DNA organization or Genetic makeup in Prokaryotic and Eukaryotic SystemsBir Bahadur Thapa
DNA organization or Genetic makeup in Prokaryotic and Eukaryotic Systems!! It is prepared under the syllabus of Tribhuwan University, Nepal, MSc. 3rd Semester as a lecture class!!
Chromatin is the complex combination of DNA and proteins that makes up chromosomes. It can be made visible by staining with specific techniques and stain (thus the name chromatin which literally means colored material). The major proteins involved in chromatin are histone proteins; although many other chromosomal proteins have prominent roles too. The functions of chromatin is to package DNA into smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and to serve as a mechanism to control gene expression and DNA replication.
DNA organization or Genetic makeup in Prokaryotic and Eukaryotic SystemsBir Bahadur Thapa
DNA organization or Genetic makeup in Prokaryotic and Eukaryotic Systems!! It is prepared under the syllabus of Tribhuwan University, Nepal, MSc. 3rd Semester as a lecture class!!
Chromatin is the complex combination of DNA and proteins that makes up chromosomes. It can be made visible by staining with specific techniques and stain (thus the name chromatin which literally means colored material). The major proteins involved in chromatin are histone proteins; although many other chromosomal proteins have prominent roles too. The functions of chromatin is to package DNA into smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and to serve as a mechanism to control gene expression and DNA replication.
Dna supercoiling and role of topoisomerasesYashwanth B S
supercoiling is one of the important process to condenses the huge amount of DNA to fit inside the histone and its also plays a role during the replication ,transcription etc..,these activities is carried out by an enzyme called topoisomerases.
It is the DNA located in the mitochondria.Mitochondrial DNA (mtDNA or mDNA) is the DNA located in the mitochondria.
They are double stranded circular DNA molecule.
It is only 16 kb in length – contains 16,600 bp.
It is haploid in nature.
It codes for 37 genes.
13 genes provide instructions for making enzymes involved in oxidative phosphorylation.
It is a process that uses oxygen and simple sugars to create ATP, the cells main energy source.
Transcription and synthesis of different RNAs
Processing of RNA transcript
Catalytic RNA
RNA splicing and Spliceosome
Transport of RNA through nuclear pore
Translation and polypeptide synthesis
Posttranslational modification
Protein trafficking and degradation
Antibiotics and inhibition of protein synthesis.
Dna supercoiling and role of topoisomerasesYashwanth B S
supercoiling is one of the important process to condenses the huge amount of DNA to fit inside the histone and its also plays a role during the replication ,transcription etc..,these activities is carried out by an enzyme called topoisomerases.
It is the DNA located in the mitochondria.Mitochondrial DNA (mtDNA or mDNA) is the DNA located in the mitochondria.
They are double stranded circular DNA molecule.
It is only 16 kb in length – contains 16,600 bp.
It is haploid in nature.
It codes for 37 genes.
13 genes provide instructions for making enzymes involved in oxidative phosphorylation.
It is a process that uses oxygen and simple sugars to create ATP, the cells main energy source.
Transcription and synthesis of different RNAs
Processing of RNA transcript
Catalytic RNA
RNA splicing and Spliceosome
Transport of RNA through nuclear pore
Translation and polypeptide synthesis
Posttranslational modification
Protein trafficking and degradation
Antibiotics and inhibition of protein synthesis.
The Monarch butterfly population is declining due to decreasing habitat in Mexico and the USA. You can help the Monarch planting milkweed in yards, gardens and open areas in the Monarch migration paths. There are vacant lands where seeds of milkweeds and wild flowers can be planted, this includes roadsides and power line right-of-ways. This year the monarch started their migration north, but the climate prevented milkweed plants from maturing enough to provide leaves for female butterflies to lay eggs and to feed the newly hatched caterpillars. Starting milkweed plants inside, then replanting them outside for the migrating butterflies to use will help sustain the Monarch butterfly population. Harvesting Milkweed seeds in the fall will provide seeds to plant in the spring. Your area may have seen a decline in Monarch butterflies. Monarch eggs, caterpillars and chrysalises can be purchased online or from local butterfly farms.
PomBase conventions for improving annotation depth, breadth, consistency and ...Valerie Wood
PomBase uses a combination of annotation conventions and QC mechanisms. In addition to identifying annotation inconsistencies and errors, these combined methods improve information content, annotation coverage, depth or specificity and redundancy.
Genome wide association studies---In genomics, a genome-wide association stud...DrAmitJoshi9
In genomics, a genome-wide association study (GWA study, or GWAS), is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait.
GWA studies typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major human diseases, but can equally be applied to any other genetic variants and any other organisms.
