Different 3'-end processing produces two independently regulated mRNAs from a single H1 histone gene

Loss of Histone Locus Bodies in the Mature Hemocytes of Larval Lymph Gland Result in Hyperplasia of the Tissue in mxc Mutants of Drosophila

Mutations in the multi sex combs (mxc) gene in Drosophila results in malignant hyperplasia in larval hematopoietic tissues, called lymph glands (LG). mxc encodes a component of the histone locus body (HLB) that is essential for cell cycle-dependent transcription and processing of histone mRNAs. The mammalian nuclear protein ataxia-telangiectasia (NPAT) gene, encoded by the responsible gene for ataxia telangiectasia, is a functional Mxc orthologue. However, their roles in tumorigenesis are unclear. Genetic analyses of the mxc mutants and larvae having LG-specific depletion revealed that a reduced activity of the gene resulted in the hyperplasia, which is caused by hyper-proliferation of immature LG cells. The depletion of mxc in mature hemocytes of the LG resulted in the hyperplasia. Furthermore, the inhibition of HLB formation was required for LG hyperplasia. In the mutant larvae, the total mRNA levels of the five canonical histones decreased, and abnormal forms of polyadenylated histone mRNAs, detected rarely in normal larvae, were generated. The ectopic expression of the polyadenylated mRNAs was sufficient for the reproduction of the hyperplasia. The loss of HLB function, especially 3-end processing of histone mRNAs, is critical for malignant LG hyperplasia in this leukemia model in Drosophila. We propose that mxc is involved in the activation to induce adenosine deaminase-related growth factor A (Adgf-A), which suppresses immature cell proliferation in LG.

sCLIP-an integrated platform to study RNA-protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs

RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here, we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing. sCLIP exploits linear amplification of the immunoprecipitated RNA improving the complexity of the sequencing-library despite significantly reducing the amount of input material and omitting several purification steps. Additionally, it permits a radiolabel-free visualization of immunoprecipitated RNA. In a proof of concept, we identify that CSTF2tau binds many previously not recognized RNAs including histone, snoRNA and snRNAs. CSTF2tau-binding is associated with internal oligoadenylation resulting in shortened snRNA isoforms subjected to rapid degradation. We provide evidence for a new mechanism whereby CSTF2tau controls the abundance of snRNAs resulting in alternative splicing of several RNAs including ANK2 with critical roles in tumorigenesis and cardiac function. Combined with a bioinformatic pipeline sCLIP thus uncovers new functions for established RBPs and fosters the illumination of RBP-protein interaction landscapes in health and disease.

A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues

Histone proteins are synthesized in large amounts during S-phase to package the newly replicated DNA, and are among the most stable proteins in the cell. The replication-dependent (RD)-histone mRNAs expressed during S-phase end in a conserved stem-loop rather than a polyA tail. In addition, there are replication-independent (RI)-histone genes that encode histone variants as polyadenylated mRNAs. Most variants have specific functions in chromatin, but H3.3 also serves as a replacement histone for damaged histones in long-lived terminally differentiated cells. There are no reported replacement histone genes for histones H2A, H2B or H4. We report that a subset of RD-histone genes are expressed in terminally differentiated tissues as polyadenylated mRNAs, likely serving as replacement histone genes in long-lived non-dividing cells. Expression of two genes, HIST2H2AA3 and HIST1H2BC, is conserved in mammals. They are expressed as polyadenylated mRNAs in fibroblasts differentiated in vitro, but not in serum starved fibroblasts, suggesting that their expression is part of the terminal differentiation program. There are two histone H4 genes and an H3 gene that encode mRNAs that are polyadenylated and expressed at 5- to 10-fold lower levels than the mRNAs from H2A and H2B genes, which may be replacement genes for the H3.1 and H4 proteins.

Role of H1 linker histones in mammalian development and stem cell differentiation

H1 linker histones are key chromatin architectural proteins facilitating the formation of higher order chromatin structures. The H1 family constitutes the most heterogeneous group of histone proteins, with eleven non-allelic H1 variants in mammals. H1 variants differ in their biochemical properties and exhibit significant sequence divergence from one another, yet most of them are highly conserved during evolution from mouse to human. H1 variants are differentially regulated during development and their cellular compositions undergo dramatic changes in embryogenesis, gametogenesis, tissue maturation and cellular differentiation. As a group, H1 histones are essential for mouse development and proper stem cell differentiation. Here we summarize our current knowledge on the expression and functions of H1 variants in mammalian development and stem cell differentiation. Their diversity, sequence conservation, complex expression and distinct functions suggest that H1s mediate chromatin reprogramming and contribute to the large variations and complexity of chromatin structure and gene expression in the mammalian genome.

What is the role of histone H1 heterogeneity? A functional model emerges from a 50 year mystery

For the past 50 years, understanding the function of histone H1 heterogeneity has been mired in confusion and contradiction. Part of the reason for this is the lack of a working model that tries to explain the large body of data that has been collected about the H1 subtypes so far. In this review, a global model is described largely based on published data from the author and other researchers over the past 20 years. The intrinsic disorder built into H1 protein structure is discussed to help the reader understand that these histones are multi-conformational and adaptable to interactions with different targets. We discuss the role of each structural section of H1 (as we currently understand it), but we focus on the H1's C-terminal domain and its effect on each subtype's affinity, mobility and compaction of chromatin. We review the multiple ways these characteristics have been measured from circular dichroism to FRAP analysis, which has added to the sometimes contradictory assumptions made about each subtype. Based on a tabulation of these measurements, we then organize the H1 variants according to their ability to condense chromatin and produce nucleosome repeat lengths amenable to that compaction. This subtype variation generates a continuum of different chromatin states allowing for fine regulatory control and some overlap in the event one or two subtypes are lost to mutation. We also review the myriad of disparate observations made about each subtype, both somatic and germline specific ones, that lend support to the proposed model. Finally, to demonstrate its adaptability as new data further refines our understanding of H1 subtypes, we show how the model can be applied to experimental observations of telomeric heterochromatin in aging cells.

