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Antibody class switch recombination (CSR) in B lymphocytes replaces immunoglobulin heavy chain locus (Igh) C[mu] constant region exons (C.sub.Hs) with one of six C.sub.Hs lying 100-200 kb downstream.sup.1. Each C.sub.H is flanked upstream by an I promoter and long repetitive switch (S) region.sup.1. Cytokines and activators induce activation-induced cytidine deaminase (AID).sup.2 and I-promoter transcription, with 3' IgH regulatory region (3' IgHRR) enhancers controlling the latter via I-promoter competition for long-range 3' IgHRR interactions.sup.3-8. Transcription through donor S[mu] and an activated downstream acceptor S-region targets AID-generated deamination lesions at, potentially, any of hundreds of individual S-region deamination motifs.sup.9-11. General DNA repair pathways convert these lesions to double-stranded breaks (DSBs) and join an S[mu]-upstream DSB-end to an acceptor S-region-downstream DSB-end for deletional CSR.sup.12. AID-initiated DSBs at targets spread across activated S regions routinely participate in such deletional CSR joining.sup.11. Here we report that chromatin loop extrusion underlies the mechanism.sup.11 by which IgH organization in cis promotes deletional CSR. In naive B cells, loop extrusion dynamically juxtaposes 3' IgHRR enhancers with the 200-kb upstream S[mu] to generate a CSR centre (CSRC). In CSR-activated primary B cells, I-promoter transcription activates cohesin loading, leading to generation of dynamic subdomains that directionally align a downstream S region with S[mu] for deletional CSR. During constitutive S[alpha] CSR in CH12F3 B lymphoma cells, inversional CSR can be activated by insertion of a CTCF-binding element (CBE)-based impediment in the extrusion path. CBE insertion also inactivates upstream S-region CSR and converts adjacent downstream sequences into an ectopic S region by inhibiting and promoting their dynamic alignment with S[mu] in the CSRC, respectively. Our findings suggest that, in a CSRC, dynamically impeded cohesin-mediated loop extrusion juxtaposes proper ends of AID-initiated donor and acceptor S-region DSBs for deletional CSR. Such a mechanism might also contribute to pathogenic DSB joining genome-wide. Chromatin loop extrusion has fundamental mechanistic roles in immunoglobulin heavy chain class switch recombination., Author(s): Xuefei Zhang [sup.1] [sup.2] [sup.3] , Yu Zhang [sup.1] [sup.2] [sup.3] [sup.6] , Zhaoqing Ba [sup.1] [sup.2] [sup.3] , Nia Kyritsis [sup.1] [sup.2] [sup.3] , Rafael Casellas [sup.4] [sup.5] [...]

53BP1 governs a specialized, context-specific branch of the classical non-homologous end joining DNA double-strand break repair pathway. Mice lacking 53bp1 (also known as Trp53bp1) are immunodeficient owing to a complete loss of immunoglobulin class-switch recombination.sup.1,2, and reduced fidelity of long-range V(D)J recombination.sup.3. The 53BP1-dependent pathway is also responsible for pathological joining events at dysfunctional telomeres.sup.4, and its unrestricted activity in Brca1-deficient cellular and tumour models causes genomic instability and oncogenesis.sup.5-7. Cells that lack core non-homologous end joining proteins are profoundly radiosensitive.sup.8, unlike 53BP1-deficient cells.sup.9,10, which suggests that 53BP1 and its co-factors act on specific DNA substrates. Here we show that 53BP1 cooperates with its downstream effector protein REV7 to promote non-homologous end joining during class-switch recombination, but REV7 is not required for 53BP1-dependent V(D)J recombination. We identify shieldin--a four-subunit putative single-stranded DNA-binding complex comprising REV7, c20orf196 (SHLD1), FAM35A (SHLD2) and FLJ26957 (SHLD3)--as the factor that explains this specificity. Shieldin is essential for REV7-dependent DNA end-protection and non-homologous end joining during class-switch recombination, and supports toxic non-homologous end joining in Brca1-deficient cells, yet is dispensable for REV7-dependent interstrand cross-link repair. The 53BP1 pathway therefore comprises distinct double-strand break repair activities within chromatin and single-stranded DNA compartments, which explains both the immunological differences between 53bp1- and Rev7- deficient mice and the context specificity of the pathway.The specificity of 53BP1 and its co-factors for particular DNA substrates during non-homologous end joining (NHEJ) derives from REV7-shieldin, a four-subunit DNA-binding complex that is required for REV7-dependent NHEJ but not for REV7-dependent DNA interstrand cross-link repair., Author(s): Hind Ghezraoui [sup.1] , Catarina Oliveira [sup.1] , Jordan R. Becker [sup.1] , Kirstin Bilham [sup.1] , Daniela Moralli [sup.2] , Consuelo Anzilotti [sup.3] , Roman Fischer [sup.4] , [...]

Distant DNA regions are juxtaposed and joined to form diverse immune-system genes encoding antibodies and T-cell receptors. It seems that both types of gene form by relying on DNA extrusion through a protein ring called cohesin. DNA extrusion through a cohesin complex aids recombination in immune cells., Author(s): Ferenc Livak, André Nussenzweig Author Affiliations: One ring to rule them all Our ability to fight the multitude of potential disease-causing agents that we encounter depends on a process [...]

