Substantial Histone Reduction Modulates Genomewide Nucleosomal Occupancy and Global Transcriptional Output

We previously showed in Drosophila melanogaster embryos that low-affinity Ultrabithorax (Ubx)-responsive shavenbaby (svb) enhancers drive expression using localized transcriptional environments and that active svb enhancers on different chromosomes tended to colocalize (Tsai et al., 2017). Here, we test the hypothesis that these multi-enhancer ‘hubs’ improve phenotypic resilience to stress by buffering against decreases in transcription factor concentrations and transcriptional output. Deleting a redundant enhancer from the svb locus led to reduced trichome numbers in embryos raised at elevated temperatures. Using high-resolution fluorescence microscopy, we observed lower Ubx concentration and transcriptional output in this deletion allele. Transcription sites of the full svb cis-regulatory region inserted into a different chromosome colocalized with the svb locus, increasing Ubx concentration, the transcriptional output of svb, and partially rescuing the phenotype. Thus, multiple enhancers could reinforce a local transcriptional hub to buffer against environmental stresses and genetic perturbations, providing a mechanism for phenotypical robustness.

Download Full-text

Auxin requirements for a meristematic state in roots depend on a dual brassinosteroid function

10.1101/2020.11.24.395483 ◽

2020 ◽

Author(s):

M. Ackerman-Lavert ◽

Y. Fridman ◽

R Matosevich ◽

H Khandal ◽

L. Friedlander ◽

...

Keyword(s):

Signaling Pathways ◽

Auxin Biosynthesis ◽

Auxin Signaling ◽

Critical Ratio ◽

Dual Effect ◽

Normal Morphology ◽

Arabidopsis Root ◽

Auxin Synthesis ◽

Meristem Maintenance ◽

Transcriptional Output

SummaryThe organization of the root meristem is maintained by a complex interplay between plant hormones signaling pathways that both interpret and determine their accumulation and distribution. Brassinosteroids (BR) and auxin signaling pathways control the number of meristematic cells in the Arabidopsis root, via an interaction that appears to involve contradicting molecular outcomes, with BR promoting auxin signaling input but also repressing its output. However, whether this seemingly incoherent effect is significant for meristem function is unclear. Here, we established that a dual effect of BR on auxin, with BR simultaneously promoting auxin biosynthesis and repressing auxin transcriptional output, is essential for meristem maintenance. Blocking BR-induced auxin synthesis resulted in rapid BR-mediated meristem loss. Conversely, plants with reduced BR levels were resistant to loss of auxin biosynthesis and these meristems maintained their normal morphology despite a 10-fold decrease in auxin levels. In agreement, injured root meristems which rely solely on local auxin synthesis, regenerated when both auxin and BR synthesis were inhibited. Use of BIN2 as a tool to selectively inhibit BR signaling, revealed meristems with distinct phenotypes depending on the perturbed tissue; meristem reminiscent of BR-deficient mutants or of high BR exposure. This enabled mapping BR-auxin interactions to the outer epidermis and lateral root cap tissues, and demonstrated the essentiality of BR signaling in these tissues for meristem maintenance. BR activity in internal tissues however, proved necessary to control BR homeostasis. Together, we demonstrate a basis for inter-tissue coordination and how a critical ratio between these hormones determines the meristematic state.

Download Full-text

TDP-43 dysfunction restricts dendritic complexity by inhibiting CREB activation and altering gene expression

10.1101/2019.12.12.874735 ◽

2019 ◽

Cited By ~ 1

Author(s):

Josiah J. Herzog ◽

Mugdha Deshpande ◽

Weijin Xu ◽

Reazur Rahman ◽

Hannah Suib ◽

...

