scholarly journals Phase separation in transcription factor dynamics and chromatin organization

2021 ◽  
Vol 71 ◽  
pp. 148-155
Author(s):  
Kaustubh Wagh ◽  
David A. Garcia ◽  
Arpita Upadhyaya
Keyword(s):  
Transcription Factor ◽  
Phase Separation ◽  
Chromatin Organization

scholarly journals Transcription-independent TFIIIC-bound sites cluster near heterochromatin boundaries within lamina-associated domains in C. elegans

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Alexis V. Stutzman ◽  
April S. Liang ◽  
Vera Beilinson ◽  
Kohta Ikegami
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Mammalian Cells ◽  
Sex Chromosome ◽  
Rna Polymerase Iii ◽  
Chromatin Organization ◽  
Control Of Gene Expression ◽  
C Elegans ◽  
Polymerase Iii ◽  
The Individual

Abstract Background Chromatin organization is central to precise control of gene expression. In various eukaryotic species, domains of pervasive cis-chromatin interactions demarcate functional domains of the genomes. In nematode Caenorhabditis elegans, however, pervasive chromatin contact domains are limited to the dosage-compensated sex chromosome, leaving the principle of C. elegans chromatin organization unclear. Transcription factor III C (TFIIIC) is a basal transcription factor complex for RNA polymerase III, and is implicated in chromatin organization. TFIIIC binding without RNA polymerase III co-occupancy, referred to as extra-TFIIIC binding, has been implicated in insulating active and inactive chromatin domains in yeasts, flies, and mammalian cells. Whether extra-TFIIIC sites are present and contribute to chromatin organization in C. elegans remains unknown. Results We identified 504 TFIIIC-bound sites absent of RNA polymerase III and TATA-binding protein co-occupancy characteristic of extra-TFIIIC sites in C. elegans embryos. Extra-TFIIIC sites constituted half of all identified TFIIIC binding sites in the genome. Extra-TFIIIC sites formed dense clusters in cis. The clusters of extra-TFIIIC sites were highly over-represented within the distal arm domains of the autosomes that presented a high level of heterochromatin-associated histone H3K9 trimethylation (H3K9me3). Furthermore, extra-TFIIIC clusters were embedded in the lamina-associated domains. Despite the heterochromatin environment of extra-TFIIIC sites, the individual clusters of extra-TFIIIC sites were devoid of and resided near the individual H3K9me3-marked regions. Conclusion Clusters of extra-TFIIIC sites were pervasive in the arm domains of C. elegans autosomes, near the outer boundaries of H3K9me3-marked regions. Given the reported activity of extra-TFIIIC sites in heterochromatin insulation in yeasts, our observation raised the possibility that TFIIIC may also demarcate heterochromatin in C. elegans.

The winged-helix transcription factor JUMU regulates development, nucleolus morphology and function, and chromatin organization of Drosophila melanogaster

2010 ◽  
Vol 18 (3) ◽  
pp. 307-324 ◽  
Author(s):  
Annemarie Hofmann ◽  
Madeleine Brünner ◽  
Alexander Schwendemann ◽  
Martin Strödicke ◽  
Sascha Karberg ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Drosophila Melanogaster ◽  
Chromatin Organization ◽  
Winged Helix ◽  
And Function ◽  
Winged Helix Transcription Factor

scholarly journals Undifferentiated Embryonic Cell Transcription Factor 1 Regulates ESC Chromatin Organization and Gene Expression

Stem Cells ◽  
2010 ◽  
Vol 28 (10) ◽  
pp. 1703-1714 ◽  
Author(s):  
Susanne M. Kooistra ◽  
Vincent van den Boom ◽  
Rajkumar P. Thummer ◽  
Frank Johannes ◽  
René Wardenaar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Embryonic Cell ◽  
Chromatin Organization ◽  
Transcription Factor 1

scholarly journals Mitotic Implantation of the Transcription Factor Prospero via Phase Separation Drives Terminal Neuronal Differentiation

2020 ◽  
Vol 52 (3) ◽  
pp. 277-293.e8 ◽  
Author(s):  
Xiaodan Liu ◽  
Jingwen Shen ◽  
Leiming Xie ◽  
Zelin Wei ◽  
Chouin Wong ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Phase Separation ◽  
Neuronal Differentiation

scholarly journals Quantifying liquid-liquid phase separation property of chromatin under physiological conditions using Hi-MS and Hi-C