PPS: A computing engine to find Palindromes in all Protein sequences

The primary structure of a protein molecule comprises a linear chain of amino acid residues. Certain parts of this linear chain are unique in nature and function. They can be classified under different categories and their roles studied in detail. Two such unique categories are the palindromic sequences and the Single Amino Acid Repeats (SAARs), which plays a major role in the structure, function and evolution of the protein molecule. In spite of their presence in various protein sequences, palindromes have not yet been investigated in detail. Thus, to enable a comprehensive understanding of these sequences, a computing engine, PPS, has been developed. The users can search the occurrences of palindromes and SAARs in all the protein sequences available in various databases and can view the three-dimensional structures (in case it is available in the known three-dimensional protein structures deposited to the Protein Data Bank) using the graphics plug-in Jmol. The proposed server is the first of its kind and can be freely accessed through the World Wide Web.

AVAILABILITY

URL http://pranag.physics.iisc.ernet.in/pps/

An algorithm to find all palindromic sequences in proteins

A palindrome is a set of characters that reads the same forwards and backwards. Since the discovery of palindromic peptide sequences two decades ago, little effort has been made to understand its structural, functional and evolutionary significance. Therefore, in view of this, an algorithm has been developed to identify all perfect palindromes (excluding the palindromic subset and tandem repeats) in a single protein sequence. The proposed algorithm does not impose any restriction on the number of residues to be given in the input sequence. This avant-garde algorithm will aid in the identification of palindromic peptide sequences of varying lengths in a single protein sequence.

H1 linker histone promotes epigenetic silencing by regulating both DNA methylation and histone H3 methylation

Epigenetic silencing in mammals involves DNA methylation and posttranslational modifications of core histones. Here we show that the H1 linker histone plays a key role in regulating both DNA methylation and histone H3 methylation at the H19 and Gtl2 loci in mouse ES cells. Some, but not all, murine H1 subtypes interact with DNA methyltransferases DNMT1 and DNMT3B. The interactions are direct and require a portion of the H1 C-terminal domain. Expression of an H1 subtype that interacts with DNMT1 and DNMT3B in ES cells leads to their recruitment and DNA methylation of the H19 and Gtl2 imprinting control regions. H1 also interferes with binding of the SET7/9 histone methyltransferase to the imprinting control regions, inhibiting production of an activating methylation mark on histone H3 lysine 4. H1-dependent recruitment of DNMT1 and DNMT3B and interference with the binding of SET7/9 also were observed with chromatin reconstituted in vitro. The data support a model in which H1 plays an active role in helping direct two processes that lead to the formation of epigenetic silencing marks. The data also provide evidence for functional differences among the H1 subtypes expressed in somatic mammalian cells.

Early evolution of histone mRNA 3' end processing

The replication-dependent histone mRNAs in metazoa are not polyadenylated, in contrast to the bulk of mRNA. Instead, they contain an RNA stem-loop (SL) structure close to the 3' end of the mature RNA, and this 3' end is generated by cleavage using a machinery involving the U7 snRNP and protein factors such as the stem-loop binding protein (SLBP). This machinery of 3' end processing is related to that of polyadenylation as protein components are shared between the systems. It is commonly believed that histone 3' end processing is restricted to metazoa and green algae. In contrast, polyadenylation is ubiquitous in Eukarya. However, using computational approaches, we have now identified components of histone 3' end processing in a number of protozoa. Thus, the histone mRNA stem-loop structure as well as the SLBP protein are present in many different protozoa, including Dictyostelium, alveolates, Trypanosoma, and Trichomonas. These results show that the histone 3' end processing machinery is more ancient than previously anticipated and can be traced to the root of the eukaryotic phylogenetic tree. We also identified histone mRNAs from both metazoa and protozoa that are polyadenylated but also contain the signals characteristic of histone 3' end processing. These results provide further evidence that some histone genes are regulated at the level of 3' end processing to produce either polyadenylated RNAs or RNAs with the 3' end characteristic of replication-dependent histone mRNAs.

Characterization, localization and possible anti-inflammatory function of rat histone H4 mRNA variants

Two histone H4 mRNA variants, H4-v.1 and histogranin mRNAs, were detected in the rat genome and measured in various tissues and isolated alveolar macrophages. Medium to high levels of both mRNAs were present in the liver, adrenal glands, thymus, bone marrow and alveolar macrophages. H4-v.1 cDNA contained an open reading frame that coded for unmodified whole histone H4, whereas histogranin cDNA lacked the first ATG codon and contained an open reading frame that coded for modified (Thr89) H4-(84-102). The two genes displayed a sequence homologous (> 80%) to the open reading frame of core H4 somatic (H4s) and H4 germinal (H4g) and their variant nature was supported by the absence of histone consensus palindromic and purine-rich sequences in the proximal 3'UTR, and the presence of a polyadenylation signal in the distal 3'UTR and of specific upstream transcription factor-binding sites. H4-v.1 and histogranin transcripts, but not H4s transcript, were selectively induced by lipopolysaccharide and/or interferon gamma in alveolar macrophages. In vitro transcription/translation experiments with H4-v.1 and histogranin cDNA pCMV constructs produced peptides with the molecular mass (2 kDa) of the alternative histone H4 translation product which, like synthetic H4-(86-100) and [Thr89]H4-(86-100) or rat histogranin, inhibited lipopolysaccharide-induced prostaglandin E(2) release from rat alveolar macrophages. The synthetic peptides also inhibited the secretion of the CXC chemokine interleukin-8 (GRO/CINC-1) in response to lipopolysaccharide. The presence of H4-v.1 and histogranin mRNAs in tissues wherein immune reactions take place and the inhibitory effects of their translation products on prostaglandin E(2) and interkeukin-8 secretion by activated alveolar macrophages suggest an anti-inflammatory function.