Keyword(s):

Neurodegenerative Diseases ◽

Rna Binding ◽

Rna Binding Proteins ◽

Dendritic Morphology ◽

New Approach ◽

Creb Activation ◽

Dendritic Branching ◽

Transcriptional Output ◽

Dendritic Complexity ◽

Lateral Sclerosis

AbstractAmyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two related neurodegenerative diseases that present with similar TDP-43 pathology in patient tissue. TDP-43 is an RNA-binding protein and forms aggregates in neurons of ALS and FTD patients as well as in a subset of patients diagnosed with other neurodegenerative diseases. Despite our understanding that TDP-43 is essential for many aspects of RNA metabolism, it remains obscure how TDP-43 dysfunction contributes to neurodegeneration. Interestingly, several neurological disorders display altered dendritic morphology and complexity, which are thought to precede neurodegeneration. In this study, we used TRIBE (targets of RNA-binding proteins identified by editing) as a new approach to identify signaling pathways that regulate dendritic branching downstream of TDP-43. We found that TDP-43 targets are enriched for pathways that signal to the CREB transcription factor. We further found that TDP-43 dysfunction inhibits CREB activation and CREB transcriptional output, and restoring CREB signaling rescued defects in dendritic branching. Our data therefore provide a novel mechanism by which TDP-43 dysfunction interferes with dendritic branching, and define new pathways for therapeutic intervention in neurodegenerative diseases.

Download Full-text

ABHD1/12‐mediated TEADs depalmitoylation regulates Hippo pathway transcriptional output

The FASEB Journal ◽

10.1096/fasebj.2021.35.s1.00243 ◽

2021 ◽

Vol 35 (S1) ◽

Author(s):

Zhipeng Tao ◽

Yang Sun ◽

Baoen Chen ◽

Carla Guarino ◽

Hannah Erb ◽

...

Keyword(s):

Hippo Pathway ◽

Transcriptional Output

Download Full-text

Estrogen receptor alpha controls gene expression via translational offsetting

10.1101/507574 ◽

2018 ◽

Author(s):

Julie Lorent ◽

Richard J. Rebello ◽

Vincent van Hoef ◽

Mitchell G. Lawrence ◽

Krzysztof J. Szkop ◽

...

Keyword(s):

Estrogen Receptor ◽

Estrogen Receptor Alpha ◽

Mrna Translation ◽

Translational Efficiency ◽

Cancer Cell Proliferation ◽

Altered Expression ◽

Receptor Alpha ◽

Protein Levels ◽

Transcriptional Output ◽

The Impact

AbstractEstrogen receptor alpha (ERα) activity is associated with increased cancer cell proliferation. Studies aiming to understand the impact of ERα on cancer-associated phenotypes have largely been limited to its transcriptional activity. Herein, we demonstrate that ERα coordinates its transcriptional output with selective modulation of mRNA translation. Importantly, translational perturbations caused by depletion of ERα largely manifest as “translational offsetting” of the transcriptome, whereby amounts of translated mRNA and protein levels are maintained constant despite changes in mRNA abundance. Transcripts whose levels, but not polysome-association, are reduced following ERα depletion lack features which limit translational efficiency including structured 5’UTRs and miRNA target sites. In contrast, mRNAs induced upon ERα depletion whose polysome-association remains unaltered are enriched in codons requiring U34-modified tRNAs for efficient decoding. Consistently, ERα regulates levels of U34-modification enzymes, whereas altered expression of U34-modification enzymes disrupts ERα dependent translational offsetting. Altogether, we unravel a hitherto unprecedented mechanism of ERα-dependent orchestration of transcriptional and translational programs, and highlight that translational offsetting may be a pervasive mechanism of proteome maintenance in hormone-dependent cancers.

Download Full-text

Two classes of active transcription sites and their roles in developmental regulation

10.1101/2020.06.23.167338 ◽

2020 ◽

Author(s):

Sarah Robinson-Thiewes ◽

John McCloskey ◽

Judith Kimble

Keyword(s):

Single Molecule ◽

Developmental Regulation ◽

Full Length ◽

Genes Encoding ◽

Transcription Sites ◽

Core Components ◽

Active Transcription ◽

Multiple Levels ◽

Nascent Transcripts ◽

Transcriptional Output

AbstractGenes encoding powerful developmental regulators are exquisitely controlled, often at multiple levels. Here, we use single molecule FISH (smFISH) to investigate nuclear active transcription sites (ATS) and cytoplasmic mRNAs of three key regulatory genes along the C. elegans germline developmental axis. The genes encode ERK/MAP kinase and core components of the Notch-dependent transcription complex. Using differentially-labeled probes spanning either a long first intron or downstream exons, we identify two ATS classes that differ in transcriptional progression: iATS harbor partial nascent transcripts while cATS harbor full-length nascent transcripts. Remarkably, the frequencies of iATS and cATS are patterned along the germline axis in a gene-, stage- and sex-specific manner. Moreover, regions with more frequent iATS make fewer full-length nascent transcripts and mRNAs, whereas those with more frequent cATS produce more of them. We propose that the regulated balance of these two ATS classes has a major impact on transcriptional output during development.

