| What is a nucleosome? | The basic structural subunit of chromatin, consisting of ~200 bp of DNA and an octamer of histone proteins. |
| What are histone tails? | Flexible amino- or carboxy-terminal regions of the core histones that extend beyond the surface of the nucleosome. |
| What events take place in histone tails? | Histone tails are sites of extensive posttranslational modification. |
| What is a 10nm fiber? | A linear array of nucleosomes generated by unfolding from the natural condition of chromatin. |
| What are linker histone? | A family of histones (such as histone H1) that are not components of the nucleosome core.
Linker DNA is the region of 8 to 114 bp that is susceptible to early cleavage by nucleases. |
| What’s the function of linker histones? | Linker histones bind nucleosomes and/or linker DNA and promote 30 nm fiber formation. |
| What is a 30 nm fiber? | A coil of nucleosomes.
It is the basic level of organization of nucleosomes in chromatin. |
| What is a nonhistone? | Any structural protein found in a chromosome except one of the histones. |
| How is the DNA organized? | DNA Is Organized in Arrays of Nucleosomes |
| What is the function of MNase? | MNase cleaves linker DNA and releases individual nucleosomes from chromatin.
>95% of the DNA is recovered in nucleosomes or multimers when MNase cleaves DNA in chromatin. |
| How does The length of DNA per nucleosome varies? | The length of DNA per nucleosome varies for individual tissues or species in a range from 154 to 260 bp. |
| What are the two divisions of Nucleosomal DNA and what it depends on? | Nucleosomal DNA is divided into the core DNA and linker DNA depending on its susceptibility to MNase. |
| What can you say about the length of the coreDNA? | The core DNA is the length of 146 bp that is found on the core particles produced by prolonged digestion with MNase. |
| What is the Subunit of All Chromatin ? | The Nucleosome Is the Subunit of All Chromatin |
| What does nucleosomes contain? | A nucleosome contains ~200 bp of DNA and two copies of each core histone (H2A, H2B, H3, and H4). |
| Where can you find the DNA in relation to the histones? | DNA is wrapped around the outside surface of the protein octamer. |
| What is the structure of a histone octamer? | The histone octamer has a structure of an H32-H42 tetramer associated with two H2A-H2B dimers. |
| T/F The nucleosome consists of approximately equal masses of DNA and histones? | True |
| T/F The nucleosome is a cylinder with DNA organized into ~1 2/3 turns around the surface. | True |
| T/F Each histone is extensively interdigitated with its partner. | true |
| What is common with all core histones? | All core histones have the structural motif of the histone fold. N- and C-terminal histone tails extend out of the nucleosome. |
| what is the the function of H1? | H1 is associated with linker DNA and may lie at the point where DNA enters or exits the nucleosome. |
| Where are the histone fold domains located? | The histone fold domains of the histones are located in the core of the nucleosome. |
| How are histones modified? | Histones are modified by methylation, acetylation, phosphorylation, ubiquitylation, sumoylation, ADP-ribosylation, and other modifications. |
| What is the histone code? | Combinations of specific histone modifications define the function of local regions of chromatin; this is known as the histone code. |
| What is a bromodomain And what it’s functions? | The bromodomain is found in a variety of proteins that interact with chromatin.
It is used to recognize acetylated sites on histones. |
| What can recognize methyl lysines? | Several protein motifs recognize methyl lysines, such as chromodomains, PHD domains, and Tudor domains. |
| Where and when does acetylation happen? | Acetylation during replication occurs on specific sites on histones before they are incorporated into nucleosomes. |
| Acetylatin is associated with what function? | Acetylation associated with gene activation. |
| What does histone variants produce? | Histone Variants Produce Alternative Nucleosomes |
| Which histones are members of families of related variants? | All core histones except H4 are members of families of related variants. |
| What can you say about histone variants? | Histone variants can be closely related to or highly divergent from canonical histones.
Different variants serve different functions in the cell. |
| What does the major core histones have in common? | The major core histones contain a conserved histone-fold domain. |
| What are the 10 nm chromatin fibers and 30 nm fibers | 10 nm chromatin fibers consist of a string of nucleosomes.
