Cell Nucleus

Vidisha Tripathi, University of Illinois at Urbana‐Champaign, Urbana, Illinois, USA
Kannanganattu V Prasanth, University of Illinois at Urbana‐Champaign, Urbana, Illinois, USA

Published online: July 2011

DOI: 10.1002/9780470015902.a0001337.pub2

The cell nucleus is a double membrane-bound organelle that contains the genetic information of the cell packaged in the form of chromatin. The nucleus is a characteristic feature of most eukaryotic cells.

The nucleus is considered to be one of the most important structures of eukaryotic cells as it serves the function of information storage, retrieval and duplication of genetic information. It is a double membrane-bound organelle that harbours the genetic material in the form of chromatin. It consists of a dynamic mix of nonmembranous subcompartments of varying functional capacity. The specific features of a cell nucleus, especially in terms of the nature and distribution of the subnuclear compartments and the positioning of the chromosomes, depend upon their differentiated state in the organism. The key functions of the cell nucleus include deoxyribonucleic acid replication and further to control gene expression during the cell cycle. Transcription and further post-transcriptional processing of pre-messenger ribonucleic acids (mRNAs) occur inside the nucleus and the mature mRNAs are transported into the cytoplasm where the translational events occur. Thus, nucleus provides functional compartmentalisation inside the cell allowing higher levels of gene regulation.

Key Concepts:

  • The cell nucleus contains nonmembranous distinct substructures that are characterised by having a specific subset of proteins and RNA.
  • The nuclear envelope is a highly regulated membrane barrier that allows the compartmentalisation of the nucleus from the cytoplasm.
  • Nuclear pore complexes (NPCs) are large proteinaceous channels that perforate the nuclear membrane and allow transport of molecules into and out of the nucleus. In general, proteins destined for import contain nuclear localisation signal (NLS) and proteins destined for export contain nuclear export signal (NES).
  • Genes are located in chromosomes inside the nucleus, which consists of a single long DNA that is highly coiled and folded by proteins. A chromosome is confined to a distinct ‘territory’ within the interphase nucleus.
  • Histone modifications of the nucleosomes differentiate between the euchromatic and heterochromatic chromatin states and allow higher order of gene regulation.
  • The genetic material, DNA is transcribed into pre-messenger RNA (pre-mRNAs) inside the nucleus. Further intron splicing of the pre-mRNA takes place according to a precise and complex arrangement of proteins and ribonuclear particles. The mature mRNA is exported to the cytoplasm for translation.
  • Gene expression is regulated at several steps including pre-mRNA processing, nucleoplasmic export and degradation of RNA.
  • The clearest substructure in the nucleus in most eukaryotes is the nucleolus, which is the site of rDNA transcription and ribosome biosynthesis. Apart from that it is also involved in biogenesis of other RNP complexes, mRNA surveillance, stress sensing and control of cell proliferation.
  • Nuclear speckles are highly dynamic, irregularly shaped nuclear domains enriched with pre-mRNA splicing factors.
  • SR family splicing factors are phosphoproteins that regulate both constitutive and alternative splicing and also the export of mRNAs from the nucleus to cytoplasm.
  • Nuclear-retained regulatory noncoding RNAs (ncRNAs) constitute a fraction of ncRNAs and play pivotal role in the control of gene expression, affecting chromatin structure, post-transcriptional modifications and stability of RNA.

Keywords: nuclear domains; transcription; chromatin; noncoding RNA; nuclear-retained RNA; pre-mRNA splicing; nuclear lamina