The mitochondrial genomes of flowering plants possess a promiscuous proclivity for taking up sequences from the chloroplast genome. All characterized chloroplast integrants exist apart from native mitochondrial genes, and only a few, involving chloroplast tRNA genes that have functionally supplanted their mitochondrial counterparts, appear to be of functional consequence. We developed a novel computational approach to search for homologous recombination (gene conversion) in a large number of sequences and applied it to 22 mitochondrial and chloroplast gene pairs, which last shared common ancestry some 2 billion years ago. We found evidence of recurrent conversion of short patches of mitochondrial genes by chloroplast homologs during angiosperm evolution, but no evidence of gene conversion in the opposite direction. All 9 putative conversion events involve the atp1/atpA gene encoding the alpha subunit of ATP synthase, which is unusually well conserved between the 2 organelles and the only shared gene that is widely sequenced across plant mitochondria. Moreover, all conversions were limited to the 2 regions of greatest nucleotide and amino acid conservation of atp1/atpA. These observations probably reflect constraints operating on both the occurrence and fixation of recombination between ancient homologs. These findings indicate that recombination between anciently related sequences is more frequent than previously appreciated and creates functional mitochondrial genes of chimeric origin. These results also have implications for the widespread use of mitochondrial atp1 in phylogeny reconstruction. gene conversion | gene transfer | recombination

The mating-type bias (mat-bias) of gene conversion was previously described as a phenomenon in which the number of prototrophic recombinants in an ura4A heteroallelic two-factor cross relates to the mating types of the parents. We show now that the mat-bias is restricted neither to ura4A nor to recombination hotspots, but occurs at other genomic loci, too. It is specific for gene conversion and absent in azygotic meiosis. Thus, the mat-bias must originate from mating-type-specific 'imprinting' events before karyogamy takes place. Structural variations of the mating-type locus, such as [h.sup.+N], [h.sup.+s], [h.sup.-s], [h.sup.+smt[DELTA]], or [h.sup.-smt[DELTA]], showed mat-bias manifestation. Mutations in genes coding for histone acetylase (gcn5, ada2) and histone deacetylase (hos2, clr6) activities smooth or abolish the mat-bias. In addition, the mat-bias depends on the presence of Swi5. We propose a new role for Swi5 and the histone acetylation status in mat-bias establishment through directionality of repair from the intact chromatid to the broken chromatid.

DNA double-strand breaks (DSB) are repaired through two different pathways, homologous recombination (HR) and nonhomologous end joining (NHEJ). Yeast Xrs2, a homolog of human Nbsl, is a component of the Mrel1-Rad50-Xrs2 (MRX) complex required tot both HR and NHEJ. Previous studies showed that the N-terminal forkhead-associated (FHA) domain of Xrs2/Nbs1 in yeast is not involved in HR, but is likely to be in NHEJ. In this study, we showed that the FHA domain of Xrs2 plays a critical role in efficient DSB repair by NHEJ. The FHA domain of Xrs2 specifically interacts with Lif1, a component of the ligase IV complex, Dn14-Nej1-Lif1 (DNL). Lif1, which is phosphorylated in vivo, contains two Xrs2-binding regions. Serine 383 of Lif1 plays an important role in the interaction with Xrs2 as well as in NHEJ. interestingly, the phospho-mimetic substitutions of serine 383 enhance the NHEJ activity of Lif1. Our results suggest that the phosphorylation of Lif1 at serine 383 is recognized by the Xrs2 FHA domain, which in turn may promote recruitment of the DNL complex to DSB for NHEJ. The interaction between Xrs2 and Lift through the FHA domain is conserved in humans; the FHA domain Nbs1 interacts with Xrcc4, a Lif1 homolog of human.

Niddm1i, a 16-Mb locus within the major diabetes QTL in the diabetic GK rat, causes impaired glucose tolerance in the congenic NIDDM1I strain. Niddm1i is homologous to both human and mouse regions linked with type 2 diabetes susceptibility. We employed multiple QTL analyses of congenic [F.sub.2] progeny selected for one recombination event within Niddm1i combined with characterization of subcongenic strains. Fine mapping located one hyperglycemia locus within 700 kb (Niddm1i4, P = 5 x [10.sup.-6]). Two adjacent loci were also detected, and the GK allele at Niddm1i2 (500 kb) showed a glucose-raising effect, whereas it had a glucose-lowering effect at Niddm1i3 (400 kb). Most proximally, Niddm1i1 (800 kb) affecting body weight was identified. Experimental data from subcongenics supported the four loci. Sorcs1, one of the two known diabetes susceptibilily genes in the region, resides within Niddm1i3, while Tcf712 maps outside all four loci. Multiple-marker QTL analysis incorporating the effect of cosegregating QTL as cofactors together with genetically selected progeny can remarkably enhance resolution of QTL. The data demonstrate that the species-conserved Niddm1i is a composite of at least four QTL affecting type 2 diabetes susceptibility and that two adjacent QTL ([Niddm1i2.sup.3K] and [Niddm1i3.sup.GK]) act in opposite directions.

