Editing Cell nucleus (section)

===Other nuclear bodies===

{{main|Nuclear bodies}}

{| class="wikitable" style="float:right; font-size:100%; margin-left:15px;"
|- bgcolor="#efefef"
|+ '''Subnuclear structure sizes'''
|- bgcolor="#efefef"
! style="width: 120px" abbr="name"     |'''Structure name'''
! style="width: 130px" abbr="diameter" |'''Structure diameter'''
! scope="col" | {{nowrap|{{Abbr|Ref.|Reference}}}}
|-
| Cajal bodies || 0.2–2.0&nbsp;μm || <ref name="Cioce">{{cite journal | vauthors = Cioce M, Lamond AI | title = Cajal bodies: a long history of discovery | journal = Annual Review of Cell and Developmental Biology | volume = 21 | pages = 105–31 | year = 2005 | pmid = 16212489 | doi = 10.1146/annurev.cellbio.20.010403.103738 | s2cid = 8807316 | department = Review }}</ref>
|-
|Clastosomes 
|0.2–0.5&nbsp;μm
|<ref name="Lafarga-2002" />
|-
| PIKA || 5&nbsp;μm || <ref name="Pollard">{{cite book | last1 = Pollard | first1 = Thomas D. | first2 = William C. | last2 = Earnshaw | name-list-style = vanc | title = Cell Biology | publisher = Saunders | year = 2004 | location = Philadelphia | isbn = 978-0-7216-3360-2 | url-access = registration | url = https://archive.org/details/cellbiology0000poll }}</ref>
|-
| PML bodies || 0.2–1.0&nbsp;μm || <ref name="Dundr">{{cite journal | vauthors = Dundr M, Misteli T | title = Functional architecture in the cell nucleus | journal = The Biochemical Journal | volume = 356 | issue = Pt 2 | pages = 297–310 | date = June 2001 | pmid = 11368755 | pmc = 1221839 | doi = 10.1042/0264-6021:3560297 | department = Review }}</ref>
|-
| Paraspeckles || 0.5–1.0&nbsp;μm || <ref>{{cite journal | vauthors = Bond CS, Fox AH | title = Paraspeckles: nuclear bodies built on long noncoding RNA | journal = The Journal of Cell Biology | volume = 186 | issue = 5 | pages = 637–44 | date = September 2009 | pmid = 19720872 | pmc = 2742191 | doi = 10.1083/jcb.200906113 | department = Review }}</ref>
|-
| Speckles || 20–25&nbsp;nm || <ref name="Pollard" />
|}
Beyond the nuclear bodies first described by [[Santiago Ramón y Cajal]] above (e.g., nucleolus, nuclear speckles, Cajal bodies) the nucleus contains a number of other nuclear bodies. These include polymorphic interphase karyosomal association (PIKA), promyelocytic leukaemia (PML) bodies, and [[paraspeckle]]s. Although little is known about a number of these domains, they are significant in that they show that the nucleoplasm is not a uniform mixture, but rather contains organized functional subdomains.<ref name="Dundr" />

Other subnuclear structures appear as part of abnormal disease processes. For example, the presence of small intranuclear rods has been reported in some cases of [[nemaline myopathy]]. This condition typically results from mutations in [[actin]], and the rods themselves consist of mutant actin as well as other cytoskeletal proteins.<ref name="Goebel">{{cite journal | vauthors = Goebel HH, Warlo I | title = Nemaline myopathy with intranuclear rods--intranuclear rod myopathy | journal = Neuromuscular Disorders | volume = 7 | issue = 1 | pages = 13–9 | date = January 1997 | pmid = 9132135 | doi = 10.1016/S0960-8966(96)00404-X | s2cid = 29584217 | department = Review }}</ref>

====PIKA and PTF domains====
PIKA domains, or polymorphic interphase karyosomal associations, were first described in microscopy studies in 1991. Their function remains unclear, though they were not thought to be associated with active DNA replication, transcription, or RNA processing.<ref name="Saunders">{{cite journal | vauthors = Saunders WS, Cooke CA, Earnshaw WC | title = Compartmentalization within the nucleus: discovery of a novel subnuclear region | journal = The Journal of Cell Biology | volume = 115 | issue = 4 | pages = 919–31 | date = November 1991 | pmid = 1955462 | pmc = 2289954 | doi = 10.1083/jcb.115.4.919 | department = Primary }}</ref> They have been found to often associate with discrete domains defined by dense localization of the transcription factor PTF, which promotes transcription of [[small nuclear RNA]] (snRNA).<ref name="Pombo">{{cite journal | vauthors = Pombo A, Cuello P, Schul W, Yoon JB, Roeder RG, Cook PR, Murphy S | title = Regional and temporal specialization in the nucleus: a transcriptionally-active nuclear domain rich in PTF, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle | journal = The EMBO Journal | volume = 17 | issue = 6 | pages = 1768–78 | date = March 1998 | pmid = 9501098 | pmc = 1170524 | doi = 10.1093/emboj/17.6.1768 | department = Primary }}</ref>

====PML-nuclear bodies====
[[Promyelocytic leukemia protein]] (PML-nuclear bodies) are spherical bodies found scattered throughout the nucleoplasm, measuring around 0.1–1.0&nbsp;μm. They are known by a number of other names, including nuclear domain 10 (ND10), Kremer bodies, and PML oncogenic domains.<ref name="Zimber">{{cite journal | vauthors = Zimber A, Nguyen QD, Gespach C | title = Nuclear bodies and compartments: functional roles and cellular signalling in health and disease | journal = Cellular Signalling | volume = 16 | issue = 10 | pages = 1085–104 | date = October 2004 | pmid = 15240004 | doi = 10.1016/j.cellsig.2004.03.020 | department = Review }}</ref> PML-nuclear bodies are named after one of their major components, the promyelocytic leukemia protein (PML). They are often seen in the nucleus in association with Cajal bodies and cleavage bodies.<ref name="Dundr"/> Pml-/- mice, which are unable to create PML-nuclear bodies, develop normally without obvious ill effects, showing that PML-nuclear bodies are not required for most essential biological processes.<ref name="Lallemand2010">{{cite journal | vauthors = Lallemand-Breitenbach V, de Thé H | title = PML nuclear bodies | journal = Cold Spring Harbor Perspectives in Biology | volume = 2 | issue = 5 | pages = a000661 | date = May 2010 | pmid = 20452955 | pmc = 2857171 | doi = 10.1101/cshperspect.a000661 | department = Review }}</ref>

====Paraspeckles====
{{Main|Paraspeckle}}
Discovered by Fox et al. in 2002, paraspeckles are irregularly shaped compartments in the interchromatin space of the nucleus.<ref name="Fox_2010">{{cite journal | vauthors = Fox AH, Lamond AI | title = Paraspeckles | journal = Cold Spring Harbor Perspectives in Biology | volume = 2 | issue = 7 | pages = a000687 | date = July 2010 | pmid = 20573717 | pmc = 2890200 | doi = 10.1101/cshperspect.a000687 | department = Review }}</ref>  First documented in HeLa cells, where there are generally 10–30 per nucleus,<ref name="para2">{{cite web | last1 =Fox | first1 =Archa | first2 = Wendy | last2 = Bickmore | name-list-style = vanc | title = Nuclear Compartments: Paraspeckles | publisher = Nuclear Protein Database | year = 2004 | url =http://npd.hgu.mrc.ac.uk/compartments/paraspeckles.html | archive-url = http://webarchive.nationalarchives.gov.uk/20080910110920/http://npd.hgu.mrc.ac.uk/compartments/paraspeckles.html | url-status =dead | archive-date =10 September 2008 | access-date = 6 March 2007 }}</ref> paraspeckles are now known to also exist in all human primary cells, transformed cell lines, and tissue sections.<ref name="para3">{{cite journal | vauthors = Fox AH, Bond CS, Lamond AI | title = P54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in an RNA-dependent manner | journal = Molecular Biology of the Cell | volume = 16 | issue = 11 | pages = 5304–15 | date = November 2005 | pmid = 16148043 | pmc = 1266428 | doi = 10.1091/mbc.E05-06-0587 | department = Primary }}</ref> Their name is derived from their distribution in the nucleus; the "para" is short for parallel and the "speckles" refers to the splicing speckles to which they are always in close proximity.<ref name="para2"/>