Figure 1. Nuclear domains immunolabelled with specific antibodies (green). (a) Immunostaining by lamin B1 representing nuclear lamina. (b) Heterochromatin labelled with antibody recognising HP1. (c) Immunostaining by nucleolin representing Nucleolus. (d) Nuclear speckles labelled with antibody-recognising SON protein. (e) Immunolocalisation with P54/NRB representing paraspeckles. (f) Immunolacalisation with p80 coilin representing Cajal bodies. The DNA is counterstained with DAPI (Blue). Bar, 10 m.
Figure 2. Nuclear-retained regulatory RNAs. (a) RNA-FISH using probe against the Xist RNA. (b) RNA-FISH analysis reveal Nuclear speckle localisation of MALAT1 RNA and (c) Paraspeckle localisation of NEAT1 RNA and (d) CTN-RNA. (e) Hsrw RNA-FISH representing its localisation to omega-speckles. (f) RNA-FISH reveals the nuclear distribution of Gomafu ncRNA and (g) GRC-RNA. DNA is counterstained with DAPI (Blue). Bar, 10 m. (a) (Xist-RNA), (f) (Gomafu-RNA), courtesy of Shinichi Nakagawa Riken, Japan. (e) (Hsrw), courtesy of Lakhotia SC, Banaras Hindu University, Varanasi, India.
Figure 3. Patterns of DNA replication identified in HeLa cells by BrdU labelling followed by immunofluorescence. (a) Early S-phase pattern, the sites of replicating DNA are distributed throughout the nucleoplasm. However, there is no apparent labelling of the nucleolus and nucleolar periphery. (b–d) Mid S-phase pattern. There is a decrease in internal and an increase in peripheral sites of replication. The sites of replication are associated with the periphery of the nucleus and nucleolus. (e and f) Late S-phase, in this pattern the sites of replication are characterised by large areas of replicating DNA that span portions of the interior as well as smaller areas of replication at the periphery of the nucleus. Bar, 5 m. Images courtesy of Dr Prasanth SG, UIUC, Urbana-Champaign, IL, USA.
close
 References
    Anderson DJ and Hetzer MW (2007) Nuclear envelope formation by chromatin-mediated reorganization of the endoplasmic reticulum. Nature Cell Biology 9: 1160–1166.
    Anderson DJ and Hetzer MW (2008) Reshaping of the endoplasmic reticulum limits the rate for nuclear envelope formation. Journal of Cell Biology 182: 911–924.
    Bannister AJ and Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Research 21: 381–395.
    Bartke T and Kouzarides T (2011) Decoding the chromatin modification landscape. Cell Cycle 10: 182.
    Bernardi R and Pandolfi PP (2007) Structure, dynamics and functions of promyelocytic leukaemia nuclear bodies. Nature Reviews in Molecular and Cellular Biology 8: 1006–1016.
    Biamonti G (2004) Nuclear stress bodies: a heterochromatin affair? Nature Reviews in Molecular and Cellular Biology 5: 493–498.
    Boisvert FM, van Koningsbruggen S, Navascués J and Lamond AI (2007) The multifunctional nucleolus. Nature Reviews Molecular and Cellular Biology 8: 574–585.
    Burke B and Stewart CL (2006) The laminopathies: the functional architecture of the nucleus and its contribution to disease. Annual Reviews of Genomics and Human Genetics 7: 369–405.
    Capelson M and Hetzer MW (2009) The role of nuclear pores in gene regulation, development and disease. EMBO Reports 10: 697–705.
    Chen LL and Carmichael GG (2009) Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Molecular Cell 35: 467–478.
    Clemson CM, Hutchinson JN, Sara SA et al. (2009) An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Molecular Cell 33: 717–726.
    Cmarko D, Smigova J, Minichova L and Popov A (2008) Nucleolus: the ribosome factory. Histology and Histopathology 23: 1291–1298.
    Cohen TV, Hernandez L and Stewart CL (2008) Functions of the nuclear envelope and lamina in development and disease. Biochemical Society Transactions 36: 1329–1334.
    Cremer T and Cremer M (2010) Chromosome territories. Cold Spring Harbor Perspectives in Biology 2: a003889.
    D'Angelo MA and Hetzer MW (2008) Structure, dynamics and function of nuclear pore complexes. Trends in Cell Biology 18: 456–466.
    Dechat T, Adam SA, Taimen P et al. (2010) Nuclear lamins. Cold Spring Harbour Perspectives in Biology 2: a000547.
