End-of-year preprints – the genetics & genomics edition

Genomics

Comparative analysis of 43 distinct RNA modifications by nanopore tRNA sequencing

Laura K. White, Kezia Dobson, Samantha del Pozo, Jill M. Bilodeaux, Shelby E. Andersen, Amber Baldwin, Chloe Barrington, Nadine Körtel, Federico Martinez-Seidel, Saylor M. Strugar, Kristin E.N. Watt, Neelanjan Mukherjee, Jay R. Hesselberth

https://www.biorxiv.org/content/10.1101/2024.07.23.604651v1

Modifications on tRNAs play important roles in many cellular processes but they are usually missed in conventional Next Gen sequencing. This preprint provides important guidelines on how to robustly detect tRNA modifications using nanopore sequencing.

Picked by: Chee Kiang (Ethan) Ewe

Single-cell multiomics reveals the oscillatory dynamics of mRNA metabolism and chromatin accessibility during the cell cycle

Maulik K. Nariya, David Santiago-Algarra, Olivier Tassy, Marie Cerciat, Tao Ye, Andrea Riba, Nacho Molina

https://www.biorxiv.org/content/10.1101/2024.01.11.575159v2

This preprint demonstrates that gene expression and chromatin oscillate during the cell cycle with waves of nuclear mRNA export at different stages.

Picked by: Chee Kiang (Ethan) Ewe

From Nariya et al. (2024). This image is made available under a CC-BY-NC-ND 4.0 International license.

A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation

Alex Y. Ge, Abolfazl Arab, Raymond Dai, Albertas Navickas, Lisa Fish, Kristle Garcia, Hosseinali Asgharian, Jackson Goudreau, Sean Lee, Kathryn Keenan, Melissa B. Pappalardi, Michael T. McCabe, Laralynne Przybyla, Hani Goodarzi, Luke A. Gilbert

https://www.biorxiv.org/content/10.1101/2022.12.14.518457v4

Picked by: Mansi Srivastava

Note: this preprint has (already) been published in Scientific Reports doi: 10.1038/s41598-024-77314-9

Buffering and non-monotonic behavior of gene dosage response curves for human complex traits

Nikhil Milind, Courtney J. Smith, Huisheng Zhu, Jeffrey P. Spence, Jonathan K. Pritchard

https://www.medrxiv.org/content/10.1101/2024.11.11.24317065v1

The authors found that duplication and deletion affects many traits in the same direction and defined a concept called “gene dosage response curve”.

Picked by: Chee Kiang (Ethan) Ewe

Divergent C. elegans toxin alleles are suppressed by distinct mechanisms

Stefan Zdraljevic, Laura Walter-McNeill, Giancarlo N. Bruni, Joshua S. Bloom, Daniel H.W. Leighton, J.B. Collins, Heriberto Marquez, Noah Alexander, Leonid Kruglyak

https://www.biorxiv.org/content/10.1101/2024.04.26.591160v2

This interesting study found that toxin-antitoxin, important for species competition and evolution, can be regulated by RNAi in C. elegans!

Picked by: Chee Kiang (Ethan) Ewe

Super-enhancer interactomes from single cells link clustering and transcription

Derek J. Le, Antonina Hafner, Sadhana Gaddam, Kevin C. Wang, Alistair N. Boettiger

https://www.biorxiv.org/content/10.1101/2024.05.08.593251v1.full

This paper looks at multi-way interactions between chromatin regions at the single-cell level to assess the frequency of contacts between super enhancers. They observe that while specific multi-way contacts are rare, enhancers are likely to form transient communities within which transcription is boosted.

Picked by: Deevitha Balasubramanian

From Le et al. (2024). This image is made available under a CC-BY 4.0 International license.

Bioinformatics

IMMClock reveals immune aging and T cell function at single-cell resolution

Yael Gurevich Schmidt, Di Wu, Sanna Madan, Sanju Sinha, Sahil Sahni, Vishaka Gopalan, Binbin Wang, Saugato Rahman Dhruba, Alejandro A. Schäffer, Nan-ping Weng, Nicholas P. Restifo, Kun Wang, Eytan Ruppin

https://www.biorxiv.org/content/10.1101/2024.11.13.623449v1

This preprint is centered on the development of IMMClock, a machine learning model that infers cell-type biological states from single-cell RNA-seq data. This model is then used by the authors to study T-cell functionality during aging.

Picked by: Jessica Chevallier

From Gurevich Schmidt et al. (2024). This image is made available under a CC-BY-NC 4.0 International license.

Gene regulation

High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes

Emma L. Peterman, Deon S. Ploessl, Kasey S. Love, Valeria Sanabria, Rachel F. Daniels, Christopher P. Johnstone, Diya R. Godavarti, Sneha R. Kabaria, Conrad G. Oakes, Athma A. Pai, Kate E. Galloway

https://www.biorxiv.org/content/10.1101/2024.11.26.625483v2.full

The authors used a variety of transgenic constructs in HCR Flow-FISH to detect mRNA and protein levels, to dissect the various genetic features (promoter sequence, coding sequence, polyadenyation signal, etc.) that differentially impact transcription and translation.

Picked by: Deevitha Balasubramanian

TurboID-based proximity labeling identifies novel germline proteins that maintain E granule integrity and small RNA homeostasis in C. elegans

Kun Li, Xuezhu Feng, Ke Wang, Xiaona Huang, Chengming Zhu, Xinya Huang, Quan Wen, Shouhong Guang, Xiangyang Chen

https://www.biorxiv.org/content/10.1101/2024.12.03.626736v1

Germ granules are essential for maintaining gene expression homeostasis in the germline. This paper found novel proteins localized to a sub-compartment of germ granules important for the synthesis of some small RNA and balance piRNA silencing in the germline.

Picked by: Chee Kiang (Ethan) Ewe

Epigenetics

DAF-16/Foxo suppresses the transgenerational sterility of prg-1 piRNA mutants via a systemic small RNA pathway

Matt Simon, Maya Spichal, Bree Heestand, Stephen Frenk, Ashley Hedges, Malik Godwin, Alicia S. Wellman, Aisa Sakaguchi, Shawn Ahmed

https://www.biorxiv.org/content/10.1101/326751v2

This paper demonstrates how conversed insulin signaling in the soma communicates with the germline to regulate epigenetic inheritance and germline mortality in C. elegans.

Picked by: Chee Kiang (Ethan) Ewe

Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome folding

Flora Paldi, Michael F Szalay, Marco Di Stefano, Daniel Jost, Hadrien Reboul, Giacomo Cavalli

https://www.biorxiv.org/content/10.1101/2024.11.21.624660v1

This preprint shows that transients perturbation of the genome causes persistent changes in genome architecture, priming certain loci for subsequent stress.

Picked by: Chee Kiang (Ethan) Ewe

From Paldi et al. (2024). This image is made available under a CC-BY-NC-ND 4.0 International license.

Limited impact of the siRNA pathway on transposable element expression in Aedes aegypti

Alexander Bergman, Anna B. Crist, Hélène Lopez-Maestre, Hervé Blanc, Mauro Castelló-Sanjuán, Lionel Frangeul, Hugo Varet, Josquin Daron, Sarah H. Merkling, Maria-Carla Saleh, Louis Lambrechts

https://www.biorxiv.org/content/10.1101/2024.11.26.625377v1

siRNA plays major role in controlling transposons in many animals, but apparently not in mosquitoes.

Picked by: Chee Kiang (Ethan) Ewe