We describe a novel method for jointly estimating crossing-over and gene-conversion rates from population genetic data using summary statistics. The performance of our method was tested on simulated data sets and compared with the composite-likelihood method of R. R. Hudson. For several realistic parameter values, the new method performed similarly to the composite-likelihood approach for estimating crossing-over rates and better when estimating gene-conversion rates. We used our method to analyze a human data set recently genotyped by Perlegen Sciences.

Natural genetic transformation in Streptococcus pneumoniae entails transcriptional activation of at least two sets of genes. One set of genes, activated by the competence-specific response regulator ComE, is involved in initiating competence, whereas a second set is activated by the competence-specific alternative sigma factor ComX and functions in DNA uptake and recombination. Here we report an initial characterization of CoiA, a ComX-dependent gene product that is induced during competence and is required for transformation. CoiA is widely conserved among gram-positive bacteria, and in streptococci, the entire coiA locus composed of four genes is conserved. By use of immunoblot assay, we show that, similar to its message, CoiA protein is transient, appearing at 10 min and largely disappearing by 30 min post-competence induction. Using complementation analysis, we establish that coiA is the only gene of this induced locus needed for transformability. We find no indication of CoiA having a role in regulating competence. Finally, using [sup.32]P. and [sup.3]H-labeled donor DNA, we demonstrate that a coiA mutant can internalize normal amounts of donor DNA compared to the wild-type strain but is unable to process it into viable transformants, suggesting a role for CoiA after DNA uptake, either in DNA processing or recombination.

Ectopic recombination between locally repeated DNA sequences is of fundamental importance in the evolution of gene families, generating copy-number variation in human DNA and often leading to pathological rearrangements. Despite its importance, little is known about the dynamics and processes of these unequal crossovers and the degree to which meiotic recombination plays a role in instability. We address this issue by using as a highly informative system the duplicated [alpha]-globin genes in which ectopic recombination can lead to gene deletions, often very prevalent in populations affected by malaria, as well as reduplications. Here we show that spontaneous deletions can be accessed directly in genomic DNA by using single-DNA-molecule methods. These deletions proved to be remarkably common in both blood and sperm. Somatic deletions arise by a strictly intrachromosomal pathway of homologous exchange that also operates in the germ line and can generate mutational mosaicism, whereas sperm deletions frequently involve recombinational interactions between homologous chromosomes that most likely occur at meiosis. Ectopic recombination frequencies show surprisingly little requirement for long, identical homology blocks shared by paralogous sequences, and exchanges can occur even between short regions of sequence identity. Finally, direct knowledge of germ-line deletion rates can give insights into the fitness of individuals with these [alpha]-globin gene deletions, providing a new approach to investigating historical levels of selection operating in human populations. ectopic| recombination | selection | mutation | mosaicism

A recent sperm-typing study by Jeffreys and Neumann suggested that recombination rates in different individuals at the DNA2 recombination hotspot appeared to be highly dependent on their genotype at a particular A/G SNP, FG11. Specifically, individuals who carried at least one copy of the A allele at this SNP exhibited rates of crossover considerably higher than those of individuals with no copies. Further, recombinant sperm from heterozygous individuals showed a preferential tendency to carry the G allele. We consider the effects of these phenomena on patterns of linkage disequilibrium and find them to be more subtle than might have been expected. In particular, our analysis suggests that, perhaps surprisingly, patterns of LD among chromosomes carrying the 'hot' allele (in this case, A) will typically be similar to those among chromosomes carrying the 'cold' allele (G).

Several streptococcal species are able to take up naked DNA from the environment and integrate it into their genomes by homologous recombination. This process is called natural transformation. In Streptococcus pneumoniae and related streptococcal species, competence for natural transformation is induced by a peptide pheromone through a quorum-sensing mechanism. Recently we showed that induction of the competent state initiates lysis and release of DNA from a subfraction of the bacterial population and that the efficiency of this process is influenced by cell density. Here we have further investigated the nature of this cell density-dependent release mechanism. Interestingly, we found that competence-induced pneumococci lysed competence-deficient cells of the same strain during cocultivation and that the efficiency of this heterolysis increased as the ratio of competent to noncompetent cells increased. Furthermore, our results indicate that the lysins made by competent pneumococci are not released into the growth medium. More likely, they are anchored to the surface of the competent cells by choline-binding domains and cause lysis of noncompetent pneumococci through cell-to-cell contact.

Bacteriophage Mx9 is a temperate phage that infects Myxococcus xanthus. It lysogenizes the bacteria by integrating into the bacterial chromosome by site-specific recombination at one of two sites, attB1 or attB2. Integration at attB1 results in deletion of DNA between the two attB sites. The attB2 site lies within the 5' region of the M. xanthus [tRNA.sup.Gly] gene. Mx9 integration requires a single protein, Int. Analysis of integration revealed that the phage attachment site (attP) is contained in the int gene and that upon integration, the 3' end of the int gene is altered. Plasmids containing fusions of the pilA or mgl promoter to lacZ integrated at either Mx9 attB site have higher levels of transcription than the same fusions integrated at the Mx8 attB site.

