scholarly journals RNA Elimination Machinery Targeting Meiotic mRNAs Promotes Facultative Heterochromatin Formation

Science ◽  
2011 ◽  
Vol 335 (6064) ◽  
pp. 96-100 ◽  
Author(s):  
Martin Zofall ◽  
Soichiro Yamanaka ◽  
Francisca E. Reyes-Turcu ◽  
Ke Zhang ◽  
Chanan Rubin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sexual Differentiation ◽  
Cellular Differentiation ◽  
Mrna Processing ◽  
Messenger Rnas ◽  
Facultative Heterochromatin ◽  
Heterochromatin Formation ◽  
Regulated Gene Expression ◽  
Heterochromatin Assembly ◽  
Processing Factors

Facultative heterochromatin that changes during cellular differentiation coordinates regulated gene expression, but its assembly is poorly understood. Here, we describe facultative heterochromatin islands in fission yeast and show that their formation at meiotic genes requires factors that eliminate meiotic messenger RNAs (mRNAs) during vegetative growth. Blocking production of meiotic mRNA or loss of RNA elimination factors, including Mmi1 and Red1 proteins, abolishes heterochromatin islands. RNA elimination machinery is enriched at meiotic loci and interacts with Clr4/SUV39h, a methyltransferase involved in heterochromatin assembly. Heterochromatin islands disassemble in response to nutritional signals that induce sexual differentiation. This process involves the antisilencing factor Epe1, the loss of which causes dramatic increase in heterochromatic loci. Our analyses uncover unexpected regulatory roles for mRNA-processing factors that assemble dynamic heterochromatin to modulate gene expression.

Regulation of α- and β-myosin heavy chain messenger RNAs in the rat myocardium by amiodarone and by thyroid status

1989 ◽  
Vol 76 (5) ◽  
pp. 463-467 ◽  
Author(s):  
J. A. Franklyn ◽  
N. K. Green ◽  
M. D. Gammage ◽  
J. A. O. Ahlquist ◽  
M. C. Sheppard
Keyword(s):  
Gene Expression ◽  
Myosin Heavy Chain ◽  
Heavy Chain ◽  
Cdna Probe ◽  
Messenger Rnas ◽  
Thyroid Status ◽  
Dot Hybridization ◽  
Spot 14 ◽  
Amiodarone Treatment ◽  
Regulated Gene Expression

1. A number of the cardiovascular effects of amiodarone resemble those of hypothyroidism, prompting examination of the relationship between the actions of the drug and thyroid hormones. Amiodarone treatment of the rat was used as a model to determine the influence of the drug on thyroid hormone-regulated gene expression in the myocardium and liver; interactions between amiodarone and thyroid status were examined in hypothyroid and tri-iodothyronine (T3)-treated animals. 2. Myocardial levels of α- and β-myosin heavy chain (MHC) messenger RNAs (mRNAs) were measured by dot hybridization to specific oligonucleotide probes; myocardial actin mRNA was measured in parallel by hybridization to a complementary DNA (cDNA) probe. Hepatic levels of Spot 14 and thyroxine-binding prealbumin mRNA were similarly determined by dot hybridization to radiolabelled cDNAs. 3. Amiodarone treatment of the rat resulted in specific increases in both α- and β-MHC mRNAs in the myocardium, as well as hepatic Spot 14 mRNA, changes reversed by T3 administration. 4. Hypothyroidism resulted in a reduction in myocardial α-MHC and hepatic Spot 14 mRNAs, in contrast to amiodarone, whilst hypothyroidism and amiodarone both exerted stimulatory influences on β-MHC mRNA. Treatment of hypothyroid rats with amiodarone had no significant effect on β-MHC or Spot 14 mRNAs, but a further reduction in α-MHC mRNA, compared with the untreated hypothyroid state, was evident. 5. The demonstrated influence of amiodarone on both α- and β-MHC mRNAs and interactions between amiodarone and thyroid status in regulating MHC gene expression may be relevant to its therapeutic effect in man.

scholarly journals The frequency natural antisense transcript first promotes, then represses, frequency gene expression via facultative heterochromatin

