Transcription & Epigenetics Flashcards
What is epigenetics?
- Epigenetics: The study of heritable changes in gene expression (usually silencing) that occur without alterations to the underlying DNA sequence.
- Epigenetic changes include chromatin conformational changes (via histone modifications) and DNA methylation.
What are epimutations?
Epimutations: heritable changes in gene expression that are not caused by genetic alterations (heritable through cell divisions and sometimes across generations) → epialleles
How is the chromosomal organization of the human genome?
- Each chromosome contains a single molecule of DNA associated with proteins (including histones)
- DNA double helix -> DNA wraps around histone proteins, forming nucleosomes - “Beads on a string” (euchromatin) -> 30nm chromatin fibre of packed nucleosomes (heterochromatin) -> chromatin loops -> chromatin domains (TADs) -> chromatin compartments -> chromosomes
How is the structure of a nucleosome?
Nucleosome: 147 bp of DNA wrapped around a histone octamer (2 copies from each H2A, H2B, H3 and H4, or their variants
How many variants are there of the linker histone H1 and what are its functions?
Linker histone H1:
* 11 variants in humans
* control of local chromatin compaction
* 3D genome organization
* Modulation of some histone post translational modifications (PTMs)
Give examples for different chromosome regions harbouring distinct histones.
- Facultative Heterochromatin (lower side): mH2A1.1, mH2A1.2, mH2A2.2 (in inactive X chromosomes)
- Centromere: CENP-A
Which histone variants are found in centromeres?
- Centromeres harbour the histone H3 variant CENP-A (centromere protein A), which is essential for the centromere architecture
- CENP-N (instead of the linker histone H1) recognizes CENP-A-containing nucleosomes and stabilizes inter-nucleosome compaction
What is CENP-A?
- It is a Histone H3 variant, found in centromeres
- It is essential for the centromere architecture
What is CENP-N?
- It is a Histone H3 variant, found in centromeres
- It recognizes and stabilizes inter-nucleosome compaction
How are chromatins organized?
In loops and domains
What does the radial positioning of chromosomes and genomic regions in the nucleus depend on?
Gene activity
Where is active chromatin (euchromatin) located?
In A compartments, towards nuclear interior
Where is inactive chromatin (heterochromatin) located?
In B compartments, close to the nuclear periphery
* Inactive regions are close to the nuclear lamina (lamina-associated domains = LADs)
What are TADs?
- Local chromatin forms submegabase self-interacting domains called topologically associating domains (TADs)
- TADs are fundamental regulatory units of the genome that are limited by boundaries, enriched in structural proteins such as CTCF (CCCTCbinding factor) and cohesin
How are TADs stabilized?
By CTCF and cohesin
What are histone tails?
Nucleosomal histones have intrinsically disordered and flexible N-/C-termini extending from the globular structure of the nucleosome = histone tails
What are general examples of histone modifications?
Histone tails are subject to reversible, covalent post-translational modifications (PTMs):
- acetylation
- methylation
- phosphorylation
- ubiquitinylation
What is a histone code and what is its function?
- A hypothesis that certain functions of the genome are governed by recognition of combinatorial chemical modifications of histones
- The combination of histone-tail PTMs found in a chromatin region constitute a „histone code“ that affects chromatin structure and function
What PTMs are possible for the amino acid S/T?
P
What PTMs are possible for the amino acid K?
Ac, Mono-methyl, Di-methyl, Tri-methyl, Ub, SUMO
What PTMs are possible for the amino acid R?
Mono-methyl, symmetric di-methyl, asymmetric di-methyl
In which regions of the genome can histone modifications be found?
Histone modifications demarcate functional elements in mammalian genomes; Promoters, enhancers, TSS, gene bodies - introns and exons, heterochromatic regions, centromeres, telomeres, insulators and boundary elements, polycomb repressive regions
How do histone modifications affect DNA and transcription?
Affect how tightly or loosely DNA is packaged in chromatin -> which affects the gene accessibility for transcription
How does acetylation affect DNA and transcription?
Loosens the DNA-histone interaction and promotes active transcription → Hyper-acetylation favours transcription
How does methylation affect DNA and transcription?
Can have positive or negative effects – depending on the position, the number of methyl groups and the interplay with other histone marks
Which histone marks always inhibit transcription?
H3K9me3, H3K27me3
Which histone marks always activate transcription?
