Nuclear Speckles

Abstract

Nuclear speckles, also known as interchromatin granule clusters, are nuclear domains enriched in pre-mRNA splicing factors, located in the interchromatin regions of the nucleoplasm of mammalian cells. When observed by immunofluorescence microscopy, they usually appear as 20-50 irregularly shaped structures that vary in size. Speckles are dynamic structures, and their constituents can exchange continuously with the nucleoplasm and other nuclear locations, including active transcription sites. Studies on the composition, structure, and dynamics of speckles have provided an important paradigm for understanding the functional organization of the nucleus and the dynamics of the gene expression machinery.T he mammalian cell nucleus is a highly compartmentalized yet extremely dynamic organelle (reviewed in Misteli 2001a;Spector 2006;Zhao et al. 2009). Many nuclear factors are localized in distinct structures, such as speckles, paraspeckles, nucleoli, Cajal bodies, polycomb bodies, and promyelocytic leukemia bodies and show punctate staining patterns when analyzed by indirect immunofluorescence microscopy (reviewed in Lamond et al. 1998;Spector 2001;Spector 2006).In mammalian cells the pre-mRNA splicing machinery, including small nuclear ribonucleoprotein particles (snRNPs), spliceosome subunits, and other non-snRNP protein splicing factors, shows a punctate nuclear localization pattern that is usually termed "a speckled pattern" but has also been referred to as "SC35 domains (Wansink et al. 1993)" or "splicing factor compartments (Phair et al. 2000)" (Figs. 1 and 2). The first detailed description of the nuclear domains that we presently refer to as nuclear speckles was reported by Santiago Ramó n y Cajal in 1910 (Ramó n y Cajal 1910; reviewed in Lafarga et al. 2009). Ramó n y Cajal used acid aniline stains to identify structures he referred to as "grumos hialinas" (literally "translucent clumps"). The term "speckles" was first put forth in 1961 by J. Swanson Beck (Beck 1961) upon examination of rat liver sections immunolabeled with the serum of individuals with autoimmune disorders. Although the connection was not made at the time, these speckles had been identified two years earlier by Hewson Swift (Swift 1959) at the electron microscopic level and called interchromatin particles. Swift observed that these particles were not randomly distributed but that they occurred in localized "clouds," and cytochemical analysis indicated that they contained RNA (Swift 1959). However, the first link between pre-mRNA splicing and nuclear speckles or interchromatin granule clusters came from an examination of the distribution of snRNPs using anti-splicing factor-specific antibodies, demonstrating a speckled distribution pattern of snRNPs in cell nuclei (Lerner et al. 1981;Perraud et al. 1979;Spector et al. 1983).It is now clear that much of the punctate localization of splicing factors observed by immunofluorescence microscopy corresponds to the presence of these factors in nuclear speckles of variable size and irregular shape that...

Transcriptionally correlated subcellular dynamics of MBNL1 during lens development and their implication for the molecular pathology of myotonic dystrophy type 1

“…Of particular interest is the non--uniform distribution of MBNL1 within the nucleus in some, but not all, cells where MBNL1 accumulates in structures resembling splicing factor 'speckles' (figure 2A arrowheads). While this is not unexpected, as MBNL1 has a well--documented role as an alternative splicing factor and splicing factors characteristically accumulate in speckles [25], it has not been documented previously. We therefore sought to confirm the identity of the structures accumulating MBNL1.…”

“…A smaller proportion of cells show clear co--localization of MBNL1 with nuclear speckles containing splicing factors. Accumulation in splicing speckles is characteristic of many splicing factors, with the speckles thought to serve as a reservoir from which they are recruited to participate in splicing at sites of transcription when required [25]. The diffuse localization of MBNL1, while uncharacteristic for a pre mRNA splicing factor, is similar to the distribution seen for snRNP proteins associated with the minor U11/12 spliceosome, present at 1/100 th the amount of the major spliceosome [36--39] .…”

Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

“…Subnuclear domains, so called nuclear speckles, correspond to sites with active transcription in the interchromatin regions. They are connected with the presence of splicing factors, but less with the accumulation of other factors participating on RNA processing in microscope localization studies (Spector & Lamond, 2011; Reddy et al ., 2012). Analogously to their animal orthologues (Liu et al ., 2014; Ping et al ., 2014), plant writers also show a similar punctate pattern (Zhong et al ., 2008) and co‐localize with the splicing factor SR34‐RFP.…”

“…This splicing factor, as well as the co‐localizing writers, shows a more diffuse pattern in the meristematic cells, whereas in the cells above the elongation zone the speckle pattern is more prevalent. This likely coincides with differential transcriptional activities in rapidly dividing and differentiated cells, similar to observations from animal systems (Tillemans et al ., 2006; Spector & Lamond, 2011; Reddy et al ., 2012). Because m 6 A affects splicing in mammals and D. melanogaster (Liu et al ., 2014; Ping et al ., 2014; Alarcón et al ., 2015a; Haussmann et al ., 2016; Lence et al ., 2016) possibly by recruiting splicing factors (Xiao et al ., 2016), it is interesting to speculate whether m 6 A could also regulate splicing in plants.…”

FTO levels affect RNA modification and the transcriptome

“…They contain transcription factors, 3 0 -end RNA processing factors, translation regulation factors and the large subunit of RNA polymerase II. 28,29 Jia et al have shown also that the inhibition of transcription changes the nucleoplasmic distribution of FTO, which becomes more concentrated at speckles. Of note, we observed different pattern of nucleoplasmic FTO staining in cells with different proliferation rates.…”