Correlation between the expression of the histone H4 mRNA variant H4-v.1 and the levels of histone H4-(86-100) and H4-(89-102) (OGP) in various rat tissues and alveolar macrophages

We studied the expression of the osteogenic and antinociceptive C-terminal histone H4-related peptide fragments, H4-(89-102) (OGP) and H4-(86-100), respectively, within various rat tissues and isolated alveolar macrophages (AM) by radioimmunoassay (RIA). OGP was located mainly within the bone marrow, spleen, thymus, and lungs whereas H4-(86-100) was more concentrated within the bone marrow, lymph nodes, spinal cord, pituitaries and thymus. The expression pattern of the two peptides showed similarities with the tissue expression pattern of the histone H4 mRNA variant H4-v.1. In rat AM, OGP and H4-(86-100) levels were significantly stimulated (2.6- and 1.9-fold, respectively) by LPS (1 microg/ml), along with H4-v.1 mRNA (4.1-fold), but not whole histone H4 (1.1-fold) nor total histone H4 mRNA (1.1-fold). The results suggest that H4-v.1 mRNA may play a role in the synthesis of the naturally occurring peptides H4-(86-100) and OGP via the alternative translation product H4-(84-102), but not whole histone H4.

Comparative studies between in vivo and in vitro spermatogenesis of Japanese eel (Anguilla japonica)

In order to check the quality of in vitro spermatogenesis of Japanese eel, in vitrol 1-ketotestosterone (11-KT) induced spermatogenesis was compared with in vivo spermatogenesis induced by a single injection of human chorionic gonadotropin (hCG) in detail. DNA contents of germ cells from in vitro and in vivo testicular fragments were compared using flow cytometry. Since the in vitro result of flow cytometry showed prominent 1C peak including spermatozoa and spermatids, the reduction of DNA by meiosis was assumed to progress normally, (i.e., haploid spermatozoa were produced in this in vitro system). In the testes of in vitro culture, however, spermatozoa were not released into lumen. Furthermore, the number of mitotic divisions of the in vitro experiment (6 divisions) was fewer than that of in vivo (10 divisions). In electron microscopy observations, both of in vivo and in vitro spermatozoon had a crescent-shaped nucleus with a flagellum, and a single large spherical mitochondrion. However, the elongation of the sperm head was not sufficient and the mitochondrion was not always located at the anterior end as is observed for the spermatozoa obtained from hCG injected eels. Eel spermatogenesis related substance-11 (eSRS11) is homologue of histone H1 which is up-regulated during spermatogenesis. Using this probe, in vitro spermatogenesis was also evaluated in molecular levels. In Northern blot analysis, eSRS11 mRNA was detected in both in vivo and in vitro testes. However, the expression of in vitro was much weaker than that of in vivo. These differences indicate that the stimulation of 11-KT is not sufficient, and another factors are needed to induce complete spermatogenesis in vitro.

A compendium of the histone H1 family of somatic subtypes: An elusive cast of characters and their characteristics

The last 35 years has seen a substantial amount of information collected about the somatic H1 subtypes, yet much of this work has been overshadowed by research into highly divergent isoforms of H1, such as H5. Reports from several laboratories in the past few years have begun to call into question some of the traditional views regarding the general function of linker histones and their heterogeneity. Hence, the impression in some circles is that less is known about these ubiquitous nuclear proteins as compared with the core histones. The goal of the following review is to acquaint the reader with the ubiquitous somatic H1s by categorizing them and their characteristics into several classes. The reasons for our current state of misunderstanding is put into a historical context along with recent controversies centering on the role of H1 in the nucleus. Finally, we propose a model that may explain the functional role of H1 heterogeneity in chromatin compaction.Key words: histone H1, linker histones, chromatin organization, chromatin compaction, heat shock.

Linker histone transitions during mammalian oogenesis and embryogenesis

A unique characteristic of the oocyte is that, although it is a differentiated cell, it can to give rise to a population of undifferentiated embryonic cells. This transition from a differentiated to a totipotential condition is thought to be mediated in part by changes in chromatin composition or configuration. In many non-mammalian organisms, oocytes contain unique subtypes of the linker histone H1, which are replaced in early embryos by the so-called somatic histone H1 subtypes. We review evidence that such histone H1 subtype switches also occur in mammals. Immunologically detectable somatic H1 is present in mitotically proliferating oogonia but gradually becomes undetectable after the oocytes enter meiosis. Immunoreactive somatic H1 remains undetectable throughout oogenesis and the early cell cycles after fertilization. Following activation of the embryonic genome, it is assembled onto chromatin. In contrast to the absence of immunoreactive protein, mRNAs encoding each of the five mammalian somatic H1 subtypes are present in growing oocytes and newly fertilized embryos, indicating that post-transcriptional mechanisms regulate expression of these genes. This maternal mRNA is degraded at the late 2-cell stage, and embryonically encoded mRNAs accumulate after embryos reach the 4-cell stage. During the period when somatic H1 is not detectable, oocytes and embryos contain mRNA encoding a sixth subtype, histone H1(0) which accumulates in differentiated somatic cells, and the nuclei can be stained with an H1(0)-specific antibody. We propose that the linker histone composition of the oocyte lineage resembles that of other mammalian cells, namely, that the somatic H1 subtypes predominate in mitotically active oogonia, that histone H1(0) becomes prominent in differentiated oocytes, and that following fertilization and transcriptional activation of the embryonic somatic H1 genes, the somatic H1 subtypes are reassembled onto chromatin of the embryonic cells. Potential functions of these linker histone subtype switches are discussed, including stabilization by H1(0) of the differentiated state of the oocytes, protection of the oocyte chromatin from factors that remodel sperm chromatin after fertilization, and restoration by the incorporation of the somatic H1 subtypes of the totipotential state of embryonic nuclei.

Regulated transcription of the histone H2B genes of Trypanosoma brucei

In Trypanosoma brucei, the genes encoding histone H2B are organized in a cluster of about 10-15 tandemly linked copies per haploid genome. The H2B transcripts are processed by trans-splicing and polyadenylation, and encode a polypeptide of 111 residues with a molecular mass of 12.5 kDa. H2B mRNAs are differentially expressed during the parasite life-cycle and are present at higher levels in dividing procyclic and bloodstream slender forms than in the nondividing bloodstream stumpy forms. Analysis of H2B mRNA levels during the synchronous differentiation from stumpy to procyclics forms revealed that the abundance of these transcripts is regulated through the cell-cycle, reaching maximum levels during S-phase. Addition of hydroxyurea to procyclic forms in culture specifically decreased H2B mRNA levels by about twofold, an effect not linked to its 3' untranslated region. Inhibition of protein synthesis prevented this decrease.

Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis

Formation of mRNA 3' ends in eukaryotes requires the interaction of transacting factors with cis-acting signal elements on the RNA precursor by two distinct mechanisms, one for the cleavage of most replication-dependent histone transcripts and the other for cleavage and polyadenylation of the majority of eukaryotic mRNAs. Most of the basic factors have now been identified, as well as some of the key protein-protein and RNA-protein interactions. This processing can be regulated by changing the levels or activity of basic factors or by using activators and repressors, many of which are components of the splicing machinery. These regulatory mechanisms act during differentiation, progression through the cell cycle, or viral infections. Recent findings suggest that the association of cleavage/polyadenylation factors with the transcriptional complex via the carboxyl-terminal domain of the RNA polymerase II (Pol II) large subunit is the means by which the cell restricts polyadenylation to Pol II transcripts. The processing of 3' ends is also important for transcription termination downstream of cleavage sites and for assembly of an export-competent mRNA. The progress of the last few years points to a remarkable coordination and cooperativity in the steps leading to the appearance of translatable mRNA in the cytoplasm.

Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis

Formation of mRNA 3' ends in eukaryotes requires the interaction of transacting factors with cis-acting signal elements on the RNA precursor by two distinct mechanisms, one for the cleavage of most replication-dependent histone transcripts and the other for cleavage and polyadenylation of the majority of eukaryotic mRNAs. Most of the basic factors have now been identified, as well as some of the key protein-protein and RNA-protein interactions. This processing can be regulated by changing the levels or activity of basic factors or by using activators and repressors, many of which are components of the splicing machinery. These regulatory mechanisms act during differentiation, progression through the cell cycle, or viral infections. Recent findings suggest that the association of cleavage/polyadenylation factors with the transcriptional complex via the carboxyl-terminal domain of the RNA polymerase II (Pol II) large subunit is the means by which the cell restricts polyadenylation to Pol II transcripts. The processing of 3' ends is also important for transcription termination downstream of cleavage sites and for assembly of an export-competent mRNA. The progress of the last few years points to a remarkable coordination and cooperativity in the steps leading to the appearance of translatable mRNA in the cytoplasm.

Intronless mRNA transport elements may affect multiple steps of pre-mRNA processing

We have reported recently that a small element within the mouse histone H2a-coding region permits efficient cytoplasmic accumulation of intronless beta-globin cDNA transcripts. This sequence lowers the levels of spliced products from intron-containing constructs and can functionally replace Rev and the Rev-responsive element (RRE) in the nuclear export of unspliced HIV-1-related mRNAs. In work reported here, we further investigate the molecular mechanisms by which this element might work. We demonstrate here through both in vivo and in vitro assays that, in addition to promoting mRNA nuclear export, this element acts as a polyadenylation enhancer and as a potent inhibitor of splicing. Surprisingly, two other described intronless mRNA transport elements (from the herpes simplex virus thymidine kinase gene and hepatitis B virus) appear to function in a similar manner. These findings prompt us to suggest that a general feature of intronless mRNA transport elements might be a collection of phenotypes, including the inhibition of splicing and the enhancement of both polyadenylation and mRNA export.

Expression of murine H1 histone genes during postnatal development

Murine genes encoding the seven H1 histone isoforms H1.1-H1.5, H1(o) and H1t have been isolated and sequenced. We have established expression patterns of these genes in several tissues during postnatal development. For that analysis, RNase protection assay rather than Northern blot hybridization was used, since the sequences of these genes are highly similar and would cross-hybridize under Northern blot conditions. Expression patterns of H1.1 to H1.5 and H1(o) were determined in tissues of animals at days 5, 9 and 20 after birth and of adult mice. In addition, RNA was analyzed in three mouse cell lines (NIH3T3, P19, TM4). Transcription of the subtype genes H1.2 and H1.4 was found in all tissues and cell lines studied. The most varied expression patterns were obtained with the H1.1 subtype. H1.1 mRNA was found at high concentrations in thymus and spleen throughout development and in testis beginning with a low expression in 5-day-old animals and increasing levels in testis RNA from 9- and 20-day-old and adult mice. H1(o) mRNA was found primarily in highly differentiated tissues with concentrations decreasing from 5-day-old to adult animals.

The high molecular weight chromatin proteins of winter flounder sperm are related to an extreme histone H1 variant

Unlike mammals, birds, and most other fishes, winter flounder completes spermatogenesis without replacing its germ cell histones with protamines. Instead, during spermiogenesis, these fish produce a family of high molecular weight (80,000-200,000) basic nuclear proteins (HMrBNPs) that bind to sperm chromatin containing the normal complement of histones. These large, basic proteins are built up of tandem iterations of oligopeptide repeats that contain phosphorylatable DNA-binding motifs. Although the HMrBNPs have no obvious homology to histones, protamines, or other sperm-specific chromatin proteins, we report here the isolation of a clone (2B) from a winter flounder genomic DNA library that establishes a link between the HMrBNPs and histone H1. The 2B sequence contains an open reading frame, which, when conceptually translated, encodes a 265-residue protein. At its N terminus the translation product contains numerous simple repeats that match the oligopeptides contained within the HMrBNPs. Unexpectedly, the C terminus of the putative protein shows 66% identity and 76% conservation to the histone H1 globular domain. This connection suggests that the HMrBNPs may have originated from the extended N-terminal tail region of a testis-specific, H1-like linker histone.

Poly A-containing histone H4 mRNA variant (H4-v. 1): isolation and sequence determination from bovine adrenal medulla

A histone H4 cDNA variant (H4-v.1) was cloned from a bovine adrenal medullary phage library using PCR as a method of detection. The isolated clones contained a short 5' untranslated region (UTR) followed by the histone H4 coding region and a long atypical 3'UTR. The 3'UTR comprised the palindromic and purine-rich sequences typical of cell-cycle dependent histone mRNAs, and a 1.1 kb extension downstream of the palindromic sequence ending with a poly(A) track typical of cell-cycle independent histone mRNAs. Northern blot and RT-PCR analyses indicate that the transcript is fully expressed in bovine adrenal medulla. Thus, bovine histone H4-v.1 mRNA represents the first example of a histone H4 transcript that contains both 3'UTR characteristics of cell-cycle dependent and cell-cycle independent histone mRNAs.

