User:Avouzas/sandbox

Significance
Chromatin remodeling plays a central role in the regulation of gene expression by providing the transcription machinery with dynamic access to an otherwise tightly packaged genome. Further, nucleosome movement by chromatin remodelers is essential to several important biological processes, including chromosome assembly and segregation, DNA replication and repair, embryonic development and pluripotency, and cell-cycle progression. Deregulation of chromatin remodeling causes loss of transcriptional regulation at these critical check-points required for proper cellular functions, and thus causes various disease syndromes, including cancer.

Response to DNA damage
Chromatin relaxation is one of the earliest cellular responses to DNA damage. The relaxation appears to be initiated by PARP1, whose accumulation at DNA damage is half complete by 1.6 seconds after DNA damage occurs. This is quickly followed by accumulation of chromatin remodeler Alc1, which has an ADP-ribose–binding domain, allowing it to be quickly attracted to the product of PARP1. The maximum recruitment of Alc1 occurs within 10 seconds of DNA damage. About half of the maximum chromatin relaxation, presumably due to action of Alc1, occurs by 10 seconds. PARP1 action at the site of a double-strand break allows recruitment of the two DNA repair enzymes MRE11 and NBS1. Half maximum recruitment of these two DNA repair enzymes takes 13 seconds for MRE11 and 28 seconds for NBS1.

Another process of chromatin relaxation, after formation of a DNA double-strand break, employs γH2AX, the phosphorylated form of the H2AX protein. The histone variant H2AX constitutes about 10% of the H2A histones in human chromatin. γH2AX (phosphorylated on serine 139 of H2AX) was detected at 20 seconds after irradiation of cells (with DNA double-strand break formation), and half maximum accumulation of γH2AX occurred in one minute. The extent of chromatin with phosphorylated γH2AX is about two million base pairs at the site of a DNA double-strand break.

γH2AX does not, by itself, cause chromatin decondenstaion, but within seconds of irradiation the protein “Mediator of the DNA damage checkpoint 1” (MDC1) specifically attaches to γH2AX. This is accompanied by simultaneous accumulation of RNF8 protein and the DNA repair protein NBS1 which bind to MDC1 as MDC1 attaches to γH2AX. RNF8 mediates extensive chromatin decondensation, through its subsequent interaction with CHD4 protein , a component of the nucleosome remodeling and deacetylase complex NuRD. CHD4 accumulation at the site of the double-strand break is rapid, with half-maximum accumulation occurring by 40 seconds after irradiation.

The fast initial chromatin relaxation upon DNA damage (with rapid initiation of DNA repair) is followed by a slow recondensation, with chromatin recovering a compaction state close to its predamage level in ∼ 20 min.

Cancer
Various forms of chromatin remodeling are involved at crucial cell growth and division steps, such as cell-cycle progression, DNA repair and chromosome segregation. Therefore, disruption of regular chromatin remodeling during such steps could lead to tumor development. Certain mutations in some chromatin remodelers, such as the SWI/SNF chromatin remodeling complex, could favor self-sufficiency in cell growth and escape from growth-regulatory cell signals - two important hallmarks of cancer.
 * Inactivating mutations in SMARCB1, formerly known as hSNF5/INI1 and a component of the human SWI/SNF remodeling complex have been found in large number of rhabdoid tumors, commonly affecting pediatric population . Similar mutations are also present in other childhood cancers, such as choroid plexus carcinoma, medulloblastoma and in some acute leukemias. Further, mouse knock-out studies strongly support SMARCB1 as a tumor suppressor protein. Since the original observation of SMARCB1 mutations in rhabdoid tumors, several more subunits of the human SWI/SNF chromatin remodeling complex have been found mutated in a wide range of neoplasms.
 * PML-RAR fusion protein in acute myeloid leukemia recruits histone deacetylases. This leads to repression of gene responsible for myelocytes to differentiate, leading to leukemia.
 * Tumor suppressor Rb protein functions by the recruitment of the human homologs of the SWI/SNF enzymes BRG1, histone deacetylase and DNA methyltransferase. Mutations in BRG1 are reported in several cancers causing loss of tumor suppressor action of Rb.
 * Recent reports indicate DNA hypermethylation in the promoter region of major tumor suppressor genes in several cancers. Although few mutations are reported in histone methyltransferases yet, correlation of DNA hypermethylation and histone H3 lysine-9 methylation has been reported in several cancers, mainly in colorectal and breast cancers.
 * Mutations in Histone Acetyl Transferases (HAT) p300 (missense and truncating type) are most commonly reported in colorectal, pancreatic, breast and gastric carcinomas. Loss of heterozygosity in coding region of p300 (chromosome 22q13) is present in large number of glioblastomas.
 * Further, HATs have diverse role as transcription factors beside having histone acetylase activity, e.g., HAT subunit, hADA3 may act as an adaptor protein linking transcription factors with other HAT complexes. In the absence of hADA3, TP53 transcriptional activity is significantly reduced, suggesting role of hADA3 in activating TP53 function in response to DNA-damage.
 * Similarly, TRRAP, the human homolog to yeast Tra1, has been shown to directly interact with c-Myc and E2F1 - known oncoproteins.

