Haplotype variation and linkage disequilibrium in 313 human genes.

Variation within genes has important implications for all biological traits. We identified 3899 single nucleotide polymorphisms (SNPs) that were present within 313 genes from 82 unrelated individuals of diverse ancestry, and we organized the SNPs into 4304 different haplotypes. Each gene had several variable SNPs and haplotypes that were present in all populations, as well as a number that were population-specific. Pairs of SNPs exhibited variability in the degree of linkage disequilibrium that was a function of their location within a gene, distance from each other, population distribution, and population frequency. Haplotypes generally had more information content (heterozygosity) than did individual SNPs. Our analysis of the pattern of variation strongly supports the recent expansion of the human population.

Cutting edge: differential signaling requirements for activation of assembled cyclin D3-cdk4 complexes in B-1 and B-2 lymphocyte subsets.

B-1 lymphocytes represent a distinct B cell subset with unusual mitogenic responses. PMA alone promotes proliferation in B-1 cells, but not in splenic B-2 cells. Although cyclin D2-cyclin-dependent kinase 4 (cdk4) complexes mediate early retinoblastoma gene product (pRb) phosphorylation in B-1 cells, the transient nature of their accumulation cannot account for the continued increase in pRb phosphorylation, which is maximal at 24 h. We show herein that PMA promotes the accumulation of functional cyclin D3-cdk4 complexes in B-1 cells following loss of cyclin D2. PMA also induces accumulation of cyclin D3-cdk4 complexes in B-2 cells; however, these complexes do not phosphorylate pRb. Thus, PMA is sufficient to induce synthesis and assembly of cyclin D3-cdk4 complexes in B-1 and B-2 cells; however, PMA triggers cyclin D3-cdk4 activation only in B-1 cells. These results reveal a novel regulatory step that controls activation of cyclin D3-cdk4 complexes whose function segregates differentially in B cell subsets.

Early induction of cyclin D2 expression in phorbol ester-responsive B-1 lymphocytes.

B-1 lymphocytes represent a distinct B cell subset with characteristic features that include self-renewing capacity and unusual mitogenic responses. B-1 cells differ from conventional B cells in terms of the consequences of phorbol ester treatment: B-1 cells rapidly enter S phase in response to phorbol ester alone, whereas B-2 cells require a calcium ionophore in addition to phorbol ester to trigger cell cycle progression. To address the mechanism underlying the varied proliferative responses of B-1 and B-2 cells, we evaluated the expression and activity of the G1 cell cycle regulator, cyclin D2, and its associated cyclin-dependent kinases (Cdks). Cyclin D2 expression was upregulated rapidly, within 2-4 h, in phorbol ester-stimulated B-1 cells, in a manner dependent on intact transcription/translation, but was not increased in phorbol ester- stimulated B-2 cells. Phorbol ester-stimulated cyclin D2 expression was accompanied by the formation of cyclin D2-Cdk4, and, to a lesser extent, cyclin D2-Cdk6, complexes; cyclin D2- containing complexes were found to be catalytically functional, in terms of their ability to phosphorylate exogenous Rb in vitro and to specifically phosphorylate endogenous Rb on serine780 in vivo. These results strongly suggest that the rapid induction of cyclin D2 by a normally nonmitogenic phorbol ester stimulus is responsible for B-1 cell progression through G1 phase. The ease and rapidity with which cyclin D2 responds in B-1 cells may contribute to the proliferative features of this subset.

Regulation of the catalytic subunit (p34PSK-J3/cdk4) for the major D-type cyclin in mature B lymphocytes.