2015 ◽  
Vol 112 (14) ◽  
pp. 4357-4362 ◽  
Author(s):  
Na Li ◽  
Tammy M. Joska ◽  
Catherine E. Ruesch ◽  
Samuel J. Coster ◽  
William J. Belden
Keyword(s):  
Gene Expression ◽  
Antisense Transcript ◽  
Inducible Promoter ◽  
Facultative Heterochromatin ◽  
Heterochromatin Formation ◽  
Circadian Phase ◽  
Parallel Pathway ◽  
Hygromycin Resistance Gene ◽  
Heterochromatin Silencing

The circadian clock is controlled by a network of interconnected feedback loops that require histone modifications and chromatin remodeling. Long noncoding natural antisense transcripts (NATs) originate from Period in mammals and frequency (frq) in Neurospora. To understand the role of NATs in the clock, we put the frq antisense transcript qrf (frq spelled backwards) under the control of an inducible promoter. Replacing the endogenous qrf promoter altered heterochromatin formation and DNA methylation at frq. In addition, constitutive, low-level induction of qrf caused a dramatic effect on the endogenous rhythm and elevated circadian output. Surprisingly, even though qrf is needed for heterochromatic silencing, induction of qrf initially promoted frq gene expression by creating a more permissible local chromatin environment. The observation that antisense expression can initially promote sense gene expression before silencing via heterochromatin formation at convergent loci is also found when a NAT to hygromycin resistance gene is driven off the endogenous vivid (vvd) promoter in the Δvvd strain. Facultative heterochromatin silencing at frq functions in a parallel pathway to previously characterized VVD-dependent silencing and is needed to establish the appropriate circadian phase. Thus, repression via dicer-independent siRNA-mediated facultative heterochromatin is largely independent of, and occurs alongside, other feedback processes.

scholarly journals Sequential Entry of Components of Gene Expression Machinery into Daughter Nuclei

2003 ◽  
Vol 14 (3) ◽  
pp. 1043-1057 ◽  
Author(s):  
Kannanganattu V. Prasanth ◽  
Paula A. Sacco-Bubulya ◽  
Supriya G. Prasanth ◽  
David L. Spector
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Mrna Processing ◽  
Mrna Splicing ◽  
Splicing Factors ◽  
Rna Pol Ii ◽  
Pol Ii ◽  
General Transcription Factors ◽  
Sequential Entry ◽  
Processing Factors

In eukaryotic cells, RNA polymerase II (RNA pol II) transcription and pre-mRNA processing are coordinated events. We have addressed how individual components of the transcription and pre-mRNA processing machinery are organized during mitosis and subsequently recruited into the newly formed daughter nuclei. Interestingly, localization studies of numerous RNA pol II transcription and pre-mRNA processing factors revealed a nonrandom and sequential entry of these factors into daughter nuclei after nuclear envelope/lamina formation. The initiation competent form of RNA pol II and general transcription factors appeared in the daughter nuclei simultaneously, but prior to pre-mRNA processing factors, whereas the elongation competent form of RNA pol II was detected even later. The differential entry of these factors rules out the possibility that they are transported as a unitary complex. Telophase nuclei were competent for transcription and pre-mRNA splicing concomitant with the initial entry of the respective factors. In addition, our results revealed a low turnover rate of transcription and pre-mRNA splicing factors during mitosis. We provide evidence to support a model in which the entry of the RNA pol II gene expression machinery into newly forming daughter nuclei is a staged and ordered process.

scholarly journals EPCR-dependent PAR2 activation by the blood coagulation initiation complex regulates LPS-triggered interferon responses in mice

Blood ◽  
2015 ◽  
Vol 125 (18) ◽  
pp. 2845-2854 ◽  
Author(s):  
Hai Po H. Liang ◽  
Edward J. Kerschen ◽  
Irene Hernandez ◽  
Sreemanti Basu ◽  
Mark Zogg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Blood Coagulation ◽  
Target Genes ◽  
Adaptor Protein ◽  
Messenger Rnas ◽  
Initiation Complex ◽  
Induced Expression ◽  
Regulated Gene Expression

