Regulation of mammalian gene expression by retroelements and non‐coding tandem repeats

Abstract

Genomes of higher eukaryotes contain abundant non‐coding repeated sequences whose overall biological impact is unclear. They comprise two categories. The first consists of retrotransposon‐derived elements. These are three major families of retroelements (LINEs, SINEs and LTRs). SINEs are clustered in gene‐rich regions and are found in promoters of genes while LINEs are concentrated in gene‐poor regions and are depleted from promoters. The second class consists of non‐coding tandem repeats (satellite DNAs and TTAGGG arrays), which are associated with mammalian centromeres, heterochromatin and telomeres. Terminal TTAGGG arrays are involved in telomere capping and satellite DNAs are located in heterochromatin, which is implicated in transcription silencing by gene repositioning (relocalization). It is unknown whether interstitial TTAGGG sequences, which are present in many vertebrates, have a function. Here, evidence will be presented that retroelements and TTAGGG arrays are involved in regulation of gene expression. Retroelements can provide binding sites for transcription factors and protect promoter CpG islands from repressive chromatin modifications, and may be also involved in nuclear compartmentalization of transcriptionally active and inactive domains. Interstitial telomere‐like sequences can form dynamically maintained three‐dimensional nuclear networks of transcriptionally inactive domains, which may be involved in transcription silencing like classic heterochromatin. BioEssays 30:338–348, 2008. © 2008 Wiley Periodicals, Inc.

Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

“…For these intergenic binding sites, we searched for TSCs located from 1 kb upstream to 10 kb downstream of the HIF-1a binding sites and identified 262 and 105 putative HIF-1a target TSCs in DLD-1 and TIG-3 cells, respectively (Table 2). Twenty-one and 21 binding sites were located in repetitive regions (see also Supplementary Table 5), which suggested that some HIF-1a target sites might also have arose from repetitive regions, as previously reported for several transcription factors (Tomilin 2008;Polak and Domany 2006) (see Supplementary Fig. 14 for one of these examples).…”

Sequence variability of the MspI satellite DNA family of the pinewood nematode Bursaphelenchus xylophilus at different geographic scales

“…The variability patterns observed here for B. xylophilus monomeric sequences follow the hypothesis that some repeat regions are under selective pressure to maintain a particular DNA sequence, whereas other regions evolve without any constraint. The growing knowledge on the effective functional roles of the highly conserved domains underpins the idea that this non-random pattern of variability could enhance binding with specific centromere proteins (Ugarković , 2008), or even the control of gene expression (Ugarković , 2005;Tomilin, 2008). The phylogenetic inference based on the different sets of MspI satellite DNA family for this species shows a broad polymorphism of the individual monomers, when compared for example to other species of nematodes (e.g.…”

“…These sequences are generally A-T rich and show variability affecting monomer size, nucleotide sequence and copy number. Contrary to a former established idea, the chromosomal regions consisting of satDNA are now known to play important but incompletely understood roles in some intragenomic mechanisms, such as centromeric condensation, sister chromatid pairing, karyotypic evolution and chromosome arrangement (Plohl et al, 2008;Malik and Henikoff, 2009) and also seem to play some role in gene regulation (Ugarković , 2005;Tomilin, 2008).…”

On the Concept Of Retrotransposons: Controlling Genome and Making Stress Memories

“…The corollary of retrotransposons' regulatory effects resides in their contribution to genome evolution, modulating several cellular processes mainly through the increase of genome plasticity, creation of pseudogenes as well as creation and remodeling of gene regulatory networks [83,123] . A flourish of works has documented the involvement of retrotransposons in embryogenesis, cell differentiation, pluripotency, cell cycle, DNA repair, aging, genomic imprinting, X-chromosome inactivation, behavior, metabolism and immune responses [42,91,[124][125][126][127][128][129][130][131][132][133][134][135][136][137] .…”