Transcriptional memory

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Principle of transcriptional memory. A pulse of an inducer (priming) results in expression of target genes, which subsides upon withdrawal. During a window of no induction (window of memory), some genes maintain a poised but transcriptionally silent state that results in a stronger gene activation upon a second challenge. Transcriptional memory.png
Principle of transcriptional memory. A pulse of an inducer (priming) results in expression of target genes, which subsides upon withdrawal. During a window of no induction (window of memory), some genes maintain a poised but transcriptionally silent state that results in a stronger gene activation upon a second challenge.

Transcriptional memory is a biological phenomenon, initially discovered in yeast, [1] during which cells primed with a particular cue show increased rates of gene expression after re-stimulation at a later time. This event was shown to take place: in yeast during growth in galactose [1] [2] and inositol starvation; [3] plants during environmental stress; [4] [5] [6] in mammalian cells during LPS [7] and interferon [8] [9] [10] induction. Prior work has shown that certain characteristics of chromatin may contribute to the poised transcriptional state allowing faster re-induction. These include: activity of specific transcription factors, [11] [12] [13] retention of RNA polymerase II at the promoters of poised genes, [9] activity of chromatin remodeling complexes, [2] propagation of H3K4me2 [8] [13] and H3K36me3 [10] histone modifications, occupancy of the H3.3 histone variant, [10] as well as binding of nuclear pore components. [9] [14] Moreover, locally bound cohesin was shown to inhibit establishment of transcriptional memory in human cells during interferon gamma stimulation. [15]

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Chromatin is a complex of DNA and protein found in 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 roles in reinforcing the DNA during cell division, preventing DNA damage, and regulating gene expression and DNA replication. During mitosis and meiosis, chromatin facilitates proper segregation of the chromosomes in anaphase; the characteristic shapes of chromosomes visible during this stage are the result of DNA being coiled into highly condensed chromatin.

<span class="mw-page-title-main">Histone</span> Family proteins package and order the DNA into structural units called nucleosomes.

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. Nucleosomes in turn are wrapped into 30-nanometer fibers that form tightly packed chromatin. Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene regulation and DNA replication. Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if completely stretched out; however, when wound about histones, this length is reduced to about 90 micrometers (0.09 mm) of 30 nm diameter chromatin fibers.

<span class="mw-page-title-main">Epigenetics</span> Study of DNA modifications that do not change its sequence

In biology, epigenetics is the study of heritable traits, or a stable change of cell function, that happen without changes to the DNA sequence. The Greek prefix epi- in epigenetics implies features that are "on top of" or "in addition to" the traditional genetic mechanism of inheritance. Epigenetics usually involves a change that is not erased by cell division, and affects the regulation of gene expression. Such effects on cellular and physiological phenotypic traits may result from environmental factors, or be part of normal development. They can lead to cancer.

<span class="mw-page-title-main">Euchromatin</span> Lightly packed form of chromatin that is enriched in genes

Euchromatin is a lightly packed form of chromatin that is enriched in genes, and is often under active transcription. Euchromatin stands in contrast to heterochromatin, which is tightly packed and less accessible for transcription. 92% of the human genome is euchromatic.

Heterochromatin is a tightly packed form of DNA or condensed DNA, which comes in multiple varieties. These varieties lie on a continuum between the two extremes of constitutive heterochromatin and facultative heterochromatin. Both play a role in the expression of genes. Because it is tightly packed, it was thought to be inaccessible to polymerases and therefore not transcribed; however, according to Volpe et al. (2002), and many other papers since, much of this DNA is in fact transcribed, but it is continuously turned over via RNA-induced transcriptional silencing (RITS). Recent studies with electron microscopy and OsO4 staining reveal that the dense packing is not due to the chromatin.

<span class="mw-page-title-main">Histone acetyltransferase</span> Enzymes that catalyze acyl group transfer from acetyl-CoA to histones

Histone acetyltransferases (HATs) are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl-CoA to form ε-N-acetyllysine. DNA is wrapped around histones, and, by transferring an acetyl group to the histones, genes can be turned on and off. In general, histone acetylation increases gene expression.

