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The chromatin scaffold protein SAFB1 localizes SUMO-1 to the promoters of ribosomal protein genes to facilitate transcription initiation and splicing

, Columbus, OH 43210 , USA 1 Present addresses: Hui-wen Liu, Oregon Health and Science University , Portland, OR 97239 , USA. Xiaoyan Guan, Florida State University , Tallahassee, FL , USA 2 Department of

Promoters active in interphase are bookmarked during mitosis by ubiquitination

We analyzed modification of chromatin by ubiquitination in human cells and whether this mark changes through the cell cycle. HeLa cells were synchronized at different stages and regions of the genome with ubiquitinated chromatin were identified by affinity purification coupled with next-generation sequencing. During interphase, ubiquitin marked the chromatin on the transcribed...

Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes

SUMOylation of transcription factors and chromatin proteins is in many cases a negative mark that recruits factors that repress gene expression. In this study, we determined the occupancy of Small Ubiquitin-like MOdifier (SUMO)-1 on chromatin in HeLa cells by use of chromatin affinity purification coupled with next-generation sequencing. We found SUMO-1 localization on chromatin...

RMCE-ASAP: a gene targeting method for ES and somatic cells to accelerate phenotype analyses

In recent years, tremendous insight has been gained on p53 regulation by targeting mutations at the p53 locus using homologous recombination in ES cells to generate mutant mice. Although informative, this approach is inefficient, slow and expensive. To facilitate targeting at the p53 locus, we developed an improved Recombinase-Mediated Cassette Exchange (RMCE) method. Our...

Analysis of variation in NF-κB genes and expression levels of NF-κB-regulated molecules

The nuclear factor-kappaB (NF-κB) family of transcription factors regulates the expression of a variety of genes involved in apoptosis and immune response. We examined relationships between genotypes at five NF-κB subunits (NFKB1, NFKB2, REL, RELA, and RELB) and variable expression levels of 15 NF-κB regulated proteins with heritability greater than 0.40: BCL2A1, BIRC2, CD40...

Analysis of variation in NF-κB genes and expression levels of NF-κB-regulated molecules

The nuclear factor-kappaB (NF-κB) family of transcription factors regulates the expression of a variety of genes involved in apoptosis and immune response. We examined relationships between genotypes at five NF-κB subunits (NFKB1, NFKB2, REL, RELA, and RELB) and variable expression levels of 15 NF-κB regulated proteins with heritability greater than 0.40: BCL2A1, BIRC2, CD40...

The genetics of gene expression: comparison of linkage scans using two phenotype normalization methods

The goal of this paper is to investigate the effects of normalization procedures for expression data on linkage results. We selected the two most commonly used expression data extraction and normalization methods, Affymetrix global scaling and dChip invariant. After applying these two methods in 3554 expression phenotypes, we identified 45 phenotypes that were more likely to be...

Linkage analysis using principal components of gene expression data

The goal of this paper is to investigate the effect of using principal components as a data reduction method for expression data in linkage analysis. We used 45 probes normalized using the Affymetrix Global Scaling that had evidence of high heritability to estimate the first 10 principal components (PC). A genome-wide linkage scan was performed on the 45 expression values and the...

Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium

Ribosomal RNAs (rRNAs) are encoded by multicopy families of identical genes. In Dictyostelium and other protists, the rDNA is carried on extrachromosomal palindromic elements that comprise up to 20% of the nuclear DNA. We present the sequence of the 88 kb Dictyostelium rDNA element, noting that the rRNA genes are likely to be the only transcribed regions. By interrogating a...

The zinc ion in the HNH motif of the endonuclease domain of colicin E7 is not required for DNA binding but is essential for DNA hydrolysis

The HNH motif was originally identified in the subfamily of HNH homing endonucleases, which initiate the process of the insertion of mobile genetic elements into specific sites. Several bacteria toxins, including colicin E7 (ColE7), also contain the 30 amino acid HNH motif in their nuclease domains. In this work, we found that the nuclease domain of ColE7 (nuclease-ColE7...