The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk”
The chromatin of the human genome was analyzed at three DNA size levels. At the first, compartment level, two “gene spaces” were found many years ago: A GC-rich, gene-rich “genome core” and a GC-poor, gene-poor “genome desert”, the former corresponding to open chromatin centrally located in the inte...
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MDPI AG
2021-04-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/11/4/342 |
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| author | Giorgio Bernardi |
| author_facet | Giorgio Bernardi |
| author_sort | Giorgio Bernardi |
| collection | DOAJ |
| description | The chromatin of the human genome was analyzed at three DNA size levels. At the first, compartment level, two “gene spaces” were found many years ago: A GC-rich, gene-rich “genome core” and a GC-poor, gene-poor “genome desert”, the former corresponding to open chromatin centrally located in the interphase nucleus, the latter to closed chromatin located peripherally. This bimodality was later confirmed and extended by the discoveries (1) of LADs, the Lamina-Associated Domains, and InterLADs; (2) of two “spatial compartments”, A and B, identified on the basis of chromatin interactions; and (3) of “forests and prairies” characterized by high and low CpG islands densities. Chromatin compartments were shown to be associated with the compositionally different, flat and single- or multi-peak DNA structures of the two, GC-poor and GC-rich, “super-families” of isochores. At the second, sub-compartment, level, chromatin corresponds to flat isochores and to isochore loops (due to compositional DNA gradients) that are susceptible to extrusion. Finally, at the short-sequence level, two sets of sequences, GC-poor and GC-rich, define two different nucleosome spacings, a short one and a long one. In conclusion, chromatin structures are moulded according to a “genomic code” by DNA sequences that pervade the genome and leave no room for “junk”. |
| first_indexed | 2024-03-10T12:21:41Z |
| format | Article |
| id | doaj.art-e3d68760a17a4487b921b1751b4f141f |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-10T12:21:41Z |
| publishDate | 2021-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-e3d68760a17a4487b921b1751b4f141f2023-11-21T15:27:07ZengMDPI AGLife2075-17292021-04-0111434210.3390/life11040342The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk”Giorgio Bernardi0Science Department, Roma Tre University, Viale Marconi 446, 00146 Rome, ItalyThe chromatin of the human genome was analyzed at three DNA size levels. At the first, compartment level, two “gene spaces” were found many years ago: A GC-rich, gene-rich “genome core” and a GC-poor, gene-poor “genome desert”, the former corresponding to open chromatin centrally located in the interphase nucleus, the latter to closed chromatin located peripherally. This bimodality was later confirmed and extended by the discoveries (1) of LADs, the Lamina-Associated Domains, and InterLADs; (2) of two “spatial compartments”, A and B, identified on the basis of chromatin interactions; and (3) of “forests and prairies” characterized by high and low CpG islands densities. Chromatin compartments were shown to be associated with the compositionally different, flat and single- or multi-peak DNA structures of the two, GC-poor and GC-rich, “super-families” of isochores. At the second, sub-compartment, level, chromatin corresponds to flat isochores and to isochore loops (due to compositional DNA gradients) that are susceptible to extrusion. Finally, at the short-sequence level, two sets of sequences, GC-poor and GC-rich, define two different nucleosome spacings, a short one and a long one. In conclusion, chromatin structures are moulded according to a “genomic code” by DNA sequences that pervade the genome and leave no room for “junk”.https://www.mdpi.com/2075-1729/11/4/342Genomic codechromatin structurejunk DNA |
| spellingShingle | Giorgio Bernardi The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk” Life Genomic code chromatin structure junk DNA |
| title | The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk” |
| title_full | The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk” |
| title_fullStr | The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk” |
| title_full_unstemmed | The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk” |
| title_short | The “Genomic Code”: DNA Pervasively Moulds Chromatin Structures Leaving no Room for “Junk” |
| title_sort | genomic code dna pervasively moulds chromatin structures leaving no room for junk |
| topic | Genomic code chromatin structure junk DNA |
| url | https://www.mdpi.com/2075-1729/11/4/342 |
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