<span class="mw-page-title-main">Cohesin</span> Protein complex that regulates the separation of sister chromatids during cell division

Cohesin is a protein complex that mediates sister chromatid cohesion, homologous recombination, and DNA looping. Cohesin is formed of SMC3, SMC1, SCC1 and SCC3. Cohesin holds sister chromatids together after DNA replication until anaphase when removal of cohesin leads to separation of sister chromatids. The complex forms a ring-like structure and it is believed that sister chromatids are held together by entrapment inside the cohesin ring. Cohesin is a member of the SMC family of protein complexes which includes Condensin, MukBEF and SMC-ScpAB.

Histone methylation is a process by which methyl groups are transferred to amino acids of histone proteins that make up nucleosomes, which the DNA double helix wraps around to form chromosomes. Methylation of histones can either increase or decrease transcription of genes, depending on which amino acids in the histones are methylated, and how many methyl groups are attached. Methylation events that weaken chemical attractions between histone tails and DNA increase transcription because they enable the DNA to uncoil from nucleosomes so that transcription factor proteins and RNA polymerase can access the DNA. This process is critical for the regulation of gene expression that allows different cells to express different genes.

The histone code is a hypothesis that the transcription of genetic information encoded in DNA is in part regulated by chemical modifications to histone proteins, primarily on their unstructured ends. Together with similar modifications such as DNA methylation it is part of the epigenetic code. Histones associate with DNA to form nucleosomes, which themselves bundle to form chromatin fibers, which in turn make up the more familiar chromosome. Histones are globular proteins with a flexible N-terminus that protrudes from the nucleosome. Many of the histone tail modifications correlate very well to chromatin structure and both histone modification state and chromatin structure correlate well to gene expression levels. The critical concept of the histone code hypothesis is that the histone modifications serve to recruit other proteins by specific recognition of the modified histone via protein domains specialized for such purposes, rather than through simply stabilizing or destabilizing the interaction between histone and the underlying DNA. These recruited proteins then act to alter chromatin structure actively or to promote transcription. For details of gene expression regulation by histone modifications see table below.

<span class="mw-page-title-main">Histone-modifying enzymes</span> Type of enzymes

Histone-modifying enzymes are enzymes involved in the modification of histone substrates after protein translation and affect cellular processes including gene expression. To safely store the eukaryotic genome, DNA is wrapped around four core histone proteins, which then join to form nucleosomes. These nucleosomes further fold together into highly condensed chromatin, which renders the organism's genetic material far less accessible to the factors required for gene transcription, DNA replication, recombination and repair. Subsequently, eukaryotic organisms have developed intricate mechanisms to overcome this repressive barrier imposed by the chromatin through histone modification, a type of post-translational modification which typically involves covalently attaching certain groups to histone residues. Once added to the histone, these groups elicit either a loose and open histone conformation, euchromatin, or a tight and closed histone conformation, heterochromatin. Euchromatin marks active transcription and gene expression, as the light packing of histones in this way allows entry for proteins involved in the transcription process. As such, the tightly packed heterochromatin marks the absence of current gene expression.

Chromatin remodeling is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression. Such remodeling is principally carried out by 1) covalent histone modifications by specific enzymes, e.g., histone acetyltransferases (HATs), deacetylases, methyltransferases, and kinases, and 2) ATP-dependent chromatin remodeling complexes which either move, eject or restructure nucleosomes. Besides actively regulating gene expression, dynamic remodeling of chromatin imparts an epigenetic regulatory role in several key biological processes, egg cells DNA replication and repair; apoptosis; chromosome segregation as well as development and pluripotency. Aberrations in chromatin remodeling proteins are found to be associated with human diseases, including cancer. Targeting chromatin remodeling pathways is currently evolving as a major therapeutic strategy in the treatment of several cancers.

Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. The field is analogous to genomics and proteomics, which are the study of the genome and proteome of a cell. Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence. Epigenomic maintenance is a continuous process and plays an important role in stability of eukaryotic genomes by taking part in crucial biological mechanisms like DNA repair. Plant flavones are said to be inhibiting epigenomic marks that cause cancers. Two of the most characterized epigenetic modifications are DNA methylation and histone modification. Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in differentiation/development and tumorigenesis. The study of epigenetics on a global level has been made possible only recently through the adaptation of genomic high-throughput assays.

<span class="mw-page-title-main">Biomarkers of aging</span> Type of biomarkers

Biomarkers of aging are biomarkers that could predict functional capacity at some later age better than chronological age. Stated another way, biomarkers of aging would give the true "biological age", which may be different from the chronological age.

