Jin J , He X , Silva E .

	Figure 1- sisRNAs are identified from GV RNA-seq data according to Ensemble and RefSeq gene sets in X. tropicalis. a Venn diagram of peaks called by MACS with FDR=0.01 and determined to be sisRNAs according to refSeq and Ensembl gene sets. b UCSC screenshot of identified sisRNAs in the gene E2F3. Red and blue blocks indicate exons, red peaks indicate mRNA detected in the cytoplasm, blue peaks indicate RNA detected in the GV, grey blocks indicate sisRNAs identified, orange lines indicate the summits of sisRNA peaks. c-d Histograms of length distributions for (c) refSeq and (d) Ensembl sisRNAs
	Figure 2-sisRNAs are highly expressed from genes with multiple introns. a-b Histograms show (a) the percentage of genes with sisRNAs, and (b) the average number of sisRNAs per gene in refSeq (red) and Ensembl (blue) genes. Genes are grouped by the intron number. The dashed line indicates the average value for all genes.
	Figure 3-The sequences of sisRNAs have higher GC and TG content, while CpG poor compared to the genome. a-b The ratio of observed/expected (O/E) for the occurrence of dinucleotide (a) and trinucleotide (b) combinations in sisRNAs identified by refSeq genes (red) and by Ensembl genes (blue). c-e Boxplots show the GC% (c), CpG density (d) and CA/TG density (e) of the genome (green) compared to sisRNAs identified by refSeq (red) and Ensembl (blue) genes
	Figure 4- sisRNAs are specific regions of the introns. Boxplots of the comparisons of GC% (a), CpG density (b) and CA|TG density (c) of the introns from genes without any sisRNA (grey), introns without sisRNA from host genes with sisRNAs (orange), and introns with sisRNAs (purple) to sisRNAs identified by refSeq (red) and Ensembl (blue) genes
	Figure 5-sisRNAs are enriched at both the start and the end of transcript, preferentially the 3′ end of transcript. a The density of sisRNAs in introns. For each transcript, all the introns are concatenated from 5′ to 3′ end, and then divided into 100 bins. b UCSC genome browser screenshot of sisRNAs distribution along the introns of the gene nasp. A higher number of sisRNAs are located at the 3′ end. c Scatter plot of sisRNA peak signals versus host gene expression level (FPKM)
	Figure 6-Specific TFBSs are enriched in sisRNAs. The enrichment of TFBS motifs was plotted for (a) the introns without any sisRNAs versus the sisRNAs identified by RefSeq genes, and (b) the RefSeq sisRNAs versus the Ensembl sisRNAs. c UCSC genome browser screenshot of Stat3 shows it is highly expressed in the cytoplasm
	Figure 7- sisRNAs are as evolutionary conserved as introns, but much less than exons. Average PhastCons conservation scores of sisRNAs and introns for upstream and downstream (±150-bps) relative to (a) 5′ end, (b) midpoint, and (c) 3′ end. Boxplots of the comparisons of GC% (d), CpG density (e) and CA|TG density (f) of the human red blood cells (grey), human Hela cells (orange), mouse red blood cells (brown), mouse 3 T3 cells (yellow), chicken DF1 cells (purple), and Xenopus laevis XTC cells (light blue) cytoplasmic sisRNAs, to sisRNAs identified by refSeq (red) and Ensembl (blue) genes. g Venn diagram shows the overlap of host genes with sisRNAs identified by RefSeq genes in Xenopus tropicalis GV and host genes with cytoplasmic sisRNAs in Xenopus laevis XTC
	Supplementary Figure 1. Longer introns have more sisRNAs. (A) Boxplot of lengths of introns grouped by the number of bearing sisRNAs: 0 (green), 1 (orange), 2 (purple), 3 (red) and >3 (blue). (B) Scatter plot of sisRNA numbers versus length of introns. (C) Scatter plot of sisRNA numbers versus total length of introns per gene. (D) Scatter plot of sisRNA numbers versus normalized intron number per Mbps per gene
	Supplementary Figure 2. sisRNAs are specific regions of the introns. Boxplots of the comparisons of GC% (A), CpG density (B), CA|TG density (C), and length (D) of the 1st introns (green), middle introns (orange), and last introns (purple) of genes with more than 3 introns, to sisRNAs identified by refSeq (red) and Ensembl (blue) genes.
