Rhythmic SAF-A Binding Underlies Circadian Transcription of the <i>Bmal1</i> Gene

Onishi, Yoshiaki; Hanai, Syuji; Ohno, Tomoya; Hara, Yasuhiro; Ishida, Norio

doi:10.1128/mcb.02227-07

Cited by 30 publications

(67 citation statements)

References 48 publications

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“…Previous reports have indicated that SAF-A interacts with gene promoters and its interaction is controlled by external factors for example circadian rhythm (Ahmad and Lingrel, 2005;Gao et al, 2005;Onishi et al, 2008;Zhao et al, 2009 (Kim and Nikodem, 1999;Kukalev et al, 2005). Using in situ PLA and co-IP we confirm that SAF-A interacts with RNA pol II in ES cells.…”

supporting

confidence: 69%

SAF-A Has a Role in Transcriptional Regulation ofOct4in ES Cells Through Promoter Binding

Vizlin‐Hodzic

Johansson

Ryme

et al. 2011

Cellular Reprogramming

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Methodologies to reprogram somatic cells into patient-specific pluripotent cells, which could potentially be used in personalized drug discovery and cell replacement therapies, are currently under development. Oct4 activation is essential for successful reprogramming and pluripotency of embryonic stem (ES) cells, albeit molecular details of Oct4 activation are not completely understood. Here we report that endogenous SAF-A is involved in regulation of Oct4 expression, binds the Oct4 proximal promoter in ES cells, and dissociates from the promoter upon early differentiation induced by LIF withdrawal. Depletion of SAF-A decreases Oct4 expression even in the presence of LIF, and results in an increase of the mesodermal marker Brachyury. The overexpression of wild-type human SAF-A rescues the mouse knock-down phenotype and results in increased Oct4 level. We also demonstrate that endogenous SAF-A interacts with the C-terminal domain (CTD) of endogenous RNA polymerase II and that the interaction is independent of CTD phosphorylation and mRNA. Moreover, we show that SAF-A exist in complexes with transcription factors Sox2 and Oct4 as well as STAT3 in ES cells. The number of endogenous SAF-A:Oct4 and SAF-A:Sox2 complexes decreases upon LIF depletion. These discoveries allow us to propose a model for activation of Oct4 transcription.

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supporting

confidence: 69%

SAF-A Has a Role in Transcriptional Regulation ofOct4in ES Cells Through Promoter Binding

Vizlin‐Hodzic

Johansson

Ryme

et al. 2011

Cellular Reprogramming

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“…Perhaps as a binder of both DNA and RNA, SP120 plays multiple roles in transcriptional regulation, both in repression and activation (23)(24)(25)(26). The protein appears to be a pleiotropic regulator of gene expression and is very likely to take an important part in additional systems, as well.…”

Section: Discussionmentioning

confidence: 99%

Regulation of DNA Topoisomerase IIβ through RNA-dependent Association with Heterogeneous Nuclear Ribonucleoprotein U (hnRNP U)