    Dechat T, Pfleghaar K, Sengupta K et al. (2008) Nuclear lamins: major factors in the structural organization and function of the nucleus and chromatin. Genes & Development 22: 832–853.
    Denegri M, Chiodi I, Corioni M et al. (2001) Stress-induced nuclear bodies are sites of accumulation of pre-mRNA processing factors. Molecular Biology of the Cell 12: 3502–3514.
    Finlan LE, Sproul D, Thomson I et al. (2008) Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genetics 4: e1000039.
    Fox AH, Lam YW, Leung AK et al. (2002) Paraspeckles: a novel nuclear domain. Current Biology 12: 13–25.
    Fox AH and Lamond AI (2010) Paraspeckles. Cold Spring Harbor Perspectives in Biology 2: a000687.
    Fridkin A, Penkner A, Jantsch V and Gruenbaum Y (2009) SUN-domain and KASH-domain proteins during development, meiosis and disease. Cellular and Molecular Life Sciences 66: 1518–1533.
    book Gall JG (1996) Views of the Cell: A Pictorial History. Bethesda, MD: American Society for Cell Biology.
    Galiova G, Bartova E, Raska I et al. (2008) Chromatin changes induced by lamin A/C deficiency and the histone deacetylase inhibitor trichostatin A. European Journal of Cell Biology 87: 291–303.
    Guttinger S, Laurell E and Kutay U (2009) Orchestrating nuclear envelope disassembly and reassembly during mitosis. Nature Reviews in Molecular and Cellular Biology 10: 178–191.
    book Harris H (1999) The Birth of the Cell. New Haven: Yale University Press.
    Huang S, Deerinck MH, Ellisman MH and Spector DL (1994) In vivo analysis of the stability and transport of nuclear poly(A) RNA. Journal of Cell Biology 126: 877–899.
    Hung T and Chang HY (2010) Long noncoding RNA in genome regulation: Prospects and mechanisms. RNA Biology 7: 582–585.
    Kouzarides T (2007) Chromatin modifications and their function. Cell 128: 693–705.
    Lamond AI and Spector DL (2003) Nuclear speckles: A model for nuclear organelles. Nature Reviews in Molecular and Cellular Biology 4: 605–612.
    Lutz RJ, Trujillo MA, Denham KS, Wenger L and Sinensky M (1992) Nucleoplasmic localization of prelamin A: Implications for prenylation-dependent lamin A assembly into the nuclear lamina. Proceedings of National Academy of Sciences of the USA 89: 3000–3004.
    Ma L, Tsai MY, Wang S et al. (2009) Requirement for Nudel and dynein for assembly of the lamin B spindle matrix. Nature Cell Biology 11: 247–256.
    Mattout A, Goldberg M, Tzur Y et al. (2007) Specific and conserved sequences in D. melanogaster and C. elegans lamins and histone H2A mediate the attachment of lamins to chromosomes. Journal of Cell Sciences 120: 77–85.
    Méchali M (2010) Eukaryotic DNA replication origins: many choices for appropriate answers. Nature Reviews in Molecular and Cellular Biology 11: 728–738.
    Meyer H, Drozdowska A and Dobrynin G (2010) A role for Cdc48/p97 and Aurora B in controlling chromatin condensation during exit from mitosis. Biochemistry and Cell Biology 88: 23–28.
    Neilan EG (2009) Laminopathies, other progeroid disorders, and aging: common pathogenic themes and possible treatments. American Journal of Medical Genetics 149A: 563–566.
    Nizami Z, Deryusheva S and Gall JG (2010) The Cajal body and histone locus body. Cold Spring Harbor Perspectives in Biology 2: a000653.
    Pollock C and Huang S (2009) The perinucleolar compartment. Journal of Cellular Biochemistry 107: 189–193.
    Popov N and Gil J (2010) Epigenetic regulation of the INK4b-ARF-INK4a locus: in sickness and in health. Epigenetics 5: 685–690.
    Prasanth KV, Prasanth SG, Xuan Z et al. (2005) Regulating gene expression through RNA nuclear retention. Cell 123: 249–263.
    Prokocimer M, Davidovich M, Nissim-Rafinia M et al. (2009) Nuclear lamins: key regulators of nuclear structure and activities. Journal of Cellular and Molecular Medicine 13: 1059–1085.
    Reddy KL, Zullo JM, Bertolino E and Singh H (2008) Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452: 243–247.
    Shimi T, Pfleghaar K, Kojima S et al. (2008) The A- and B-type nuclear lamin networks: microdomains involved in chromatin organization and transcription. Genes & Development 22: 3409–3421.
