Three new papers (Kilpinen et al., 2013; McVickers et al., 2013; Kasowski et al., 2013) published earlier this month in Science all address the effects on human patterns of gene expression and other phenotypes of 1) genetic variation in non-protein coding regions of the genome and 2) covalent modifications of chromatin, the complex of DNA and proteins that facilitates the packaging and organization of DNA in the limited volume of the cell nucleus. Regulation of gene expression is known to involve enzymes that covalently modify the chromatin proteins, known as histones, by attaching such moieties as methyl, acetyl, or phosphate groups to the so-called histone tails. These post-translational modifications are commonly known as epigenetic marks and different marks, distinguished by both the chemical structure of the added substituent and the particular histone and precise amino acid modified, are associated with consistent and distinct effects on gene expression.
The term epigenetics is much in fashion in recent years with articles in non-academic publications suggesting that our understanding of evolution has been upended by the ‘new’ appreciation that phenotypes are the result of both genetic and epigenetic factors (Shulevitz, 2011). Of course, the term “epigenetics” can be traced back at least to 1942 (Lederberg, 2001) and it has been clear for decades that environmental factors can regulate gene expression and thereby influence phenotype (Pardee et al., 1959). Putting aside the least cogent claims about the newness or implications of epigenetics, a truly critical question for investigators has been whether the covalent modifications of chromatin that correlate with gene expression are prime movers of gene expression or are mostly secondary effects caused by the binding of proteins, known as transcription factors (TF), to DNA. Mark Ptashne, an eminent molecular biologist who was one of the first two scientists (the other being Wally Gilbert) to identify a protein that regulates the expression of a particular gene (Ptashne, 1967), has forcefully expounded the view that TF are the ultimate causal factors (2007; 2013) determining both the patterns of histone modification and gene expression.
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Ptashne’s argument is centered on the crucial facts that, 1) whereas TF are nucleotide sequence-specific in their interactions with DNA (i.e., even a single nucleotide substitution can substantially alter the affinity of the TF for the binding site and thereby influence TF function), 2) the enzymes that modify histones are nucleotide sequence non-specific. Thus the enzymes mediating these post-translational modifications have no way to select one histone over another among the vast number they would encounter by random diffusion among the chromosomes in the nucleus. So, it makes sense in Ptashne’s view that TF select the appropriate portions of the genome for chemical modification and then recruit the relevant enzymes through protein-protein interactions. It is already clear that TF regulate gene expression in part through recruitment of RNA polymerase, the complex enzyme that carries out transcription from DNA into RNA.
A strikingly similar strategy is also observed in dramatically different contexts in host defense, such as in the mediation of immunity by antibodies (Schroeder and Greenspan, 2008). In the immunological setting, an antibody provides the specificity for antigen and after binding recruits other proteins through protein-protein interactions, such as complement proteins, that then facilitate, in an antigen-non-specific fashion, clearance or destruction of the foreign material.
The authors of all three of the new studies used lymphoblastoid cell lines from various sources, including cell lines from the members of parent-offspring trios in two of the studies, to correlate genetic polymporphisms in sites of TF binding with patterns of histone modification, DNAse I sensitivity, and gene expression. Based on the data generated in each study, the authors concluded that genetic polymorphisms in TF-binding sites influence the extent of TF binding. Variations in TF binding are then reflected in variation in chromatin modification and gene expression. Kilpinen et al. note that histone modifications are more subject to stochastic effects than is TF binding, and “likely reflect, rather than define, coordinated regulatory interactions.”
Thus, one conlusion from these three studies is that allelic variations in the non-coding regulatory regions of genes can result in variations in histone modification, gene expression, and traits. This model of the molecular control of gene expression, in which TF are the key agents, is also supported by independent studies that demonstrate the ability of transfected TF to mediate cellular reprogramming and wholesale changes in the pattern of chromatin modification (Takahashi and Yamanaka, 2006). However, as noted by Furey and Sethupathy (2013) in an editorial in the same issue of Science as the three papers cited above, not every nucleotide substitution in a regulatory region causes phenotypic variation or even changes in gene expression. To determine why some polymorphisms in non-coding regions are more and others less consequential, additional experiments will be required.
Another conclusion is that genetic variations can cause epigenetic variation, so that the boundary between “genetic” and “epigenetic” phenomena is necessarily less sharply defined than some may have assumed. More than ten years ago, Feinberg (2001) presciently anticipated this perspective on the integrated nature of genetic and epigenetic effects.
Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science. 2013 Nov 8;342(6159):744-7. doi: 10.1126/science.1242463. Epub 2013 Oct 17. PubMed PMID: 24136355.
McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, Pritchard JK. Identification of genetic variants that affect histone modifications in human cells. Science. 2013 Nov 8;342(6159):747-9. doi: 10.1126/science.1242429. Epub 2013 Oct 17. PubMed PMID: 24136359.
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Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Extensive variation in chromatin states across humans. Science. 2013 Nov 8;342(6159):750-2. doi: 10.1126/science.1242510. Epub 2013 Oct 17. PubMed PMID: 24136358.
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