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Sperm and oocyte has equal or comparable number of expressed transcripts
Venn diagrams showing the number of sperm and oocyte expressed long intergenic noncoding RNAs (lincRNAs) and protein-coding genes (PCGs) from human represented in three categories: sperm or oocyte (Oc) specific, commonly expressed in sperm and oocyte (SpOc), and Miscellaneous (inconsistently expressed between replicates samples from gametes).
Boxplots from human data showing the expression of Sp and SpOc lincRNAs and PCGs in sperm and oocyte.
Sperm established chromatin patterns well correlate with the expression levels
Heatmaps showing H3K27me3 and H3K4me3 enrichment over Sp and SpOc lincRNA (a) and PCG (b) promoters (extended ±10 kb from transcription start site, TSS) and the clusters are categorized into three to four optimal sperm-derived chromatin clusters.
Boxplot showing expression levels of Sp and SpOc-lincRNAs (b) and PCGs (b) from individual sperm-derived chromatin clusters.
Sperm lncRNAs during pre-implantation stages of development
Schematics representation of preimplantation stages of embryo development. Upper panel depits the status of RNAs/genome throughout the stages. At the initial stages of development after fertilization, the maternal transcripts starts degrading. Upon offset of maternal transcript degradation, the transcription of zygotic genome gets activated.
Heatmaps showing stage-specific expression of Sp and SpOc transcripts (lincRNAs and PCGs) during preimplantation stages of embryos. Sp-lincRNAs and PCGs were see active during zygotic genome activation (ZGA) of preimplantation embryos whereas SpOc lincRNAs are active during pre-ZGA corresponds to parental transcript degradation. SpOc PCGs were expressed consistantly throughout the stages of preimplantation embryos. Additionally, Sp-lincRNAs and PCGs are having stage-specific expression pattern, but this stage-specific patterns are abscent in commonly expressed SpOc transcripts.
Sperm lncRNAs during post-implantation development (embryonic germ layers) and germ layer derived somatic tissues
Enrichment of H3K27me3 (K27) and H3K4me3 (K4) ChIP-seq signals from the three embryonic germ layers, human embryonic stem cells (hESC), and the germ-layer-derived tissues (brain, thyroid, and heart) over the promoters of Sp and SpOc lincRNA and PCGs (extended ±10 kb from TSS) from sperm-derived chromatin clusters.
Boxplots with expression of Sp- and SpOc lincRNAs and PCGs in the three germ layers, hESCs and germ-layer derived somatic tissues ( brain, thyroid, and heart ).
Bottom panel shows schematic of samples chosen from three germ layers (ectoderm, mesoderm, and endoderm) and matured tissues (brain, heart, and thyroid), derived from respective germ layers.
Sperm specific-lncRNAs were aberrantly activated in multiple cancer types
Status of Sp and SpOc transcripts in germ cells, preimplantation stage embryos, the human body map tissues, TCGA tumors compared with the corresponding healthy samples, or TCGA tumors compared with GTEx health samples.
Note: Above findings are published in iScience (cell press), Issue 23 (Subhash S et al, 2020). Only computational analysis results contributed by me is included in above summary. For complete research, please have a look at this original article.
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