Paul D. Kaufman
University of Massachusetts Medical School
Histone codeHistone H1HeterochromatinGeneHistone methyltransferaseMolecular biologyHistone octamerNucleolusChemistryHistone H3Chromatin Assembly Factor IChromatin Assembly Factor-1GeneticsBiochemistryHistone H2AHistoneDNA replicationChromatinNucleosomeBiologyCell biology
85Publications
36H-index
7,596Citations
Publications 74
Newest
#1Osama Garwain (UMMS: University of Massachusetts Medical School)
#2Xiaoming Sun (UMMS: University of Massachusetts Medical School)H-Index: 3
Last. Paul D. Kaufman (UMMS: University of Massachusetts Medical School)H-Index: 36
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Vertebrate mammals express a protein called Ki-67 which is most widely known as a clinically useful marker of highly proliferative cells. Previous studies of human cells indicated that acute depletion of Ki-67 can elicit a delay at the G1/S boundary of the cell cycle, dependent on induction of the checkpoint protein p21. Consistent with those observations, we show here that acute Ki-67 depletion causes hallmarks of DNA damage, and the damage occurs even in the absence of checkpoint signaling. Th...
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#1Aizhan Bizhanova (UMMS: University of Massachusetts Medical School)H-Index: 4
#2Paul D. Kaufman (UMMS: University of Massachusetts Medical School)H-Index: 36
Chromatin is a dynamic structure composed of DNA, RNA, and proteins, regulating storage and expression of the genetic material in the nucleus. Heterochromatin plays a crucial role in driving the three-dimensional arrangement of the interphase genome, and in preserving genome stability by maintaining a subset of the genome in a silent state. Spatial genome organization contributes to normal patterns of gene function and expression, and is therefore of broad interest. Mammalian heterochromatin, th...
7 CitationsSource
#1Aizhan Bizhanova (UMMS: University of Massachusetts Medical School)H-Index: 4
#2Aimin Yan (UMMS: University of Massachusetts Medical School)H-Index: 8
Last. Paul D. Kaufman (UMMS: University of Massachusetts Medical School)H-Index: 36
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Heterochromatin in eukaryotic interphase cells frequently localizes to the nucleolar periphery (nucleolus-associated domains (NADs)) and the nuclear lamina (lamina-associated domains (LADs)). Gene expression in somatic cell NADs is generally low, but NADs have not been characterized in mammalian stem cells. Here, we generated the first genome-wide map of NADs in mouse embryonic stem cells (mESCs) via deep sequencing of chromatin associated with biochemically purified nucleoli. As we had observed...
7 CitationsSource
#1Anastassiia Vertii (UMMS: University of Massachusetts Medical School)H-Index: 11
#2Jianhong Ou (UMMS: University of Massachusetts Medical School)H-Index: 26
Last. Paul D. Kaufman (UMMS: University of Massachusetts Medical School)H-Index: 36
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: In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining nucleolus-associated domains (NADs) and lamina-associated domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts (MEFs) via deep sequencing of chromatin associated with purified nucleoli. We developed a Bioconductor package called NADfinder and demonstrated that it identifies NADs more accurat...
30 CitationsSource
#1Yuichi IchikawaH-Index: 4
#2Paul D. Kaufman (UMMS: University of Massachusetts Medical School)H-Index: 36
In the original publication, Fig. 1 was incorrectly published. The amino acid sequence was shifted to the left relative to the rest of the diagram in the published version and the corrected figure is given here.
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#1Yuichi IchikawaH-Index: 4
#2Paul D. Kaufman (UMMS: University of Massachusetts Medical School)H-Index: 36
In eukaryotes, genomic DNA is packaged into the nucleus together with histone proteins, forming chromatin. The fundamental repeating unit of chromatin is the nucleosome, a naturally symmetric structure that wraps DNA and is the substrate for numerous regulatory post-translational modifications. However, the biological significance of nucleosomal symmetry until recently had been unexplored. To investigate this issue, we developed an obligate pair of histone H3 heterodimers, a novel genetic tool t...
3 CitationsSource
#1Aizhan BizhanovaH-Index: 4
#2Aimin YanH-Index: 8
Last. Paul D. KaufmanH-Index: 36
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#1Yuichi Ichikawa (UMMS: University of Massachusetts Medical School)H-Index: 4
#2Noriko SaitohH-Index: 15
Last. Paul D. Kaufman (UMMS: University of Massachusetts Medical School)H-Index: 36
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: Nucleosomes contain two copies of each core histone, held together by a naturally symmetric, homodimeric histone H3-H3 interface. This symmetry has complicated efforts to determine the regulatory potential of this architecture. Through molecular design and in vivo selection, we recently generated obligately heterodimeric H3s, providing a powerful tool for discovery of the degree to which nucleosome symmetry regulates chromosomal functions in living cells (Ichikawa et al., 2017). We now have ex...
4 CitationsSource
#1Yuichi Ichikawa (UMMS: University of Massachusetts Medical School)H-Index: 4
#2Noriko SaitohH-Index: 15
Last. Paul D. Kaufman (UMMS: University of Massachusetts Medical School)H-Index: 36
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#1Yuichi Ichikawa (UMMS: University of Massachusetts Medical School)H-Index: 4
#2Paul D. KaufmanH-Index: 36
: Nucleosomes are the fundamental unit of eukaryotic chromosome packaging, comprised of 147 bp of DNA wrapped around two molecules of each of the core histone proteins H2A, H2B, H3, and H4. Nucleosomes are symmetrical, with one axis of symmetry centered on the homodimeric interaction between the C-termini of the H3 molecules. To explore the functional consequences of nucleosome symmetry, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, allowing us to compare cells with single...
1 CitationsSource