<span class="mw-page-title-main">Nuclear organization</span> Spatial distribution of chromatin within a cell nucleus

Nuclear organization refers to the spatial distribution of chromatin within a cell nucleus. There are many different levels and scales of nuclear organisation. Chromatin is a higher order structure of DNA.

<span class="mw-page-title-main">Robin Allshire</span>

Robin Campbell Allshire is Professor of Chromosome Biology at University of Edinburgh and a Wellcome Trust Principal Research Fellow. His research group at the Wellcome Trust Centre for Cell Biology focuses on the epigenetic mechanisms governing the assembly of specialised domains of chromatin and their transmission through cell division.

H3K9me2 is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the di-methylation at the 9th lysine residue of the histone H3 protein. H3K9me2 is strongly associated with transcriptional repression. H3K9me2 levels are higher at silent compared to active genes in a 10kb region surrounding the transcriptional start site. H3K9me2 represses gene expression both passively, by prohibiting acetylation as therefore binding of RNA polymerase or its regulatory factors, and actively, by recruiting transcriptional repressors. H3K9me2 has also been found in megabase blocks, termed Large Organised Chromatin K9 domains (LOCKS), which are primarily located within gene-sparse regions but also encompass genic and intergenic intervals. Its synthesis is catalyzed by G9a, G9a-like protein, and PRDM2. H3K9me2 can be removed by a wide range of histone lysine demethylases (KDMs) including KDM1, KDM3, KDM4 and KDM7 family members. H3K9me2 is important for various biological processes including cell lineage commitment, the reprogramming of somatic cells to induced pluripotent stem cells, regulation of the inflammatory response, and addiction to drug use.

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.

H4K16ac is an epigenetic modification to the DNA packaging protein Histone H4. It is a mark that indicates the acetylation at the 16th lysine residue of the histone H4 protein.

H3K36ac is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the acetylation at the 36th lysine residue of the histone H3 protein.

Transgenerational epigenetic inheritance in plants involves mechanisms for the passing of epigenetic marks from parent to offspring that differ from those reported in animals. There are several kinds of epigenetic markers, but they all provide a mechanism to facilitate greater phenotypic plasticity by influencing the expression of genes without altering the DNA code. These modifications represent responses to environmental input and are reversible changes to gene expression patterns that can be passed down through generations. In plants, transgenerational epigenetic inheritance could potentially represent an evolutionary adaptation for sessile organisms to quickly adapt to their changing environment.

