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Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Abstract

RNA, including long noncoding RNA (lncRNA), is known to be an abundant and important structural component of the nuclear matrix. However, the molecular identities, functional roles and localization dynamics of lncRNAs that influence nuclear architecture remain poorly understood. Here, we describe one lncRNA, Firre, that interacts with the nuclear-matrix factor hnRNPU through a 156-bp repeating sequence and localizes across an ~5-Mb domain on the X chromosome. We further observed Firre localization across five distinct trans-chromosomal loci, which reside in spatial proximity to the Firre genomic locus on the X chromosome. Both genetic deletion of the Firre locus and knockdown of hnRNPU resulted in loss of colocalization of these trans-chromosomal interacting loci. Thus, our data suggest a model in which lncRNAs such as Firre can interface with and modulate nuclear architecture across chromosomes.

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Figure 1: Firre is a new X-chromosome–localized lincRNA.
Figure 2: Firre is a new, strictly nuclear lincRNA that escapes X-chromosome inactivation.
Figure 3: Firre forms cis and trans chromosomal contacts.
Figure 4: The trans-chromosomal contacts of Firre are colocalized within the nucleus.
Figure 5: Characterization of Firre knockout in male mESCs.
Figure 6: hnRNPU binds to the RRD of Firre and regulates its nuclear localization.
Figure 7: The trans-chromosomal contacts of Firre are mediated via its interaction with the nuclear-matrix protein hnRNPU.

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Acknowledgements

We thank Biosearch, especially M. Beal, H. Johansson, A. Orjalo, S. Coassin and R. Cook, for materials, advice and help with FISH experiments. We are grateful to the entire Rinn and Raj laboratories for generous help with experiments, bioinformatics and preparation of the manuscript. This work was supported by US National Institutes of Health grants 1DP2OD00667 (J.L.R.), P01GM099117 (J.L.R.), 1DP20D008514 (A.R.) and P50HG006193-01 (J.L.R.) and by the Howard Hughes Medical Institute (R.F.).

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Authors and Affiliations

Authors

Contributions

E.H. designed and performed experiments. L.A.G. performed computational analysis. J.L.R. directed research. E.H., L.A.G. and J.L.R. wrote the manuscript. C.T. and D.R.K. helped with computational analysis. M.S., D.G.H., P.M., J.E., M.G., A.R., M.M. and E.S.L. contributed experiments. A.W., J.H.-M. and R.F. generated knockout mESCs. L.S. and H.F.L. helped with experimental techniques.

Corresponding author

Correspondence to John L Rinn.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Firre is a stable transcript.

(a) Cloning of 50 different mouse isoforms of Firre, with most exons demarcated by the inclusion of the repeat domain RRD (purple tracks). (b) The isoform assemblies for human FIRRE are shown, again with most exons marked by RRD (purple marks). (c) Actinomycin-D treatment of male mESCs followed by RNA FISH for Firre over a course of 6 hours. (d) The number of nascent versus mature transcripts counted by image processing in Matlab.

Supplementary Figure 2 Firre is a strictly nuclear lncRNA.

Single molecule RNA fluorescence in situ hybridization (FISH) in HEK293s and HeLa cells, with introns labeled in “green” and exons in “red”, as described in Raj et al. (2008).

Supplementary Figure 3 Firre RNA is sufficient to form ectopic expression domains.

(a) qRT-PCR analysis of the viral overexpression of the human isoform of FIRRE in HEK293, HeLa, and human lung fibroblasts (hLF), and the mouse isoform of Firre in mouse lung fibroblasts (mLF). Normalized to untransduced samples after all CT values are normalized to Gapdh. (b) Single molecule RNA FISH in transduced HeLa and HEK293 cells, which have endogenous Firre expression; introns labeled in “green” and exons in “red”.

Supplementary Figure 4 Firre forms transchromosomal contacts.

(a) Genes that were not detected to be bound by Firre by RAP were used as negative controls for FISH. Firre intron is shown in “green” and Sox2 exons are shown in “red.” (b) RNA co-FISH between the trans targets of Firre: Slc25a12 and Ypel4 (yellow arrows for co-localization): Slc25a12 intron in “green” and Ypel4 intron in “red.”

Supplementary Figure 5 Firre interacts with hnRNPU in mESc and adipose contexts.

(a) The RNA pull-down technique was developed and optimized by testing known lncRNA-protein interactions. For optimization, telomerase RNA TERC was chosen as well as others, such as SRP and 7SK (data not shown). The binding partners of TERC, Dyskerin and TERT, were recovered with high efficiency and specificity. (b) The optimized RNA pull-down technique was used to find the binding partners of Firre. The analysis of mass spectrometry data is outlined. (c) Based on the highest unique peptide counts across different isoforms and lysate conditions, we identified 8 candidate proteins that physically associate with Firre in an RRD-dependent manner. The top candidate was hnRNPU. (d) Firre interacts with hnRNPU in mouse adipose tissue as well as in mESC lysate. Western blots are shown for the pull-downs using in vitro biotinylated isoforms of Firre: five with RRD and one without. We compared end labeling (EL) and body labeling (BL) to exclude the possibility of a bias in binding and used TERC antisense (AS) and sense (S) as negative controls. hnRNPK and A1 are shown for RRD-specific interactions. 20% of the input protein lysate was loaded in the first lane for each Western blot. Input protein lysate and input RNA are included as loading controls.

Supplementary Figure 6 Firre-hnRNPU interaction is biologically relevant, and hnRNPU has a previously shown role in Xist localization.

(a) Endogenous Firre was captured by desthiobiotin-modified DNA oligos in mESCs. The efficiency of capture was measured by qRT-PCR by comparing the RNA levels in the eluate and what is left on the beads post-elution after normalizing to 10% of the total input. The specificity of capture was measured by comparing the eluates from the targeting and scramble oligos. The endogenous RNA pull-down was repeated in mESCs, in which Firre was knocked down to test the specificity of the oligo for the RNA. (b) The endogenous pull-down was repeated in HEK293s to test for the human FIRRE. Additionally, specificity of the oligo was tested by measuring the elutions for the enrichment or depletion of an unrelated lincRNA, linc-Arid4a. (c) Western blot of HEK293 lysates before and after transfection with siRNAs targeting hnRNPU and scramble siRNAs. (d) RNA FISH of Xist in HEK293s after siRNA-mediated depletion of hnRNPU.

Supplementary Figure 7 Uncropped versions of Figure 6a,b.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 (PDF 8212 kb)

Supplementary Table 1

Sequences of Firre transcripts (GenBank KJ638680–KJ638686) In the version of this Table title originally published online, the GenBank accession codes were not included. The information is included as of 10 September 2014. (TXT 28 kb)

Supplementary Table 2

RNA FISH probe sequences (XLSX 58 kb)

Supplementary Table 3

RAP probe sequences (XLSX 29 kb)

Supplementary Table 4

All qRT-PCR primer sequences (XLSX 13 kb)

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Hacisuleyman, E., Goff, L., Trapnell, C. et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol 21, 198–206 (2014). https://doi.org/10.1038/nsmb.2764

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