Alterations in titer and distribution of high mobility group proteins during embryonic development of Drosophila melanogaster

Dynamics of Gene Co-expression Networks in Time-Series Data: A Case Study in Drosophila melanogaster Embryogenesis

Co-expression networks tightly coordinate the spatiotemporal patterns of gene expression unfolding during development. Due to the dynamic nature of developmental processes simply overlaying gene expression patterns onto static representations of co-expression networks may be misleading. Here, we aim to formally quantitate topological changes of co-expression networks during embryonic development using a publicly available Drosophila melanogaster transcriptome data set comprising 14 time points. We deployed a network approach which inferred 10 discrete co-expression networks by smoothly sliding along from early to late development using 5 consecutive time points per window. Such an approach allows changing network structure, including the presence of hubs, modules and other topological parameters to be quantitated. To explore the dynamic aspects of gene expression captured by our approach, we focused on regulator genes with apparent influence over particular aspects of development. Those key regulators were selected using a differential network algorithm to contrast the first 7 (early) with the last 7 (late) developmental time points. This assigns high scores to genes whose connectivity to abundant differentially expressed target genes has changed dramatically between states. We have produced a list of key regulators – some increasing (e.g., Tusp, slbo, Sidpn, DCAF12, and chinmo) and some decreasing (Rfx, bap, Hmx, Awh, and mld) connectivity during development – which reflects their role in different stages of embryogenesis. The networks we have constructed can be explored and interpreted within Cytoscape software and provide a new systems biology approach for the Drosophila research community to better visualize and interpret developmental regulation of gene expression.

Drosophila D1 overexpression induces ectopic pairing of polytene chromosomes and is deleterious to development

Eukaryotic genomes function in the context of chromatin, but the roles of most nonhistone chromosomal proteins are far from understood. The D1 protein of Drosophila is an example of a chromosomal protein that has been fairly well characterized biochemically, but has nevertheless eluded functional description. To this end, we have undertaken a gain-of-function genetical analysis of D1, utilizing the GAL4-UAS system. We determined that ubiquitous overexpression of D1 using the Act5C- or tubP-GAL4 drivers was lethal to the organism during larval growth. We also ectopically expressed D1 in a tissue-limited manner using other GAL4 drivers. In general, ectopic D1 was observed to inhibit differentiation and/or development. We observed effects on pattern formation of the adult eye, bristle morphogenesis, and spermatogenesis. These phenotypes may be the consequence of misregulation of D1 target genes. A surprising result was obtained when D1 was overexpressed in the third instar salivary gland. The polytene chromosomes exhibited numerous ectopic associations such that spreading of the chromosome arms was precluded. We mapped the sites of ectopic pairing along the polytene chromosome arms, and found a correlation with sites of intercalary heterochromatin. We speculate that these sites comprise the natural targets of D1 protein activity and that D1 is involved in the ectopic pairing observed for wild-type chromosomes. Together, our data suggest that D1 may influence multiple biochemical activities within the nucleus.

The multi-AT-hook chromosomal protein of Drosophila melanogaster, D1, is dispensable for viability

The D1 protein is a high mobility group A (HMGA)-like nonhistone chromosomal protein with primary localization to certain AT-rich satellite DNA sequences within heterochromatin. The binding of D1 to euchromatic sequences is less studied and the functional significance of its chromosomal associations is unclear. By taking advantage of existing P-insertion alleles of the D1 gene, I generated D1 null mutations to investigate the phenotypic effect of loss of the D1 gene. In contrast to a previous report, I determined that the D1 gene is not essential for viability of Drosophila melanogaster, and moreover, that loss of D1 has no obvious phenotypic effects. My tests for an effect of D1 mutations on PEV revealed that it is not a suppressor of variegation, as concluded by other investigators. In fact, the consequence of loss of D1 on one of six variegating rearrangements tested, T(2;3)Sb(V), was dominant enhancement of PEV, suggesting a role for the protein in euchromatic chromatin structure and/or transcription. A study of D1 protein sequence conservation highlighted features shared with mammalian HMGA proteins, which function as architectural transcription factors.

Overexpression of HmgD causes the failure of pupariation in Drosophila by affecting ecdysone receptor pathway

HmgD encodes Drosophila homologue of high mobility group proteins (HMGD), which are thought to have an architectural function in chromatin organization. However, current opinions about the function of HMGD in Drosophila development are controversial. Our previous studies have shown that ubiquitous overexpression of HmgD caused the formation of melanotic tumors in the Drosophila larvae by prematurely activating the Ras-MAPK pathway. Here we report that under maternal control, the viability of flies links with overexpression of HmgD, while under ubiquitous control, ActGal4, overexpressing HmgD animals, which display prolonged larval stages around day 13, developmentally stagnate in the larva-white pupa transition. Ecdysone feeding did not rescue overexpressing HmgD animals. RT-PCR analyses show that overexpression of HmgD does not affect the temporal expression pattern of ecdysone receptor gene EcR, whereas transcriptional patterns of some key regulatory genes, such as E74A, E74B, E75A, E75B, betaFTZ-F1, are changed greatly. These results suggest that ubiquitous overexpression of HmgD results in the failure of pupariation neither by affecting the process of ecdysone synthesis and release nor by abnormal EcR transcription, but by causing expression of EcR regulatory nuclear receptors out of schedule. The results led us to postulate that overexpression of HMGD likely changes the signaling cascade of Drosophila metamorphosis by an interaction between HMGD and DNA strands, and subsequently by an error of DNA binding abilities and transcriptional activities of some nuclear receptor genes. Arch. Insect Biochem. Physiol. 2008.