Presentation by Justin Zook at GRC/GIAB ASHG 2017 workshop "Getting the most from the reference assembly and reference materials" on benchmarks for indels and structural variants.
Journal club slides for "Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches" and a description of the software pipeline digit
2. Promoters is a region of DNA
that initiates the transcription
of a particular gene.
What is Promoter?
3. Promoter is a Important element for gene regulation.
TSS
4. Assumptions
• Promoters are
Usually
conceptualized as
upstream of the
sequences they
promote.
Facts
• Scientist do not really
know in which
direction promoters
usually transcribe or
if they only
transcribe in one
direction or not.
Present-Research
• Their Directions
possibilities and
parts of
promoter which
plays role in
deciding direction.
5. Promoter is a Important element for gene regulation.
TSS
6. On Basis of Directions they can
transcribe, Promoters can be
classified into two sub-classes-
1.Unidirectional
2.Bi-Directional*
13. what is the promoter length Distribution then?
14. Promoter Length Histogram (window =1500)
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15. 0
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Chart Title
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Series1 Log. (Series1)
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On Basis of these Results:
Mean Promoter length is : 335 Median of Promoter length is: 189
16. Conclusion we can draw:
• Clusters near the gene starting position in
range of 189.
• The probability of occurrence of another
gene at a distance from one gene first
increases exponentially till 335 and then
decreases and then saturates tending to
constant*.
*Not sure as second differentiation is still positive and can even change its concavity.
17. Visions and Logics to verify data:
• Making a artificial gene distribution
like system.
• A Cyber-Refgene.txt file.
• Using the same tunnel and get the
distribution.
• Comparing the Distribution.
18. 1. All Further Data is being
taken from a review paper.
2. All the sources and platforms
are mentioned on last slide.
PART - 2
19. Is it possible to identify consistent
pattern that distinguish
Bidirectional and Unidirectional ???
What to Look for …..
25. INR-Initiator element
• Functionally similar to TATA box.
• Accurate transcription initiation ,
INR btw -3 to +5 is necessary.
• Increases the strength of TATA
containing promoters.
Bidirectional: 25.3%
Unidirectional: 30.8%
31. DPE(Downstream Promoter Element)
• Located at +30 position
• Binds to common transcription
factor(TFIID) in absence of TATA
Bidirectional: 46.6%
Unidirectional: 50.6%
35. CpG islands:
The CpG sites or CG sites are regions of DNA where
a cytosine nucleotide occurs next to a guanine
Source:Trinklein, N. D., Aldred, S. H., Hartman, S. J., Schroeder, D. I., Otillar, R. P., and Myers, R. M. (2004) Genome Res.,14, 6266.
• 77% B-DP located in CpG islands
compared with 38% of U-DP.
• 90% B-DP located in CpG islands
compared with 45% of U-DP.
Source: Yang, M. Q., and Elnitski, L. L. (2008) BMC Genom., 9 (Suppl. 2), S3.
36. Bi-Directional promoters enrich with
following specific Binding sites of TF.
• GABPA
• MYC
• E2F1
• E2F4
• Nrf1
• YY1
• NFY
• SP1
38. Lets check the GC content-
Wait..Wait..Wait..
Where’s the length of
Unidirectional Promoters??
39. No, We Don’t . But we
have some Important
values which can help us.
1. Mean length of Bidirectional Promoter.
2. Median Length of Bidirectional Promoters.
3. We Know in Paper they take 1000BP
40. Comparison of GC content between
Unidirectional (Mean Length)
Bidirectional VS Unidirectional (Median Length)
Unidirectional (1000bp Length)
41. GC content Distribution- Unidirectional_MEAN
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AVERAGE: 54.6%
42. GC content Distribution- Unidirectional_MEDIAN
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AVERAGE: 56.9%
43. GC content Distribution- Unidirectional_1000 BP
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Histogram
Frequency
AVERAGE: 49.7%
44. Comparison of GC content between
Unidirectional (Mean Length)
Bidirectional VS Unidirectional (Median Length)
Unidirectional (1000bp Length)
45. GC content Distribution- BIDIRECTIONAL
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AVERAGE: 64%
47. NOTE**DATA SOURCE and Platforms
1. All the Data mentioned in Slides 17-36 are taken from Review:
Bidirectional Promoters in the Transcription of Mammalian Genomes.
A. S. Orekhova and P. M. Rubtsov*
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, 119991
Moscow, Russia; fax: (499) 1351405; Email: rubtsov@eimb.ru
2. All other data in these presentation belong to Sanju Sinha and he have all rights on those.
Any copying without mentioning the relevance source shall be considered as plagiarism.
3.twoBitToFa on linux platform is being used to done the calculations.
4. All coding is being done via Python language.