| Pointer Session |
00:00 Intro
11:37 #Chromosome has to be read under following heads
12:41 The #capsid is assembled around the genome for single-stranded #RNA viruses.
13:36 Inserting DNA into a phage head involves two types of reaction: #translocation and #condensation.
17:37 In E.coli, Protein HU is a dimer that condenses DNA, possibly wrapping it into a #beadlike structure.
18:51 The bacterial #genome consists of a large number of loops of duplex DNA (in the form of a fiber).
21:16 Each domain consists of -40 kilobases (kb) of DNA, or may be smaller, 10 kb each. About -400 domains in the E. coli genome.
28:24 An unrestrained supercoil in the DNA path creates tension, but no tension is transmitted along DNA when a supercoil is restrained by protein binding.
30:06 Chromosomal packaging is maintained by supercoiling of DNA in case of bacteria 30:13 Because supercoiled DNA molecules are more compact than relaxed molecules, they migrate more rapidly during gel electrophoresis.
36:30 E. coli has at least four individual topoisomerases (I through IV). Those of type I (topoisomerases I and III) generally, relax DNA by removing negative supercoils (increasing Lk).
59:40 A bacterial type II enzyme, called either topoisomerase II or DNA gyrase, can introduce negative supercoils (decrease Lk).
1:07:49 Eukaryotic cells also have type I and type II topoisomerases.
1:11:41 The quinolone antibiotics, inhibits bacterial DNA gyrase and topoisomerase IV, as ciprofloxacin (Cipro).
1:13:41 Camptothecin is an inhibitor of eukaryotic type I topoisomerases.
Irinotecan (Campto) and topotecan (Hycamtin)—used to treat colorectal cancer and ovarian cancer.
1:20:13 The human type II topoisomerases are targeted doxorubicin (Adriamycin), etoposide (Etopophos), and ellipticine.
1:23:40 Addition of a topoisomerase greatly facilitates nucleosome association with cccDNA.
1:27:56 By maintaining the unbound DNA in a relaxed state, topoisomerases facilitate the binding of histones to the DNA and the formation of additional nucleosomes.
1:30:36 This discrepancy is referred to as the “nucleosome linking number paradox,”
1:36:06 When an ethidium ion intercalates between two base pairs, it causes the DNA to unwind by 260, reducing the normal rotation per base pair from 360 to 100.
1:39:42 One approach is to measure the effect of nicking the DNA. Unconstrained supercoils are released by nicking, whereas constrained supercoils are unaffected.
1:46:28 First the DNA is wrapped around histone octamers, then H1 stimulates formation of the 30 nm fiber.
1:47:29 Interphase chromatin is a tangled-appearing mass occupying a large part of the nuclear volume, in contrast with the highly organized and reproducible ultrastructure of mitotic chromosomes.
1:50:53 Histone-depleted chromosomes consist of a protein scaffold to which loops of DNA are anchored.
1:52:56 DNA is attached to the nuclear matrix or scaffold at specific sequences called MARs or SARs.
2:00:04 Matrix-associated regions (MARs) may be identified by characterizing the DNA retained by the matrix isolated in vivo (left) or by identifying the fragments that can bind to the matrix from which all DNA has been removed (right).
2:02:28 A surprising feature is the lack of conservation of sequence in MAR fragments. They are usually 70% A-T rich. cis-acting sites that regulate transcription are common, as are 5’ introns, and a recognition site for topoisomerase II is usually present in the MAR.
2:03:59The nuclear matrix and chromosome scaffold consist of different proteins, although there are some common components.
2:05:41Chromosomes occupy chromosome territories in the nucleus and are not entangled with each other.
2:08:44 In most regions, the fibers are much less densely packed than in the mitotic chromosome. This material is called euchromatin.
2:09:35 Some regions of chromatin are very densely packed with fibers, displaying a condition comparable to that of the chromosome at mitosis. This material is called heterochromatin.
2:10:26In some cases, the various heterochromatic regions, especially those associated with centromeres, aggregate into a densely staining chromocenter.
2:13:20 G-bands are distinguished from interbands by their lower G-C content. This is a peculiar result.
2:13:31In the case of human chromosomes, approximately 300 G bands can usually be distinguished during metaphase.
2:14:00 Chromosome Conformation Capture. 3C assays involve three basic steps:
2:15:46This is used to identify when regulatory proteins bound at an enhancer are in close proximity to the transcriptional machinery at a given promoter—a physical proximity interpreted to show looping out of the DNA
2:19:18 The interphase nuclei of some tissues of the larvae of dipteran flies contain chromosomes that are greatly enlarged relative to their usual condition.
2:19:31 The centromeres of all four chromosomes of D. melanogaster aggregate to form a chromocenter that consists largely of heterochromatin.
