Transcriptional memory explained

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[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, activity of chromatin remodeling complexes, propagation of H3K4me2 and H3K36me3 histone modifications, occupancy of the H3.3 histone variant, as well as binding of nuclear pore components.[14] Moreover, locally bound cohesin was shown to inhibit establishment of transcriptional memory in human cells during interferon gamma stimulation.[15]

Notes and References

  1. Acar. Murat. Becskei. Attila. van Oudenaarden. Alexander. 2005-05-12. Enhancement of cellular memory by reducing stochastic transitions. Nature. 435. 7039. 228–232. 10.1038/nature03524. 1476-4687. 15889097. 2005Natur.435..228A. 4429383.
  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. 10.1101/gad.1506607. 0890-9369. 1847716. 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. 10.1371/journal.pbio.0050081. 1544-9173. 1828143. 17373856 . free .
  4. Ding. Yong. Fromm. Michael. Avramova. Zoya. January 2012. Multiple exposures to drought 'train' transcriptional responses in Arabidopsis. Nature Communications. 3. 1. 740. 10.1038/ncomms1732. 22415831. 2041-1723. 2012NatCo...3..740D. free.
  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. 10.1186/1471-2229-13-229. 1471-2229. 3879431. 24377444 . free .
  6. Sani. Emanuela. Herzyk. Pawel. Perrella. Giorgio. Colot. Vincent. Amtmann. Anna. Anna Amtmann. 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. 10.1186/gb-2013-14-6-r59. 1474-760X. 3707022. 23767915 . free .
  7. Foster. Simmie L.. Hargreaves. Diana C.. Diana Hargreaves. Medzhitov. Ruslan. 2007-05-30. Gene-specific control of inflammation by TLR-induced chromatin modifications. Nature. 447. 7147. 972–978. 10.1038/nature05836. 17538624. 0028-0836. 2007Natur.447..972F. 4426398.
  8. 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. 10.1128/MCB.00906-09. 0270-7306. 2849471. 20123968.
  9. Light. William H.. Freaney. Jonathan. Sood. Varun. Thompson. Abbey. D'Urso. Agustina. Horvath. Curt M.. Brickner. Jason H.. 2013-03-26. Misteli. Tom. A Conserved Role for Human Nup98 in Altering Chromatin Structure and Promoting Epigenetic Transcriptional Memory. PLOS Biology. 11. 3. e1001524. 10.1371/journal.pbio.1001524. 1545-7885. 3608542. 23555195 . free .
  10. 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. 10.1073/pnas.1720930115. 30201712. 6166839. 2018PNAS..115E9162K . 0027-8424. free .
  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. 10.7554/eLife.16691. 2050-084X. 4951200. 27336723 . free .
  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. 10.1534/genetics.117.201632. 1943-2631. 5560796. 28607146.
  13. 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. 10.15252/embj.201592593. 1460-2075. 4718455. 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. 10.1016/j.molcel.2017.02.020. 1097-4164. 28366641. 7439321. free.
  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. 10.1016/j.molcel.2020.10.005. 7657446. 33108759. 225100808. 1097-2765. free.

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