	Fig. 1. sisRNAs are identified from GV RNA-seq data according to Ensemble and RefSeq gene sets in X. tropicalis. a Venn diagram of peaks called by MACS with FDR=0.01 and determined to be sisRNAs according to refSeq and Ensembl gene sets. b UCSC screenshot of identified sisRNAs in the gene E2F3. Red and blue blocks indicate exons, red peaks indicate mRNA detected in the cytoplasm, blue peaks indicate RNA detected in the GV, grey blocks indicate sisRNAs identified, orange lines indicate the summits of sisRNA peaks. c-d Histograms of length distributions for (c) refSeq and (d) Ensembl sisRNAs
	Fig. 2. sisRNAs are highly expressed from genes with multiple introns. a-b Histograms show (a) the percentage of genes with sisRNAs, and (b) the average number of sisRNAs per gene in refSeq (red) and Ensembl (blue) genes. Genes are grouped by the intron number. The dashed line indicates the average value for all genes
	Fig. 3. The sequences of sisRNAs have higher GC and TG content, while CpG poor compared to the genome. a-b The ratio of observed/expected (O/E) for the occurrence of dinucleotide (a) and trinucleotide (b) combinations in sisRNAs identified by refSeq genes (red) and by Ensembl genes (blue). c-e Boxplots show the GC% (c), CpG density (d) and CA/TG density (e) of the genome (green) compared to sisRNAs identified by refSeq (red) and Ensembl (blue) genes
	Fig. 4. sisRNAs are specific regions of the introns. Boxplots of the comparisons of GC% (a), CpG density (b) and CA|TG density (c) of the introns from genes without any sisRNA (grey), introns without sisRNA from host genes with sisRNAs (orange), and introns with sisRNAs (purple) to sisRNAs identified by refSeq (red) and Ensembl (blue) genes
	Fig. 5. sisRNAs are enriched at both the start and the end of transcript, preferentially the 3′ end of transcript. a The density of sisRNAs in introns. For each transcript, all the introns are concatenated from 5′ to 3′ end, and then divided into 100 bins. b UCSC genome browser screenshot of sisRNAs distribution along the introns of the gene nasp. A higher number of sisRNAs are located at the 3′ end. c Scatter plot of sisRNA peak signals versus host gene expression level (FPKM)
	Fig. 6. Specific TFBSs are enriched in sisRNAs. The enrichment of TFBS motifs was plotted for (a) the introns without any sisRNAs versus the sisRNAs identified by RefSeq genes, and (b) the RefSeq sisRNAs versus the Ensembl sisRNAs. c UCSC genome browser screenshot of Stat3 shows it is highly expressed in the cytoplasm
	Fig. 7. sisRNAs are as evolutionary conserved as introns, but much less than exons. Average PhastCons conservation scores of sisRNAs and introns for upstream and downstream (±150-bps) relative to (a) 5′ end, (b) midpoint, and (c) 3′ end. Boxplots of the comparisons of GC% (d), CpG density (e) and CA|TG density (f) of the human red blood cells (grey), human Hela cells (orange), mouse red blood cells (brown), mouse 3 T3 cells (yellow), chicken DF1 cells (purple), and Xenopus laevis XTC cells (light blue) cytoplasmic sisRNAs, to sisRNAs identified by refSeq (red) and Ensembl (blue) genes. g Venn diagram shows the overlap of host genes with sisRNAs identified by RefSeq genes in Xenopus tropicalis GV and host genes with cytoplasmic sisRNAs in Xenopus laevis XTC

Adkins, GAGA protein: a multi-faceted transcription factor. 2006, Pubmed

Adkins, GAGA protein: a multi-faceted transcription factor. 2006, Pubmed
Akira, Molecular cloning of APRF, a novel IFN-stimulated gene factor 3 p91-related transcription factor involved in the gp130-mediated signaling pathway. 1994, Pubmed
Ambros, The functions of animal microRNAs. 2004, Pubmed
Ashburner, Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. 2000, Pubmed
Bailey, MEME SUITE: tools for motif discovery and searching. 2009, Pubmed
Bird, Studies of DNA methylation in animals. 1995, Pubmed
Bogdanovic, Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. 2011, Pubmed , Xenbase
Brocke-Heidrich, BCL3 is induced by IL-6 via Stat3 binding to intronic enhancer HS4 and represses its own transcription. 2006, Pubmed
Burge, Over- and under-representation of short oligonucleotides in DNA sequences. 1992, Pubmed
Callan, Lampbrush chromosomes. 1986, Pubmed
Carpenter, STAT3 Target Genes Relevant to Human Cancers. 2014, Pubmed
Chan, Stable Intronic Sequence RNAs (sisRNAs): An Expanding Universe. 2019, Pubmed