High mobility group proteins of the plant HMGB family: dynamic chromatin modulators

In plants, the chromosomal high mobility group (HMG) proteins of the HMGB family typically contain a central HMG-box DNA-binding domain that is flanked by a basic N-terminal and an acidic C-terminal domain. The HMGB proteins are abundant and highly mobile proteins in the cell nucleus that influence chromatin structure and enhance the accessibility of binding sites to regulatory factors. Due to their remarkable DNA bending activity, HMGB proteins can increase the structural flexibility of DNA, promoting the assembly of nucleoprotein complexes that control DNA-dependent processes including transcription. Therefore, members of the HMGB family act as versatile modulators of chromatin function.

Mass spectrometric mapping of linker histone H1 variants reveals multiple acetylations, methylations, and phosphorylation as well as differences between cell culture and tissue

Posttranslational modifications of histones are involved in regulation of chromatin structure and gene activity. Whereas the modifications of the core histones H2A, H2B, H3, and H4 have been extensively studied, our knowledge of H1 modifications remained mainly limited to its phosphorylation. Here we analyzed the composition of histone H1 variants and their modifications in two human cell lines and nine mouse tissues. Use of a hybrid linear ion trap-orbitrap mass spectrometer facilitated assignment of modifications by high resolution and low ppm mass accuracy for both the precursor and product mass spectra. Across different tissues we identified a range of phosphorylation, acetylation, and methylation sites. We also mapped sites of ubiquitination and report identification of formylated lysine residues. Interestingly many of the mapped modifications are located within the globular domain of the histones at sites that are thought to be involved in binding to nucleosomal DNA. Investigation of mouse tissue in addition to cell lines uncovered a number of interesting differences. For example, whereas methylation sites are frequent in tissues, this type of modification was much less abundant in cultured cells and escaped detection. Our study significantly extends the known spectrum of linker histone variability.

Many players, one goal: how chromatin states are inherited during cell division

Replication of genomic material is a process that requires not only high fidelity in the duplication of DNA sequences but also inheritance of the chromatin states. In the last few years enormous effort has been put into elucidating the mechanisms involved in the correct propagation of chromatin states. From all these studies it emerges that an epigenetic network is at the base of this process. A coordinated interplay between histone modifications and histone variants, DNA methylation, RNA components, ATP-dependent chromatin remodeling, and histone-specific assembly factors regulates establishment of the replication timing program, initiation of replication, and propagation of chromatin domains. The aim of this review is to examine, in light of recent findings, how so many players can be coordinated with each other to achieve the same goal, a correct inheritance of the chromatin state.

Transcriptional frequency and cell determination

The relative base composition of DNA regulatory sequences of certain genes of undetermined multipotent progenitor cells may account for the frequency of transcription of these genes in cell determination. The sequences of these regulatory regions of cell determination genes that are more AT-rich would create the potential for transcription at a higher frequency due to their lower melting temperature, as well as propensity to bend. An increase of one or more of the high mobility group (HMG) chromatin proteins would preferentially bind the more AT-rich regulatory sequences, thereby increasing the rate of transcription. The amount of unphosphorylated H1 histone reacting with these same regulatory sites may decrease transcription frequency. The level of cell growth, i.e. total protein synthesis of a cell, is correlated positively with the synthesis of HMG proteins. H1 histone synthesis is linked to DNA replication. Unbalanced growth would alter the amounts of HMG proteins and H1 histone, thus changing transcriptional frequency. The greater the enrichment of AT sequences in the regulatory regions of the cell determination genes, the greater may be the extent of evolutionary conservation. Higher frequency of transcription of the cell determination genes with the more AT-rich regulatory sequences could account for the earlier expression of the more conserved cell determination genes during embryonic development. Preferential binding of H1 histone to the more AT-rich regulatory sequences would subsequently restrict their transcription before that of less conserved cell determination genes.

Identification of novel Drosophila neural precursor genes using a differential embryonic head cDNA screen

During Drosophila neuroblast lineage development, temporally ordered transitions in neuroblast gene expression have been shown to accompany the changing repertoire of functionally diverse cells generated by neuroblasts. To broaden our understanding of the biological significance of these ordered transitions in neuroblast gene expression and the events that regulate them, additional genes have been sought that participate in the timing and execution of these temporally controlled events. To identify dynamically expressed neural precursor genes, we have performed a differential cDNA hybridization screen on a stage specific embryonic head cDNA library, followed by whole-mount embryo in situ hybridizations. Described here are the embryonic expression profiles of 57 developmentally regulated neural precursor genes. Information about 2389 additional genes identified in this screen, including 1614 uncharacterized genes, is available on-line at 'BrainGenes: a search for Drosophila neural precursor genes' (http://sdb.bio.purdue.edu/fly/brain/ahome.htm).

