David J Tremethick - Academia.edu (original) (raw)

Papers by David J Tremethick

Table S12. Results of the differential splicing analysis showing alternative first exon usage com... more Table S12. Results of the differential splicing analysis showing alternative first exon usage comparing wt with H2A.B.3 KO round spermatids. (XLSX 90 kb)

Journal of Biological Chemistry, Nov 1, 1994

Recently, using a well defined nucleosomal assembly system, we demonstrated that high mobility gr... more Recently, using a well defined nucleosomal assembly system, we demonstrated that high mobility group proteins (HMGs) 14 and 17 can organize nucleosomes into a regular array with a nucleosomal repeat length of 160-165 base pairs in vitro. Interestingly, such a short repeat length has been described for lower eukaryotes and for active chromatin. To begin to investigate how these proteins may prevent the close packing of nucleosomes, assembly reactions were carried out in which the relative amounts of HMGs 14 and 17, histones H2A and H2B, and the N1/N2.(H3, H4) complex were varied in assembly reactions. Under conditions in which histones H2A and H2B were limiting and in the absence of HMGs 14 and 17, micrococcal nuclease digestion of the assembled product produced a ladder of DNA fragments that was much less well defined and which included DNA that was associated with subnucleosomal structures. The apparent repeat length for this chromatin template was around 125 base pairs. Most interestingly, when HMGs 14 and 17 were added to this assembly reaction, "nucleosome-like" structures were reassembled as shown by the restoration of a regular, well defined ladder of DNA fragments upon micrococcal nuclease digestion. The apparent repeat length increased from 125 to approximately 145 base pairs. Analysis of the protein composition of chromatin formed in the presence or absence of HMGs 14 and 17 reveals that HMGs 14 and 17 might be able to substitute for a histone H2A-H2B dimer in a H2A/H2B-deficient nucleosome. The ability to form a regularly spaced nucleosomal template is also lost when excess HMGs 14 and 17 are used in assembly reactions. Spacing can be restored by the addition of poly(glutamate, alanine), a chemical polymer of negative charge, which may indicate that carrier proteins (specific or nonspecific) may be required for the proper incorporation of all chromatin assembly components into chromatin in vivo. Finally, although the mechanism of action is not known, HMGs 14 and 17 can partially overcome inhibition of initiation of transcription caused by the formation of nucleosomal particles deficient in histones H2A and H2B.

Humana Press eBooks, Nov 15, 2003

Journal of Biological Chemistry, Mar 1, 1990

Assembly of nucleosomes on a 5 S DNA plasmid with histone H3.H4-N1 complex and histone H2A-H2B di... more Assembly of nucleosomes on a 5 S DNA plasmid with histone H3.H4-N1 complex and histone H2A-H2B dimers causes a marked, 30-300-fold repression of 5 S RNA transcription. This repression is a time-dependent process that parallels the process of nucleosome formation. At physiological histone levels, DNA plasmids carrying nucleosomes with only histones H3 and H4 are transcriptionally permissive. The histone H3-H4 chromatin becomes transcriptionally nonpermissive when histone H2A-H2B dimers complement the nucleosome assembly reaction. H3-H4-H2A-H2B nucleosomes, but not H3-H4 nucleosomes, displace a DNA-bound transcription factor IIIA. In contrast, a preassembled 5 S RNA transcription complex is refractory to inactivation by nucleosomes.

