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Additional file 10: Table S7. LINE-1 subclass elements identification. Table represents the number of different types of subclasses of LINE-1 repeat elements associated with HILS1 and percentage of HILS1 occupancy to each subclass with respect to the total number of each in the rat genome

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Additional file 7: Table S6. Repeat elements identification. Table represents the number of different types of repeat elements associated with HILS1

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Additional file 13: Table S9. PCR primer sequences used for ChIP-qPCR analysis

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Additional file 9: Figure 3B. Chr 17-20 and ChrX. Chromosome-wise distribution of rat linker histone HILS1. Each vertical line on the chromosomal map represents location of enriched regions as viewed in UCSC genome browser

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Additional file 3: Table S2. Chromosome-wise fold enrichment of HILS1 peaks. Excel file represents the fold enrichment values for HILS1 peaks across all chromosomes of the rat genome

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Additional file 5: Table S4. ChIP peaks (32731) overlapping with UCSC CpG islands. List of CpG islands were obtained from UCSC table browser and used to find overlaps with 32731 HILS1 ChIP peaks using Bed tools Intersect

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Additional file 6: Table S5. Annotation of the overlapping peaks using HOMER. Overlapping peaks were re-annotated using HOMERv4.7 with newly defined overlap peak lengths and table represents the chromosome-wise number of peaks associated with specific genomic regions like intergenic, intron, exon, 3′UTR, TTS, and promoter-TSS

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Additional file 1: Figure S1. Mass spectrometric analysis of HILS1 IP bands confirms the specificity of HILS1 antibody. Specificity of the antibody raised against CTD of HILS1 was confirmed by the mass spec analysis of the immunoprecipitated bands. Results represent the peptides identified from 25 kDa and ~15kDa bands detected in western blot in both input and immunoprecipitated lane as represented in Figure 5A. Note that the prominent 25kDa band is the full-length form of HILS1, whereas ~15kDa showed different migration in HILS1 IP lane in comparison with input, which is the cleaved product. Coverage represents the percentage of sequence matching with peptides found in the analysis

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Additional file 4: Table S3. Chromosome-wise peak length of HILS1 peaks. Excel file represents the length of HILS1 peaks across the chromosomes confirming their broad natur

DDX5/p68 associated lncRNA <i>LOC284454</i> is differentially expressed in human cancers and modulates gene expression

<p>Long non-coding RNAs (lncRNAs) are emerging as important players in regulation of gene expression in higher eukaryotes. DDX5/p68 RNA helicase protein which is involved in splicing of precursor mRNAs also interacts with lncRNAs like, SRA and <i>mrhl</i>, to modulate gene expression. We performed RIP-seq analysis in HEK293T cells to identify the complete repertoire of DDX5/p68 interacting transcripts including 73 single exonic (SE) lncRNAs. The <i>LOC284454</i> lncRNA is the second top hit of the list of SE lncRNAs which we have characterized in detail for its molecular features and cellular functions. The RNA is located in the same primary transcript harboring miR-23a∼27a∼24-2 cluster. <i>LOC284454</i> is a stable, nuclear restricted and chromatin associated lncRNA. The sequence is conserved only in primates among 26 different species and is expressed in multiple human tissues. Expression of <i>LOC284454</i> is significantly reduced in breast, prostate, uterus and kidney cancer and also in breast cancer cell lines (MCF7 and T47D). Global gene expression studies upon loss and gain of function of <i>LOC284454</i> revealed perturbation of genes related to cancer-related pathways. Focal adhesion and cell migration pathway genes are downregulated under overexpression condition, and these genes are significantly upregulated in breast cancer cell lines as well as breast cancer tissue samples suggesting a functional role of <i>LOC284454</i> lncRNA in breast cancer pathobiology.</p