Natural selection is expected to leave a characteristic footprint on neighboring nucleotide variation through the effects of genetic linkage. The size of the region affected is proportional to the strength of selection and greatly reduced with the recombinational distance from the selected site. Thus, the genomic footprint of selection is generally believed to be restricted to a small DNA stretch in normal and highly recombining regions. Here, we study the effect of selection on linked polymorphism (hitchhiking effect) by surveying nucleotide variation across a highly recombining ~88-kb genomic fragment in an African population of Drosophila simulans. We find a core region of up to 38 kb with a major haplotype at intermediate frequency. The extended haplotype structure that gradually vanishes until disappearing is unusual for a highly recombining region. Both the presence in the structured genomic domain of a single major haplotype depleted of variability and the detected spatial pattern of variation along the ~88-kb fragment are incompatible with neutral predictions in a panmictic population. A major role of demographic effects could also be discarded. The observed pattern of variation clearly provides evidence that directional selection has acted recently on this region, sweeping out variation around a strongly adaptive mutation. Our findings suggest a major role of positive selection in shaping DNA variability even in highly recombining regions.

The subtelomeric DNA sequences from chromosome I of Saccharomyces cerevisiae are shown to be inherently poor substrates for meiotic recombination. On the basis of these results and prior observations that crossovers near telomeres do not promote efficient meiosis I segregation, we suggest that subtelomeric sequences evolved to prevent recombination from occurring where it cannot promote efficient segregation.

Recombination nodules (RNs) are closely correlated with crossing over, and, because they are observed by electron microscopy of synaptonemal complexes (SCs) in extended pachytene chromosomes, RNs provide the highest-resolution cytological marker currently available for defining the frequency and distribution of crossovers along the length of chromosomes. Using the maize inbred line KYS, we prepared an SC karyotype in which each SC was identified by relative length and arm ratio and related to the proper linkage group using inversion heterozygotes. We mapped 4267 RNs on 2080 identified SCs to produce high-resolution maps of RN frequency and distribution on each bivalent. RN frequencies are closely correlated with both chiasma frequencies and SC length. The total length of the RN recombination map is about twofold shorter than that of most maize linkage maps, but there is good correspondence between the relative lengths of the different maps when individual bivalents are considered. Each bivalent has a unique distribution of crossing over, but all bivalents share a high frequency of distal RNs and a severe reduction of RNs at and near kinetochores. The frequency of RNs at knobs is either similar to or higher than the average frequency of RNs along the SCs. These RN maps represent an independent measure of crossing over along maize bivalents.

We employed quantitative trait locus (QTL) mapping to dissect the genetic architecture of a hierarchy of functionally related physiological traits, including metabolic enzyme activity, metabolite storage, metabolic rate, and free-flight performance in recombinant inbred lines of Drosophila melanogaster. We identified QTL underlying variation in glycogen synthase, hexokinase, phosphoglucomutase, and trehalase activity. In each case variation mapped away from the enzyme-encoding loci, indicating that transacting regions of the genome are important sources of variation within the metabolic network. Individual QTL associated with variation in metabolic rate and flight performance explained between 9 and 35% of the phenotypic variance. Bayesian QTL analysis identified epistatic effects underlying variation in flight velocity, metabolic rate, glycogen content, and several metabolic enzyme activities. A region on the third chromosome was associated with expression of the glucose-6-phosphate branchpoint enzymes and with metabolic rate and flight performance. These genomic regions are of special interest as they may coordinately regulate components of energy metabolism with effects on whole-organism physiological performance. The complex biochemical network is encoded by an equally complex network of interacting genetic elements with potentially pleiotropic effects. This has important consequences for the evolution of performance traits that depend upon these metabolic networks.

Chromatin remodeling plays crucial roles in the regulation of gene expression and recombination. Transcription of the fission yeast [fbp1.sup.+] gene and recombination at the meiotic recombination hotspot ade6-M26 (M26) are both regulated by cAMP responsive element (CRE)-like sequences and the CREB/ ATF-type transcription factor Atf1*Pcr1. The Tup11 and Tup12 proteins, the fission yeast counterparts of the Saccharomyces cerevisiae Tup1 corepressor, are involved in glucose repression of the [fbp1.sup.+] transcription. We have analyzed roles of the Tup1-like corepressors in chromatin regulation around the [fbp1.sup.+] promoter and the M26 hotspot. We found that the chromatin structure around two regulatory elements for [fbp1.sup.+] was remodeled under derepressed conditions in concert with the robust activation of [fbp1.sup.+] transcription. Strains with tup11[DELTA] tup12[DELTA] double deletions grown in repressed conditions exhibited the chromatin state associated with wild-type cells grown in derepressed conditions. Interestingly, deletion of [rst2.sup.+], encoding a transcription factor controlled by the cAMP-dependent kinase, alleviated the tup11[DELTA] tup12[DELTA] defects in chromatin regulation but not in transcription repression. The chromatin at the M26 site in mitotic cultures of a tup11[DELTA] tup12[DELTA] mutant resembled that of wild-type meiotic cells. These observations suggest that these fission yeast Tup1-like corepressors repress chromatin remodeling at CRE-related sequences and that Rst2 antagonizes this function.

