Genomics

Covid-19 genomic analysis reveals clusters of emerging sublineages within the delta variant

1. Evans K. Rono

Reviewed by ScreenIT

A test of the pioneer factor hypothesis using ectopic liver gene activation

1. Jeffrey L Hansen
2. Kaiser J Loell
3. Barak A Cohen

• Curated by eLife

  Evaluation Summary:

  How transcription factors access their DNA binding motifs in chromatin and cooperate with other transcription factors in DNA binding remains a contentious question. It is clear that some transcription factors ("pioneer transcription factors") play a dominant role in opening chromatin during development and reprogramming, but it has also been clear that the ability of transcription factors to do so lies on a spectrum, that pioneer transcription factors may mutually interact with other transcription factors in their pioneering activity and that their mode of binding is still poorly understood. This manuscript's presentation attempts to refute an overly simplified pioneer factor hypothesis. Overall, this is an important topic and the authors use a good experimental approach, but the analyses are limited and the interpretation too simplified.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Angiotensin converting enzyme 2 (ACE2) is expressed in murine cutaneous under single-cell transcriptome resolution

1. Chenyu Chu
2. Chen Hu
3. Li Liu
4. Yuanjing Wang
5. Yili Qu
6. Yi Man

Reviewed by ScreenIT

Diversity of SARS-CoV-2 genome among various strains identified in Lucknow, Uttar Pradesh

1. Biswajit Sahoo
2. Pramod Kumar Maurya
3. Ratnesh Kumar Tripathi
4. Jyotsana Agarwal
5. Swasti Tiwari

Reviewed by ScreenIT

De Novo-Whole Genome Assembly of the Roborovski Dwarf Hamster ( Phodopus roborovskii ) Genome: An Animal Model for Severe/Critical COVID-19

1. Sandro Andreotti
2. Janine Altmüller
3. Claudia Quedenau
4. Tatiana Borodina
5. Geraldine Nouailles
6. Luiz Gustavo Teixeira Alves
7. Markus Landthaler
8. Maximilian Bieniara
9. Jakob Trimpert
10. Emanuel Wyler

Reviewed by ScreenIT

Sequence features of retrotransposons allow for epigenetic variability

1. Kevin R Costello
2. Amy Leung
3. Candi Trac
4. Michael Lee
5. Mudaser Basam
6. J Andrew Pospisilik
7. Dustin E Schones

• Curated by eLife

  Evaluation Summary:

  The authors aim to understand how certain transposable elements escape chromatin-based silencing. Focusing on variably methylated copies of IAP (VM-IAPs) in the mouse, the authors show that elements that can escape silencing share sequence variations that alter KRAB zinc finger protein (KZFP) binding and KAP1 recruitment, proximity to expressed genes and high CpG content. Analysis of human elements in human KZFP-free mouse cells recapitulates some of these observations. The authors propose that ZF-CxxxC proteins play a role in establishing permissive chromatin at transposable elements that harbor high CpG content and weak KZFP binding. The data are mostly correlative and open the path for further mechanistic analyses. The paper is of interest to readers in the field of epigenetics, genome biology and transposable elements.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Reviewed by eLife

Reciprocal differentiation via GABAergic components and ASD-related phenotypes in hES with 1q21.1 CNV

1. Yoshiko Nomura
2. Jun Nomura
3. Toru Nishikawa
4. Toru Takumi

Reviewed by Review Commons

Remote immune processes revealed by immune-derived circulating cell-free DNA

1. Ilana Fox-Fisher
2. Sheina Piyanzin
3. Bracha Lea Ochana
4. Agnes Klochendler
5. Judith Magenheim
6. Ayelet Peretz
7. Netanel Loyfer
8. Joshua Moss
9. Daniel Cohen
10. Yaron Drori
11. Nehemya Friedman
12. Michal Mandelboim
13. Marc E Rothenberg
14. Julie M Caldwell
15. Mark Rochman
16. Arash Jamshidi
17. Gordon Cann
18. David Lavi
19. Tommy Kaplan
20. Benjamin Glaser
21. Ruth Shemer
22. Yuval Dor

• Curated by eLife

  Evaluation Summary:

  This manuscript introduces a novel method for the monitoring of immune dynamics from blood, based on a measurement of the burden of cell-free DNA derived from seven key immune cell types in blood. The authors demonstrate the possibility to quantify the specific amounts of cell-free DNA by assaying cell-type specific CpG methylation marks via a targeted DNA sequencing assay. Assays of specific immune cell counts in blood are commonplace in modern diagnostic medicine. Rather than counting cells, the assay reported in this manuscript measures the burden of DNA released by dying immune cells, and this new assay may provide information about the immune system beyond what is possible with mere cell counting. The authors test their assay in three different settings (vaccination, inflammation and cancer), and provide significant support for the utility of their assay for immune monitoring in health and disease.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

3′HS1 CTCF binding site in human β-globin locus regulates fetal hemoglobin expression

1. Pamela Himadewi
2. Xue Qing David Wang
3. Fan Feng
4. Haley Gore
5. Yushuai Liu
6. Lei Yu
7. Ryo Kurita
8. Yukio Nakamura
9. Gerd P Pfeifer
10. Jie Liu
11. Xiaotian Zhang

• Curated by eLife

  Evaluation Summary:

  The authors investigate the contribution of a CTCF binding site located 3' of the beta-globin locus to the relative expression of the genes within the cluster. Their results serve to further clarify a longstanding model for how relatively high levels of fetal beta-globin are observed in some individuals harboring a deletion of this region, and contribute to existing models of the function of CTCF binding sites in genome organization.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Geometrical Study of Virus RNA Sequences

1. Alex Belinsky
2. Guennadi Kouzaev

Reviewed by ScreenIT