PLOS Genetics, Mar 16, 2018

Ambient temperature affects plant growth and even minor changes can substantially impact crop yie... more Ambient temperature affects plant growth and even minor changes can substantially impact crop yields. The underlying mechanisms of temperature perception and response are just beginning to emerge. Chromatin remodeling, via the eviction of the histone variant H2A.Z containing nucleosomes, is a critical component of thermal response in plants. However, the role of histone modifications remains unknown. Here, through a forward genetic screen, we identify POWERDRESS (PWR), a SANT-domain containing protein known to interact with HISTONE DEACETYLASE 9 (HDA9), as a novel factor required for thermomorphogenesis in Arabidopsis thaliana. We show that mutations in PWR impede thermomorphogenesis, exemplified by attenuated warm temperature-induced hypocotyl/petiole elongation and early flowering. We show that inhibitors of histone deacetylases diminish temperatureinduced hypocotyl elongation, which demonstrates a requirement for histone deacetylation in thermomorphogenesis. We also show that elevated temperature is associated with deacetylation of H3K9 at the +1 nucleosomes of PHYTOCHROME INTERACTING FACTOR4 (PIF4) and YUCCA8 (YUC8), and that PWR is required for this response. There is global misregulation of genes in pwr mutants at elevated temperatures. Meta-analysis revealed that genes that are misregulated in pwr mutants display a significant overlap with genes that are H2A.Z-enriched in their gene bodies, and with genes that are differentially expressed in mutants of the components of the SWR1 complex that deposits H2A.Z. Our findings thus uncover a role for PWR in facilitating thermomorphogenesis and suggest a potential link between histone deacetylation and H2A.Z nucleosome dynamics in plants.

Nature Genetics, Apr 22, 2019

Genomic information is selectively used to direct spatial and temporal gene expression during dif... more Genomic information is selectively used to direct spatial and temporal gene expression during differentiation. Interactions between topologically associating domains (TADs) and between chromatin and the nuclear lamina organize and position chromosomes in the nucleus. However, how these genomic organizers together shape genome architecture is unclear. Here, using a dual-lineage differentiation system, we report long-range TAD–TAD interactions that form constitutive and variable TAD cliques. A differentiation-coupled relationship between TAD cliques and lamina-associated domains suggests that TAD cliques stabilize heterochromatin at the nuclear periphery. We also provide evidence of dynamic TAD cliques during mouse embryonic stem-cell differentiation and somatic cell reprogramming and of inter-TAD associations in single-cell high-resolution chromosome conformation capture (Hi-C) data. TAD cliques represent a level of four-dimensional genome conformation that reinforces the silencing of repressed developmental genes.The authors identify the formation of dynamic topologically associating domain (TAD) cliques during differentiation and reprogramming. Their analysis indicates that TAD cliques stabilize heterochromatin at the nuclear periphery.

The EMBO Journal, Apr 15, 1997

and in vitro studies, has shown that the assembly of a Divisions of 1 Biochemistry and Molecular ... more and in vitro studies, has shown that the assembly of a Divisions of 1 Biochemistry and Molecular Biology and eukaryotic promoter into chromatin can block the estab

Copyright information:Taken from "The replacement histone H2A.Z in a hype... more Copyright information:Taken from "The replacement histone H2A.Z in a hyperacetylated form is a feature of active genes in the chicken"Nucleic Acids Research 2005;33(17):5633-5639.Published online 4 Oct 2005PMCID:PMC1243646.© The Author 2005. Published by Oxford University Press. All rights reservedZ and anti-AcH2A.Z affinity purified antibodies. HB, butyrate-treated HeLa histones; CE, 15-day embryo chicken erythrocyte histones; rH2A.Z, recombinant H2A.Z. ( and ) Characterization of proteins from ChIPs using these affinity purified antibodies with nucleosomes from 10-day chicken brain tissue (10DCB). , , : nput, nbound, ound histones; Ab, carry-over products of primary antibodies.

Journal of Biological Chemistry, 1986

We have used specific in vitro transcription as a functional assay to study the effects of the ma... more We have used specific in vitro transcription as a functional assay to study the effects of the major chromosomal proteins, histones and high mobility group (HMG) proteins 1 and 2, on transcription by RNA polymerases II and III. HMG proteins 1 and 2 can stimulate transcription by both RNA polymerases II and III; maximal stimulation (up to 20-fold) is seen when HMG proteins 1 and 2 are mixed with template DNA prior to the addition of whole cell transcription lysate. HMG proteins 1 and 2 are also able to overcome inhibition of transcription caused by histones; maximal enhancement of transcription (at least 60-fold) is seen when histones and then HMG proteins 1 and 2 are added to DNA before addition of transcription lysate. This suggests that stimulation of transcription by HMG proteins 1 and 2 in the presence of histones is not due to a simple competition between histones and HMG proteins for binding to DNA. It appears likely that HMG proteins 1 and 2 stimulate transcription in a nonspecific manner, perhaps altering the template in such a way as to allow increased accessibility of transcription factors or rate of elongation for both RNA polymerases II and III.

