Connecting nuclear architecture and genomic function

Berezney, Ronald; Mortillaro, M; Ma, Hong; Meng, Chong; Samarabandu, Jagath; Wei, Xiangyun; Somanathan, Suryanarayan; Liou, W.S.; Pan, Shih Jung; Cheng, Pengfei

doi:10.1002/(sici)1097-4644(199608)62:2<223::aid-jcb10>3.0.co;2-m

Cited by 32 publications

(4 citation statements)

References 11 publications

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“…An interesting hypothesis is therefore that RUNX1 may be required to bring together promoter‐distal regulatory elements at nuclear ‘transcription factories’ (Jackson et al , 1993; Osborne et al , 2004), where genes are dynamically recruited during activation and abatement of their transcription (Schoenfelder et al , 2010). Moreover, RUNX1 proteins localize in defined subnuclear domains (Berezney et al , 1996; Stein et al , 1999; Li et al , 2005), and a unique intranuclear trafficking sequence that targets RUNX1 to these sites has been identified (Zeng et al , 1997, 1998; Zaidi et al , 2002). Interestingly, molecular alterations that cause misrouting of RUNX1 in the nucleus result in abnormal synergism with other transcription factors (Li et al , 2005), aberrant gene expression and development of disease (Jackson, 1997; Stein et al , 2000a, 2000b), suggesting that the correct subnuclear targeting of RUNX1 is an integral component of multifactor interaction to control cell‐specific gene expression.…”

Section: Discussionmentioning

confidence: 99%

RUNX1 regulates theCD34gene in haematopoietic stem cells by mediating interactions with a distal regulatory element

et al. 2011

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The transcription factor RUNX1 is essential to establish the haematopoietic gene expression programme; however, the mechanism of how it activates transcription of haematopoietic stem cell (HSC) genes is still elusive. Here, we obtained novel insights into RUNX1 function by studying regulation of the human CD34 gene, which is expressed in HSCs. Using transgenic mice carrying human CD34 PAC constructs, we identified a novel downstream regulatory element (DRE), which is bound by RUNX1 and is necessary for human CD34 expression in long-term (LT)-HSCs. Conditional deletion of Runx1 in mice harbouring human CD34 promoter-DRE constructs abrogates human CD34 expression. We demonstrate by chromosome conformation capture assays in LT-HSCs that the DRE physically interacts with the human CD34 promoter. Targeted mutagenesis of RUNX binding sites leads to perturbation of this interaction and decreased human CD34 expression in LT-HSCs. Overall, our in vivo data provide novel evidence about the role of RUNX1 in mediating interactions between distal and proximal elements of the HSC gene CD34.

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Section: Discussionmentioning

confidence: 99%

RUNX1 regulates theCD34gene in haematopoietic stem cells by mediating interactions with a distal regulatory element

et al. 2011

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“…Nuclear matrix proteins (NMPs) are the non‐histone proteins, which contain nuclear matrix (NM) following nuclease, salt, and detergent extraction of isolated cell nuclei [Berezney et al, 1996]. Despite the high complexity, NMPs can be classified into at least two major types: (1) those which are commonly found in a variety of eukaryotic cells.…”

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confidence: 99%

Nuclear matrix protein expressions in hepatocytes of normal and cirrhotic rat livers under normal and regenerating conditions

Yun¹,

Liew²,

Chew³

et al. 2004

J of Cellular Biochemistry

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We explored the feasibility of studying nuclear matrix protein (NMP) expressions of the hepatocytes in normal and cirrhotic rat livers with liver regeneration after partial hepatectomy. Sixteen Wistar healthy rats were studied with experimental liver regeneration and/or liver cirrhosis. Two-dimensional (2-D) gel electrophoresis was used to generate these NMP compositions from these rat liver samples. Several antibodies against cytokeratin, vimentin, actin, B23, HNF4alpha, and heat shock protein 70 were used for identification by Western blot. Totally, 41 strongly stained protein spots were characterized on the 2-D gels. Thirty-four protein spots were detected in all of these rat livers, of which, cytokeratin, vimentin, actin, HNF4alpha, and heat shock protein 70 were identified. B23 was detected in the regenerated livers. Three protein spots (s33, s34, and s35) were detectable only in NMP preparation extracted from the regenerating rat livers after hepatectomy. Another three protein spots (s36, s37, and s38) were detectable only in NMP preparation extracted from thioacetamide-induced cirrhotic rat livers. Under these conditions including experimental liver regeneration and/or liver cirrhosis, Over thirty higher abundance NMPs of hepatocytes were consistently expressed and considered as common and basic NMPs. Some of the NMPs are specific for liver regeneration and may play a critical role in cell proliferation and cell cycle, and some are specific for liver cirrhosis.

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“…3). A decade later with the advent of digital imaging and computational image analysis tools, these numbers grew to around one thousand (Berezney et al 1996; Fox et al 1991; Jackson and Pombo 1998; Ma et al 1998), where they remained for several years (see Fig. 3).…”

Section: To Go Where No One Has Gone Before: Beyond the Abbe Limitmentioning

confidence: 99%

A journey through the microscopic ages of DNA replication

Reinhart

Cardoso

2016

Protoplasma

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Scientific discoveries and technological advancements are inseparable but not always take place in a coherent chronological manner. In the next, we will provide a seemingly unconnected and serendipitous series of scientific facts that, in the whole, converged to unveil DNA and its duplication. We will not cover here the many and fundamental contributions from microbial genetics and in vitro biochemistry. Rather, in this journey, we will emphasize the interplay between microscopy development culminating on super resolution fluorescence microscopy (i.e., nanoscopy) and digital image analysis and its impact on our understanding of DNA duplication. We will interlace the journey with landmark concepts and experiments that have brought the cellular DNA replication field to its present state.

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Connecting nuclear architecture and genomic function

Cited by 32 publications

References 11 publications

RUNX1 regulates theCD34gene in haematopoietic stem cells by mediating interactions with a distal regulatory element

RUNX1 regulates theCD34gene in haematopoietic stem cells by mediating interactions with a distal regulatory element

Nuclear matrix protein expressions in hepatocytes of normal and cirrhotic rat livers under normal and regenerating conditions

A journey through the microscopic ages of DNA replication

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