Pioneer Factor
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Pioneer factors are
transcription factor In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription (genetics), transcription of genetics, genetic information from DNA to messenger RNA, by binding t ...
s that can directly bind condensed
chromatin Chromatin is a complex of DNA and protein found in eukaryote, eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures. This prevents the strands from becoming tangled and also plays important r ...
. They can have positive and negative effects on transcription and are important in recruiting other transcription factors and
histone In biology, histones are highly basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei and in most Archaeal phyla. They act as spools around which DNA winds to create structural units called nucleosomes ...
modification enzymes as well as controlling
DNA methylation DNA methylation is a biological process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence. When located in a gene promoter (genetics), promoter, DNA methylati ...
. They were first discovered in 2002 as factors capable of binding to target sites on nucleosomal DNA in compacted chromatin and endowing competency for gene activity during hepatogenesis. Pioneer factors are involved in initiating
cell differentiation Cellular differentiation is the process in which a stem cell changes from one type to a differentiated one. Usually, the cell changes to a more specialized type. Differentiation happens multiple times during the development of a multicellular ...
and activation of cell-specific
gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s. This property is observed in histone fold-domain containing transcription factors (fork head box (FOX) and NF-Y) and other transcription factors that use zinc finger(s) for DNA binding (Groucho TLE, Gal4, and GATA). The
eukaryotic cell The eukaryotes ( ) constitute the domain of Eukaryota or Eukarya, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, seaweeds, and many unicellular organisms are eukaryotes. They constitute a major group of Out ...
condenses its genome into tightly packed chromatin and
nucleosome A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone, histone proteins and resembles thread wrapped around a bobbin, spool. The nucleosome ...
s. This ability saves space in the
nucleus Nucleus (: nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom *Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA Nucleu ...
for only actively transcribed
gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s and hides unnecessary or detrimental genes from being transcribed. Access to these condensed regions is done by chromatin remodelling by either balancing histone modifications or directly with pioneer factors that can loosen the chromatin themselves or as a flag recruiting other factors. Pioneer factors are not necessarily required for assembly of the transcription apparatus and may dissociate after being replaced by other factors.


Active rearrangement

Pioneer factors can also actively affect transcription by directly opening up condensed chromatin in an ATP-independent process. This is a common trait of fork head box factors (which contain a winged helix DNA-binding domain that mimics the DNA-binding domain of the linker H1 histone), and NF-Y (whose NF-YB and NF-YC subunits contain histone-fold domains similar to those of the core histones H2A/H2B).


Fork head box factors

The similarity to
histone H1 Histone H1 is one of the five main histone protein families which are components of chromatin in eukaryotic cells. Though highly conserved, it is nevertheless the most variable histone in sequence across species. Structure Metazoan H1 prote ...
explains how fork head factors are able to bind chromatin by interacting with the major groove of only the one available side of DNA wrapped around a nucleosome. Fork head domains also have a helix that confers sequence specificity unlike linker histone. The C terminus is associated with higher mobility around the nucleosome than linker histone, displacing it and rearranging nucleosomal landscapes effectively. This active re-arrangement of the nucleosomes allows for other transcription factors to bind the available DNA. In thyroid cell differentiation FoxE binds to compacted chromatin of the
thyroid peroxidase Thyroid peroxidase, also called thyroperoxidase (TPO), thyroid specific peroxidase or iodide peroxidase, is an enzyme expressed mainly in the thyroid where it is secreted into colloid. Thyroid peroxidase oxidizes iodide ions to form iodine atoms ...
promoter and opens it for NF1 binding.


NF-Y

NF-Y is a heterotrimeric complex composed of NF-YA, NF-YB, and NF-YC subunits. The key structural feature of the NF-Y/DNA complex is the minor-groove interaction of its DNA binding domain-containing subunit NF-YA, which induces an ~80° bend in the DNA. NF-YB and NF-YC interact with DNA through non-specific histone-fold domain-DNA contacts. NF-YA's unique DNA-binding mode and NF-YB/NF-YC's nucleosome-like properties of non-specific DNA binding impose sufficient spatial constraints to induce flanking nucleosomes to slide outward, making nearby recognition sites for other transcription factors accessible.