Suggested new section for Chromatin remodeling
wiki education program. Grad

LncRnas
The development of advanced sequencing technologies in the recent years has provided us with a more clear picture of what is being transcribed in the human genome. Despite only 2% of our DNA carrying protein-coding information, it is now clear that over 70% of the human genome is being transcribed. A large part of that 70% codes for long non-coding RNAs (lncRNAs), whose function we just started to explore in the last decade. However, it has been suggested that some are indirectly associated with different cancers through their association with chromatin-modification complexes, such as histone methyltransferases and the polycomb repressive complex 2 (PRC2). There is a number of lncRNAs that have been shown to associate with a number of different alterations in chromatin architecture in various cancers. These discoveries could provide with important insight as to the mechanisms of cancer development and metastasis as well as provide with diagnostic tools for certain forms of cancer.

One lncRNA associated with cancer is HOTAIR. Studies have shown that there is a correlation between HOTAIR and cancer metastasis. HOTAIR has been shown to regulate polycomp repressive complex 2 (PRC2) to affect chromatin organization and remodeling. HOTAIR levels could also be used as a potential prognostic tool in certain types of cancer, including colorectal cancers among others. Other ways lncRNAs could affect cancer development could be more indirect. For example, lncRNA HULC affects histone acetyl-transferase P300, by controlling levels of certain microRNAs and cAMP response element-binding protein (CREB), leading to alteration in deacetylation and methylation patterns in liver cancer. Additionally, some lncRNAs can affect the density of chromatin. One such lncRNA is XIST RNA, which is correlated with heterochromatin defects in BRCA1-related breast cancers. Finally, in some cases the absence of certain lncRNAs can be correlated with chromatin architecture alterations. In the case of certain colorectal cancers, a decrease in the expression of the LIT1/KCNQ1IT1 lncRNA is correlated with a decrease in H3K4 dimethylation and an enrichment in H3K9 dimethylation.

Therapeutic intervention
Epigenetic instability caused by deregulation in chromatin remodeling is studied in several cancers, including breast cancer, colorectal cancer, pancreatic cancer. Such instability largely cause widespread silencing of genes with primary impact on tumor-suppressor genes. Hence, strategies are now being tried to overcome epigenetic silencing with synergistic combination of HDAC inhibitors or HDI and DNA-demethylating agents. HDIs are primarily used as adjunct therapy in several cancer types. HDAC inhibitors can induce p21 (WAF1) expression, a regulator of p53's tumor suppressoractivity. HDACs are involved in the pathway by which the retinoblastoma protein (pRb) suppresses cell proliferation. Estrogen is well-established as a mitogenic factor implicated in the tumorigenesis and progression of breast cancer via its binding to the estrogen receptor alpha (ERα). Recent data indicate that chromatin inactivation mediated by HDAC and DNA methylation is a critical component of ERα silencing in human breast cancer cells. Started pivotal phase II clinical trials Current front-runner candidates for new drug targets are Histone Lysine Methyltransferases (KMT) and Protein Arginine Methyltransferases (PRMT).
 * Approved usage:
 * Vorinostat was licensed by the U.S. FDA in October 2006 for the treatment of cutaneous T cell lymphoma (CTCL).
 * Romidepsin (trade name Istodax) was licensed by the US FDA in Nov 2009 for cutaneous T-cell lymphoma (CTCL).
 * Phase III Clinical trials:
 * Panobinostat (LBH589) is in clinical trials for various cancers including a phase III trial for cutaneous T cell lymphoma (CTCL).
 * Valproic acid (as Mg valproate) in phase III trials for cervical cancer and ovarian cancer.
 * Belinostat (PXD101) has had a phase II trial for relapsed ovarian cancer, and reported good results for T cell lymphoma.
 * Click here for more

Other disease syndromes

 * ATRX-syndrome (α-thalassemia X-linked mental retardation) and α-thalassemia myelodysplasia syndrome are caused by mutations in ATRX, a SNF2-related ATPase with a PHD.
 * CHARGEsyndrome, an autosomal dominant disorder, has been linked recently to haploinsufficiency of CHD7, which encodes the CHD family ATPase CHD7.

Aging
As pointed out by Liu et al., defects in DNA repair, with accumulation of DNA damage, underlie premature aging syndromes (also see DNA damage theory of aging). Deficiencies in chromatin remodeling, reducing DNA repair, appear to directly contribute to the process of aging.