Paraspeckles sequester nuclear proteins and RNA and thus appear to function as a molecular sponge<ref name="Nakagawa_2018">{{cite journal | vauthors = Nakagawa S, Yamazaki T, Hirose T | title = Molecular dissection of nuclear paraspeckles: towards understanding the emerging world of the RNP milieu | journal = Open Biology | volume = 8 | issue = 10 | date = October 2018 | page = 180150 | pmid = 30355755 | pmc = 6223218 | doi = 10.1098/rsob.180150 | department = Review }}</ref> that is involved in the regulation of gene expression.<ref name="Pisani_2019">{{cite journal | vauthors = Pisani G, Baron B | title = Nuclear paraspeckles function in mediating gene regulatory and apoptotic pathways | journal = Non-Coding RNA Research | volume = 4 | issue = 4 | pages = 128–134 | date = December 2019 | pmid = 32072080 | pmc = 7012776 | doi = 10.1016/j.ncrna.2019.11.002 | department = Review }}</ref> Furthermore, paraspeckles are dynamic structures that are altered in response to changes in cellular metabolic activity. They are transcription dependent<ref name="Fox_2010" /> and in the absence of RNA Pol II transcription, the paraspeckle disappears and all of its associated protein components  (PSP1, p54nrb, PSP2, CFI(m)68, and PSF) form a crescent shaped perinucleolar cap in the nucleolus. This phenomenon is demonstrated during the cell cycle. In the [[cell cycle]], paraspeckles are present during [[interphase]] and during all of [[mitosis]] except for [[telophase]]. During telophase, when the two daughter nuclei are formed, there is no [[RNA]] Pol II [[Transcription (genetics)|transcription]] so the protein components instead form a perinucleolar cap.<ref name="para3"/>

===={{anchor|Perichromatin fibrils}} Perichromatin fibrils====

Perichromatin fibrils are visible only under electron microscope. They are located next to the transcriptionally active chromatin and are hypothesized to be the sites of active [[precursor mRNA|pre-mRNA]] processing.<ref name="Matera2007_NatureMolCellBio" />

====Clastosomes====

Clastosomes are small nuclear bodies (0.2–0.5&nbsp;μm) described as having a thick ring-shape due to the peripheral capsule around these bodies.<ref name="Lafarga-2002">{{cite journal | vauthors = Lafarga M, Berciano MT, Pena E, Mayo I, Castaño JG, Bohmann D, Rodrigues JP, Tavanez JP, Carmo-Fonseca M | display-authors = 6 | title = Clastosome: a subtype of nuclear body enriched in 19S and 20S proteasomes, ubiquitin, and protein substrates of proteasome | journal = Molecular Biology of the Cell | volume = 13 | issue = 8 | pages = 2771–82 | date = August 2002 | pmid = 12181345 | pmc = 117941 | doi = 10.1091/mbc.e02-03-0122 | citeseerx = 10.1.1.321.6138 | department = Primary }}</ref> This name is derived from the Greek ''klastos'' ([[wikt:κλαστός|κλαστός]]), broken and ''soma'' ([[wikt:σῶμα|σῶμα]]), body.<ref name="Lafarga-2002" /> Clastosomes are not typically present in normal cells, making them hard to detect. They form under high [[Proteolysis|proteolytic]] conditions within the nucleus and degrade once there is a decrease in activity or if cells are treated with [[proteasome inhibitor]]s.<ref name="Lafarga-2002" /><ref>{{cite journal | vauthors = Kong XN, Yan HX, Chen L, Dong LW, Yang W, Liu Q, Yu LX, Huang DD, Liu SQ, Liu H, Wu MC, Wang HY | display-authors = 6 | title = LPS-induced down-regulation of signal regulatory protein {alpha} contributes to innate immune activation in macrophages | journal = The Journal of Experimental Medicine | volume = 204 | issue = 11 | pages = 2719–31 | date = October 2007 | pmid = 17954568 | pmc = 2118489 | doi = 10.1084/jem.20062611 | department = Primary }}</ref> The scarcity of clastosomes in cells indicates that they are not required for [[proteasome]] function.<ref name="Carmo-Fonseca-2010">{{cite journal | vauthors = Carmo-Fonseca M, Berciano MT, Lafarga M | title = Orphan nuclear bodies | journal = Cold Spring Harbor Perspectives in Biology | volume = 2 | issue = 9 | pages = a000703 | date = September 2010 | pmid = 20610547 | pmc = 2926751 | doi = 10.1101/cshperspect.a000703 | department = Review }}</ref> [[Osmotic shock|Osmotic stress]] has also been shown to cause the formation of clastosomes.<ref>{{cite journal | vauthors = Sampuda KM, Riley M, Boyd L | title = Stress induced nuclear granules form in response to accumulation of misfolded proteins in Caenorhabditis elegans | journal = BMC Cell Biology | volume = 18 | issue = 1 | pages = 18 | date = April 2017 | pmid = 28424053 | pmc = 5395811 | doi = 10.1186/s12860-017-0136-x | department = Primary | doi-access = free }}</ref> These nuclear bodies contain catalytic and regulatory subunits of the proteasome and its substrates, indicating that clastosomes are sites for degrading proteins.<ref name="Carmo-Fonseca-2010" />