Passive factors

Pioneer factors can function passively, by acting as a bookmark for the cell to recruit other transcription factors to specific genes in condensed chromatin. This can be important for priming the cell for a rapid response as the enhancer is already bound by a pioneer transcription factor giving it a head start towards assembling the
transcription preinitiation complex The preinitiation complex (abbreviated PIC) is a complex of approximately 100 proteins that is necessary for the transcription (genetics), transcription of protein-coding genes in eukaryotes and archaea. The preinitiation complex positions RNA po ...
.
Hormone A hormone (from the Ancient Greek, Greek participle , "setting in motion") is a class of cell signaling, signaling molecules in multicellular organisms that are sent to distant organs or tissues by complex biological processes to regulate physio ...
responses are often quickly induced in the cell using this priming method such as with the
estrogen receptor Estrogen receptors (ERs) are proteins found in cell (biology), cells that function as receptor (biochemistry), receptors for the hormone estrogen (17β-estradiol). There are two main classes of ERs. The first includes the intracellular estrogen ...
. Another form of priming is when an enhancer is simultaneously bound by activating and repressing pioneer factors. This balance can be tipped by dissociation of one of the factors. In hepatic cell differentiation the activating pioneer factor FOXA1 recruits a
repressor In molecular genetics, a repressor is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers. A DNA-binding repressor blocks the attachment of RNA polymerase to the ...
, grg3, that prevents transcription until the repressor is down-regulated later on in the differentiation process.
In a direct role pioneer factors can bind an enhancer and recruit activation complex that will modify the chromatin directly. The change in the chromatin changes the affinity, decreasing the affinity of the pioneer factor such that it is replaced by a transcription factor that has a higher affinity. This is a mechanism for the cell to switch a gene on was observed with
glucocorticoid receptor The glucocorticoid receptor (GR or GCR) also known by its gene name ''NR3C1'' ( nuclear receptor subfamily 3, group C, member 1) is the steroid receptor for glucocorticoids such as cortisol. The GR is expressed in almost every cell in the bod ...
recruiting modification factors that then modify the site to bind activated estrogen receptor which was coined as a “bait and switch” mechanism.


Epigenetic effects

Pioneer factors can exhibit their greatest range of effects on transcription through the modulation of epigenetic factors by recruiting activating or repressing histone modification enzymes and controlling CpG methylation by protecting specific
cysteine Cysteine (; symbol Cys or C) is a semiessential proteinogenic amino acid with the chemical formula, formula . The thiol side chain in cysteine enables the formation of Disulfide, disulfide bonds, and often participates in enzymatic reactions as ...
residues. This has effects on controlling the timing of transcription during cell differentiation processes.


Histone modification

Histone modification is a well-studied mechanism to transiently adjust chromatin density. Pioneer factors can play a role in this by binding specific enhancers and flagging histone modification enzymes to that specific gene. Repressive pioneer factors can inhibit transcription by recruiting factors that modify histones that further tighten the chromatin. This is important to limit gene expression to specific cell types and has to be removed only when cell differentiation begins. FoxD3 has been associated as a repressor of both
B-cell B cells, also known as B lymphocytes, are a type of the lymphocyte subtype. They function in the humoral immunity component of the adaptive immune system. B cells produce antibody molecules which may be either secreted or inserted into the plasm ...
and melanocytic cell differentiation pathways, maintaining repressive histone modifications where bound, that have to be overcome to start differentiation. Pioneer factors can also be associated with recruiting transcription-activating histone modifications. Enzymes that modify H3K4 with mono and di-methylation are associated with increasing transcription and have been shown to bind pioneer factors. In B cell differentiation PU.1 is necessary to signal specific histones for activating H3K4me1 modifications that differentiate hematopoietic stem cells into either the B-cell or macrophage lineage. FoxA1 binding induces HSK4me2 during neuronal differentiation of
pluripotent Cell potency is a cell's ability to differentiate into other cell types. The more cell types a cell can differentiate into, the greater its potency. Potency is also described as the gene activation potential within a cell, which like a continuum ...
stem cells as well as the loss of DNA methylation. SOX9 recruits histone modification enzymes MLL3 and MLL4 to deposit
H3K4me1 H3K4me1 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the mono-methylation at the 4th lysine residue of the histone H3 protein and often associated with gene enhancers. Nomenclature H3K4me1 i ...
prior to the opening of enhancers in developing hair follicle and basal cell carcinoma.


DNA methylation

Pioneer factors can also affect transcription and differentiation through the control of DNA methylation. Pioneer factors that bind to CpG islands and cytosine residues block access to methyltransferases. Many eukaryotic cells have CpG islands in their promoters that can be modified by methylation having adverse effects on their ability to control transcription. This phenomenon is also present in promoters without CpG islands where single cytosine residues are protected from methylation until further cell differentiation. An example is FoxD3 preventing methylation of a cytosine residue in Alb1 enhancer, acting as a place holder for FoxA1 later in hepatic as well as in CpG islands of genes in
chronic lymphocytic leukemia Chronic lymphocytic leukemia (CLL) is a type of cancer that affects the blood and bone marrow. In CLL, the bone marrow makes too many lymphocytes, which are a type of white blood cell. In patients with CLL, B cell lymphocytes can begin to colle ...
. For stable control of methylation state the cytosine residues are covered during
mitosis Mitosis () is a part of the cell cycle in eukaryote, eukaryotic cells in which replicated chromosomes are separated into two new Cell nucleus, nuclei. Cell division by mitosis is an equational division which gives rise to genetically identic ...
, unlike most other transcription factors, to prevent methylation. Studies have shown that during mitosis 15% of all interphase FoxA1 binding sites were bound. The protection of cytosine methylation can be quickly removed allowing for rapid induction when a signal is present.