H3K4me2/3, H3K36me2/3, H3K27ac
What are examples of histone-associated enzymes?
writers, erasers, readers
What are examples of histone-associated enzymes responsible for writing?
Acetylases, Methylases, Phosphorylases
What are examples of histone-associated enzymes responsible for reading?
Deacetylases, Demethylases, Phosphatases
What are examples of histone-associated enzymes responsible for erasing?
Bromodomain (-> acetylated histones), Chromodomain (-> methylated lysines), PHD finger, WD40 repeat
What are different compaction states that chromatin is found in?
euchromatin, facultative heterochromatin, constitutive heterochromatin
What is a heterochromatin?
- It is a condensed form of chromatin
- The genomic DNA in heterochromatin is mostly inactive (transcription, replication, recombination and repair are suppressed)
What are typical hallmarks for heterochromatin?
Methylation (mainly trimethylation) of the histone H3 lysine 9 (H3K9me3) and/or 27 (H3K27me3) are typical hallmarks for heterochromatin formation (repressive marks)
Which histone variant is herterochromatin enriched in and why?
Linker histone H1-> Compact nucleosome packaging
What causes compact nucleosome packaging in heterochromatin?
Linker histone H1
How does linker histone 1 cause gene repression?
Spatially restricted H1 recruitment represses genes, presumably by localized chromatin condensation or alternate nucleosome spacing
What are the 2 types of heterochromatins?
Facultative & Constitutive
What effect does facultative heterochromatins have on transcription? What is a mark for facultative heterochromatins?
- maintains genes transcriptionally silent, but may be dismantled upon e.g. developmental cues
- can alternate between repressive and active states depending on the cellular context or environmental signals
- usually contains the H3K27me3 mark
Where are constitutive heterochromatins found? What is a mark for constitutive heterochromatins?
- Telomeres, centromeres; epigenetically maintained at the same genomic loci in every cell type
- Contains H3K9me3 mark
What is heterochromatin protein (HP1)?
HP1 (heterochromatin protein 1) specifically binds to the chromatin containing H3K9me3 („H3K9me3 reader“) and contributes to the formation and maintenance of heterochromatin
How does HP1 bind to H3K9me3?
Chromodomain
What are the two domains of HP1 and what do they interact with?
Chromodomain -> methylated K9 of H3
Chromoshadow domain -> HP1α, HP1β, p150 of CAF1, (Suv39h), Dnmt1, Dnmt3a
What is the linker region of HP1 and what does it interact with?
Hinge region -> RNA, DNA, chromatin
What does HP1 dimer bind?
HP1 dimer binds H3K9me on two nucleosomes
Can heterochromatin spread?
Heterochromatin can spread, but spreading is restrained by boundaries:
- Nucleosome depletion
- Nucleosome turnover
- Opposing PTMs (Ac)
- PTM-mediated eraser recruitment (Epe1)
What are some boundaries that prevent heterochromatin spreading?
- Nucleosome depletion
- Nucleosome turnover
- Opposing PTMs (Ac)
- PTM-mediated eraser recruitment (Epe1)
What does unblocked spread of heterochromatin lead to?
Position-effect variegation
What is variegation?
The occurrence within a tissue of sectors or clones with differing phenotypes
What is position-effect variegation?
Stochastic, meta-stable and heritable silencing of a euchromatic gene through the spread of heterochromatin formation
What protects against position-effect variegation?
Barrier elements protect against position-effect variegation (PEV)
What do barrier elements do?
Protect against position-effect variegation (PEV)
Where were polycomb genes first discovered and what were they required for?
- Polycomb genes discovered in Drosophila; required for the repression of homeotic genes and thus for body plan specification
- Evolutionary conserved
- They have mammalian orthologs involved in controlling gene expression throughout development
What are polycomb proteins responsible for?
- Polycomb proteins establish facultative heterochromatin domains that are involved in developmental gene regulation
- Role in X-chromosome inactivation
What are polycomb repressive complexes (PRC) and what is their main function?
Polycomb proteins assemble in large multiprotein complexes that post-translationally modify histones: Polycomb Repressive Complexes
What is the function of PRC1?
PRC1: E3 ubiquitin ligase activity → H2AK119Ub1
(Remember: regressive mark!!!)
What is the function of PRC2?
PRC2: methyltransferase activity → H3K27me1, me2, me3
(Remember: regressive mark!!!)