Abstract Infection and inflammation are invariably associated with activation of the blood coagulation mechanism, secondary to the inflammation-induced expression of the coagulation initiator tissue factor (TF) on innate immune cells. By investigating the role of cell-surface receptors for coagulation factors in mouse endotoxemia, we found that the protein C receptor (ProcR; EPCR) was required for the normal in vivo and in vitro induction of lipopolysaccharide (LPS)-regulated gene expression. In cultured bone marrow–derived myeloid cells and in monocytic RAW264.7 cells, the LPS-induced expression of functionally active TF, assembly of the ternary TF-VIIa-Xa initiation complex of blood coagulation, and the EPCR-dependent activation of protease-activated receptor 2 (PAR2) by the ternary TF-VIIa-Xa complex were required for the normal LPS induction of messenger RNAs encoding the TLR3/4 signaling adaptor protein Pellino-1 and the transcription factor interferon regulatory factor 8. In response to in vivo challenge with LPS, mice lacking EPCR or PAR2 failed to fully initiate an interferon-regulated gene expression program that included the Irf8 target genes Lif, Iigp1, Gbp2, Gbp3, and Gbp6. The inflammation-induced expression of TF and crosstalk with EPCR, PAR2, and TLR4 therefore appear necessary for the normal evolution of interferon-regulated host responses.

scholarly journals The role of TREX in gene expression and disease

2016 ◽  
Vol 473 (19) ◽  
pp. 2911-2935 ◽  
Author(s):  
Catherine G. Heath ◽  
Nicolas Viphakone ◽  
Stuart A. Wilson
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Molecular Basis ◽  
Cellular Differentiation ◽  
Viral Infections ◽  
Vital Role ◽  
Mrna Processing ◽  
Cellular Functions ◽  
Lateral Sclerosis

TRanscription and EXport (TREX) is a conserved multisubunit complex essential for embryogenesis, organogenesis and cellular differentiation throughout life. By linking transcription, mRNA processing and export together, it exerts a physiologically vital role in the gene expression pathway. In addition, this complex prevents DNA damage and regulates the cell cycle by ensuring optimal gene expression. As the extent of TREX activity in viral infections, amyotrophic lateral sclerosis and cancer emerges, the need for a greater understanding of TREX function becomes evident. A complete elucidation of the composition, function and interactions of the complex will provide the framework for understanding the molecular basis for a variety of diseases. This review details the known composition of TREX, how it is regulated and its cellular functions with an emphasis on mammalian systems.

scholarly journals Light-regulated gene expression during maize leaf development.

1984 ◽  
Vol 98 (2) ◽  
pp. 558-564 ◽  
Author(s):  
T Nelson ◽  
M H Harpster ◽  
S P Mayfield ◽  
W C Taylor
Keyword(s):  
Gene Expression ◽  
Chlorophyll A ◽  
Phosphoenolpyruvate Carboxylase ◽  
Leaf Development ◽  
Light Harvesting ◽  
Messenger Rnas ◽  
Bisphosphate Carboxylase ◽  
Maize Leaf ◽  
Protein Gel ◽  
Regulated Gene Expression

We have established schedules of expression during maize leaf development in light and darkness for the messenger RNAs (mRNAs) and polypeptides for ribulose 1,5-bisphosphate carboxylase (RuBPCase) subunits, phosphoenolpyruvate carboxylase (PEPCase), and the light-harvesting chlorophyll a/b-binding protein (LHCP). Levels of mRNAs were measured by hybridization with cloned probes, and proteins were measured by immunodetection on protein gel blots. The initial synthesis in leaves of all four mRNAs follows a light-independent schedule; illumination influences only the level to which each mRNA accumulates. The synthesis of RuBPCase small and large subunits and of PEPCase polypeptides also follows a light-independent schedule which is modified quantitatively by light. However, the accumulation of LHCP polypeptides absolutely requires illumination. The accumulation of each protein closely follows the accumulation of its mRNA during growth in light. Higher ratios of PEPCase and RuBPCase protein to mRNA occur during dark growth.