Homologous recombination of a particular DNA sequence is strongly stimulated by transcription, a phenomenon observed from bacteria to mammals, which we refer to as transcription-associated recombination (TAR). TAR might be an accidental feature of DNA chemistry with important consequences for genetic stability. However, it is also essential for developmentally regulated processes such as class switching of immunoglobulin genes. Consequently, it is likely that TAR embraces more than one mechanism. In this study we tested the possibility that transcription induces recombination by making DNA more susceptible to recombinogenic DNA damage. Using different plasmid-chromosome and direct-repeat recombination constructs in which transcription is driven from either the [P.sub.GAL1]- or the [P.sub.tet]-regulated promoters, we have shown that either 4-nitroquinoline-N-oxide (4-NQO) or methyl methanesulfonate (MMS) produces a synergistic increase of recombination when combined with transcription. 4-NQO and MMS stimulated recombination of a transcriptionally active DNA sequence up to 12,800-and 130-fold above the spontaneous levels observed in the absence of transcription, whereas 4-NQO and MMS alone increased recombination 193- and 4.5-fold, respectively. Our results provide evidence that TAR is due, at least in part, to the ability of transcription to enhance the accessibility of DNA to exogenous chemicals and internal metabolites responsible for recombinogenic lesions. We discuss possible parallelisms between the mechanisms of induction of recombination and mutation by transcription.

Plasmid pTC-F14 is a 14.2-kb plasmid isolated from Acidithiobacius caldus that has a replicon that is closely related to the promiscuous, broad-host-range IncQ family of plasmids. The region containing the mobilization genes was sequenced and encoded five Mob proteins that were related to those of the DNA processing (Dtr or Tral) region of IncP plasmids rather than to the three-Mob-protein system of the IncQ group 1 plasmids (e.g., plasmid RSF1010 or R1162). Plasmid pTC-F14 is the second example of an IncQ family plasmid that has five mob genes, the other being pTF-FC2. The minimal region that was essential for mobilization included the mobA, mobB, and mobC genes, as well as the oriT gene. The mobD and mobE genes were nonessential, but together, they enhanced the mobilization frequency by approximately 300-fold. Mobilization of pTC-F14 between Escherichia coli strains by a chromosomally integrated RP4 plasmid was more than 3,500-fold less efficient than the mobilization of pTF-FC2. When both plasmids were coresident in the same E. coli host, pTC-F14 was mobilized at almost the same frequency as pTF-FC2. This enhanced pTC-F14 mobilization frequency was due to the presence of a combination of the pTF-FC2 mobD and mobE gene products, the functions of which are still unknown. Mob protein interaction at the oriT regions was unidirectionally plasmid specific in that a plasmid with the oriT region of pTC-F14 could be mobilized by pTF-FC2 but not vice versa. No evidence for any negative effect on the transfer of one plasmid by the related, potentially competitive plasmid was obtained.

Large-scale genomic rearrangements including inversions, deletions, and duplications are significant in bacterial evolution. The recently completed Brucella melitensis 16M and Brucella suis 1330 genomes have facilitated the investigation of such events in the Brucella spp. Suppressive subtractive hybridization (SSH) was employed in identifying genomic differences between B. melitensis 16M and Brucella abortus 2308. Analysis of 45 SSH clones revealed several deletions on chromosomes of B. abortus and B. melitensis that encoded proteins of various metabolic pathways. A 640-kb inversion on chromosome II of B. abortus has been reported previously (S. Michaux Charachon, G. Bourg, E. Jumas Bilak, P. Guigue Talet, A. Allardet Servent, D. O'Callaghan, and M. Ramuz, J. Bacteriol. 179:3244-3249, 1997) and is further described in this study. One end of the inverted region is located on a deleted TATGC site between open reading frames BMEII0292 and BMEII0293. The other end inserted at a GTGTC site of the cyclic-di-GMP phosphodiesterase A (PDEA) gene (BMEII1009), dividing PDEA into two unequal DNA segments of 160 and 977 bp. As a consequence of inversion, the 160-bp segment that encodes the N-terminal region of PDEA was relocated at the opposite end of the inverted chromosomal region. The splitting of the PDEA gene most likely inactivated the function of this enzyme. A recombination mechanism responsible for this inversion is proposed.

Cardiomyocyte differentiation overall has been analyzed in vivo and in vitro at the molecular level by homologous recombination, gene mutation studies, and by transgenics; however, the roles of many signal transduction mechanisms that drive this differentiation process are still not fully understood. One set of signal transduction components that has been studied in detail in mature, differentiated cardiomyocytes is the PKC isotype superfamily. However, while the function of each isotype is slowly being uncovered in adult cardiomyocytes, limited information persists concerning their function in the differentiation process of cardiomyocytes. To begin analyzing the function of specific PKC isotypes in the differentiation process, we employed an established model for differentiating ES cells into cardiomyocyte-positive embryoid bodies (EBs) in vitro. RT-PCR, Western analyses, and confocal microscopy all showed that the expression of specific PKC isotypes was significantly changed as ES cells differentiated into cardiomyocytes. More importantly, by using antagonists specific for each isotype we found that this change was a final step in the differentiation process. PKC[beta] and [integral] downregulation served to promote differentiation (beating), while upregulation of PKC[epsilon] appeared to amplify differentiation (beating). Finally, melding classical tools (i.e., ionic exchange glass beads) with recently developed methods for differentiating ES cells creates a possible novel technique for investigating differentiation of ES cells into cardiomyocytes as well as other cell types. Keywords: Embryonic stem cells; Cardiomyocytes; PKC, Heart development; Embryogenesis