How do Polycomb complexes recognize their target sites?
- Sequence-specific DNA-binding factors are incorporated in or bind some PRCs (e.g. E2F6-DP1 motif, E-box motif, T-box motif)
- lncRNAs binding to specific chromatin sites (e.g. XIST lncRNA during X chromosome inactivation, Airn and Kcnq1ot1 in autosomal imprinted regions → adaptor protein hnRNPK recruits PRC complex)
- Some PRC subunits recognize non-methylated CpG → target PRCs to CpG islands
What are polycomb chromatin domains and what is their main function?
PRC1 and 2 converge spatially and work together to form Polycomb chromatin domains, which counteract transcription
What are key characteristics of polycomb chromatin domains?
- Very high levels of H2AK119ubi, H3K27me3 and Polycomb complex occupancy
- Domains that can extend up to tens of kbp
Where are polycomb chromatins typically found and what is their function?
Polycomb chromatin domains form at non- or low-transcribed genes → might maintain, rather than initiate, gene expression
* Only some Polycomb target sites form Polycomb chromatin domains
What are polycomb bodies?
Repressive Polycomb chromatin domains can form long-range interactions in 3D space, possibly within dynamic condensates, which are polycomb bodies
What is the role of cohesin in polycom bodies?
Cohesin is involved in extruding chromatin loops → counteracting interaction between Polycomb chromatin domains and stabilizing its structure
When can polycomb target genes be activated and how does this occur?
During cellular differentiation:
- Loss of Polycomb chromatin domains (associated with gene repression)
- Formation and spreading of transcription-permissive, H3K4me3-containing Trithorax chromatin domains (associated with gene activation)
What does the antagonistic interaction between Polycomb (repression) and Trithorax (activation) allow for?
Switch-like transitions in gene expression (on/off) -> useful for master regulators of cell fate to support decisive gene expression transitions during development (binary gene expression)
What modification is meant by DNA methylation?
5-methylcytosine (5mC) modification of DNA:
DNA methylation occurs at cytosine bases when a methyl group is added at the 5′ position on the pyrimidine ring
Where does the 5-methylcytosine (5mC) modification of DNA (DNA methylation) occur and which protein is responsible for it?
- Occurs at cytosine bases when a methyl group is added at the 5′ position on the pyrimidine ring by a DNMT (DNA methyltransferase)
- Occurs within CpG dinucleotides (CpG sites) and intergenic regions
- Writers, readers and erasers establish, recognize and remove DNA methylation
What are the 2 types of DNA methyltransferases („writers“)?
- De novo DNA methylation
- Maintenance DNA methylation
What is De novo DNA methylation?
(DNMT3a/b): methylation of naked DNA in response to signals (histone code, TFs, microenvironment…)
What is Maintenance DNA methylation?
(DNMT1): methylation of hemi-methylated DNA at the complementary strand in the replication fork during cell division => inheritance to daughter cells, maintenance of the original pattern of DNA methylation in a cell lineage
Where are CpG sites typically found and what is their state of methylation?
CpG sites are found spread out across the genome and are usually heavily methylated, except in CpG islands
What does DNA methylation in intergenic regions cause?
Represses potentially harmful genetic elements (e.g. transposable and viral elements)
Which DNA element is mostly found in CpG islands?
~70% of gene promoters (and in particular the promoters of housekeeping genes) reside within CpG islands
How is the general methylation state of CpG islands and as such, gene expression?
- Rarely methylation
- Low nucleosome density (low histone affinity), and the nucleosomes often harbor histone marks associated with enhanced gene expression
What effect does methylation of CpG islands have on gene expression and how?
Results in stable silencing of gene expression → impairs TF binding and recruits repressive methyl-binding proteins
What effect does methylation of gene bodies (past the first exon) have on gene expression?
Higher gene expression in dividing cells (unclear mechanisms)
Is DNA methylation a silencing / repressive mark?
Although DNA methylation is mostly seen as a silencing / repressive epigenetic mark, its effect on transcription actually depends on its position in the transcriptional unit
Other than within CpG islands and intergenic regions, in which other DNA elements can DNA methylation be found?
New roles of DNA methylation in altering the activities of regulatory elements such as enhancers and insulators
Which epigenetic regulators promote gene transcription?
