biotech

Question 1

secondary structure of chromatin

Answer 1

nucleosomal interactions, chromating folding

Question 2

PTM

Answer 2

post-translational modification

Question 2

tertiary structure of chromatin

Answer 2

interactions between folds of chromatin (higher order)

Question 2

primary structure of chromatin

Answer 2

nucleosome organization in the chromatin (beads on a string), which vary in nucleotide sequence, aminoacid sequence and post-translational modification of the histones

Question 3

chromatin structure description

Answer 3

Primary, secondary and tertiary structure of chromatin.The primary structure is shown as nucleosomal arrays consisting of nucleosomes with canonical histones (shown in light blue and yellow) and combinations of different histone variants (shown in green, purple and light blue). Nucleosomes with canonical or histone variants may vary in the degree of post-translational modifications (PTMs; such as acetylation, methylation, phosphorylation, ubiquitylation and sumoylation), generating the possibility for nucleosomes with a large number of different ‘colours’. Histone variants and PTMs may affect nucleosome structure and dynamics. The spacing between nucleosomes may vary on the basis of the underlying sequence, action of chromatin-remodelling enzymes and DNA binding by other factors (for example, transcription activators). Short-range nucleosome–nucleosome interactions result in folded chromatin fibres (secondary chromatin structure, lower left panel). Fibre–fibre interactions, which are defined by long-range interactions between individual nucleosomes, are also affected by the primary structure of chromatin fibres, including PTMs, histone variants and spacing of nucleosomes. Secondary and tertiary structures are stabilized by architectural proteins, such as linker histone H1, methyl-CpG-binding protein 2 (MeCP2), heterochromatin protein 1 (HP1), high mobility group (HMG) proteins, poly(ADP-ribose) polymerase 1 (PARP1), myeloid and erythroid nuclear termination stage-specific protein (MENT), Polycomb group proteins and many others. Transitions between the different structural states are indicated by double arrows; these may be regulated by changes in patterns of PTMs, binding or displacement of architectural proteins, exchange of histone variants and chromatin-remodelling factors.

Question 4

linker DNA

Answer 4

shord DNA segments that connect nucleosomes.

Question 5

ACP

Answer 5

architectural chromatin protein

Question 6

histone chaperone

Answer 6

histone-binding proteins that influence chromatin dynamics in an ATP-independent manner

Question 7

molecular chaperones

Answer 7

guardians of the proteome that assist in protein folding and prevent the accumulation of aberrant protein conformations that can lead to proteotoxicity

Question 8

bin

Answer 8

region of a given size or cluster in a dataset

Question 9

Hi-C

Answer 9

high-throughput genomic and epigenomic technique to capture chromatin conformation.[1] In general, Hi-C is considered as a derivative of a series of chromosome conformation capture technologies, including but not limited to 3C (chromosome conformation capture), 4C (chromosome conformation capture-on-chip/circular chromosome conformation capture), and 5C (chromosome conformation capture carbon copy).[1][2][3][4] Hi-C comprehensively detects genome-wide chromatin interactions in the cell nucleus by combining 3C and next-generation sequencing (NGS) approaches and has been considered as a qualitative leap in C-technology (chromosome conformation capture-based technologies) development and the beginning of 3D genomics.[2][3][4]

Question 10

How Hi-C works

Answer 10

Similar to the classic 3C technique, Hi-C measures the frequency (as an average over a cell population) at which two DNA fragments physically associate in 3D space, linking chromosomal structure directly to the genomic sequence

Question 11

TAD

Answer 11

topologically associated domain

Question 12

pairtools

Answer 12

tools for manipulating sequence contact data

Question 13

DNA ligation

Answer 13

joining of two fragments of DNA by ligase, which form a phosphodiester bond between adjacent nucleotides in duplex DNA.

Question 14

okazaki fragments

Answer 14

short lengths of DNA that are produced by the discontinuous replication of the lagging strand.

Question 15

how okazaki fragments are formed

Answer 15

As the DNA polymerase synthesises a part and then should wait for the helicase to open up more of the DNA helix upstream, the Okazaki fragments are formed on the lagging strand. Upon the opening up of the DNA by helicase, the primase gets in and puts down a new complementary RNA primer, which permits the DNA polymerase to associate the DNA and create the new fragment.

Question 16

in what direction is DNA synthetized by polymerase?

Answer 16

5’ to 3’

Question 17

what does it mean to say nucleosomes are well positioned (like in yeast)

Answer 17

the arrays occupy the same location
of the chromatin fiber in the majority of a cell population.

Question 18

NRL (nucleosome repeat length)

Answer 18

average distance between the centers of neighboring nucleosomes, which remains unchanged within a nucleosome array. By matching the distribution of local NRLs, it is possible to align the nucleosome
arrays in poorly-positioned regions

Question 19

contact distance (nucleosome)

Question 20

parametric model

Answer 20

summarize data with a fixed number of parameters
https://deepai.org/machine-learning-glossary-and-terms/parametric-model

Question 21

Dirichlet process

Answer 21

The Dirichlet process is a stochastic proces used in Bayesian nonparametric
models of data, particularly in Dirichlet process mixture models (also known as
infinite mixture models). It is a distribution over distributions, i.e. each draw
from a Dirichlet process is itself a distribution. It is called a Dirichlet process because it has Dirichlet distributed finite dimensional marginal distributions, just
as the Gaussian process, another popular stochastic process used for Bayesian
nonparametric regression, has Gaussian distributed finite dimensional marginal
distributions. Distributions drawn from a Dirichlet process are discrete, but
cannot be described using a finite number of parameters, thus the classification
as a nonparametric model.

Question 22

(nucleosome) ligation orientation

Question 23

(dna) ligation junction

Question 24

normalized matrix

Question 25

STORM (imaging technique)

Answer 25

STochastic Optical Reconstruction Microscopy (STORM) reconstructs a super-resolution image by combining the high-accuracy localization information of individual fluorophores in three dimensions and multiple colors

Question 26

linker histone

Answer 26

H1 or H5 histone which binds to the nucleosome at the DNA entry and exit points

Question 27

TAD

Answer 27

A topologically associating domain (TAD) is a self-interacting genomic region, meaning that DNA sequences within a TAD physically interact with each other more frequently than with sequences outside the TAD

Question 28

CTCF

Answer 28

Transcriptional repressor, binds together strands of DNA, thus forming chromatin loops, and anchors DNA to cellular structures like the nuclear lamina. It also defines the boundaries between active and heterochromatic DNA.

Question 29

cis-acting factor

Answer 29

non-coding DNA which regulate the transcription of neighboring genes

Question 30

trans-acting factor

Answer 30

molecule that binds to DNA and acts in regulation (or dna that codes for such molecule)

Question 31

virion

Answer 31

an entire virus particle (dna or rna and encapsulating)

Question 32

chromatin fibrils

Question 33

NDR

Answer 33

nucleosome depleted region

Question 34

A and B compartment

Answer 34

different regions of the genome in chromatin, A is active, B is inactive