Inactivation of Cdx2 by homologous recombination results in the development of forestomach epithelium at ectopic sites in pericaecal areas of the midgut of heterozygote mice. Local factors subsequently result in the secondary induction of tissues exhibiting an orderly sequence of tissue types between the ectopic forestomach tissue and the surrounding colon. Clonal analysis of this secondarily generated tissue using Y chromosome painting in chimaeric mice indicates that once differentiated to express Cdx2, host colonic epithelium can only form small intestinal-type epithelium, while Cdx2 mutant cells give rise to a succession of gastric-type tissue but never to a small intestine morphology. Our results indicate a difference in potency between forestomach and midgut precursor endodermal cells. Keywords: Cdx2; Homeobox; Intercalation; Gut development

In the intergeneric conjugation between Escherichia coli and Streptomyces peucetius and Streptomyces sp. strain C5, the forein genes integrate into a single chromosomal site in C5 and S. pucetius. Furthermore, integration of chiC gene into the wild-type S. peucetius chromosome results in a 30-fold increase in chitinase production.

Research reveals that Streptomyces strains with a deletion of the attB site exhibit three pseudo-attB sites with sequences resembling attB. Integrating vector insertion analysis in both attB(sup)+ and attB deletion mutants indicate that the insertion plasmid can integrate at several loci, suggesting occurrence of multiple site-specific recombination events.

By deletion of 1.8 kb of sequence between [cog.sup.L] and his-3 and replacement with sequences of different lengths, we have generated a set of Neurospora strains in which the distance between [cog.sup.L] and the site at which recombination is selected varies from 1.7 to nearly 6 kb. Each of the manipulated strains includes [cog.sup.L], a highly active recombination hotspot, and rec-2, thus allowing high-frequency recombination. In addition, each is a his-3 mutant, either K26 or K480. The frequency of [His.sup.+] recombinants in progeny of these crosses is inversely proportional to the distance between his-3 and cog. Specifically, there is a linear relationship between [log.sub.10] (recombination frequency) and the distance in base pairs, indicating that as distance decreases, the rate of interallelic recombination increases exponentially. An exponential relationship between distance separating markers and the chance of co-conversion has been found in both Drosophila and fission yeast, indicating that the extension of recombination events may be a stochastic process in most organisms. On the basis of these and additional data presented in this article, we conclude that recombination is initiated at [cog.sup.L] in > 17% of meioses, that most conversion tracts are very short, and that few extend > 14 kb.

Recombination between DNA and the chromosome using lacZ system reveal that the bacteriophage lambda gene can substitute for the Escherichia coli ruvC gene.

Comparison of the Kanagawa phenomenon-positive strain Vibrio parahaemolyticus KX-V237 genome with that of the strain AQ4673 and V. cholerae N16961 reveals that the genome of KX-V237 exhibits two circular chromosomes, a large and a small, with only the large being similar to that of AQ4673. While the open reading frames of the large is similar to V. cholerae, the small compares with N16961, suggesting intrachromosomal exchange.

Results indicate that in the recBC and sbcBC mutants of Escherichia coli, the postsynaptic recombination is dependent on the RuvABC proteins to a larger extent than the wild-type cells. In the SbcB15 mutant, the protein binds to a recombinogenic DNA, which requires RuvABC resolvase for making the final stage of recombination.

We have determined the marker separations (genetic distances) that maximize the probability, or power, of detecting meiotic recombination deficiency when only a limited number of meiotic progeny can be assayed. We find that the optimal marker separation is as large as 30-100 cM in many cases. Provided the appropriate marker separation is used, small reductions in recombination potential (as little as 50%) can be detected by assaying a single interval in as few as 100 progeny. If recombination is uniformly altered across the genomic region of interest, the same sensitivity can be obtained by assaying multiple independent intervals in correspondingly fewer progeny. A reduction or abolition of crossover interference, with or without a reduction of recombination proficiency, can be detected with similar sensitivity. We present a set of graphs that display the optimal marker separation and the number of meiotic progeny that must be assayed to detect a given recombination deficiency in the presence of various levels of crossover interference. These results will aid the optimal design of experiments to detect meiotic recombination deficiency in any organism.

Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity [pi]s varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent, simulations and estimate that up to 90% of recombination is due to gene conversion.

Cells can repair DNA double-strand breaks by both homologous and nonhomologous mechanisms. To explore the basis of pathway utilization, we developed both plasmid and chromosomal yeast repair assays in which breaks are created with restriction endonucleases so that nonhomologous end-joining (NHEJ) competes with the single-strand annealing (SSA) recombination pathway, which we show acts with high efficiency via terminal direct repeats of only 28 bp and with reduced but measurable efficiency at 10 bp. The chromosomal assay utilizes a novel approach termed suicide deletion in which the endonuclease cleaves its own gene from the chromosome, thereby ending the futile cleavage cycle that otherwise prevents detection of simple-religation events. Eliminating SSA as a possibility in either assay, either by removal of the direct repeat or by mutation of RAD52, increased the relative but not the absolute efficiency of NHEJ. In contrast, the apparent efficiency of NHEJ was specifically increased in the G1 stage of the haploid cell cycle, as well as by the glucose depletion-signaled transition to stationary phase. The combined results argue against a model in which pathway utilization is determined by a passive competition. Instead, they demonstrate an active regulation designed to optimize the likelihood of genome restoration based on cell state.