Kawano

Miyaji

Ichiyasu

et al. 2010

Journal of Biological Chemistry

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Recent studies suggest that DNA topoisomerase II␤ (topo II␤) is involved in transcriptional activation of certain genes, which assumes accurate targeting of the enzyme to its action site. The target selection may be achieved by cooperation with unknown regulatory factors. To seek out such factors, we looked for proteins associated with the enzyme in differentiating cerebellar neurons. Antibody against topo II␤ co-precipitated RNA-binding proteins including PSF, NonO/p54nrb, as well as hnRNP U/SAF-A/SP120. Reconstitution experiments with tag-purified proteins showed that topo II␤ associates stoichiometrically with SP120 in the presence of RNA that was co-purified with SP120. The most effective RNA species for the complex formation was a subset of cellular polyadenylated RNAs. The C-terminal 187-residue domain of SP120 was necessary and sufficient for the association with both topo II␤ and the endogenous RNA. The RNA isolated from the tag-purified SP120 inhibited the relaxation of supercoiled DNA by topo II␤. When the enzyme associates with SP120, however, the inhibition was abolished and the catalytic property was modulated to more processive mode, which may prolong its residence time at the genomic target site. Furthermore, the presence of SP120 was required for the stable expression of topo II␤ in vivo. Thus, SP120 regulates the enzyme in dual ways. DNA topoisomerase II (topo II)2 can be described as an enzyme with two different catalytic activities, deoxyribonuclease and DNA ligase. Between the cleavage and religation of one duplex DNA (G-segment), another duplex (T-segment) is transferred through the gate between the cleaved ends that are held through a covalent linkage to the tyrosine residues of two identical subunits (1). Multiple cycles of these events dissipate the supercoiling or intertwining structures in substrate DNA. Thus, the enzyme plays a major role in cellular processes such as DNA replication, transcription, and recombination (2). Topo II orthologs are widely distributed in organisms from bacteria to mammals and two paralogs, named ␣ and ␤, were first identified in human cells (3). These paralogs (isozymes) that are present in most vertebrates show similar enzymatic properties in vitro but their expression is regulated quite differently. Topo II␣ is essential in cell proliferation because it catalyzes the segregation of daughter chromosomes at the mitotic phase. This role is played by a unique topo II in lower eukaryotes. In contrast, the biological function of topo II␤ had been totally ambiguous until we compared the isozyme expression patterns in developing cerebellar cortex (4, 5). As expected, topo II␣ is the predominant isozyme expressed in proliferating precursors of granule neurons. When cells begin to differentiate after the final cell division, the isozyme expression pattern switches from topo II␣ to topo II␤. Later studies with cultured granule neurons and topo II-specific inhibitors revealed that the activity of topo II␤ is required for the transcriptional activation of a subset of g...

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“…Both Xist RNA and SAF-A have been detected in the nuclear matrix fraction after removal of chromatin (Clemson et al, 1996;Helbig and Fackelmayer, 2003). Saf-A has been implicated in many processes, including transcription, RNA transport, DNA replication and circadian rhythm (Onishi et al, 2008). Saf-A is required for cell proliferation and a hypomorphic mutation in mice causes embryonic lethality (Roshon and Ruley, 2005).…”

Section: Saf-a Ash2l and Macroh2a Recruitment Requiresmentioning

confidence: 99%

The Trithorax group protein Ash2l and Saf-A are recruited to the inactive X chromosome at the onset of stable X inactivation

et al. 2010

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SUMMARYMammals compensate X chromosome gene dosage between the sexes by silencing of one of the two female X chromosomes. X inactivation is initiated in the early embryo and requires the non-coding Xist RNA, which encompasses the inactive X chromosome (Xi) and triggers its silencing. In differentiated cells, several factors including the histone variant macroH2A and the scaffold attachment factor SAF-A are recruited to the Xi and maintain its repression. Consequently, in female somatic cells the Xi remains stably silenced independently of Xist. Here, we identify the Trithorax group protein Ash2l as a novel component of the Xi. Ash2l is recruited by Xist concomitantly with Saf-A and macroH2A at the transition to Xi maintenance. Recruitment of these factors characterizes a developmental transition point for the chromatin composition of the Xi. Surprisingly, expression of a mutant Xist RNA that does not cause gene repression can trigger recruitment of Ash2l, Saf-A and macroH2A to the X chromosome, and can cause chromosome-wide histone H4 hypoacetylation. This suggests that a chromatin configuration is established on non-genic chromatin on the Xi by Xist to provide a repressive compartment that could be used for maintaining gene silencing. Gene silencing is mechanistically separable from the formation of this repressive compartment and, thus, requires additional pathways. This observation highlights a crucial role for spatial organization of chromatin changes in the maintenance of X inactivation.

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Rhythmic SAF-A Binding Underlies Circadian Transcription of the Bmal1 Gene

Cited by 30 publications

References 48 publications

SAF-A Has a Role in Transcriptional Regulation ofOct4in ES Cells Through Promoter Binding

SAF-A Has a Role in Transcriptional Regulation ofOct4in ES Cells Through Promoter Binding

Regulation of DNA Topoisomerase IIβ through RNA-dependent Association with Heterogeneous Nuclear Ribonucleoprotein U (hnRNP U)

The Trithorax group protein Ash2l and Saf-A are recruited to the inactive X chromosome at the onset of stable X inactivation

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