Resynchronising returns to service in anoestrous dairy cows in the South Island of New Zealand.

AIMS: To investigate the effect of targeted resynchronisation of cows treated for non-observed oestrus before the planned start of mating (PSM), that were not detected in oestrus or pregnant 23 days after treatment (phantom cows), on the proportion pregnant at 42 days after PSM and the end of mating. METHODS: Farm staff from eight herds in two regions of the South Island of New Zealand identified 1,819 cows not showing oestrus by 10 days before PSM. These cows were treated with intravaginal progesterone for 7 days, and I/M gonadorelin 10 days and 1 day before PSM. Three days before PSM they were injected with cloprostenol and equine chorionic gonadotrophin, with fixed time artificial insemination (FTAI) at PSM. By 23 days after PSM, 1,218 cows had not returned to oestrus. Of these, 161 cows confirmed not pregnant by transrectal ultrasonography were randomly assigned to no treatment (control group; n=74) or were resynchronised 25 days after PSM using the same treatment programme as above, with FTAI 35 days after PSM (n=87). All cows that returned to oestrus were artificially inseminated until 42 days after PSM, when natural mating was used. All cows were examined using transrectal ultrasonography 80 to 90 days after PSM to confirm conception dates. RESULTS: Of the 1,819 anoestrous cows treated before PSM, 526 (29 (95% CI=23.1-34.0)%) had not been observed in oestrus by 23 days after PSM and had not conceived, so were diagnosed as phantoms cows. For resynchronised cows, 42/87 (48 (95% CI=37.8-58.8)%) were pregnant by 42 days after PSM compared to 21/74 (28 (95% CI=18.1-38.7)%) control cows (p=0.009). At the end of mating 58/87 (67 (95% CI=56.6-76.7)%) cows in the resynchronised group were pregnant and 46/74 (62 (95% CI=50.9-73.2)%) in the control group (p=0.554). The hazard of conception from 21 to 42 days after PSM was 1.9 (95% CI=1.07-3.12) times greater for resynchronised than control cows (p=0.026). CONCLUSION: In cows not observed in oestrus and treated before PSM, resynchronisation increased the proportion pregnant by 42 days after PSM. CLINICAL RELEVANCE: The benefit of resynchronisation depends on the number of anoestrous cows before PSM and the number of phantom cows after PSM. However at the herd-level it is likely that providing advice to reduce the known risk factors for cows not being observed in oestrus before the PSM may well be more cost effective than identifying and treating a sub-population of phantom cows.

Comparative analyses of multi-species sequences from targeted genomic regions.

The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.

Structural and functional cross-talk between a distant enhancer and the epsilon-globin gene promoter shows interdependence of the two elements in chromatin.

We investigated the requirements for enhancer-promoter communication by using the human beta-globin locus control region (LCR) DNase I-hypersensitive site 2 (HS2) enhancer and the epsilon-globin gene in chromatinized minichromosomes in erythroid cells. Activation of globin genes during development is accompanied by localized alterations of chromatin structure, and CACCC binding factors and GATA-1, which interact with both globin promoters and the LCR, are believed to be critical for globin gene transcription activation. We found that an HS2 element mutated in its GATA motif failed to remodel the epsilon-globin promoter or activate transcription yet HS2 nuclease accessibility did not change. Accessibility and transcription were reduced at promoters with mutated GATA-1 or CACCC sites. Strikingly, these mutations also resulted in reduced accessibility at HS2. In the absence of a globin gene, HS2 is similarly resistant to nuclease digestion. In contrast to observations in Saccharomyces cerevisiae, HS2-dependent promoter remodeling was diminished when we mutated the TATA box, crippling transcription. This mutation also reduced HS2 accessibility. The results indicate that the epsilon-globin promoter and HS2 interact both structurally and functionally and that both upstream activators and the basal transcription apparatus contribute to the interaction. Further, at least in this instance, transcription activation and promoter remodeling by a distant enhancer are not separable.

Essential role of NF-E2 in remodeling of chromatin structure and transcriptional activation of the epsilon-globin gene in vivo by 5' hypersensitive site 2 of the beta-globin locus control region.

Much of our understanding of the process by which enhancers activate transcription has been gained from transient-transfection studies in which the DNA is not assembled with histones and other chromatin proteins as it is in the cell nucleus. To study the activation of a mammalian gene in a natural chromatin context in vivo, we constructed a minichromosome containing the human epsilon-globin gene and portions of the beta-globin locus control region (LCR). The minichromosomes replicate and are maintained at stable copy number in human erythroid cells. Expression of the minichromosomal epsilon-globin gene requires the presence of beta-globin LCR elements in cis, as is the case for the chromosomal gene. We determined the chromatin structure of the epsilon-globin gene in both the active and inactive states. The transcriptionally inactive locus is covered by an array of positioned nucleosomes extending over 1,400 bp. In minichromosomes with a (mu)LCR or DNase I-hypersensitive site 2 (HS2) which actively transcribe the epsilon-globin gene, the nucleosome at the promoter is altered or disrupted while positioning of nucleosomes in the rest of the locus is retained. All or virtually all minichromosomes are simultaneously hypersensitive to DNase I both at the promoter and at HS2. Transcriptional activation and promoter remodeling, as well as formation of the HS2 structure itself, depended on the presence of the NF-E2 binding motif in HS2. The nucleosome at the promoter which is altered upon activation is positioned over the transcriptional elements of the epsilon-globin gene, i.e., the TATA, CCAAT, and CACCC elements, and the GATA-1 site at -165. The simple availability of erythroid transcription factors that recognize these motifs is insufficient to allow expression. As in the chromosomal globin locus, regulation also occurs at the level of chromatin structure. These observations are consistent with the idea that one role of the beta-globin LCR is to maintain promoters free of nucleosomes. The restricted structural change observed upon transcriptional activation may indicate that the LCR need only make a specific contact with the proximal gene promoter to activate transcription.

Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate.

Transcription terminators recognized by several RNA polymerases include a DNA segment encoding uridine-rich RNA and, for bacterial RNA polymerase, a hairpin loop located immediately upstream. Here, mutationally altered Escherichia coli RNA polymerase enzymes that have different termination efficiencies were used to show that the extent of transcription through the uridine-rich encoding segment is controlled by the substrate concentration of nucleoside triphosphate. This result implies that the rate of elongation determines the probability of transcript release. Moreover, the position of release sites suggests an important spatial relation between the RNA hairpin and the boundary of the terminator.