Nature Genetics, 2019

The EMBO Journal, 1997

Genome Research, 2011

Histone H2A.Z (H2A.Z) is an evolutionarily conserved H2A variant implicated in the regulation of ... more Histone H2A.Z (H2A.Z) is an evolutionarily conserved H2A variant implicated in the regulation of gene expression; however, its role in transcriptional deregulation in cancer remains poorly understood. Using genome-wide studies, we investigated the role of promoter-associated H2A.Z and acetylated H2A.Z (acH2A.Z) in gene deregulation and its relationship with DNA methylation and H3K27me3 in prostate cancer. Our results reconcile the conflicting reports of positive and negative roles for histone H2A.Z and gene expression states. We find that H2A.Z is enriched in a bimodal distribution at nucleosomes, surrounding the transcription start sites (TSSs) of both active and poised gene promoters. In addition, H2A.Z spreads across the entire promoter of inactive genes in a deacetylated state. In contrast, acH2A.Z is only localized at the TSSs of active genes. Gene deregulation in cancer is also associated with a reorganization of acH2A.Z and H2A.Z nucleosome occupancy across the promoter regio...

Molecular and Cellular Biology, Oct 1, 1988

We describe an in vitro system, based on the Xenopus laevis oocyte supernatant of Glikin et al. (... more We describe an in vitro system, based on the Xenopus laevis oocyte supernatant of Glikin et al. (G. Glikin, I. Ruberti, and A. Worcel, Cell 37:33-41, 1984), that packages DNA into minichromosomes with regularly spaced nucleosomes containing histones H3, H4, H2A, and H2B but no histone Hi. The same supernatant also assembles the 5S RNA transcription complex; however, under the conditions that favor chromatin assembly, transcription is inhibited and a phased nucleosome forms over the 5S RNA gene. The minichromosomes that are fully loaded with nucleosomes remain refractory to transcriptional activation by 5S RNA transcription factors. Our data suggest that this repression is caused by a nucleosome covering the 5S RNA gene and that histone Hi is not required for regular nucleosome spacing or for gene repression in this system.

Journal of Biological Chemistry, Jul 1, 1992

Summary acidic patch is a critical molecular determinant required for the formation of higher ord... more Summary acidic patch is a critical molecular determinant required for the formation of higher order chromatin structures Controlling the degree of higher order chromatin fold- and that H2A.Z modulates this process.ing is a key element in partitioning the metazoan ge- Recently, we supported our prediction by demonstra- nomeintofunctionallydistinctchromosomaldomains. ting that H2A.Z alters the dynamics of the chromatin However, the mechanism of this fundamental process fiber-folding pathway in a unique way using the model is poorly understood. Our recent studies suggested 12-208 nucleosomal array system. H2A.Z facilitates in- thattheessentialhistonevariantH2A.Zandthesilenc- tramolecular folding of nucleosomal arrays to generate ing protein HP1 may function together to establish highlycompactedchromatinsecondarystructureswhile aspecializedconformationatconstitutiveheterochro- simultaneously inhibiting interfiber interactions (Fan et matic domains. We demonstrate here that HP1 is a al.,...

This article cites 52 articles, 18 of which can be accessed free

Ambient temperature influences plant growth and development and minor changes can substantially i... more Ambient temperature influences plant growth and development and minor changes can substantially impact crop yields. The underlying mechanisms for temperature perception and response are just beginning to emerge. Chromatin remodeling via the eviction of the histone variant H2A.Z in nucleosomes that alters gene expression is a critical component of thermal response in plants. However, whether chromatin-remodeling processes such as histone modifications play a global role in thermal response remains unknown. Using a combination of genetic analysis, chemical inhibition studies and RNA-seq analysis coupled with meta-analysis, here we identify POWERDRESS (PWR), a SANT-domain containing protein that is known to interact with HISTONE DEACETYLASE 9 (HDA9), as a novel key factor required for thermomorphogenesis inArabidopsis thaliana. We identify that mutations inPWRimpede thermomorphogenesis exemplified by severely attenuated temperature-induced hypocotyl/petiole elongation and early floweri...