Differential effect of H1 variant overproduction on gene expression is due to differences in the central globular domain

The in vivo overproduction of two mouse histone H1 variants in homologous mouse fibroblasts has opposite effects on gene expression. Overproduction of H1(0) results in repression of transcript levels of all polymerase II genes tested. In contrast, overproduction of H1c results in elevated levels of transcripts. We created a series of chimeric H1 genes in which the regions encoding the three structural domains common to this family of these proteins were systematically switched. Overexpression of these genes in vivo resulted in the accumulation of large amounts of the chimeric H1 in chromatin. Analysis of the effects of overproduction of these proteins revealed that the differential effect of H1 variant overproduction on gene expression is due to differences in the central globular domain.

The histone H1 genes of the dipteran insect, Chironomus thummi, fall under two divergent classes and encode proteins with distinct intranuclear distribution and potentially different functions

Four histone H1 genes of the midge, Chironomus thummi piger, and three H1 genes of the subspecies C. thummi thummi have been cloned and assigned to the four different H1 proteins from C. thummi larvae. Together with an earlier cloned H1 gene from C. thummi thummi [Hankeln, T. & Schmidt, E. R. (1991) Chromosoma 101, 25-31], these genes probably constitute the complete complement of H1 genes in both subspecies. They were found to fall under two classes that differ remarkably in their gene copy numbers, genomic organization, structure of flanking sequences, codon usage, and expression during embryonic development, and that encode H1 proteins of divergent structure. Histone H1 I-1 contains an inserted sequence, KAPKAPKAPKSPKAE in C. thummi piger, and KAPKAPKSPKAE in C. thummi thummi, that is lacking in the other H1 variants, H1 II-1, H1 II-2, and H1 III-1. In the immediate neighbourhood to the inserted sequence, a substitution in the H1 I-1 protein sequence dramatically enhances the potential to form a reversed turn. In early development, H1 I-1 is expressed at a higher rate than the other H1 genes. The transcripts have a size of about 1 kb; in addition, the H1 I-1 gene exhibited two minor transcripts of about 2.5 and > 3 kb size in middle blastoderm that are possibly polyadenylated. Together with our earlier finding that histone H1 I-1 is found in a limited number of polytene chromosome bands whereas the other H1 histones are uniformly distributed in chromatin, these results intimate functional differences between the two classes of H1 genes and their products.

The mouse histone H2a gene contains a small element that facilitates cytoplasmic accumulation of intronless gene transcripts and of unspliced HIV-1-related mRNAs

Histone mRNAs are naturally intronless and accumulate efficiently in the cytoplasm. To learn whether there are cis-acting sequences within histone genes that allow efficient cytoplasmic accumulation of RNAs, we made recombinant constructs in which sequences from the mouse H2a gene were cloned into a human beta-globin cDNA. By using transient transfection and RNase protection analysis, we demonstrate here that a 100-bp sequence within the H2a coding region permits efficient cytoplasmic accumulation of the globin cDNA transcripts. We also show that this sequence appears to suppress splicing and can functionally replace Rev and the Rev-responsive element in the cytoplasmic accumulation of unspliced HIV-1-related mRNAs. Like the Rev-responsive element, this sequence acts in an orientation-dependent manner. We thus propose that the sequence identified here may be a member of the cis-acting elements that facilitate the cytoplasmic accumulation of naturally intronless gene transcripts.

The mouse histone H1 genes: gene organization and differential regulation

There are six mouse histone H1 genes present in the histone gene cluster on mouse chromosome 13. These genes encode five histone H1 variants expressed in somatic cells, H1a to H1e, and the testis-specific H1t histone. Two of the genes that have not been assigned previously to the five somatic H1 subtypes have been identified as encoding the H1b and H1d subtypes. Three of the H1 genes, H1a, H1c and H1t, are present on an 80 kb segment of DNA that contains nine core histone genes. Two others, H1d and H1e, are present in a second patch, while the H1b gene is at least 500 kb away in a patch containing 14 core histone genes. The histone H1 genes are differentially expressed. All five genes for the somatic histone H1 proteins are expressed in exponentially growing cells. However, the levels of H1a, H1b and H1d mRNAs are greatly reduced in cells that are terminally differentiated or arrested in G0, while the H1c and H1e mRNAs continue to be expressed. In addition to the major RNA that ends at the stem-loop, the H1c gene expresses a longer, polyadenylated mRNA in differentiated cells, although in varying amounts. None of the other histone H1 genes encodes detectable amounts of polyadenylated mRNAs.

The S.//.A.IG amino acid motif is present in a replication dependent late H3 histone variant of P. lividus sea urchin

A novel gene encoding a new H3 histone varian (H3L) has been identified in P. lividus sea urchin embryo. It encodes a H3 histone protein showing the S.//.A.IG amino acid motif typical of the replication independent H3.3 variants but in a mRNA showing the 3' terminal stem-loop nucleotide sequence that is typical of the replication dependent variants. The gene is intronless, the corresponding short transcript is non-polyadenyl ated and its expression is replication dependent with a timing of late variant. The new H3 variant is expressed as a minor component with respect to a major replication dependent late H3 histone here identified by partial cDNA sequence. These results show that classification of histones in replication dependent and independent variants only on the basis of their amino acid sequences should be reconsidered.

Two types of polyadenated mRNAs are synthesized from Drosophila replication-dependent histone genes

The polyadenylation of replication-dependent histone H2B, H3 and H4 mRNAs in Drosophila melanogaster was analysed. Two types of mRNAs, containing a poly(A) tail, can be detected in addition to non-polyadenylated messengers, which represent the majority of replication-dependent histone mRNAs. Firstly, conventional polyadenylation signals, localized downstream from the stem-loop region, are used to produce polyadenylated mRNAs. The messengers of this type, generated from the D. melanogaster H2B gene, are preferentially synthesized in the testis of the fly. Secondly, a distinct type of polyadenylated histone mRNA has been identified. This mRNA, which is present in many different tissues and constitutes a minor part of the total histone mRNA pool, contains a short poly(A) tail, added to the end of the 3' terminal stem-loop structure, which is in most cases lacking several nucleotides from its 3' end. The sites of polyadenylation within the stem-loop are not preceded by a normal polyadenylation signal. The possible functions of the polyadenylated histone transcripts are discussed.

