scholarly journals Role of the nuclear envelope in genome organization and gene expression

2010 ◽  
Vol 3 (2) ◽  
pp. 147-166 ◽  
Author(s):  
David W. Van de Vosse ◽  
Yakun Wan ◽  
Richard W. Wozniak ◽  
John D. Aitchison
Keyword(s):  
Gene Expression ◽  
Nuclear Envelope ◽  
Genome Organization

scholarly journals Role of lamins in 3D genome organization and global gene expression

Nucleus ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 33-41 ◽  
Author(s):  
Youngjo Kim ◽  
Xiaobin Zheng ◽  
Yixian Zheng
Keyword(s):  
Gene Expression ◽  
Genome Organization ◽  
Global Gene Expression ◽  
3D Genome

scholarly journals Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Parna Saha ◽  
Divya Tej Sowpati ◽  
Mamilla Soujanya ◽  
Ishanee Srivastava ◽  
Rakesh Kumar Mishra
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Transcriptional Regulation ◽  
Genome Organization ◽  
Constitutive Heterochromatin ◽  
Regulatory Mechanisms ◽  
Epigenetic Code ◽  
Chromatin Proteins ◽  
Heterochromatic Genes

Abstract Background Transcription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. The regulatory mechanisms of Drosophila melanogaster heterochromatic gene transcription remain largely unknown. Emerging evidence suggests that genome organization and transcriptional regulation are inter-linked. However, the pericentromeric genome organization is relatively less studied. Therefore, we sought to characterize the pericentromeric genome organization and understand how this organization along with the pericentromeric factors influences heterochromatic gene expression. Results Here, we characterized the pericentromeric genome organization in Drosophila melanogaster using 5C sequencing. Heterochromatic topologically associating domains (Het TADs) correlate with distinct epigenomic domains of active and repressed heterochromatic genes at the pericentromeres. These genes are known to depend on the heterochromatic landscape for their expression. However, HP1a or Su(var)3-9 RNAi has minimal effects on heterochromatic gene expression, despite causing significant changes in the global Het TAD organization. Probing further into this observation, we report the role of two other chromatin proteins enriched at the pericentromeres-dMES-4 and dADD1 in regulating the expression of a subset of heterochromatic genes. Conclusions Distinct pericentromeric genome organization and chromatin landscapes maintained by the interplay of heterochromatic factors (HP1a, H3K9me3, dMES-4 and dADD1) are sufficient to support heterochromatic gene expression despite the loss of global Het TAD structure. These findings open new avenues for future investigations into the mechanisms of heterochromatic gene expression.

The Role of Chromosome–Nuclear Envelope Attachments in 3D Genome Organization

2018 ◽  
Vol 83 (4) ◽  
pp. 350-358 ◽  
Author(s):  
I. V. Sharakhov ◽  
S. M. Bondarenko ◽  
G. N. Artemov ◽  
A. V. Onufriev
Keyword(s):  
Nuclear Envelope ◽  
Genome Organization ◽  
3D Genome

Role of small nuclear RNAs in eukaryotic gene expression

2013 ◽  
Vol 54 ◽  
pp. 79-90 ◽  
Author(s):  
Saba Valadkhan ◽  
Lalith S. Gunawardane
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Rna Stability ◽  
Splice Sites ◽  
Branch Site ◽  
Small Nuclear Rnas ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Rna Biogenesis

Eukaryotic cells contain small, highly abundant, nuclear-localized non-coding RNAs [snRNAs (small nuclear RNAs)] which play important roles in splicing of introns from primary genomic transcripts. Through a combination of RNA–RNA and RNA–protein interactions, two of the snRNPs, U1 and U2, recognize the splice sites and the branch site of introns. A complex remodelling of RNA–RNA and protein-based interactions follows, resulting in the assembly of catalytically competent spliceosomes, in which the snRNAs and their bound proteins play central roles. This process involves formation of extensive base-pairing interactions between U2 and U6, U6 and the 5′ splice site, and U5 and the exonic sequences immediately adjacent to the 5′ and 3′ splice sites. Thus RNA–RNA interactions involving U2, U5 and U6 help position the reacting groups of the first and second steps of splicing. In addition, U6 is also thought to participate in formation of the spliceosomal active site. Furthermore, emerging evidence suggests additional roles for snRNAs in regulation of various aspects of RNA biogenesis, from transcription to polyadenylation and RNA stability. These snRNP-mediated regulatory roles probably serve to ensure the co-ordination of the different processes involved in biogenesis of RNAs and point to the central importance of snRNAs in eukaryotic gene expression.

Cell-specific regulation of IRS-1 gene expression: role of E box and C/EBP binding site in HepG2 cells and CHO cells

Diabetes ◽  
1997 ◽  
Vol 46 (3) ◽  
pp. 354-362 ◽  
Author(s):  
K. Matsuda ◽  
E. Araki ◽  
R. Yoshimura ◽  
K. Tsuruzoe ◽  
N. Furukawa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Site ◽  
Cho Cells ◽  
Hepg2 Cells ◽  
E Box ◽  
Specific Regulation
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