The AT-hook protein D1 is essential for Drosophila melanogaster development and is implicated in position-effect variegation

We have analyzed the expression pattern of the D1 gene and the localization of its product, the AT hook-bearing nonhistone chromosomal protein D1, during Drosophila melanogaster development. D1 mRNAs and protein are maternally contributed, and the protein localizes to discrete foci on the chromosomes of early embryos. These foci correspond to 1.672- and 1.688-g/cm(3) AT-rich satellite repeats found in the centromeric heterochromatin of the X and Y chromosomes and on chromosomes 3 and 4. D1 mRNA levels subsequently decrease throughout later development, followed by the accumulation of the D1 protein in adult gonads, where two distributions of D1 can be correlated to different states of gene activity. We show that the EP473 mutation, a P-element insertion upstream of D1 coding sequences, affects the expression of the D1 gene and results in an embryonic homozygous lethal phenotype correlated with the depletion of D1 protein during embryogenesis. Remarkably, decreased levels of D1 mRNA and protein in heterozygous flies lead to the suppression of position-effect variegation (PEV) of the white gene in the white-mottled (w(m4h)) X-chromosome inversion. Our results identify D1 as a DNA-binding protein of known sequence specificity implicated in PEV. D1 is the primary factor that binds the centromeric 1.688-g/cm(3) satellite repeats which are likely involved in white-mottled variegation. We propose that the AT-hook D1 protein nucleates heterochromatin assembly by recruiting specialized transcriptional repressors and/or proteins involved in chromosome condensation.

Replication timing and cell differentiation

Cell differentiation may depend in part upon a type of unbalanced growth in which several cell cycles occur with a reduced level of total protein synthesis. During this period the synthesis of the chromatin protein HMG-I/Y is reduced since its synthesis is correlated with that of total protein. The synthesis of histone H1 shows less reduction since its synthesis is entrained with that of DNA. This greater reduction of HMG-I/Y than of histone H1 is thought to delay or prevent replicon initiations within AT-enriched isochores. This shifts their time of replication from early to late S phase. This may restrict certain pathways of cell differentiation in multipotent progenitor cells and allow one particular type of differentiation.

HMG-D and histone H1 interplay during chromatin assembly and early embryogenesis

HMG-D is an abundant chromosomal protein associated with condensed chromatin during the first nuclear cleavage cycles of the developing Drosophila embryo. We previously suggested that HMG-D might substitute for the linker histone H1 in the preblastoderm embryo and that this substitution might result in the characteristic less compacted chromatin. We have now studied the association of HMG-D with chromatin using a cell-free system for chromatin reconstitution derived from Drosophila embryos. Association of HMG-D with chromatin, like that of histone H1, increases the nucleosome spacing indicative of binding to the linker DNA between nucleosomes. HMG-D interacts with DNA during the early phases of nucleosome assembly but is gradually displaced as chromatin matures. By contrast, purified chromatin can be loaded with stoichiometric amounts of HMG-D, and this can be displaced upon addition of histone H1. A direct physical interaction between HMG-D and histone H1 was observed in a Far Western analysis. The competitive nature of this interaction is reminiscent of the apparent replacement of HMG-D by H1 during mid-blastula transition. These data are consistent with the hypothesis that HMG-D functions as a specialized linker protein prior to appearance of histone H1.

Consecutive steps of phosphorylation affect conformation and DNA binding of the chironomus high mobility group A protein

The high mobility group (HMG) proteins of the AT-hook family (HMGA) lie downstream in regulatory networks with protein kinase C, Cdc2 kinase, MAP kinase, and casein kinase 2 (CK2) as final effectors. In the cells of the midge Chironomus, almost all of the HMGA protein (cHMGA) is phosphorylated by CK2 at two adjacent sites. 40% of the protein population is additionally modified by MAP kinase. Using spectroscopic and protein footprinting techniques, we analyzed how individual and consecutive steps of phosphorylation change the conformation of an HMGA protein and affect its contacts with poly(dA-dT).poly(dA-dT) and a fragment of the interferon-beta promoter. We demonstrate that phosphorylation of cHMGA by CK2 alters its conformation and modulates its DNA binding properties such that a subsequent phosphorylation by Cdc2 kinase changes the organization of the protein-DNA complex. In contrast, consecutive phosphorylation by MAP kinase, which results in a dramatic change in cHMGA conformation, has no direct effect on the complex. Because the phosphorylation of the HMGA proteins attenuates binding affinity and reduces the extent of contacts between the DNA and protein, it is likely that this process mirrors the dynamics and diversity of regulatory processes in chromatin.