Chromatin modifications during oogenesis in the mouse: removal of somatic subtypes of histone H1 from oocyte chromatin occurs post-natally through a post-transcriptional mechanism

We examined the distribution of the somatic subtypes of histone H1 and the variant subtype, H1(0), and their encoding mRNAs during oogenesis and early embryogenesis in the mouse. As detected using immunocytochemistry, somatic H1 was present in the nuclei of oocytes of 18-day embryos. Following birth, however, somatic H1 became less abundant in both growing and non-growing oocytes, beginning as early as 4 days of age in the growing oocytes, and was scarcely detectable by 19 days. Together with previous results, this defines a period of time when somatic H1 is depleted in oocytes, namely, from shortly after birth when the oocytes are at prophase I until the 4-cell stage following fertilization. At the stages when somatic H1 was undetectable, oocyte nuclei could be stained using an antibody raised against histone H1(0), which suggests that this may be a major linker histone in these cells. In contrast to the post-natal loss of somatic H1 protein, mRNAs encoding four (H1a, H1b, H1d, H1e) of the five somatic subtypes were present, as detected using RT-PCR in growing oocytes of 9-day pups, and all five subtypes including H1c were present in fully grown oocytes of adults. All five subtypes were also present in embryos, both before and after activation of the embryonic genome. mRNA encoding H1(0) was also detected in oocytes and early embryos. Whole-mount in situ hybridization using cloned H1c and H1e cDNAs revealed that the mRNAs were present in the cytoplasm of oocytes and 1-cell embryos, in contrast to the sea urchin early embryo where they are sequestered in the cell nucleus. We suggest that, as in many somatic cell types, the chromatin of mouse oocytes becomes depleted of somatic H1 and relatively enriched in histone H1(0) postnatally, and that somatic H1 is reassembled onto chromatin in cleavage-stage embryos. The post-natal loss of somatic H1 appears to be regulated post-transcriptionally by a mechanism not involving nuclear localization.

Differential effect of H1 variant overexpression on cell cycle progression and gene expression

To identify functional differences among non-allelic variants of the mammalian H1 linker histones a system for the overexpression of individual H1 variants in vivo was developed. Mouse 3T3 cells were transformed with an expression vector containing the coding regions for the H1c or H10 variant under the control of an inducible promoter. Stable, single colony transformants, in which the normal stoichiometry of H1 variants was perturbed, displayed normal viability, unaltered morphology and no long-term growth arrest. However, upon release from synchronization at different points in the cell cycle transformants significantly overproducing H10 exhibited transient inhibition of both G1 and S phase progression. Overexpression of H1c to comparable levels had no effect on cell cycle progression. Analysis of transcript levels for several cell cycle-regulated and housekeeping genes indicated that overexpression of H10 resulted in significantly reduced expression of all genes tested. Surprisingly, overexpression of H1c to comparable levels resulted in either a negligible effect or, in some cases, a dramatic increase in transcript levels. These results support the suggestion that functional differences exist among H1 variants.

A proline-rich TGF-beta-responsive transcriptional activator interacts with histone H3

The molecular mechanisms involved in the regulation of gene expression by transforming growth factor-beta (TGF-beta) have been analyzed. We show that TGF-beta specifically induces the activity of the proline-rich trans-activation domain of CTF-1, a member of the CTF/NF-I family of transcription factors. A TGF-beta-responsive domain (TRD) in the proline-rich transcriptional activation sequence of CTF-1 was shown to mediate TGF-beta induction in NIH-3T3 cells. Mutagenesis studies indicated that this domain is not the primary target of regulatory phosphorylations, suggesting that the growth factor may regulate a CTF-1-interacting protein. A two-hybrid screening assay identified a nucleosome component, histone H3, as a specific CTF-1-interacting protein in yeast. Furthermore, the CTF-1 trans-activation domain was shown to interact with histone H3 in both transiently and stably transfected mammalian cells. This interaction requires the TRD, and it appears to be upregulated by TGF-beta in vivo. Moreover, point mutations in the TRD that inhibit TGF-beta induction also reduce interaction with histone H3. In vitro, the trans-activation domain of CTF-1 specifically contacts histone H3 and oligomers of histones H3 and H4, and full-length CTF-1 was shown to alter the interaction of reconstituted nucleosomal cores with DNA. Thus, the growth factor-regulated trans-activation domain of CTF-1 can interact with chromatin components through histone H3. These findings suggest that such interactions may regulate chromatin dynamics in response to growth factor signaling.

An upstream control region required for inducible transcription of the mouse H1(zero) histone gene during terminal differentiation

The replacement linker histone H1 (zero) is associated with terminal differentiation in many mammalian cell types, and its accumulation in chromatin may contribute to transcriptional repression occurring during terminal differentiation. H1 (zero) also accumulates in a variety of cell culture lines undergoing terminal differentiation. During in vitro mouse erythroleukemia cell differentiation, H1 (zero) gene expression is induced very rapidly, prior to the time when the cells actually commit to terminal differentiation. We have used a combination of transfection assays and in vitro DNA-protein interaction studies to identify nuclear protein binding sites in the H1 (zero) promoter that control expression and induction of the H1(zero) gene in mouse erythroleukemia cells. The results indicate that transcription of the H1 (zero) gene is controlled by three elements present in the upstream region of the promoter between positions -305 and -470. Site-directed mutagenesis of each of these elements showed that one of them controls inducibility of the gene in differentiating cells. The other two elements in the upstream control region affect primarily the level of transcription of the gene in undifferentiated and differentiating cells. These two elements share a DNA sequence motif consisting of a (dG)6 tract contained in an eight-base consensus, (A/C)GGGGGG(A/C). Additional copies of this motif are present elsewhere in the H1 (zero) promoter.

