Article Review on Polytene Chromosomes and Structural Abnormalities
Background
The interphase stage during cell division condenses the genetic material i.e. DNA into chromosomes and in salivary glands of Drosophila melanogaster, polytene chromosomes appear characteristically that are a result of repeated replication cycles but no disjunction. They have dark bands alternating with light interbands. The hypothesis tested in the research work performed by Zhimulev et al in 2014 was that the interbands incorporates transcripton initiation sites i.e. promoter binding areas that extend to coding areas in band regions. Using the modENCODE protein profiling data, DamID genome mapping has earlier classified various chromatin states. The current study performed cytological and physical mapping and evaluated transposon insertion tags to map 12 DNA sequences in interbands that were found to encompass promoters for grey area coding genes. The intercalary heterochromatin (IH) band regions were divided into grey comprised of anytime active genes coding regions (early replicating loosely packed) and black comprised of tissue specific genes (late replicating densely packed).
32 interbands (21 from previous studied and 11 novel) in total were mapped on cytological, physical maps through electron microscopy to identify their protein expression. 11 interbands from region 7F, 19E, 21D, 35D, 56A, 58A, 70A, and 100B were identified on physical map but paper elaborates on 7F1-2 and 100B regions. 7F1-2 and 7F3-4 incorporates an interband with 5’ end of Nrg gene (figure 1 demonstrated it in the paper). Region 100B had subunits 100B1-2, 100B-3 and 100B4-5. Interband between 100B3 and 100B4-5 had 5’end of dco gene and between 100B1-2 and 100B-3 was 5’end of gene l(3)03670. All of the three interband regions had characteristic CHRIZ protein.
On cytological mapping from modENCODE protein profiling, 12 interband regions were found marked with P-element transposon element insertions, considered as interband-specific protein markers. The interband specific proteins were found concentrated in the promoter and compacted gene regions that gave high probability for interband border characterization that was confirmed via HHM model analysis. The chromatin was found to be differentiated into 4 states: 5674 cyan fragments having all interband regions with an average size of 2.7 kb, then 4006 blue fragments having few, 5148 magenta fragments and green having none. 32 interbands were well identified with 65 genes and then protein and functional chromatin element mapping was done that confirmed cyan states bordering of interbands. Most of 12 genes were located between interbands 10A1-2 and 10B1-2 was classified as housekeeping or multiply active or differentially regulated genes by many literatures. An interesting observation was presence of transcriptionally active components like ORC-2, RNA polII, broad promoters and NSL. The interbands were loosely packed areas due to its transcriptional activeness leaving the promoter regions protein free so as to give ready space for initiation factors to bind.
Cyan state referred to 5’regulatory regions and blue to the space between two interbands. This confirmed the hypothesis that interband regions holds the 5’regulatory sequences of a coding gene that moves further into the band region encompassing the coding area. Cytological maps based on these observations were prepared for 7F and 100B regions. On the other hand, 238 genes were found in the black bands that were near the identified interband/grey regions and did not have any discussed features like interband specific proteins, cyan chromatin state, etc. These genes were spaced and had large sizes. IH dark bands were thus confirmed to be transcriptionally less active with underreplication during S phase. This pointed to a noticeable evolutionary conservativeness.
The genetic maps so created confirmed that 78.3% P-elements prefer to integrate in the cyan state of ORC regions of interbands. The same frequency goes on depleting for magenta, blue and green chromatic states. Along with this, it was evaluated that the 32 interband/grey area posed genes were active at all the sites with more activity of 5’ ends falling in cyan states than magenta states and 238 genes in the dark IH regions were restricted. Cyan regions were found rich in broad promoters with head to head orientation of genes.
Conclusion
The work done is exemplary and significant in biological field. The cytological and molecular level mapping of the interband regions with their encoded proteins and characteristics is a boon to the further understanding of molecular mechanisms. This study can be enhanced to higher genomes so as to unveil further secrets lying in the genomic structure and its organization patterns. It will aid in devising treatments for various abnormalities and dysfunctions.
References
Zhimulev, F, I., Zykova, Y, T., Goncharov, P, F., et al. Genetic Organization of Interphase Chromosome Bands and Interbands in Drosophila melanogaster. Plos One. 2014. 9(7):1-16.