References

  1. 1 2 Acar, Murat; Becskei, Attila; van Oudenaarden, Alexander (2005-05-12). "Enhancement of cellular memory by reducing stochastic transitions". Nature. 435 (7039): 228–232. Bibcode:2005Natur.435..228A. doi:10.1038/nature03524. ISSN   1476-4687. PMID   15889097. S2CID   4429383.
  2. 1 2 Kundu, Sharmistha; Horn, Peter J.; Peterson, Craig L. (2007-04-15). "SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster". Genes & Development. 21 (8): 997–1004. doi:10.1101/gad.1506607. ISSN   0890-9369. PMC   1847716 . PMID   17438002.
  3. Brickner, Donna Garvey; Cajigas, Ivelisse; Fondufe-Mittendorf, Yvonne; Ahmed, Sara; Lee, Pei-Chih; Widom, Jonathan; Brickner, Jason H (April 2007). "H2A.Z-Mediated Localization of Genes at the Nuclear Periphery Confers Epigenetic Memory of Previous Transcriptional State". PLOS Biology. 5 (4): e81. doi: 10.1371/journal.pbio.0050081 . ISSN   1544-9173. PMC   1828143 . PMID   17373856.
  4. Ding, Yong; Fromm, Michael; Avramova, Zoya (January 2012). "Multiple exposures to drought 'train' transcriptional responses in Arabidopsis". Nature Communications. 3 (1): 740. Bibcode:2012NatCo...3..740D. doi: 10.1038/ncomms1732 . ISSN   2041-1723. PMID   22415831.
  5. Ding, Yong; Liu, Ning; Virlouvet, Laetitia; Riethoven, Jean-Jack; Fromm, Michael; Avramova, Zoya (2013). "Four distinct types of dehydration stress memory genes in Arabidopsis thaliana". BMC Plant Biology. 13 (1): 229. doi: 10.1186/1471-2229-13-229 . ISSN   1471-2229. PMC   3879431 . PMID   24377444.
  6. Sani, Emanuela; Herzyk, Pawel; Perrella, Giorgio; Colot, Vincent; Amtmann, Anna (June 2013). "Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome". Genome Biology. 14 (6): R59. doi: 10.1186/gb-2013-14-6-r59 . ISSN   1474-760X. PMC   3707022 . PMID   23767915.
  7. Foster, Simmie L.; Hargreaves, Diana C.; Medzhitov, Ruslan (2007-05-30). "Gene-specific control of inflammation by TLR-induced chromatin modifications". Nature. 447 (7147): 972–978. Bibcode:2007Natur.447..972F. doi:10.1038/nature05836. ISSN   0028-0836. PMID   17538624. S2CID   4426398.
  8. 1 2 Gialitakis, M.; Arampatzi, P.; Makatounakis, T.; Papamatheakis, J. (2010-04-15). "Gamma Interferon-Dependent Transcriptional Memory via Relocalization of a Gene Locus to PML Nuclear Bodies". Molecular and Cellular Biology. 30 (8): 2046–2056. doi:10.1128/MCB.00906-09. ISSN   0270-7306. PMC   2849471 . PMID   20123968.
  9. 1 2 3 Light, William H.; Freaney, Jonathan; Sood, Varun; Thompson, Abbey; D'Urso, Agustina; Horvath, Curt M.; Brickner, Jason H. (2013-03-26). Misteli, Tom (ed.). "A Conserved Role for Human Nup98 in Altering Chromatin Structure and Promoting Epigenetic Transcriptional Memory". PLOS Biology. 11 (3): e1001524. doi: 10.1371/journal.pbio.1001524 . ISSN   1545-7885. PMC   3608542 . PMID   23555195.
  10. 1 2 3 Kamada, Rui; Yang, Wenjing; Zhang, Yubo; Patel, Mira C.; Yang, Yanqin; Ouda, Ryota; Dey, Anup; Wakabayashi, Yoshiyuki; Sakaguchi, Kazuyasu (2018-09-10). "Interferon stimulation creates chromatin marks and establishes transcriptional memory". Proceedings of the National Academy of Sciences. 115 (39): E9162–E9171. Bibcode:2018PNAS..115E9162K. doi: 10.1073/pnas.1720930115 . ISSN   0027-8424. PMC   6166839 . PMID   30201712.
  11. D'Urso, Agustina; Takahashi, Yoh-Hei; Xiong, Bin; Marone, Jessica; Coukos, Robert; Randise-Hinchliff, Carlo; Wang, Ji-Ping; Shilatifard, Ali; Brickner, Jason H. (23 June 2016). "Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory". eLife. 5. doi: 10.7554/eLife.16691 . ISSN   2050-084X. PMC   4951200 . PMID   27336723.
  12. Sood, Varun; Cajigas, Ivelisse; D'Urso, Agustina; Light, William H.; Brickner, Jason H. (August 2017). "Epigenetic Transcriptional Memory of GAL Genes Depends on Growth in Glucose and the Tup1 Transcription Factor in Saccharomyces cerevisiae". Genetics. 206 (4): 1895–1907. doi:10.1534/genetics.117.201632. ISSN   1943-2631. PMC   5560796 . PMID   28607146.
  13. 1 2 Lämke, Jörn; Brzezinka, Krzysztof; Altmann, Simone; Bäurle, Isabel (2016-01-18). "A hit-and-run heat shock factor governs sustained histone methylation and transcriptional stress memory". The EMBO Journal. 35 (2): 162–175. doi:10.15252/embj.201592593. ISSN   1460-2075. PMC   4718455 . PMID   26657708.
  14. Pascual-Garcia, Pau; Debo, Brian; Aleman, Jennifer R.; Talamas, Jessica A.; Lan, Yemin; Nguyen, Nha H.; Won, Kyoung J.; Capelson, Maya (2017-04-06). "Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts". Molecular Cell. 66 (1): 63–76.e6. doi: 10.1016/j.molcel.2017.02.020 . ISSN   1097-4164. PMC   7439321 . PMID   28366641.
  15. Siwek, Wojciech; Tehrani, Sahar S.H.; Mata, João F.; Jansen, Lars E.T. (November 2020). "Activation of Clustered IFNγ Target Genes Drives Cohesin-Controlled Transcriptional Memory". Molecular Cell. 80 (3): 396–409.e6. doi: 10.1016/j.molcel.2020.10.005 . ISSN   1097-2765. PMC   7657446 . PMID   33108759. S2CID   225100808.