An alternative pathway of histone mRNA 3' end formation in mouse round spermatids

During mammalian spermiogenesis, the post-meiotic stage of spermatogenesis, histones are replaced by protamines on the DNA. Despite this histone elimination, novel polyadenylated histone transcripts were detected in mouse round spermatids. Sequence analysis of a spermatid-specific H2a cDNA clone indicated that it was derived from a mRNA of a replication-dependent histone gene even though its transcript was not polyadenylated in somatic and earlier spermatogenic cells. In round spermatids, both the hairpin and purine-rich elements in the 3' untranslated region of the somatic pre-mRNA were retained in the mature poly(A)+ mRNA transcripts. Polyadenylation occurred downstream of the purine-rich element and was not preceded by the somatic AATAAA polyadenylation signal sequence. While polyadenylated histone transcripts from replication-dependent genes have been observed previously in somatic cells, characteristics of this type of 3'-end formation in mammalian round spermatids were unique. In particular, a specific replication-dependent H2a gene was transcribed either as a polyadenylated or non-polyadenylated transcript in these cells, suggesting that the type of transcript present was dependent on the RNA sequence. Finally, both poly(A)- and poly(A)+ mRNAs were found on polyribosomes from round spermatids, indicating that histones were being translated in these cells and that the polyadenylation status of these transcripts did not affect their translatability.

Isolation and characterization of two replication-dependent mouse H1 histone genes

Mice contain at least seven nonallelic forms of the H1 histones, including the somatic variants H1a-e and less closely related variants H1 degrees and H1t. The mouse H1 degrees and H1c (H1var.1) genes were isolated and characterized previously. We have now isolated, sequenced and studied the expression properties of two additional mouse H1 genes, termed H1var.2 and H1var.3. Extensive amino acid and nucleotide sequence comparisons were made between the two genes and other mammalian H1 histone genes. A high degree of nucleotide sequence identity was seen between the H1var.2, rat H1d and human H1b genes, even well beyond the coding region, indicating that these genes are likely homologues. Unlike the previously characterized mouse H1var.1 gene which produces both nonpolyadenylated and polyadenylated mRNAs, the H1var.2 and H1var.3 genes produce only typical, replication dependent, nonpolyadenylated mRNAs.

A proposal for a coherent mammalian histone H1 nomenclature correlated with amino acid sequences

Bio-Rex 70 chromatography was combined with reverse-phase (RP) HPLC to fractionate histone H1 zero and 4 histone H1 subtypes from human placental nuclei as previously described (Parseghian MH et al., 1993, Chromosome Res 1:127-139). After proteolytic digestion of the subtypes with Staphylococcus aureus V8 protease, peptides were fractionated by RP-HPLC and partially sequenced by Edman degradation in order to correlate them with human spleen subtypes (Ohe Y, Hayashi H, Iwai K, 1986, J Biochem (Tokyo) 100:359-368; 1989, J Biochem (Tokyo) 106:844-857). Based on comparisons with the sequence data available from other mammalian species, subtypes were grouped. These groupings were used to construct a coherent nomenclature for mammalian somatic H1s. Homologous subtypes possess characteristic patterns of growth-related and cAMP-dependent phosphorylation sites. The groupings defined by amino acid sequence also were used to correlate the elution profiles and electrophoretic mobilities of subtypes derived from different species. Previous attempts at establishing an H1 nomenclature by chromatographic or electrophoretic fractionations has resulted in several misidentifications. We present here, for the first time, a nomenclature for somatic H1s based on amino acid sequences that are analogous to those for H1 zero and H1t. The groupings defined should be useful in correlating the many observations regarding H1 subtypes in the literature.

Induction of H3.3 replacement histone mRNAs during the precommitment period of murine erythroleukemia cell differentiation

Differential hybridization to a cDNA library made from the mRNA of differentiating mouse erythroleukemia (MEL) cells has been used to identify sequences that are induced during the early stages of MEL cell differentiation. One of the differentially expressed genes identified encodes the H3.3 histone subtype. We show here that the three polyadenylated mRNAs produced from the H3.3B gene, as well as the single mRNA produced from the related H3.3A gene, are coordinately induced during the first few hours of MEL cell differentiation and subsequently down regulated as cells undergo terminal differentiation. Nuclear run-on transcription experiments indicate that the accumulation and decay of these mRNAs are controlled at the post-transcriptional level. Unlike the polyadenylated mRNAs of two H1 histone genes that exhibit similar kinetics of induction and decay controlled by c-myc, induction of the H3.3 mRNAs is unaffected by deregulated expression of c-myc.

Variable effects of the conserved RNA hairpin element upon 3' end processing of histone pre-mRNA in vitro

We have studied the requirements for efficient histone-specific RNA 3' processing in nuclear extract from mammalian tissue culture cells. Processing is strongly impaired by mutations in the pre-mRNA spacer element that reduce the base-pairing potential with U7 RNA. Moreover, by exchanging the hairpin and spacer elements of two differently processed H4 genes, we find that this difference is exclusively due to the spacer element. Finally, processing is inhibited by the addition of competitor RNAs, if these contain a wild-type spacer sequence, but not if their spacer element is mutated. Conversely, the importance of the hairpin for histone RNA 3' processing is highly variable: A hairpin mutant of the H4-12 gene is processed with almost wild-type efficiency in extract from K21 mouse mastocytoma cells but is strongly affected in HeLa cell extract, whereas an identical hairpin mutant of the H4-1 gene is affected in both extracts. The hairpin defect of H4-12-specific RNA in HeLa cells can be overcome by a compensatory mutation that increases the base complementarity to U7 snRNA. Very similar results were also obtained in RNA competition experiments: processing of H4-12-specific RNA can be competed by RNA carrying a wild-type hairpin element in extract from HeLa, but not K21 cells, whereas processing of H4-1-specific RNA can be competed in both extracts. With two additional histone genes we obtained results that were in one case intermediate and in the other similar to those obtained with H4-1. These results suggest that hairpin binding factor(s) can cooperatively support the ability of U7 snRNPs to form an active processing complex, but is(are) not directly involved in the processing mechanism.

