Transcription initiation site with only unidirectional transcription.

<p>A: A nearly symmetrical consensus showing only unidirectional transcription. B, C & D: A variant of the consensus showing only unidirectional transcription with the presence of nearby genes. *Panel formation: 1- Scaffold browser scale. 2- Mapped RNA-seq and TSS-seq read counts in relation to the scaffold. 3- Mapped RNA-seq read distribution. 4- Mapped TSS-seq read distribution. 5- Annotated genes (including deprecated ones).</p

Conserved consensus for the transcription initiation site in <i>Giardia.</i>

<p>Conserved consensus for the transcription initiation site in <i>Giardia.</i></p

Transcription initiation site with bidirectional transcription.

<p>A & B: Bidirectional transcription starting at the same nucleotide position at different distances from nearby genes. C: Bidirectional transcription occurring at the same nucleotide position as one starting at another close transcription initiation site. D: Bidirectional transcription occurring at two overlapping transcription initiation sites. *Red oval mark was used to mark the consensus. **Panel formation: 1- Scaffold browser scale. 2- Mapped RNA-seq and TSS-seq read counts in relation to the scaffold. 3- Mapped RNA-seq read distribution. 4- Mapped TSS-seq read distribution. 5- Annotated genes (including deprecated ones).</p

Frequent transcription-initiation site consensus variants.

<p>Frequent transcription-initiation site consensus variants.</p

A Comparison of the Rest Complex Binding Patterns in Embryonic Stem Cells and Epiblast Stem Cells

<div><p>We detected and characterized the binding sites of the representative Rest complex components Rest, Sin3A, and Lsd1. We compared their binding patterns in mouse embryonic stem (ES) cells and epiblast stem (EpiS) cells. We found few Rest sites unique to the EpiS cells. The ES-unique site features were distinct from those of the common sites, namely, the signal intensities were weaker, and the characteristic gene function categories differed. Our analyses showed that the Rest binding sites do not always overlap with the Sin3A and Lsd1 binding sites. The Sin3A binding pattern differed remarkably between the ES and EpiS cells and was accompanied by significant changes in acetylated-histone patterns in the surrounding regions. A series of transcriptome analyses in the same cell types unexpectedly showed that the putative target gene transcript levels were not dramatically different despite dynamic changes in the Rest complex binding patterns and chromatin statuses, which suggests that Rest is not the sole determinant of repression at its targets. Nevertheless, we identified putative Rest targets with explicitly enhanced transcription upon Rest knock-down in 143 and 60 common and ES-unique Rest target genes, respectively. Among such sites, several genes are involved in ES cell proliferation. In addition, we also found that long, intergenic non-coding RNAs were apparent Rest targets and shared similar features with the protein-coding target genes. Interestingly, such non-coding target genes showed less conservation through evolution than protein-coding targets. As a result of differences in the components and targets of the Rest complex, its functional roles may differ in ES and EpiS cells.</p></div

List of genes with long 5′-UTR.

<p>List of genes with long 5′-UTR.</p

Combining TSS and RNA-seq with the use of IGV tool.

<p>A: GL50803_23497 (deprecated gene) has a closely positioned TR and is highly expressed in RNA-seq. B: A long 5`-UTR is observed in GL50803_29595, which is highly expressed in RNA-seq. *Panel formation: 1- Scaffold browser scale. 2- Mapped RNA-seq and TSS-seq read counts in relation to the scaffold. 3- Mapped RNA-seq read distribution. 4- Mapped TSS-seq read distribution. 5- Annotated genes (including deprecated ones).</p

Results of RT-PCR for 30 targets.

<p>All samples were run in duplicate (template added and template free). For further details about the position and size of the target, see supplemental material and methods.</p

Rest complex ChIP Seq.

<p>Examples of the Rest complex binding sites detected and associated with protein-coding genes in ES and EpiS cells. ChIP Seq tags for Rest, Sin3A, and Lsd1 in the indicated cells are shown. (A), (B), and (C) show examples of the ES-unique, common, and EpiS-unique sites in the vicinity of “Snap23”, “C2cd5 and Etnk1”, and “Cdh23”, respectively.</p

Evaluation of the correlation between TRs and genes.

<p>A: Perfectly positioned if the distance between the TR and the start codon is ±40, ±60 or ±100 nt. B: The TR is intragenic. C: If the TR was located between 500 nt up-stream of the first codon and distance A, it was considered as possibly related to the gene. D: If the TR was located more than 500 nt up-stream any annotated ORF.</p