DNA hypomethylation
Histone H2B ubiquitination
H3 acetylation
H3K4 methylation
H4 acetylation
Which epigenetic regulators inhibit gene transcription?
DNA hypermethylation
H2A ubiquitination
H3K9 methylation
H3K27 methylation
How does DNA methylation repress transcription?
- by preventing TFs from binding to the DNA
- by recruiting proteins that repress transcription
Which proteins can be recruited to repress transcription through DNA methylation?
„Readers“ recognize and bind to methyl groups to ultimately influence gene expression:
* Proteins binding 5mC can inhibit TF binding
* MBD (methyl-CpG-binding domain) proteins
How do MBD (methyl-CpG-binding domain) proteins work?
(e.g. MeCP2) recognize DNA methylation and bind a variety of repressor complexes via their transcriptional repression domain
-> histone deacetylation, de novo methylation, chromosome condensation -> stable repression
DNMTs and MBD protein MeCP2 interact with enzymes responsible for repressive histone markers. Give examples.
- Histone methyltransferases (HMT) → H3K9 methylation
- Histone deacetylases (HDACs) → DNA condensation
results in: Euchromatin → Heterochromatin
How do histone modification influence DNA methylation pattern?
Histone modifications can also influence the DNA methylation pattern by regulating the activity of the DNA methylation enzymes.
Does DNA methylation regulate the expression of miRNAs?
DNA methylation also regulates the expression of miRNAs (CpG island methylation). Conversely, miRNAs regulate histone modifications and DNA methylation (DNMT expression).
What is the importance of DNA methylation?
DNA methylation is essential for silencing retroviral elements, regulating tissue-specific gene expression, genomic imprinting, and X chromosome inactivation.
Mutations in the MeCP2 epigenetic „reader“ are associated with rare human diseases. Give examples.
- Rett syndrome: in females, loss-of-function mutations in MECP2
- MECP2 duplication syndrome: in males, extra copy of MECP2
What is rett syndrome and who does it affect? What are its symptoms?
- Neurological disorder affecting brain development and function in females in 1 in 10,000 live births
- Developmental regression, including loss of speech and hand skills, after apparently normal development
What is the cause of rett syndrome? How does it appear in men and women?
- Caused by loss-of-function mutations in the X-linked MECP2 gene, mostly de novo mutations
- In females, random X chromosome inactivation results in somatic mosaics with normal and mutant MECP2.
- In males, MECP2 mutations usually lead to severe congenital encephalopathies and death within 2 years
What are some elements of MECP2 gene and what are their functions?
Intrinsically disordered protein
* NTD: N-terminal domain. Binds HP1, heterochromatin formation
* MBD: binds methylated DNA
* TRD: transcriptional repression domain. Interacts with HDACs, NCoR, DNMT1, NCoR… Contains a NLS.
* CTD : heterochromatin condensation
* Hundreds of Rett syndrome-causing mutations identified, with 8 hotspots in NTD, MBD and the
rest of the protein
What is genomic imprinting?
- Genomic imprinting is an epigenetically regulated process that causes genes to be expressed in a parental-origin-specific manner rather than from both chromosome homologues.
- The expression of an allele can be influenced by whether it is inherited from the mother or the father.
- Imprinted genes have mono-allelic expression.
Since genomic imprinting is not dependant on the DNA sequence, what is it dependant on?
The imprint is not dependent on the DNA sequence, but on the parental germline environment through which the gene passes.
What exactly is imprinted?
Specific genes are imprinted, and in some cases (e.g. inactivated (paternal) X chromosome in marsupials), a whole chromosome!
What phenomena do genomic imprinting and X-chromosome inactivation have in common?
Genomic imprinting and X-chromosome inactivation (XCI) are classic epigenetic phenomena that involve transcriptional silencing of one parental allele
How many gene are known to imprint in humans?
There are ~ 200 imprinted genes in human: some imprinted genes are expressed from the paternally inherited allele, while others are expressed from the maternally inherited allele (21% maternal alleles, 67% paternal allele)
What is the expression of imprinted genes controlled by?
- Expression of imprinted genes is controlled by methylation at the imprinting control region (ICR) which is a differentially methylated region (DMR) between the two chromosomes.
- Genomic imprinting relies on the regulation of gene expression by DNA methylation, chromatin structure and non-coding RNA
How long do genomic imprints last for?
