11. Nucleus, chromatin

Answer 1

nucleolus
An intensively stained area (or areas) in the nucleus of eukaryotic cells during the interphase of
the cell division cycle. Nucleolus organizing regions (NOR) are particular segments of certain
chromosomes that contain tandem repeats of genes responsible for synthesis of ribosomal
RNAs (rRNA). The physical association of these NOR regions – together with nucleolar
proteins – forms the nucleolus. Ribosomal RNA is synthesized in the nucleolus, and the
ribosomal subunits are also assembled here (but not the whole ribosome).

euchromatin, heterochromatin
Euchromatin is a decondensed, transcriptionally active region of chromosome, whereas
heterochromatin is a region of chromosome that remains condensed and transcriptionally
inactive during interphase. Types: constitutive (e.g. one of the two X chromosomes, or
centromeres and telomeres (the last two are usually repetitive and play structural roles); and
facultative heterochromatin (under specific developmental or environmental signaling it loses
its condensed structure and becomes transcriptionally active).

Answer 2

histone
Simple water-soluble proteins that are rich in basic amino acids. Their positive charges allow
them to associate with the negatively charged DNA molecule, and package the DNA into
structural units of chromatin called nucleosomes. Five major families of histones exist:
Histones H2A, H2B, H3 and H4 are known as the core histones, while histones H1 are known
as the linker histones. Posttranslational chemical modification of N-terminal tails of histones
can modulate the structures and function of nucleosomes, and make the DNA accessible or
inaccessible to proteins (e.g. enzymes or transcription factors) involved in diverse biological
processes such as transcriptional activation/inactivation, chromosome packaging, or DNA
repair.
nucleosome
The repeating structural units of chromatin, each consisting of approximately 200 base pairs of
DNA wound around a protein core. This core, called histone octamer, is composed of the
histones H2A, H2B, H3, and H4. The repeating units can exhibit a beads-on-a-string structure
under no-physiological conditions. The DNA between the nucleosomes is called
internucleosomal linker DNA.

Question 3

chormatin remodeling, dnas sensivity

Answer 3

chromatin remodeling
An ATP-dependent modification of chromatin architecture during the process of turning genes
on and off, which regulates the sliding of nucleosomes along the DNA molecule or the
attachment of nucleosomes to DNA by remodeling enzymes. It occurs chiefly on regulatory
regions and has an important role in gene regulation.
DNAse sensitivity
DNase sensitivity is the relatively higher sensitivity of transcriptionally active regions of
chromatin against certain nucleases (e.g. DNase I enzyme), which is a consequence of
chromatin decondensation (euchromatisation). This sensitivity extends to the gene and its entire
regulatory environments. DNase I hypersensitivity is different in that it is the extreme
sensitivity to DNase I of some hundred basepairs long DNA of active promoters and enhancers
and is caused by the absence of nucleosomes in that particular stretch of DNA.

Question 4

chromoseome, interphase chromosome

Answer 4

chromosome
Basic units of the cell’s chromatin. The structure and function of chromosomes vary during the
cell cycle. In G0/G1 phase, chromosomes are constituted of one chromatid each, their function
is to serve as template for transcription. In S phase, chromosomes with two chromatids are
formed, which during cell division condense to form metaphase chromosomes. The two
chromatids are connected at their centromeres. Within a chromosome, the two chromatids have
the same DNA sequence since they were produced by replicating the original single chromatid.
interphase chromosome

Interphase chromosome: Each interphase chromosome consists of a linear DNA (giant)
molecule and its associated histone and non-histone proteins. The ratio of proteins and nucleic
acids is approximately 1:1. They are hierarchically packaged, but the level of their condensation
can be different, e.g. euchromatin, heterochromatin or facultative heterochromatin. Their
location inside the nucleus shows territorial distribution.

Question 5

metaphase chromosome, chromatid

Answer 5

metaphase chromosome
The metaphase chromosome is the most compact form of chromatin that contains two identical
DNA strands (that is two sister chromatids) coding the same information. This type of DNA
material is inactive. Particular parts of chromosomes are chromosome arms, centromere and
telomeres. They show special banding after different staining at processes by which
chromosomes can be distinguished from each other.
chromatid
It is made up of a DNA double helix and proteins are attached to it. Prior to cell division, the
gene pool of the cells is doubled and chromosomes, made of two chromatids are created. In the
anaphase of the mitotic cell division, and in the anaphase of the second stage of meiotic cell
division, these chromatids (sister chromatids) are separated from each other (see mitosis,
meiosis), again resulting in single-chromatid chromosomes.

Question 6

epigenom, histone code

Answer 6

epigenom
A sum of factors influencing gene activity that are over the information stored in sequences,
like as DNA methylation; posttranslation modifications of histones, e.g. methylation,
acetylation and phosphorilation (called histone code). The dynamic and reversible changes of
epigenom determine or direct the changes of gene expression. The epigenomic pattern is
hereditary during mitosis and is usually inherited by both daugter cells (excetp, e.g., asymmetric
division of stem cells).
histone code, with example
The pattern of posttranslational modifications of the histones in the nucleosomes along the
chromatin fiber. It is part of the epigenome, together with DNA methylation. There are various
histone modifications, for example methylation, acetylation, phosphorylation. Histone
acetylation, e.g. often opens up chromatin structure by neutralizing the positive charge of lysins
on the histones. The pattern is propagated into the daughter cells upon mitosis

Question 7

promoter, enhancer

Answer 7

promoter
DNA region regulating transcription. It is a sequence located 5’ upstream from the associated
gene, at which RNA polymerase can bind and which designate the initiation site of transcription
of an associated gene.
enhancer
DNA region regulating transcription. It is a sequence, which enhances/amplifies the
transcription of a gene. It can be located long distance from the gene being regulated, but always
at the same chromosome. The gene specific transcription factors associated with enhancer
connect directly with the transcription machinery through other proteins by formation of a
chromatin loop