription can have gross, but reversible, effects on chromosome architecture. Our data demonstrate that the distribution of genomic sequences between chromosomes has implications for nuclear structure and we discuss our findings in relation to a model of the human nucleus that is functionally compartmentalized.

/pdf/differences-in-the-localization-and-morphology-of-3vk26hynhc.pdf

Differences in the localization and morphology of chromosomes in the human nucleus

https://www.research.ed.ac.uk/portal/files/10739509/Chromatin_motion_is_constrained_by_association_with_nuclear_compartments_in_human_cells.pdf

Paul Perry

Papers

New Giemsa method for the differential staining of sister chromatids

Cytological detection of mutagen-carcinogen exposure by sister chromatid exchange.

Optical Projection Tomography as a Tool for 3D Microscopy and Gene Expression Studies

Differences in the localization and morphology of chromosomes in the human nucleus

Chromatin motion is constrained by association with nuclear compartments in human cells.