Chapman, Isolation and characterization of the gene encoding yeast debranching enzyme. 1991, Pubmed
Coulondre, Molecular basis of base substitution hotspots in Escherichia coli. 1978, Pubmed
Domdey, Lariat structures are in vivo intermediates in yeast pre-mRNA splicing. 1984, Pubmed
Durant, Diverse targets of the transcription factor STAT3 contribute to T cell pathogenicity and homeostasis. 2010, Pubmed
Fleming, STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer. 2015, Pubmed
Funk, Cyclic amplification and selection of targets for multicomponent complexes: myogenin interacts with factors recognizing binding sites for basic helix-loop-helix, nuclear factor 1, myocyte-specific enhancer-binding factor 2, and COMP1 factor. 1992, Pubmed
Gardiner-Garden, CpG islands in vertebrate genomes. 1987, Pubmed
Gardner, Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis. 2012, Pubmed , Xenbase
Girard, A germline-specific class of small RNAs binds mammalian Piwi proteins. 2006, Pubmed
Haerty, Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci. 2015, Pubmed
Hamilton, A species of small antisense RNA in posttranscriptional gene silencing in plants. 1999, Pubmed
Huang, Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. 2009, Pubmed
Huang, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. 2009, Pubmed
Hüttenhofer, Non-coding RNAs: hope or hype? 2005, Pubmed
JACOB, Genetic regulatory mechanisms in the synthesis of proteins. 1961, Pubmed
Katoh, STAT3-induced WNT5A signaling loop in embryonic stem cells, adult normal tissues, chronic persistent inflammation, rheumatoid arthritis and cancer (Review). 2007, Pubmed
Kopczynski, Introns excised from the Delta primary transcript are localized near sites of Delta transcription. 1992, Pubmed
Kossler, Neurofibromin (Nf1) is required for skeletal muscle development. 2011, Pubmed
Lister, Human DNA methylomes at base resolution show widespread epigenomic differences. 2009, Pubmed
Matys, TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. 2006, Pubmed
Michaeli, An excised SV40 intron accumulates and is stable in Xenopus laevis oocytes. 1988, Pubmed , Xenbase
Moss, Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA. 2013, Pubmed
Pek, Stable intronic sequence RNAs have possible regulatory roles in Drosophila melanogaster. 2015, Pubmed , Xenbase
Perkel, Visiting "noncodarnia". 2013, Pubmed
Plaksin, KBF1 (p50 NF-kappa B homodimer) acts as a repressor of H-2Kb gene expression in metastatic tumor cells. 1993, Pubmed
Qian, A spliced intron accumulates as a lariat in the nucleus of T cells. 1992, Pubmed
Rosenbloom, The UCSC Genome Browser database: 2015 update. 2015, Pubmed
Sen, Multiple nuclear factors interact with the immunoglobulin enhancer sequences. 1986, Pubmed
Sharp, Structure and transcription of eukaryotic tRNA genes. 1985, Pubmed
Siepel, Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. 2005, Pubmed
Sigova, Transcription factor trapping by RNA in gene regulatory elements. 2015, Pubmed
Talhouarne, Lariat intronic RNAs in the cytoplasm of Xenopus tropicalis oocytes. 2014, Pubmed , Xenbase
Talhouarne, Lariat intronic RNAs in the cytoplasm of vertebrate cells. 2018, Pubmed , Xenbase
Tay, Maternally Inherited Stable Intronic Sequence RNA Triggers a Self-Reinforcing Feedback Loop during Development. 2017, Pubmed , Xenbase
Trovó-Marqui, Neurofibromin: a general outlook. 2006, Pubmed
van Nues, Processing of eukaryotic pre-rRNA: the role of the transcribed spacers. 1995, Pubmed
Wahl, The spliceosome: design principles of a dynamic RNP machine. 2009, Pubmed
Wang, The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. 2014, Pubmed
Wong, DIP1 modulates stem cell homeostasis in Drosophila through regulation of sisR-1. 2017, Pubmed
Yanai, Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility. 2011, Pubmed , Xenbase
Yang, The Circular RNA Interacts with STAT3, Increasing Its Nuclear Translocation and Wound Repair by Modulating Dnmt3a and miR-17 Function. 2017, Pubmed
Yang, Genomewide characterization of non-polyadenylated RNAs. 2011, Pubmed
Zhang, Circular intronic long noncoding RNAs. 2013, Pubmed
Zhang, Model-based analysis of ChIP-Seq (MACS). 2008, Pubmed
Zorn, IL-2 regulates FOXP3 expression in human CD4+CD25+ regulatory T cells through a STAT-dependent mechanism and induces the expansion of these cells in vivo. 2006, Pubmed