Telomeres are the protective ends of linear chromosomes. Telomeric components have been identified and described by their abilities to bind telomeric DNA, affect telomere repeat length, participate in telomeric DNA replication, or modulate transcriptional silencing of telomere-adjacent genes; however, their roles in chromosome end protection are not as well defined. We have developed a genetic, quantitative assay in Saccharomyces cerevisiae to measure whether various telomeric components protect chromosome ends from homologous recombination. This 'chromosomal cap' assay has revealed that the telomeric end-binding proteins, Cdc13p and Ku, both protect the chromosome end from homologous recombination, as does the ATM-related kinase, Tel1p. We propose that Cdcl3p and Ku structurally inhibit recombination at telomeres and that Tel1p regulates the chromosomal cap, acting through Cdcl3p. Analysis with recombination mutants indicated that telomeric homologous recombination events proceeded by different mechanisms, depending on which capping component was compromised. Furthermore, we found that neither telomere repeat length nor telomeric silencing correlated with chromosomal capping efficiency. This capping assay provides a sensitive in vivo approach for identifying the components of chromosome ends and the mechanisms by which they are protected.

A single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line (2n = 2x = 14). The chromatin of F. pratensis and L. perenne can be distinguished by genomic in situ hybridization (GISH), and it is therefore possible to visualize the substituted F. pratensis chromosome in the L. perenne background and to study chiasma formation in a single marked bivalent. Recombination occurs freely in the F. pratensis/L. perenne bivalent, and chiasma frequency counts give a predicted map length for this bivalent of 76 cM. The substituted F. pratensis chromosome was also mapped with 104 EcoRI/Tru91 and HindIII/Tru91 amplified fragment length polymorphisms (AFLPs), generating a marker map of 81 cM. This map length is almost identical to the map length of 76 cM predicted from the chiasma frequency data. The work demonstrates a 1:1 correspondence between chiasma frequency and recombination and, in addition, the absence of chromatid interference across the Festuca and Lolium centromeres.

Transgenic analyses have defined two MyoD enhancers in mammals, the core enhancer and distal regulatory region (DRR); these enhancers exhibit complementary activities and together are sufficient to recapitulate MyoD expression in developing and mature skeletal muscle. DRR activity is restricted to differentiated muscle and persists postnatally, suggesting an important role in maintaining MyoD expression in myocytes and muscle fibers. Here, we use targeted mutagenesis in the mouse to define essential functions of the DRR in its normal chromosomal context. Surprisingly, deletion of the DRR resulted in reduced MyoD expression in all myogenic lineages at E10.5, at least I day prior to detection of DRR activity in limb buds and branchial arches of transgenic mice. At later embryonic and fetal stages, however, no defect in MyoD expression was observed, indicating that the DRR is dispensable for regulating MyoD during muscle differentiation. Expression analyses in wild-type and Myf-5 mutant embryos also indicate that the DRR is not an obligate target for Myf-5-and Pax-3-dependent regulation. In contrast to embryonic and fetal stages, deletion of the DRR resulted in a pronounced reduction in MyoD mRNA levels in adults, showing a functional requirement for DRR activity in mature muscle. These data reveal essential and redundant functions of the DRR and underscore the importance of loss-of-function enhancer analyses for understanding cis transcriptional circuitry. Key Words: MyoD; enhancer; myogenesis; gene targeting; Cre recombination; somite; transcription; redundancy.

Conditional mutagenesis is a powerful tool to analyze gene functions in mammalian cells. The site-specific recombinase Cre can be used to recombine loxP-modified alleles under temporal and spatial control. However, the efficient delivery of biologically active Cre recombinase to living cells represents a limiting factor. In this study we compared the potential of a hydrophobic peptide modified from Kaposi fibroblast growth factor with a basic peptide derived from HIV-TAT to promote cellular uptake of recombinant Cre. We present the production and characterization of a Cre protein that enters mammalian cells and subsequently performs recombination with high efficiency in a time- and concentration-dependent manner. Histidine-tagged Cre recombinase transduced inefficiently unless fused to a nuclear localization signal (NLS). Fusion of NLS-Cre to the fibroblast growth factor transduction peptide did not improve the transducibility, whereas fusion with the TAT peptide significantly enhanced cellular uptake and subsequent recombination. More than 95% recombination efficiency in fibroblast cells, as well as murine embryonic stem cells, was achieved after His-TAT-NLS-Cre transduction. Efficient recombination could also be obtained in primary splenocytes ex vivo. We expect that application of His-TAT-NLS-Cre, which can be produced readily in large quantities from a bacterial source, will expand our abilities to manipulate mammalian genomes.

We describe a method to simultaneously detect and fine map quantitative trait loci (QTL) that is especially suited to the mapping of modifier loci in mouse mutant models. The method exploits the high level of historical recombination present in a heterogeneous stock (HS), an outbred population of mice derived from known founder strains. The experimental design is an [F.sub.2] cross between the HS and a genetically distinct line, such as one carrying a knockout or transgene. QTL detection is performed by a standard genome scan with ~100 markers and fine mapping by typing the same animals using densely spaced markers over those candidate regions detected by the scan. The analysis uses an extension of the dynamic-programming technique employed previously to fine map QTL in HS mice. We show by simulation that a QTL accounting for 5% of the total variance can be detected and fine mapped with >50% probability to within 3 cM by genotyping ~1500 animals.

