In particular, the first meiotic division (occurring in primary spermatocytes) involves many cell-specific gene products.
In a tissue that is composed of many cell types, specific antibodies are usually necessary to identify these cell types when they are dissociated in vitro; and if one wants to study the cells live, such antibodies must recognise cell surface antigens and yet not interfere with cell function.
Even with the comprehensive annotation coverage in our analysis, we expected many germ cell specific lncRNAs would be missed.
E2A and HEB proteins bind DNA at specific E-box sites in the enhancers of many T cell specific regulatory genes like CD4 and preT α [ 2].
In cell lines and several primary tissues, FoxM1 was shown to directly regulate many cell cycle-specific genes, including the G1/S specific genes (cyclin D1, Skp2 and Cks1), the S phase-specific gene c-myc, the G2/M genes (cdc25B and cyclin B1) and those that are involved in mitosis (aurora, survivin and CENP) [15].
Additionally, the recruitment of SETD1 and MLL to specific target genes is mediated by many cell type-specific transcription factors or transcriptional coactivators 19 20 21922 23.
Although the activity of Sp1 is generally believed to be constitutive, it may have synergistic effect with many cell type-specific transcription factors such as E2F [35], HNF3 [36], RXR [37], SREBP-1 [59], NF-κB [60] and AP2 [61].
Analysis of DNase I hypersensitive sites (DHS), markers of accessible chromatin, revealed many cell line-specific changes mapping to retrotransposable elements [ 38].
However, there were also many cell type-specific sites, even when only peaks with high tag count were compared (supplementary material Fig. S5D).
This result suggests that approaches which rely solely on identifying extended blocks of extreme phylogenetic conservation may fail to detect many cell-type specific CREs.
However, many cell-type specific promoters drive relatively weak gene expression [ 20].