Journal of Developmental Biology

During the emergence and radiation of complex multicellular eukaryotes from unicellular ancestors... more During the emergence and radiation of complex multicellular eukaryotes from unicellular ancestors, transcriptional systems evolved by becoming more complex to provide the basis for this morphological diversity. The way eukaryotic genomes are packaged into a highly complex structure, known as chromatin, underpins this evolution of transcriptional regulation. Chromatin structure is controlled by a variety of different epigenetic mechanisms, including the major mechanism for altering the biochemical makeup of the nucleosome by replacing core histones with their variant forms. The histone H2A variant H2A.Z is particularly important in early metazoan development because, without it, embryos cease to develop and die. However, H2A.Z is also required for many differentiation steps beyond the stage that H2A.Z-knockout embryos die. H2A.Z can facilitate the activation and repression of genes that are important for pluripotency and differentiation, and acts through a variety of different molecu...

EMBO reports

Testis‐specific regulators of chromatin function are commonly ectopically expressed in human canc... more Testis‐specific regulators of chromatin function are commonly ectopically expressed in human cancers, but their roles are poorly understood. Examination of 81 primary Hodgkin lymphoma (HL) samples showed that the ectopic expression of the eutherian testis‐specific histone variant H2A.B is an inherent feature of HL. In experiments using two HL cell lines derived from different subtypes of HL, H2A.B knockdown inhibited cell proliferation. H2A.B was enriched in both nucleoli of these HL cell lines and primary HL samples. We found that H2A.B enhanced ribosomal DNA (rDNA) transcription, was enriched at the rDNA promoter and transcribed regions, and interacted with RNA Pol I. Depletion of H2A.B caused the loss of RNA Pol I from rDNA chromatin. Remarkably, H2A.B was also required for high levels of ribosomal protein gene expression being located at the transcriptional start site and within the gene body. H2A.B knockdown reduced gene body chromatin accessibility of active RNA Pol II genes concurrent with a decrease in transcription. Taken together, our data show that in HL H2A.B has acquired a new function, the ability to increase ribosome biogenesis.

Input nucleosomes, nucleosomes immunoprecipitated with H2A.B.3 or H3K36me3 affinity puri... more Input nucleosomes, nucleosomes immunoprecipitated with H2A.B.3 or H3K36me3 affinity purified antibodies, and poly (A)-transcripts obtained from 28–30 day old mice testes were sequenced yielding 100 base pair paired-end reads (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006633#sec011" target="_blank">Material and methods</a>). (a) The individual lines represent the normalised H2A.B.3 and total input reads aligned between -1 and +10 kb from the TSS in the testis. (b) The individual line represents the normalized input nucleosome reads (mean reads per base pair per million reads mapped (RPM)) aligned between -1 and +1 kb from the intron—exon boundary for all exons in the testis ranked according their expression level (repressed, low, medium and high). The colour-map panel shows the relationship between colour and the gene expression rank. (c) Normalized testis H2A.B.3 ChIP-Seq reads ranked according to their expression level aligned with the intron—exon boundary. (d) At each base position relative to the intron exon-boundary, a linear model was fitted to the mean H2A.B.3/input ratio versus gene log expression across all intron—exon boundaries, and the slope of the fitted model plotted for the testis. (e) Normalized testis H3K36me3 ChIP-Seq reads ranked according to their expression level aligned with the intron—exon boundary. (f) Pearson correlation of the log coverage, across 50 base pair windows, was calculated between testes H2A.B.3 ChIP-Seq reads and H3K36me3 ChIP-Seq reads for each base pair relative to the intron—exon boundary. (g) Normalized testis H3K36me3 ChIP-Seq reads ranked according to the incorporation of H2A.B.3 (very low, low, medium and high) aligned with the intron—exon boundary. 95% confidence bands are shown in grey.</p