2020 ◽  
Author(s):  
Minglei Shi ◽  
Kaiqiang You ◽  
Chao Hou ◽  
Taoyu Chen ◽  
Zhengyu Liang ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Quantitative Measurement ◽  
Biological Process ◽  
Global Analysis ◽  
Chromatin Organization ◽  
Liquid Phase Separation ◽  
Protein Functions ◽  
Associated Proteins ◽  
Liquid Liquid Phase Separation

AbstractBackgroundLiquid–liquid phase separation (LLPS) is an important organizing principle for biomolecular condensation and chromosome compartmentalization. However, while many proteins have been reported to undergo LLPS, quantitative and global analysis of chromatin LLPS property remains absent.ResultsHere, by combing chromatin associated protein pull-down, quantitative proteomics and 1,6-hexanediol treatment, we developed Hi-MS and defined anti-1,6-HD index of chromatin-associated proteins (AICAP) to quantitative measurement of LLPS property of chromatin-associated proteins in their endogenous state and physiological abundance. The AICAP values were verified by previously reported experiments and were reproducible across different MS platforms. Moreover, the AICAP values were highly correlate with protein functions. Proteins act in active/regulatory biological process often exhibit low AICAP values, while proteins act in structural and repressed biological process often exhibit high AICAP values. We further revealed that chromatin organization changes more in compartment A than B, and the changes in chromatin organization at various levels, including compartments, TADs and loops are highly correlated to the LLPS properties of their neighbor nuclear condensates.ConclusionsOur work provided the first global quantitative measurement of LLPS properties of chromatin-associated proteins and higher-order chromatin structure, and demonstrate that the active/regulatory chromatin components, both protein (trans) and DNA (cis), exhibit more hydrophobicity-dependent LLPS properties than the repressed/structural chromatin components.

scholarly journals Transcription-independent TFIIIC-bound sites cluster near heterochromatin boundaries within lamina-associated domains in C. elegans

2019 ◽  
Author(s):  
Alexis V. Stutzman ◽  
April S. Liang ◽  
Vera Beilinson ◽  
Kohta Ikegami
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Mammalian Cells ◽  
Sex Chromosome ◽  
Rna Polymerase Iii ◽  
Chromatin Organization ◽  
Control Of Gene Expression ◽  
C Elegans ◽  
Polymerase Iii ◽  
The Individual

ABSTRACTBACKGROUNDChromatin organization is central to precise control of gene expression. In various eukaryotic spieces, domains of pervasive cis-chromatin interactions demarcate functional domains of the genomes. In nematode C. elegans, however, pervasive chromatin contact domains are limited to the dosage-compensated sex chromosome, leaving the principle of C. elegans chromatin organization unclear. Transcription Factor III C (TFIIIC) is a basal transcription factor complex for RNA Polymerase III, and is implicated in chromatin organization. TFIIIC binding without RNA Polymerase III co-occupancy, referred to as extra-TFIIIC binding, has been implicated in insulating active and inactive chromatin domains in yeasts, flies, and mammalian cells. Whether extra-TFIIIC sites are present and contribute to chromatin organization in C. elegans remains unknown.RESULTSWe identified 504 TFIIIC-bound sites absent of RNA Polymerase III and TATA-binding protein co-occupancy characteristic of extra-TFIIIC sites in C. elegans embryos. Extra-TFIIIC sites constituted half of all identified TFIIIC binding sites in the genome. Extra-TFIIIC sites formed dense clusters in cis. The clusters of extra-TFIIIC sites were highly over-represented within the distal arm domains of the autosomes that presented a high level of heterochromatin-associated histone H3K9 trimethylation (H3K9me3). Furthermore, extra-TFIIIC clusters were embedded in the lamina-associated domains. Despite the heterochromatin environment of extra-TFIIIC sites, the individual clusters of extra-TFIIIC sites were devoid of and resided near the individual H3K9me3-marked regions.CONCLUSIONClusters of extra-TFIIIC sites were pervasive in the arm domains of C. elegans autosomes, near the outer boundaries of H3K9me3-marked regions. Given the reported activity of extra-TFIIIC sites in heterochromatin insulation in yeasts, our observation raised the possibility that TFIIIC may also demarcate heterochromatin in C. elegans.

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