bHLH Transcription Factors Undergo Alternative Splicing During Cold Acclimation in a Eucalyptus hybrid

Apablaza, Héctor; Solís, Myriam; Conejera, Daniel; Fonseca, Alexis; Cid, Jorge Dresdner; Tarifeño-Saldivia, Estefanía; Valenzuela, Sofía; Emhart, Verónica; Fernández, M

doi:10.1007/s11105-021-01313-7

Cited by 3 publications

(3 citation statements)

References 113 publications

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“…Transcription factors basic-helix-loop-helix (bHLH) play a key role in growth, development, and abiotic stress. In the Eucalyptus hybrid ( E. nitens × E. globulus ), 44 bHLH transcripts were transcribed under the effect of AS and two unique isoforms during cold acclimation to counter cold stress ( Apablaza et al., 2021 ). Late Elongated Hypocotyl (LHY) and Circadian Clock-Associated 1 (CCA1) coexpress to regulate the transcription of C-Repeat Binding Factor (CBF) to enhance cold tolerance ( Dong et al., 2011 ).…”

Section: Applications Of As In Transcriptional Repressionmentioning

confidence: 99%

Alternative splicing: transcriptional regulatory network in agroforestry

Hussain

Abbas

et al. 2023

Front. Plant Sci.

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Alternative splicing (AS) in plants plays a key role in regulating the expression of numerous transcripts from a single gene in a regulatory pathway. Variable concentrations of growth regulatory hormones and external stimuli trigger alternative splicing to switch among different growth stages and adapt to environmental stresses. In the AS phenomenon, a spliceosome causes differential transcriptional modifications in messenger RNA (mRNAs), resulting in partial or complete retention of one or more introns as compared to fully spliced mRNA. Differentially expressed proteins translated from intron-retaining messenger RNA (mRNAir) perform vital functions in the feedback mechanism. At the post-transcriptional level, AS causes the remodeling of transcription factors (TFs) by the addition or deletion of binding domains to activate and/or repress transcription. In this study, we have summarized the specific role of AS in the regulation of gene expression through repression and activation of the transcriptional regulatory network under external stimuli and switch among developmental stages.

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Section: Applications Of As In Transcriptional Repressionmentioning

confidence: 99%

Alternative splicing: transcriptional regulatory network in agroforestry

Hussain

Abbas

et al. 2023

Front. Plant Sci.

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“…Manual pipelines are commonly used to identify members of gene families in publications documenting the assembly of newly assembled genomes (Dong et al 2021 ; Feng et al 2021 ; Huang et al 2021a ; Li et al 2021 ; Rai et al 2021 ; Wang et al 2021a ; Apablaza et al 2022 ). When implementing a manual pipeline to identify a gene family, it is important to consider several issues that affect the confidence in the homologs that are reported.…”

Section: Automated and Manual Pipelines For Gene Family Identificationmentioning

confidence: 99%

“…A second commonly used method for homology searches is HMMER (Andolfo et al 2021 ; Dong et al 2021 ; Feng et al 2021 ; Guérin et al 2021 ; Huang et al 2021a ; Qin et al 2021 ; Wu et al 2021 ; Apablaza et al 2022 ). HMMER is used to search for homologs based on conserved sequence domains rather than sequence similarity, which allows identification of remote homologs with low overall sequence similarity (Rost 1999 ; Habermann 2016 ; de Boissier and Habermann 2020 ).…”

Section: Profile Domain Searches Using Hidden Markov Modeler (Hmmer)mentioning

confidence: 99%

Approaches to increase the validity of gene family identification using manual homology search tools

Nestor,

Bayer,

Fernandez

et al. 2023

Genetica

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Identifying homologs is an important process in the analysis of genetic patterns underlying traits and evolutionary relationships among species. Analysis of gene families is often used to form and support hypotheses on genetic patterns such as gene presence, absence, or functional divergence which underlie traits examined in functional studies. These analyses often require precise identification of all members in a targeted gene family. Manual pipelines where homology search and orthology assignment tools are used separately are the most common approach for identifying small gene families where accurate identification of all members is important. The ability to curate sequences between steps in manual pipelines allows for simple and precise identification of all possible gene family members. However, the validity of such manual pipeline analyses is often decreased by inappropriate approaches to homology searches including too relaxed or stringent statistical thresholds, inappropriate query sequences, homology classification based on sequence similarity alone, and low-quality proteome or genome sequences. In this article, we propose several approaches to mitigate these issues and allow for precise identification of gene family members and support for hypotheses linking genetic patterns to functional traits.

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