    Sone M, Hayashi T, Tarui H et al. (2007) The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. Journal of Cell Science 120: 2498–2506.
    Stanek D and Neugebauer KM (2006) The Cajal body: a meeting place for spliceosomal snRNPs in the nuclear maze. Chromosoma 115: 343–354.
    Sunwoo H, Dinger ME, Wilusz JE et al. (2009) MEN 1/b nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Research 19: 347–359.
    Tamaru H (2010) Confining euchromatin/heterochromatin territory: jumonji crosses the line. Genes & Development 24: 1465–1478.
    Tran EJ and Wente SR (2006) Dynamic nuclear pore complexes: life on the edge. Cell 125: 1041–1053.
    Tripathi V, Ellis J, Shen Z et al. (2010) Nuclear-retained non-coding RNA regulates alternative splicing by modulating SR splicing factor phosphorylation. Molecular Cell 39: 925–938.
    Tsai MY, Wang S, Heidinger JM et al. (2006) A mitotic lamin B matrix induced by RanGTP required for spindle assembly. Science 311: 1887–1893.
    Wente SR and Rout MP (2010) The nuclear pore complex and nuclear transport. Cold Spring Harbour Perspectives in Biology 2: a000562.
    Wilusz JE, Sunwoo H and Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes & Development 23: 1494–1504.
    Zhang R and Adams PD (2007) Heterochromatin and its relationship to cell senescence and cancer therapy. Cell Cycle 6: 784–789.
    Zhao K, Harel A, Stuurman N et al. (1996) Binding of matrix attachment regions to nuclear lamin is mediated by the rod domain and depends on the lamin polymerization state. FEBS Letters 380: 161–164.
    Zhao R, Bodnar MS and Spector DL (2009) Nuclear neighborhoods and gene expression. Current Opinion in Genetics and Development 19: 172–179.
    Zheng R, Shen Z, Tripathi V et al. (2010) Polypurine-repeat-containing RNAs: a novel class of long non-coding RNA in mammalian cells. Journal of Cell Sciences 123: 3734–3744.
 Further Reading
    Austin CM and Bellini M (2010) The dynamic landscape of the cell nucleus. Molecular Reproduction & Development 77: 19–28.
    Dundr M and Misteli T (2010) Biogenesis of Nuclear Bodies. Cold Spring Harbor Perspectives in Biology 2: a000711.
    Groth A, Rocha W, Verreault A and Almouzni G (2007) Chromatin challenges during DNA replication and repair. Cell 128: 721–733.
    book Hirose T (2010) "Emerging roles of long noncoding RNAs in gene expression and intracellular organization". In: Erdmann VA and Barciszewski J (eds) RNA Technologies and their Applications, 1st edn, vol. XVI, pp. 369–391. Heidelberg: Springer.
    Lallemand-Breitenbach V and de The H (2010) PML nuclear bodies. Cold Spring Harbor Perspectives in Biology 2: a000661.
    Matera GA, Izaguire-Sierra M, Praveen K and Rajendra TK (2009) Nuclear bodies: random aggregates of sticky proteins or crucibles of macromolecular assembly? Developmental Cell 17: 639–647.
    Nunez E, Fu X-D and Rosenfeld MG (2009) Nuclear organization in the 3D space of the nucleus-cause or consequence? Current Opinions in Genetics and Development 19: 424–436.
    Pederson T (2010) The nucleolus. Cold Spring Harbor Perspectives in Biology 2: a000638.
    Prasanth KV and Spector DL (2007) Eukaryotic regulatory RNAs: an answer to the genome complexity conundrum. Genes and Development 21: 11–42.
    Ruault M, Marion Dubarry and Taddei A (2008) Re-positioning genes to the nuclear envelope in mammalian cells: impact on transcription. Trends in Genetics 24: 574–581.
    Woodcock CL and Ghosh RP (2010) Chromatin higher order structure and dynamics. Cold Spring Harbor Perspectives in Biology 2: a000596.

Related Sub-Topics:

Basic Cell Biology, Protein, RNA and DNA | Cell Compartments and Cellular Organelles | Transcription of DNA | Transcriptional Regulation | Chromosomes and Chromatin Modifications | Noncoding RNA | Posttranscriptional Modification
Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

Article Title: Cell Nucleus
 
How to Cite close
Tripathi, Vidisha, and Prasanth, Kannanganattu V(Jul 2011) Cell Nucleus. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001337.pub2]