Download Full-text

Topoisomerase activity is linked to altered nucleosome positioning and transcriptional regulation in the fission yeast fbp1 gene

PLoS ONE ◽

10.1371/journal.pone.0242348 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242348

Author(s):

Ryuta Asada ◽

Satoshi Senmatsu ◽

Ben Montpetit ◽

Kouji Hirota

Keyword(s):

Transcriptional Regulation ◽

Fission Yeast ◽

Chromatin Structure ◽

Promoter Region ◽

Nucleosome Positioning ◽

Dna Topology ◽

Upstream Region ◽

Inactive Form ◽

Topological State ◽

Transcriptional Output

Chromatin structure, including nucleosome positioning, has a fundamental role in transcriptional regulation through influencing protein-DNA interactions. DNA topology is known to influence chromatin structure, and in doing so, can also alter transcription. However, detailed mechanism(s) linking transcriptional regulation events to chromatin structure that is regulated by changes in DNA topology remain to be well defined. Here we demonstrate that nucleosome positioning and transcriptional output from the fission yeast fbp1 and prp3 genes are altered by excess topoisomerase activity. Given that lncRNAs (long noncoding RNAs) are transcribed from the fbp1 upstream region and are important for fbp1 gene expression, we hypothesized that local changes in DNA topological state caused by topoisomerase activity could alter lncRNA and fbp1 transcription. In support of this, we found that topoisomerase overexpression caused destabilization of positioned nucleosomes within the fbp1 promoter region, which was accompanied by aberrant fbp1 transcription. Similarly, the direct recruitment of topoisomerase, but not a catalytically inactive form, to the promoter region of fbp1 caused local changes in nucleosome positioning that was also accompanied by altered fbp1 transcription. These data indicate that changes in DNA topological state induced by topoisomerase activity could lead to altered fbp1 transcription through modulating nucleosome positioning.

Download Full-text

Sonic hedgehog increases the commitment of pluripotent mesenchymal cells into the osteoblastic lineage and abolishes adipocytic differentiation

Journal of Cell Science ◽

10.1242/jcs.114.11.2085 ◽

2001 ◽

Vol 114 (11) ◽

pp. 2085-2094 ◽

Cited By ~ 3

Author(s):

Sylviane Spinella-Jaegle ◽

Georges Rawadi ◽

Shinji Kawai ◽

Sylvie Gallea ◽

Chi Faucheu ◽

...

Keyword(s):

Sonic Hedgehog ◽

Inverse Relationship ◽

Mesenchymal Cell ◽

Bone Morphogenetic Protein 2 ◽

Short Treatment ◽

Morphogenetic Protein ◽

Adipocytic Differentiation ◽

Hh Signaling ◽

Transcriptional Output ◽

Calvaria Cell

The proteins of the hedgehog (Hh) family regulate various aspects of development. Recently, members of this family have been shown to regulate skeletal formation in vertebrates and to control both chondrocyte and osteoblast differentiation. In the present study, we analyzed the effect of Sonic hedgehog (Shh) on the osteoblastic and adipocytic commitment/differentiation. Recombinant N-terminal Shh (N-Shh) significantly increased the percentage of both the pluripotent mesenchymal cell lines C3H10T1/2 and ST2 and calvaria cells responding to bone morphogenetic protein 2 (BMP-2), in terms of osteoblast commitment as assessed by measuring alkaline phosphatase (ALP) activity. This synergistic effect was mediated, at least partly, through the positive modulation of the transcriptional output of BMPs via Smad signaling. Furthermore, N-Shh was found to abolish adipocytic differentiation of C3H10T1/2 cells both in the presence or absence of BMP-2. A short treatment with N-Shh was sufficient to dramatically reduce the levels of the adipocytic-related transcription factors C/EBPα and PPARγ in both C3H10T1/2 and calvaria cell cultures. Given the inverse relationship between marrow adipocytes and osteoblasts with aging, agonists of the Hh signaling pathway might constitute potential drugs for preventing and/or treating osteopenic disorders.

Download Full-text