30 nm fibers have six nucleosomes/turn, which are organized into a two-start helix. |
| What promotes the formation of the 30nm fiber? | Histone H1, histone tails, and increased ionic strength all promote the formation of the 30 nm fiber. |
| What does the replication of chromatin require? | Replication of Chromatin Requires Assembly of Nucleosomes |
| Which histones octamers are conserved during replication? | Histone octamers are not conserved during replication, but H2A-H2B dimers and H32-H42 tetramers are conserved.
There are different pathways for the assembly of nucleosomes during replication and independently of replication. |
| How does nucleosomes assemble in vivo? | During nucleosome assembly in vivo, H3-H4 tetramers form and bind DNA, then H2A-H2B dimers are added to form a complete nucleosome. |
| What are accessory proteins and what is their function? | Accessory proteins are required to assist the assembly of nucleosomes.
CAF-1 and ASF1 are histone assembly proteins that are linked to the replication machinery.
A different assembly protein, HIRA, and the histone H3.3 variant are used for replication-independent assembly. |
| What does Replication fork passage do to histones? | Replication fork passage displaces histone octamers from DNA. |
| Do Nucleosomes Lie at Specific Positions? | Nucleosomes may form at specific positions as the result of either the local structure of DNA or proteins that interact with specific sequences. |
| What is indirect end labeling? | A technique for examining the organization of DNA by making a cut at a specific site and identifying all fragments containing the sequence adjacent to one side of the cut.
It reveals the distance from the cut to the next break(s) in DNA. |
| What is the cause of nucleosome positioning? | A common cause of nucleosome positioning is when proteins binding to DNA establish a boundary.
DNA sequence determinants (exclusion or preferential binding) may be responsible for half of the in vivo nucleosome positions. |
| What are the effects of nucleosome positioning? | Positioning may affect which regions of DNA are in the linker and which face of DNA is exposed on the nucleosome surface. |
| What is rotational positioning? | The location of the histone octamer relative to turns of the double helix, which determines which face of DNA is exposed on the nucleosome surface.
Rotational positioning describes the exposure of DNA on the surface of the nucleosome. |
| What is translational positioning? | The location of a histone octamer at successive turns of the double helix, which determines which sequences are located in linker regions. |
| What happens to nucleosomes during transcription? | Nucleosomes Are Displaced and Reassembled During Transcription |
| How does transcribed genes retain a nucleosomal structure? | Most transcribed genes retain a nucleosomal structure, though the organization of the chromatin changes during transcription.
Some heavily transcribed genes appear to be exceptional cases that are devoid of nucleosomes. |
| What does RNA polymerase do to histone octamers during transcription? | RNA polymerase displaces histone octamers during transcription in vitro, but octamers reassociate with DNA as soon as the polymerase has passed.
Additional factors are required both for RNA polymerase to displace octamers during transcription and for the histones to reassemble into nucleosomes after transcription. |
| What happens to nucleosomes after transcription passes through a gene? | Nucleosomes are reorganized when transcription passes through a gene. |
| What are Hypersensitive sites? | Hypersensitive sites are found at the promoters of expressed genes, as well as at other important sites such as origins of replication and centromeres. |
| How does hypersensitive sites generate? | Hypersensitive sites are generated by the binding of factors that exclude histone octamers. |
| How domains relate to hypersensitive sites? | A domain containing a transcribed gene is defined by increased sensitivity to degradation by DNase I. |
| What are insulators and what’s their function? | Insulators are able to block passage of any activating or inactivating effects from enhancers, silencers, and other control elements.
Insulators can provide barriers against the spread of heterochromatin.
Insulators are specialized chromatin structures that typically contain hypersensitive sites. |
| How two insulators function together? | In most cases, two insulators can protect the region between them from all external effects. |
| What makes distinct insulators deferent? | Different insulators are bound by different factors, and may use alternative mechanisms for enhancer blocking and/or heterochromatin barrier formation. |
| What are locus control regions(LCRs) and what is their function ? | Locus control regions (LCRs) are located at the 5′ end of a chromosomal domain and typically consist of multiple DNAse hypersensitive sites.
LCRs regulate gene clusters.
LCRs usually regulate loci that show complex developmental or cell-type specific patterns of gene expression.
LCRs control the transcription of target genes in the locus by direct interactions, forming looped structures. |
| What is conformation capture (3c)? | Chromosome conformation capture (3C) is one method to detect physical interactions between regions of chromatin in vivo. |
