BIOMAT Database Logo BIOMAT Database Logo

The Release 5.1 annotation of Drosophila melanogaster heterochromatin. 2007

Christopher D Smith, and Shengqiang Shu, and Christopher J Mungall, and Gary H Karpen
Department of Biology, San Francisco State University, San Francisco, CA 94132, USA.

The repetitive DNA that constitutes most of the heterochromatic regions of metazoan genomes has hindered the comprehensive analysis of gene content and other functions. We have generated a detailed computational and manual annotation of 24 megabases of heterochromatic sequence in the Release 5 Drosophila melanogaster genome sequence. The heterochromatin contains a minimum of 230 to 254 protein-coding genes, which are conserved in other Drosophilids and more diverged species, as well as 32 pseudogenes and 13 noncoding RNAs. Improved methods revealed that more than 77% of this heterochromatin sequence, including introns and intergenic regions, is composed of fragmented and nested transposable elements and other repeated DNAs. Drosophila heterochromatin contains "islands" of highly conserved genes embedded in these "oceans" of complex repeats, which may require special expression and splicing mechanisms.

UI MeSH Term Description Entries
D007313 Insecta Members of the phylum ARTHROPODA composed or organisms characterized by division into three parts: head, thorax, and abdomen. They are the dominant group of animals on earth with several hundred thousand different kinds. Three orders, HEMIPTERA; DIPTERA; and SIPHONAPTERA; are of medical interest in that they cause disease in humans and animals. (From Borror et al., An Introduction to the Study of Insects, 4th ed, p1). Insects,Insect
D007438 Introns Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes. Intervening Sequences,Sequences, Intervening,Intervening Sequence,Intron,Sequence, Intervening
D011544 Pseudogenes Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes. Genes, Processed,beta-Tubulin Pseudogene,Gene, Processed,Processed Gene,Processed Genes,Pseudogene,Pseudogene, beta-Tubulin,Pseudogenes, beta-Tubulin,beta Tubulin Pseudogene,beta-Tubulin Pseudogenes
D012091 Repetitive Sequences, Nucleic Acid Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES). DNA Repetitious Region,Direct Repeat,Genes, Selfish,Nucleic Acid Repetitive Sequences,Repetitive Region,Selfish DNA,Selfish Genes,DNA, Selfish,Repetitious Region, DNA,Repetitive Sequence,DNA Repetitious Regions,DNAs, Selfish,Direct Repeats,Gene, Selfish,Repeat, Direct,Repeats, Direct,Repetitious Regions, DNA,Repetitive Regions,Repetitive Sequences,Selfish DNAs,Selfish Gene
D002874 Chromosome Mapping Any method used for determining the location of and relative distances between genes on a chromosome. Gene Mapping,Linkage Mapping,Genome Mapping,Chromosome Mappings,Gene Mappings,Genome Mappings,Linkage Mappings,Mapping, Chromosome,Mapping, Gene,Mapping, Genome,Mapping, Linkage,Mappings, Chromosome,Mappings, Gene,Mappings, Genome,Mappings, Linkage
D004251 DNA Transposable Elements Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. DNA Insertion Elements,DNA Transposons,IS Elements,Insertion Sequence Elements,Tn Elements,Transposable Elements,Elements, Insertion Sequence,Sequence Elements, Insertion,DNA Insertion Element,DNA Transposable Element,DNA Transposon,Element, DNA Insertion,Element, DNA Transposable,Element, IS,Element, Insertion Sequence,Element, Tn,Element, Transposable,Elements, DNA Insertion,Elements, DNA Transposable,Elements, IS,Elements, Tn,Elements, Transposable,IS Element,Insertion Element, DNA,Insertion Elements, DNA,Insertion Sequence Element,Sequence Element, Insertion,Tn Element,Transposable Element,Transposable Element, DNA,Transposable Elements, DNA,Transposon, DNA,Transposons, DNA
D004330 Drosophila A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology. Fruit Fly, Drosophila,Drosophila Fruit Flies,Drosophila Fruit Fly,Drosophilas,Flies, Drosophila Fruit,Fly, Drosophila Fruit,Fruit Flies, Drosophila
D004331 Drosophila melanogaster A species of fruit fly frequently used in genetics because of the large size of its chromosomes. D. melanogaster,Drosophila melanogasters,melanogaster, Drosophila
D005091 Exons The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA. Mini-Exon,Exon,Mini Exon,Mini-Exons
D006570 Heterochromatin The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE. Heterochromatins

Related Publications

Christopher D Smith, and Shengqiang Shu, and Christopher J Mungall, and Gary H Karpen
Functional elements in Drosophila melanogaster heterochromatin.
January 1992, Annual review of genetics,
Christopher D Smith, and Shengqiang Shu, and Christopher J Mungall, and Gary H Karpen
Interstrain heterochromatin polymorphisms in Drosophila melanogaster.
January 1981, Chromosoma,
Christopher D Smith, and Shengqiang Shu, and Christopher J Mungall, and Gary H Karpen
Genome annotation assessment in Drosophila melanogaster.
April 2000, Genome research,
Christopher D Smith, and Shengqiang Shu, and Christopher J Mungall, and Gary H Karpen
Domains of heterochromatin protein 1 required for Drosophila melanogaster heterochromatin spreading.
August 2009, Genetics,
Christopher D Smith, and Shengqiang Shu, and Christopher J Mungall, and Gary H Karpen
A NEW HETEROCHROMATIN EFFECT IN DROSOPHILA MELANOGASTER.
April 1960, Proceedings of the National Academy of Sciences of the United States of America,
Christopher D Smith, and Shengqiang Shu, and Christopher J Mungall, and Gary H Karpen
[Structural heterochromatin in the early embryogenesis of Drosophila melanogaster].
January 1991, Doklady Akademii nauk SSSR,
Christopher D Smith, and Shengqiang Shu, and Christopher J Mungall, and Gary H Karpen
Localization and function of heterochromatin in Drosophila melanogaster.
January 1951, Advances in genetics,
Christopher D Smith, and Shengqiang Shu, and Christopher J Mungall, and Gary H Karpen
Sequence finishing and mapping of Drosophila melanogaster heterochromatin.
June 2007, Science (New York, N.Y.),
Christopher D Smith, and Shengqiang Shu, and Christopher J Mungall, and Gary H Karpen
Heterochromatin pattern in metaphase chromosomes of Drosophila melanogaster.
January 1971, The Journal of heredity,
Christopher D Smith, and Shengqiang Shu, and Christopher J Mungall, and Gary H Karpen
Essential genes in autosomal heterochromatin of Drosophila melanogaster.
January 2000, Genetica,
Copied contents to your clipboard!