We examined the expression of the cyclin-dependent kinase 4, p34PSK-J3/cdk4 protein, in small dense, activated, and proliferating primary B lymphocytes. A small steady state level of cdk4 synthesis was detected in resting B cells. Stimulation of resting B cells with mitogenic amounts of F(ab')2 fragments of goat anti-mouse IgM (anti-Ig) resulted in increased synthesis of cdk4 protein during the mid to late G1 phase of the cell cycle; LPS or the combination of phorbol ester and calcium ionophore also elevated cdk4 levels. Resting B cells that we rendered competent by treatment with IL 4 or low doses of anti-Ig or, alternatively, were activated by phorbol ester or ionomycin alone also exhibited heightened cdk4 protein levels. Subsequent analysis of potential cdk4 regulatory subunit D-type cyclins revealed that cyclin D2, not cyclin D1 or D3, is expressed in primary mature B lymphocytes. The induction of cyclin D2 synthesis in response to mitogenic anti-Ig paralleled cdk4 expression; however, IL-4 or low dose anti-Ig alone did not increase the rate of de novo cyclin D2 synthesis above that of resting B cells. The significance of the lack of cyclin D2 regulation by competence-inducing growth factors was demonstrated, in that only mitogenic factors that stimulated DNA synthesis 1) led to the formation of stable cyclin D2/cdk4 holoenzyme complexes during G1 phase progression, and 2) afforded the isolation of anti-cyclin D2 or anti-cdk4 immunoprecipitates that phosphorylated retinoblastoma. These findings suggest a role for these proteins during the mid to late G1 phase progression and possibly the G1/S phase transition in primary mature B lymphocytes.

Activation of AP-1 in primary B lymphocytes by surface immunoglobulin requires de novo Jun-B synthesis.

We demonstrate herein that resting primary B lymphocytes do not contain detectable levels of AP-1 (TRE)-binding activity. Upon cross-linking of surface immunoglobulin (sIg) receptors, TRE-binding activity is induced within 2 hr and its appearance requires de novo protein synthesis. Antisera to Jun-B inhibits the vast majority of TRE-binding activity, indicating that Jun-B is a primary component of B cell TRE-binding complexes. In keeping with this, Jun-B protein is not detectable in cytosol or nuclear extracts from resting B lymphocytes, as determined by immunoblotting with Jun-B antisera. However, the nuclear expression of Jun-B is induced within 2 hr following sIg cross-linking and is completely blocked by cycloheximide. 35S-labeling studies suggest that the increase in Jun-B expression results from de novo protein synthesis. Moreover, Jun-B migrates in SDS-polyacrylamide gels as two distinct electrophoretic proteins that correspond to a 41-kDa species and a phosphorylated 47-kDa form. These results suggest that the induction of AP-1-binding activity in primary B lymphocytes following sIg cross-linking does not result from post-translational phosphorylation of a preexisting cellular pool of Jun-B protein, but rather is coupled to the stimulation of de novo Jun-B synthesis. Thus Jun-B synthesis represents an integral event in the production of receptor-mediated AP-1 in B cells. The significance of these results with respect to the role of Jun-B in controlling gene expression during the activation of primary B cells is discussed.

Cell cycle-specific induction of Cdk2 expression in B lymphocytes following antigen receptor cross-linking.

The ligation of membrane Ig (mIg) on quiescent primary B lymphocytes by mitogenic concentrations of anti-IgM antibodies leads to cell cycle progression. The level of cyclin-dependent kinase 2 (Cdk2) expression was found to be restricted to specific phases of the cell cycle in primary cultures of murine B lymphocytes. Resting G0 phase, G1 phase, or B cells arrested near the G1/S boundary by hydroxyurea contained no detectable Cdk2 protein or associated histone H1 kinase activity. In contrast, B cell entry into S phase was accompanied by an induction in the expression of cellular Cdk2 as judged by immunoblotting of B cell lysates with anti-Cdk2 antibodies. Concomitant with S phase entry was the detection of anti-Cdk2-specific immunoprecipitable histone H1 kinase activity. Further analysis revealed that the amount of cyclin A protein also oscillated during cell cycle, appearing initially in G1 phase B cells. Cyclin A was found to be associated with Cdk2 in B cells during S phase progression. These results indicate that cross-linking of mIg on primary B lymphocytes results in the "downstream" catalytic activation of Cdk2. The timing of Cdk2 expression and its association with cyclin A suggests that Cdk2 may not be involved in the decision to enter S phase, but rather may provide a role in the maintenance of S phase progression or in preparing B cells to enter M phase.