Other pioneer factors

A well studied pioneer factor family is the Groucho-related (Gro/TLE/Grg) transcription factors that often have a negative effect on transcription. These chromatin binding domains can span up to 3-4 nucleosomes. These large domains are scaffolds for further protein interactions and also modify the chromatin for other pioneer factors such as FoxA1 which has been shown to bind to Grg3. Transcription factors with
zinc finger A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. The term ''zinc finger'' was originally coined to describe the finger-like appearance of a ...
DNA binding domains, such as the GATA family and glucocorticoid receptor. The zinc finger domains do not appear to bind nucleosomes well and can be displaced by FOX factors. In the skin epidermis, SOX family transcription factor,
SOX9 Transcription factor SOX-9 is a protein that in humans is encoded by the ''SOX9'' gene. Function SOX-9 recognizes the sequence CCTTGAG along with other members of the HMG-box class DNA-binding domain, DNA-binding proteins. It is expressed by ...
, also behaves as a pioneer factor that governs hair follicle cell fate and can reprogram epidermal stem cells to a hair follicle fate.


Role in cancer

The ability of pioneer factors to respond to extracellular signals to differentiate cell type has been studied as a potential component of hormone-dependent cancers. Hormones such as
estrogen Estrogen (also spelled oestrogen in British English; see spelling differences) is a category of sex hormone responsible for the development and regulation of the female reproductive system and secondary sex characteristics. There are three ...
and IGFI are shown to increase pioneer factor concentration leading to a change in transcription. Known pioneer factors such as FoxA1, PBX1, TLE, AP2, GATA factors 2/ 3/ 4, and PU.1 have been associated with hormone-dependent cancer . FoxA1 is necessary for estrogen and androgen mediated hepatocarcinogenesis and is a defining gene for ER+ luminal breast cancer, as is another pioneer factor GATA3. FOXA1 particularly is expressed in 90% of breast cancer metastases and 89% of metastatic prostate cancers. In the breast cancer cell line,
MCF-7 MCF-7 is a breast cancer cell line isolated in 1970 from a 69-year-old woman. MCF-7 is the acronym of Michigan Cancer Foundation-7, referring to the institute in Detroit where the cell line was established in 1973 by Herbert Soule and co-workers ...
, it was found that FoxA1 was bound to 50% of estrogen receptor binding sites independent of estrogen presence. High expression of pioneer factors is associated with poor prognosis with the exception of breast cancer where FoxA1 is associated with a stronger outcome.
The correlation between pioneer factors and cancer has led to prospective therapeutic targeting. In knockdown studies in the MCF-7 breast cancer cell line it was found that decreasing pioneer factors FoxA1 and AP2 decreased ER signalling. Other fork head proteins have been associated with cancer, including
FoxO3 Forkhead box O3, also known as FOXO3 or FOXO3a, is a human protein encoded by the ''FOXO3'' gene. Function FOXO3 belongs to the O subclass of the forkhead family of transcription factors which are characterized by a distinct fork head DNA- ...
and FoxM that repress the cell survival pathways Ras and PPI3K/AKT/IKK. Drugs such as
Paclitaxel Paclitaxel, sold under the brand name Taxol among others, is a chemotherapy medication used to treat ovarian cancer, esophageal cancer, breast cancer, lung cancer, Kaposi's sarcoma, cervical cancer, and pancreatic cancer. It is administered b ...
,
Imatinib Imatinib, sold under the brand names Gleevec and Glivec (both marketed worldwide by Novartis) among others, is an oral targeted therapy medication used to treat cancer. Imatinib is a small molecule inhibitor targeting multiple tyrosine kinases ...
, and
doxorubicin Doxorubicin, sold under the brand name Adriamycin among others, is a chemotherapy medication used to treat cancer. This includes breast cancer, bladder cancer, Kaposi's sarcoma, lymphoma, and acute lymphocytic leukemia. It is often used toge ...
which activate FoxO3a or its targets are being used. Modification to modulate related factors with pioneer activity is a topic of interest in the early stages as knocking down pioneer factors may have toxic effects through alteration of the lineage pathways of healthy cells.


References

{{Reflist, 33em Transcription factors Protein families Gene expression