scholarly journals Conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing

2015 ◽  
Vol 112 (51) ◽  
pp. 15548-15555 ◽  
Author(s):  
Venkata R. Chalamcharla ◽  
H. Diego Folco ◽  
Jothy Dhakshnamoorthy ◽  
Shiv I. S. Grewal
Keyword(s):  
Gene Silencing ◽  
Rna Processing ◽  
Premature Termination ◽  
Constitutive Heterochromatin ◽  
Transcription Termination ◽  
Facultative Heterochromatin ◽  
Rnai Machinery ◽  
Repeat Elements ◽  
Heterochromatin Formation ◽  
Heterochromatin Assembly

Cotranscriptional RNA processing and surveillance factors mediate heterochromatin formation in diverse eukaryotes. In fission yeast, RNAi machinery and RNA elimination factors including the Mtl1–Red1 core and the exosome are involved in facultative heterochromatin assembly; however, the exact mechanisms remain unclear. Here we show that RNA elimination factors cooperate with the conserved exoribonuclease Dhp1/Rat1/Xrn2, which couples pre-mRNA 3′-end processing to transcription termination, to promote premature termination and facultative heterochromatin formation at meiotic genes. We also find that Dhp1 is critical for RNAi-mediated heterochromatin assembly at retroelements and regulated gene loci and facilitates the formation of constitutive heterochromatin at centromeric and mating-type loci. Remarkably, our results reveal that Dhp1 interacts with the Clr4/Suv39h methyltransferase complex and acts directly to nucleate heterochromatin. Our work uncovers a previously unidentified role for 3′-end processing and transcription termination machinery in gene silencing through premature termination and suggests that noncanonical transcription termination by Dhp1 and RNA elimination factors is linked to heterochromatin assembly. These findings have important implications for understanding silencing mechanisms targeting genes and repeat elements in higher eukaryotes.

scholarly journals SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles

2012 ◽  
Vol 23 (18) ◽  
pp. 3694-3706 ◽  
Author(s):  
Vidisha Tripathi ◽  
David Y. Song ◽  
Xinying Zong ◽  
Sergey P. Shevtsov ◽  
Stephen Hearn ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Cell Nucleus ◽  
Interphase Nucleus ◽  
Sr Proteins ◽  
Mrna Processing ◽  
Splicing Factors ◽  
Nuclear Speckles ◽  
Nuclear Speckle ◽  
Processing Factors

The mammalian cell nucleus is compartmentalized into nonmembranous subnuclear domains that regulate key nuclear functions. Nuclear speckles are subnuclear domains that contain pre-mRNA processing factors and noncoding RNAs. Many of the nuclear speckle constituents work in concert to coordinate multiple steps of gene expression, including transcription, pre-mRNA processing and mRNA transport. The mechanism that regulates the formation and maintenance of nuclear speckles in the interphase nucleus is poorly understood. In the present study, we provide evidence for the involvement of nuclear speckle resident proteins and RNA components in the organization of nuclear speckles. SR-family splicing factors and their binding partner, long noncoding metastasis-associated lung adenocarcinoma transcript 1 RNA, can nucleate the assembly of nuclear speckles in the interphase nucleus. Depletion of SRSF1 in human cells compromises the association of splicing factors to nuclear speckles and influences the levels and activity of other SR proteins. Furthermore, on a stably integrated reporter gene locus, we demonstrate the role of SRSF1 in RNA polymerase II–mediated transcription. Our results suggest that SR proteins mediate the assembly of nuclear speckles and regulate gene expression by influencing both transcriptional and posttranscriptional activities within the cell nucleus.

scholarly journals Enhancer of Rudimentary Cooperates with Conserved RNA-Processing Factors to Promote Meiotic mRNA Decay and Facultative Heterochromatin Assembly

2016 ◽  
Vol 61 (5) ◽  
pp. 747-759 ◽  
Author(s):  
Tomoyasu Sugiyama ◽  
Gobi Thillainadesan ◽  
Venkata R. Chalamcharla ◽  
Zhaojing Meng ◽  
Vanivilasini Balachandran ◽  
...  
Keyword(s):  
Rna Processing ◽  
Mrna Decay ◽  
Facultative Heterochromatin ◽  
Enhancer Of Rudimentary ◽  
Heterochromatin Assembly ◽  
Processing Factors
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