Of palindromes and peptides

On the average, 30% of the residues in a protein are members of peptidic palindromes, tripeptidic and longer. This percentage may go up to 50% in histones and certain other DNA binding proteins. The longest peptidic palindrome encountered thus far was 14 residues in length. However, there is every reason to expect even longer peptidic palindromes in other proteins not yet analyzed.

A human histone H2B.1 variant gene, located on chromosome 1, utilizes alternative 3' end processing

A variant human H2B histone gene (GL105), previously shown to encode a 2300 nt replication independent mRNA, has been cloned. We demonstrate this gene expresses alternative mRNAs regulated differentially during the HeLa S3 cell cycle. The H2B-Gl105 gene encodes both a 500 nt cell cycle dependent mRNA and a 2300 nt constitutively expressed mRNA. The 3' end of the cell cycle regulated mRNA terminates immediately following the region of hyphenated dyad symmetry typical of most histone mRNAs, whereas the constitutively expressed mRNA has a 1798 nt non-translated trailer that contains the same region of hyphenated dyad symmetry but is polyadenylated. The cap site for the H2B-GL105 mRNAs is located 42 nt upstream of the protein coding region. The H2B-GL105 histone gene was localized to chromosome region 1q21-1q23 by chromosomal in situ hybridization and by analysis of rodent-human somatic cell hybrids using an H2B-GL105 specific probe. The H2B-GL105 gene is paired with a functional H2A histone gene and this H2A/H2B gene pair is separated by a bidirectionally transcribed intergenic promoter region containing consensus TATA and CCAAT boxes and an OTF-1 element. These results demonstrate that cell cycle regulated and constitutively expressed histone mRNAs can be encoded by the same gene, and indicate that alternative 3' end processing may be an important mechanism for regulation of histone mRNA. Such control further increases the versatility by which cells can modulate the synthesis of replication-dependent as well as variant histone proteins during the cell cycle and at the onset of differentiation.

The histone mRNA 3' end is required for localization of histone mRNA to polyribosomes

The final step in mRNA biosynthesis is transport of the mRNA from the nucleus to the cytoplasm. Histone genes from which the 3' stem-loop has been deleted are transcribed to give RNAs with heterogeneous 3' ends. These RNAs are localized in the nucleus and are stable. Addition of the histone 3' processing signal either on short (< 250 nts) or long (> 1000 nts) transcripts restores 3' processing and transport of the mRNA to the cytoplasm. In addition chimeric histone-U1 snRNA genes which produced RNAs with either histone or U1 3' ends were analyzed. Transcripts which ended with U1 snRNA 3' ends were not efficiently localized to polyribosomes. However, transcripts containing the same sequences including the snRNA 3' end followed by the histone 3' end were present in the cytoplasm on polyribosomes. Taken together these results suggest that the histone 3' end is required for export of histone mRNA to the cytoplasm and association of the mRNA with polyribosomes.

Molecular characterization of a Leishmania donovani infantum antigen identified as histone H2A

A Leishmania donovani infantum promastigote cDNA expression library was screened with a serum obtained from a dog naturally infected with this parasite. One of the positive clones obtained revealed nucleotide sequence similarities with the histone H2A genes from various organisms. Northern blot analyses and sequence data of three independently isolated cDNA clones indicated that the Leishmania H2A mRNAs are polyadenylated, as are the basal histone mRNAs of higher eukaryotes and the histone mRNAs of yeast. The analysis of the genomic distribution of the DNA coding for histone H2A suggested that, in L. d. infantum, there are at least four genes coding for the H2A protein. It is likely that there is a simultaneous expression of at least two of the H2A genes since differences in nucleotide sequence between two of the sequenced cDNAs were observed. Affinity-purified antibodies against the beta-galactosidase-fused H2A protein recognize specifically a Leishmania protein band with a molecular mass of 14 kDa.

Closely linked H2B genes in the marine copepod, Tigriopus californicus indicate a recent gene duplication or gene conversion event

Two nonallelic histone gene clusters were characterized in the marine copepod, Tigriopus californicus. The DNA sequence of one of the clusters reveals six genes in the contiguous arrangement of H2B, H1, H3, H4, H2B and H2A. The order of genes within the second cluster is H3, H4, H2B and H2A. There is no evidence for the presence of an H1 gene in this cluster. Comparison of the three copepod H2B genes reveals a high degree of similarity between the 5' upstream regions and between the amino terminal halves of the two H2B genes found within the same cluster. From these data we infer that gene duplication and/or gene conversion events occurred within this cluster in the recent past.

Relationship of eukaryotic DNA replication to committed gene expression: general theory for gene control

The historic arguments for the participation of eukaryotic DNA replication in the control of gene expression are reconsidered along with more recent evidence. An earlier view in which gene commitment was achieved with stable chromatin structures which required DNA replication to reset expression potential (D. D. Brown, Cell 37:359-365, 1984) is further considered. The participation of nonspecific stable repressor of gene activity (histones and other chromatin proteins), as previously proposed, is reexamined. The possible function of positive trans-acting factors is now further developed by considering evidence from DNA virus models. It is proposed that these positive factors act to control the initiation of replicon-specific DNA synthesis in the S phase (early or late replication timing). Stable chromatin assembles during replication into potentially active (early S) or inactive (late S) states with prevailing trans-acting factors (early) or repressing factors (late) and may asymmetrically commit daughter templates. This suggests logical schemes for programming differentiation based on replicons and trans-acting initiators. This proposal requires that DNA replication precede major changes in gene commitment. Prior evidence against a role for DNA replication during terminal differentiation is reexamined along with other results from terminal differentiation of lower eukaryotes. This leads to a proposal that DNA replication may yet underlie terminal gene commitment, but that for it to do so there must exist two distinct modes of replication control. In one mode (mitotic replication) replicon initiation is tightly linked to the cell cycle, whereas the other mode (terminal replication) initiation is not cell cycle restricted, is replicon specific, and can lead to a terminally differentiated state. Aberrant control of mitotic and terminal modes of DNA replication may underlie the transformed state. Implications of a replicon basis for chromatin structure-function and the evolution of metazoan organisms are considered.