Genomic imprints endure for one generation: from their establishment in mature germ cells of an individual to their erasure in the gamete precursors of their progeny
What is the importance of genomic imprinting?
Genomic imprinting is essential for normal mammalian growth and development. Effects on development and placental biology, before birth (males), but also after birth (females)
What are examples of imprinting genes that control embryo growth control?
Igf2/H19
* maternal chromosome: H19 is turned on, Igf2 turned off -> negative regulator of general growth (Suppression of growth)
* Paternal chromosome: H19 is turned off, Igf2 turned on -> positive regulator of general growth (Growth)
How are Igf2 and H19 genes regulated?
By an enhancer located downstream of H19
How exactly do Igf2 and H19 imprinting genes work?
- Maternal allele: ICR is not methylated, so CTCF binds the imprinting control region (ICR) insulator and blocks long-range interactions between enhancer and IGF2-promoter
- Paternal allele: the CTCF-binding sites in the ICR are methylated and CTCF is unable to bind the ICR. The enhancers can then activate the IGF2 gene while repressors bind H19
Imprinting might arise from selective pressures that differ between males and females.
What is the differnce between maternal and paternal imprinting?
- Maternal imprinting: limits use of maternal resources by baby in utero
- Paternal imprinting: maximizes use of maternal resources by baby in utero
What is an example of an imprinting disorder?
Silver–Russell syndrome
What is Silver–Russell syndrome?
- Pre- and postnatal growth retardation
- Characteristic facial features
- Body asymmetry
- Metabolic, food intake and puberty disorders
What is the cause of SRS?
- SRS often associated with molecular abnormalities of chromosome 11p15, which contains 2 imprinted domains
- The most common underlying mechanisms for SRS are loss of methylation on chromosome 11p15
- Paternal hypomethylation of H19/IGF2 IGDMR -> Reduced paternal IGF2 expression -> growth restriction
What is dosage compensation?
To achieve dosage compensation, one of the two X chromosomes in female mammalian somatic cells is stably silenced by epigenetic processes -> condensed, inactivated X-chromosome (Xi) = Barr body
Which part of the X chromosome is affected by X-Chromosome Inactivation?
- Chromosome-wide gene silencing
- BUT: A subset of X-linked genes escapes XCI and are biallelically expressed
How is the structure of an inactivated X chromosome?
- Compact heterochromatin → a paradigm for facultative heterochromatin
- Positioning close to the nuclear periphery or the nucleolus (Xi) (where as Xa is more central)
- Different shape: Unique 3D bipartite structure (2 megadomains with frequent long-range contacts, separated by a hinge, instead of >100 TADs for the active X (Xa))
What are the epigenetic modifications found in inactivated X chromosomes?
- High levels of DNA methylation
- High levels of H3K9 and H3K27 methylation
- Low levels of histone acetylation
- Low levels of histone H3K4 methylation
- Coated by Xist RNA
When does replication of the inactivated X chromosome occur?
Late replication (in the latter half of the S phase)
Which histone is associated with X chromosome inactivation?
Incorporation of the macroH2A histone variant in its nucleosomes (early indicator of XCI initiation)
What are some effects of the incorporation of macroH2A in inactivated X chromosomes?
- Increased internucleosomal contacts (compared to canonical H2A)
- Inhibition of transcription factor binding
- Inhibition of the activity of the chromatin-remodeling complex SWI/SNF
What does XCI lead to?
<XCI leads to tissue mosaicism
Is XCI a random process?
one of the 2 X chromosomes in a female cell (paternal / maternal) is randomly selected for inactivation during early embryonic development, and maintained throughout the lifetime of that cell and its daughter cells -> mosaic pattern of XCI across different tissues in the body
When does XCI happen?
During early embryonic development
* Biallelic XIST expression (also in male X chromosome) -> might dampen X-linked expression
* Monoallelic expression of XIST is only achieved later in development
Does biallelic expression of XIST happen before XCI?
Yes, in an early embryo - Biallelic XIST expression (also in male X chromosome) -> might dampen X-linked expression
What is an example of X-linked allele expression that results in tissue mosaicism?
Calico cats
How many active X chromosome (Xa) are found per celö?
Only one active X chromosome (Xa) per diploid cell irrespective of the number of X chromosomes in the cell
How does the cell know that more than one X chromosome is present?
XCI implies mechanisms to count the X chromosomes and to randomly select chromosomes for inactivation
What is the condition called in males and females, when an extra X chromosome is present?