Results show that a 2,744-basepair fragment containing the attP site and mj1 site of phage phiFC1 mediates site-specific recombination via pEMJ1-1 vector, leading to chimeric plasmids production in Enterococcus faecalis KBL 703. The attB site produces a functional target site for the vector attP site and for integrase gene integration.

Genetic recombination pathways and genes are well studied, but relatively little is known in plants, especially in lower plants. To study the recombination apparatus of a lower land plant, a recombination gene well characterized particularly in yeast, mouse, and man, the RAD51 gene, was isolated from the moss Physcomitrella patens and characterized. Two highly homologous RAD51 genes were found to be present. Duplicated RAD51 genes have been found thus far exclusively in eukaryotes with duplicated genomes. Therefore the presence of two highly homologous genes suggests a recent genome duplication event in the ancestry of Physcomitrella. Comparison of the protein sequences to Rad51 proteins from other organisms showed that both RAD51 genes originated within the group of plant Rad51 proteins. However, the two proteins form a separate clade in a phylogenetic tree of plant Rad51 proteins. In contrast to RAD51 genes from other multicellular eukaryotes, the Physcomitrella genes are not interrupted by introns. Because introns are a common feature of Physcomitrella genes, the lack of introns in the RAD51 genes is unusual and may indicate the presence of an unusual recombination apparatus in this organism. The presence of duplicated intronless RAD51 genes is unique among eukaryotes. Studies of further members of this lineage are needed to determine whether this feature may be typical of lower plants.

Results demonstrate that in addition to their DNA repair role, both recJ and recN also influence recombination-dependent processess such as pilus-dependent colony morphology variation frequency and DNA transformation efficiency in Neisseria gonorrhoeae.

Research findings suggest that within the Microcystis, the distribution of tRNA(sup)Leu(UAA) group I introns is governed by both intron transfer and recombination in tRNA and intron-containing region. Data suggest a nested evolution of the intron, in which the intron is transferred horizontally to tRNA(sup)Leu(UAA) gene.

The leukotoxin operon of the respiratory tract in gram-negative bacteria exhibits a complex mosaic structure derived from inter- and intra-species horizontal DNA transfer and intragenic recombination. Data indicate that the multiple horizontal exchanges of the operon emnate from a common mechanism of transduction.

A plasmid containing Rhizobium meliloti 41 phage 16-3 integrative element of 23-basepair integrates into the chromosomes of R. meliloti 1021 and other bacteria. Sequence data indicate that the target sites of integration is within proline tRNA (CGG) genes.

Research findings suggest that Mus81 protein possesses many of the properties of Holliday junctions such as endonucleolytic cleavage during DNA recombination and replication. Data indicate that Mus81 protein associates with the recombinat protein Rad54 and interacts with meiotic paralog Rad53.

Adeno-associated virus (AAV) is the only known eukaryotic virus capable of targeted integration in human cells. An AAV Rep binding element (RBE) and terminal resolution site (trs) identical to the viral terminal repeats required for AAV DNA replication are located on chromosome (ch) 19. Both ch-19 RBE and trs elements have been shown to be essential for viral targeting to this locus. To characterize the role of the AAV inverted terminal repeat (ITR) cis-acting sequences in targeted integration an AAV trs mutant incapable of supporting viral replication was tested. Wild-type and mutant substrates were assayed for targeted integration after cotransfection in the presence or absence of Rep. Our results demonstrated that, in the presence of Rep78, both ITR substrates targeted to ch-19 with similar frequency. Molecular characterization of the mutant ITR integrants confirmed the presence of the trs mutation in the majority of samples tested. Complementation analysis confirmed that the mutant targeted viral genomes were unable to rescue and replicate. In addition, Rep78 induced extensive rearrangement and amplification of ch-19 sequences independent of wild-type or mutant targeting substrate. These studies demonstrate that Rep-dependent nicking of the viral cis-acting trs sequence is not a prerequisite for site-specific recombination and suggests AAV targeting is mediated by Rep78/68-dependent replication from the ch-19 origin of replication (ori). These studies have significant impact toward the understanding of AAV site-specific recombination and the development of targeting vectors.

Results show that the lactococcal bacteriophage TP901-1 integrase exhibits a site-sepecific recombination utilizing a 56 base pair attP fragment that recombines with the chromosomal attB site. Data indicate that two bases outside the attB core region are involved in the in vitro binding of the enzyme.

Research demonstrates that introgression between genomes is selective and gene flow filtering between species occurs in hybrid populations as evidenced by genetically mapped restriction fragment length polymorphism of cottonwood species and their hybrids. Data show that natural hybridization has the potential to offer genetic variation that impacts evolutionary processes.

Results indicate that rates of Plasmodium falciparum evolution are governed by cross-reactivity between parental genotypes as well as between recombinant and parental genotypes. Furthermore, subsequent to parasite establishment of a recombinant in a human population, its persistence is influenced by cross-reactivity with its parental forms.

Research delineates the distinction between RecA proteins of Streptomyces and other bacteria such as Escherichia. Unlike in other bacteria, recA gene is essential for viability of streptomyces. Gene inactivation studies in the presence of a second copy of recA reveal that recA is inactivated only in mutant strains.