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Fig. 10 | Epigenetics & Chromatin

Fig. 10

From: A computational approach for the functional classification of the epigenome

Fig. 10

Examples of genomic visualization of the NMF-based epigenetic profiles on the UCSC Genome Browser. Chromatin profiles are compared with the UCSC Refseq gene annotation tracks at the TMEM139/CASP2 and the MKRN1 loci. NMF-profiles are highlighted with the same color scheme adopted in this work and are displayed in the first track of the panel, as indicated by the yellow arrow on the right. a Genomic visualization of chromatin profiles over a 25Kb-region encompassing two different genomic loci: the TMEM139 (transmembrane protein 139) and the CASP2 gene. A specific chromatin transition ‘ActProm > TxInit’ is found exactly on the TSS of the CASP2 gene, suggesting the presence of a functionally active promoter. Chromatin profile GenBd is also detected multiple times on both intronic and exonic regions of the gene, indicating that the CASP2 is transcriptionally active in hESC-H1 cells. The NMF-approach also identified a repressive chromatin region (profile RepReg) on the 3′ end and a potential enhancer element over the 5′ end of the TMEM139 gene, that are also confirmed by ChromHMM predictions in the bottom track. b Chromatin profiles at the MKRN1 locus (the Makorin ring finger protein1). MKRN1 appears to be well-expressed in hESC-H1 cells as indicated by the ‘TxInit > ActProm > TxInit’ chromatin motif over the TSS region and the Gene Body Transcription profile that frequently appears in both introns and the last exons of the gene. On the left of the figure, a putative active enhancer (i.e. the chromatin profile sequence ‘Enh > ActProm > Enh’) is predicted over the 3′ end of the gene. This prediction appears to be concordant with the ChromHMM annotation, as indicated by the ‘strong-enhancer’ label in the corresponding chromatin segmentation track. Finally, a putative CTCF-binding region (profile RegEl) also appears in the first intron, suggesting a functional role in the control of MKRN1

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