- XXY male: Klinefelter
- XXX female: triple X
Where does XCI start?
at the XIC
What is XIC?
XIC = X-inactivation centre: X-chromosome region necessary and sufficient to trigger XCI (counting X chromosomes, randomly choosing and initiating X chromosome inactivation)
Where is XIST found?
XIC contains the XIST locus
What is XIST?
XIST (X inactive-specific transcript) is a non-coding RNA triggering XCI (ncRNA) in female mammals
What functions do XIST RNA have?
- silencing activity
- coating activity
- macro recruitment
What is TISX RNA?
- antisense RNA that regulates XIST expression negatively
- transcribed in the opposite direction of XIST
- plays a key role in ensuring proper XCI dynamics
What is the function of the element LINX?
Repressor of XIST
What is the function of the elements JPX & FTX?
Activators of XIST
What is the function of TSIX RNA?
Negatively regulates XIST expression by antisense transcription
What is the function of the element RNF12?
Activators of XIST
What is the function of Tsix (lnRNA)?
Suppressor of XIST
During X-X pairing (crosstalk between chromosomes), what factors help mediate the pairing?
CTCF & OCT4
What happens during XCI onset?
- On the future Xi, Jpx activates Xist, while Tsix expression is reduced.
- On the future Xa, Tsix remains active, suppressing Xist.
What happens during Xist activation?
- YY1, a transcription factor, helps tether Xist RNA to the nucleation center on the Xi
- RNA Polymerase II facilitates the transcription of Xist
What happens during Xist spreading?
Xist coats the chromosome from which it is expressed („in cis“), first enriched around its own locus and then spreading from 28 specific entry sites distributed along the chromosome at regions that tend to be physically close in 3D space to the Xist gene itself.
What are the key phases of XCI?
- Initiation of XCI:
- Reduction in H4Ac and H3K9Ac
- Loss of transcriptionally active markers like H3Kme1/2/3
- Ejection of RNA Pol II - Recruitment of chromatin regulatory complexes:
- SAFA (Scaffold Attachment Factor A) binds Xist RNA to the chromatin
- SHARP and HDAC3 (Histone Deacetylase 3) are recruited, which deacetylate histones, leading to a repressive chromatin state - Recruitment of Gene Repression Complexes:
- PRC1 adds H2AK119ub1, a histone ubiquitination mark
- PRC2 catalyses H3K27me3, a repressive histone methylation mark
- H3K9me2/3, another repressive marker, is established
- hnRNP K (heterogeneous nuclear ribonucleoprotein K) is involved in recruiting PRC2 to chromatin - Maintenance of XCI (long-term silencing):
- DNA methylation of CpG islands by DNMT (DNA Methyltransferase)
- Incorporation of macroH2A, a histone variant associated with transcriptional silencing
Is the inactivated X chromosome imprinted?
In marsurpials, the inactivated X chromosome is imprinted with the paternal X chromosome being inactive in somatic cells -> Whole chromosome model for parental-origin effects
When does the imprinting of X chromosome inactivation happen in mice?
In mice, X-chromosome inactivation is also imprinted, but only during pre-implantation stages and in extra-embryonic lineages including the placenta.
In mice, random inactivation initiates in all embryonic components around the time of implantation
Euchromatin <–> facultative Heterochromatin
- Chromatin Components:
* Histone variant macroH2A contributes to chromatin structure
* Linker histone H1 stabilizes chromatin organization - Chromatin Modulation:
* Histone-modifying enzymes (e.g., histone acetyltransferases and deacetylases) regulate chromatin accessibility
* Histone methyltransferases (HMTs) and histone ubiquitin ligases modify histones for gene regulation
* ATP-dependent chromatin-remodelling factors influence nucleosome positioning
* DNA methyltransferases (DNMTs) add repressive methylation marks to DNA - Chromatin Trans-Acting Factors:
* Non-coding RNAs guide or recruit chromatin modifiers for regulation
Trans-acting proteins include:
* Polycomb group (PcG) proteins for gene silencing
* Lamin-associated proteins for nuclear structure
* Mediator proteins for transcriptional control
* CTCF, an insulator protein for chromatin boundaries
* PARP-1, involved in chromatin remodelling and DNA repair - Subnuclear Position: Chromatin localization within the nucleus affects its activity
