"Gene bookmarking" - to keep the molecular pages open
Authors: Rama Prashat G1, Vignesh M1 and Vinutha T2
1 Division of Genetics, ICAR-IARI, New Delhi
2 Division of Biochemistry, ICAR-IARI, New Delhi


Several mechanisms are responsible for transcription regulation in cells, that includes chromatin remodelling, differential methylation of specific DNA regions and binding of certain proteins at specific locations in chromosomes, which acts as an insulator in preventing the migration of chromatin states or transactivation between neighbouring chromosomal regions. Apart from this, there is yet another mechanism that is essential for proper gene expression called as gene bookmarking, which is less popular.

The genetic material is transferred to the daughter cells and in subsequent generations through mitosis. These cells must remember and maintain the phenotype of cell lineages. So they must have a way to remember the genes which are active before cell division and must follow the same pattern through mitosis into daughter cells. During mitosis most of the sequenceâ€"specific DNA binding proteins disassociate from the DNA. So to remember which genes were active before the onset of mitosis, the active genes are in some way ‘marked’ and the daughter cells reassemble the transcriptional machinery on the promoters of those active genes. This marking resembles the way in which a bookmark marks the position of last read page of a book and hence called as 'Gene bookmarking' and the factors or the modifications that mark the active genes are called as 'molecular bookmarks'.

Some genes like hsp70 gene that are essential for protecting the cells from stress must be activated as early as possible during or just after the completion of mitosis. During mitosis the transcription is in the state of repression. So if these essential genes were not bookmarked, the cell might not be able to transcribe until the normal decompaction process were complete, which will take some time after mitosis. Such a delay in transcription might lead to the disruption of cell function or even cell death.

Chromosomal DNA must be compacted during mitosis for the proper segregation of chromosomes into the daughter cells. When the chromosomes were condensed, they do not react to nucleases and chemical probes. But some studies found that certain specific sites in chromatin were hypersensitive to nucleases and chemical probes. This suggests that the specific region of DNA which is sensitive to nucleases were not compacted.

Mechanism of gene bookmarking

There were at least four mechanisms of gene bookmarking:.

1. The mitosis-dependent modification of histones or binding of different types of histones at the sites of active genes.

2. The persistent binding of TFIID complexes to promoters in mitotic cells.

3. The role of Polycomb and Trithorax in bookmarking their target genes.

4. HSF2-mediated bookmarking of the hsp70 promoter.

(1). Modification of histones and binding of histone variant

The chromatin structures are regulated by the modifications that occur on histones. The hyperacetylation of histone H4 in metaphase chromosome based on the staining patterns has been used to propose that the ‘memory’ of gene expression patterns could be propagated to daughter cells because of the modification of histones at the regions corresponding to active genes. Hyperacetylation of histone H3 and H4, dimethylation of Lys4 and Lys79 on histone H3 and trimethylation of Lys4 on histone H3 were found as evidence to support this hypothesis. The recruitment of histone modifying enzymes by transcription factors bound to the promoters or by the RNA polymerase II complex have been postulated to the reason for histone modifications.

Apart from these modifications of histones, the active gene regions were found to be associated with nucleosomes containing a different type of histone H3, called H3.3, in combination with acetylation and methylation of histone H3 and this pattern persisted through mitosis. The mechanism and regulation of bookmarking through histone modification and histone variants is intriguing and needs more investigation.

(2). TFIID in bookmarking

TFIID transcription factor via the TBP subunit and its associated protein complexes interact with TATA boxes of promoters in the basal transcription machinery of eukaryotes. During mitosis it was thought that, sequence-specific DNA binding proteins disassociate from chromatin. But some biochemical and immunocytochemical studies found that some portion of TFIID remains tightly associated with the condensed chromosomes in mitotic cells.

Further studies using chromatin immunoprecipitation technique showed that, in mitotic cells, TFIID along with TFIIB remain associated with the promoters of genes that are active in cells but not with inactive genes. These results support the hypothesis of TFIID as a good candidate for bookmarking the promoters of active genes. By using TFIID transcription factor for bookmarking, the cells can easily identify the active genes that should be bookmarked and by having TFIID remain bound at the promoters during mitosis, the reassembling transcription complexes on the promoters after mitosis is very straight forward.

(3). The role of Polycomb and Trithorax

Proteins belonging to Polycomb group and Trithorax group complexes bind to specific DNA sequences in target genes. The PcG complexes functions as a repressor and inactivates genes. Trithorax proteins have the opposite effect and activate genes. Both these group of proteins have histone methyl transferase activity and promote different patterns of histone modification. The pattern of histone methylation by Polycomb proteins is associated with a closed chromatin configuration and Trithorax proteins promote an open chromatin configuration. The effects of both these proteins persist through cell divisions and hence they both function as bookmarking factors for their common target genes.

(4). hsp70 promoter bookmarking

HSP70 is an important cytoprotective protein upregulated during stress, mediated by HSF1 transcription factor. Stress plays an important role in converting HSF1 into its DNA â€" binding form. HSF1 interacts with HSEs in the hsp70 promoter and increases its rate of transcription. These HSE elements are located in a region of the hsp70 promoter that conatins sites showing persistent hypersensitivity to DNase in mitotic cells, suggesting that it is a part of the bookmarked region. A study has found that HSF2 transcription factor interacts with CAP-G subunit of the condensin complex, which is important in DNA compaction in mitotic cells. Subsequent experiments showed that HSF2 have a crucial role in mediating bookmarking of the hsp70 promoter. The data from the experiments indicated that HSF2 binds to hsp70 promoter at the beginning of mitosis and recruits the serine/threonine phosphatase PP2A to this DNA region. HSF2 than interacts with the CAP-G subunit of condensing complexes that are compacting chromosomal DNA in the hsp70 promoter vicinity. The condensin is inactivated by its dephosphorylation by HSF2 asociated PP2A and hence the compaction of the DNA is stopped. So HSF2 functions both as a positioning factor, by marking the promoter to be bookmarked by specifically binding to the HSEs within it and as a binding factor, interacting with PP2A and the CAP-G subunit of condensin to promote dephosphorylation of CAP-G.


From the above discussion we conclude that there are at least two biological functions of bookmarking. One is the bookmarking of active genes to ensure transmission of phenotype through mitosis to daughter cells and the second one is the bookmarking of genes that need to be expressed in early G1, such as the hsp70 gene, which must remain inducible for the cells to survive stress.

References (if any)

1. Kevin D. Sarge and Ok-Kyong Park-Sarge (2006). Gene bookmarking: keeping the pages open. Trends in Biochemical Sciences. Vol. 30 No. 11 605-610

2. Stephen Kadauke and Gerd A Blobel (2013). Mitotic bookmarking by transcription factors. Epigenetics and chromatin. 6:6

About Author / Additional Info:
Scientist in the Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi