Hybrid allele-specific ChIP-Seq analysis links variation in transcription factor binding to traits in maize

Variation in transcriptional regulation is a major cause of phenotypic diversity. Genome-wide association studies (GWAS) have shown that most functional variants reside in non-coding regions, where they potentially affect transcription factor (TF) binding and chromatin accessibility to alter gene expression. Pinpointing such regulatory variations, however, remains challenging. Here, we developed a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach and identified variations in target binding of the brassinosteroid (BR) responsive transcription factor ZmBZR1 in maize. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) in B73xMo17 F1s identified thousands of target genes of ZmBZR1. Allele-specific ZmBZR1 binding (ASB) was observed for about 14.3% of target genes. It correlated with over 550 loci containing sequence variation in BZR1-binding motifs and over 340 loci with haplotype-specific DNA methylation, linking genetic and epigenetic variations to ZmBZR1 occupancy. Comparison with GWAS data linked hundreds of ASB loci to important yield, growth, and disease-related traits. Our study provides a robust method for analyzing genome-wide variations of transcription factor occupancy and identified genetic and epigenetic variations of the BR response transcription network in maize.

Molecular Basis of the Rare Gene Complex, D(C)-, Which Encodes Four Low Prevalence Antigens In the Rh Blood Group System.

Abstract 1117 Background: Over 40 years ago, the investigation of a case of fatal HDN in the third child of Madame Nou, a native of Ivory Coast, revealed that Madame Nou's RBCs had an unusual phenotype in the Rh blood group system denoted DIVa(C)-/DIVa(C)-. Initially, her RBCs were shown to express a partial D, a weak form of C, and Goa (RH30) [Salmon, et al., Rev Franc Transf 1969;12:239]. Later her RBCs were shown to also express RH33, Riv (RH45), and FPTT (RH50) [Bizot, et al., Transfusion 1988;28:342; Delehanty, et al., Transfusion 1983;23:410, abstract]. R0Har and CeVA phenotypes are encoded by hybrid RHCE-D(5)-CE alleles (respectively, c+ and C+) and the RBCs express RH33 and FPTT antigens but not Goa or Riv [Noizat-Pirenne, et al. Transfusion 2002;42:627]. RHD*DIVa.2 encodes a partial D and the Goa antigen and frequently travels with RHCE*ce(1025T) (RHCE*ceTI) (Vege, et al., Transfusion 2007;47:159A). The purpose of this study was to determine the molecular basis associated with the rare DIVa(C)- complex. Material and Methods: Blood samples were obtained from three donors previously identified as having the DIVa(C)- haplotype. Molecular analyses were performed by standard methods and included AS-PCR, PCR-RFLP, genomic sequencing of specific exons, and cloning and direct sequencing of cDNA. Results: At the RHD locus all donors were heterozygous for RHD and RHD*DIVa.2 and at the RHCE locus all had a compound hybrid allele, which contains exons 2 and 3 from RHD*DIVa.2 (based on RHD*186G/T, RHD*410C/T, RHD*455A/C), and exon 5 from RHD. The altered RHCE is presumed to be in cis to RHD*DIVa.2. In all three probands RHCE*48 in exon 1 is G/C; presumably the G belonging to the in trans RHCE and the nt48C to the hybrid allele, and this assumption favors exon 1 of the hybrid being from RHCE. Thus, the RHCE allele is likely RHCE*CE-DIVa.2(2,3)-CE-D(5)-CE. The in trans allele in Proband 1 is RH*cE, in Proband 2 it is RHCE*ce 254C, 733G, and in Proband 3 it is RHCE*ce. Conclusions: The compound hybrid provides an explanation for the expression of the four low prevalence antigens on RBCs with the DIVa(C)- phenotype. RHD*DIVa.2 encodes the Goa antigen. The flanking of RHD exon 5 by RHCE exons in the compound hybrid likely results in RH33 and FPTT antigen expression because R0Har and CeVA RBCs express these two antigens. It is possible that the junction of RHD exon 3 to RHCE exon 4 is involved in the expression of Riv. The weak C expression could be a consequence of exons 2 and 3 from RHD*DIVa.2 in the compound hybrid because exon 2 of the wild type RHD is identical in sequence to exon 2 of RHCE*C. The three probands in our study had RHCE nt1025C/C (wild type) and thus, are not RHCE*ce(1025T). This is the first report of RHD*DIVa.2 being involved in a hybrid gene at the RHCE locus. Such a hybrid is not unprecedented in that RHD*DIIIa is involved in the RHD*DIIIa-CE(4-7)-D hybrid [(C)ceS type 1 in the r’S haplotype] As only one example of anti-Riv has been described, our findings provide a tool by which to predict the expression of Riv. Disclosures: No relevant conflicts of interest to declare.