Michelle M. Halstead
YOU?
Author Swipe
View article: Genetic Variants in Recurrent Euploid Pregnancy Loss
Genetic Variants in Recurrent Euploid Pregnancy Loss Open
Recurrent pregnancy loss (RPL) affects ∼5% of women, yet the genetic basis of euploid losses remains unclear. We performed genome sequencing in 118 families with unexplained euploid RPL, most without fetal anomalies. We identified genomic …
View article: Maternal<i>Med12</i>safeguards trophoblast pluripotency and placental development
Maternal<i>Med12</i>safeguards trophoblast pluripotency and placental development Open
For a brief but critical period post-fertilization, the mammalian embryo is entirely dependent on maternal products inherited from the oocyte. Previous research showed that oocyte-specific loss of Med12 , an X-linked gene and Mediator comp…
View article: An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics
An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics Open
A comprehensive characterization of regulatory elements in the chicken genome across tissues will have substantial impacts on both fundamental and applied research. Here, we systematically identified and characterized regulatory elements i…
View article: Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing
Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing Open
To identify and annotate transcript isoforms in the chicken genome, we generated Nanopore long-read sequencing data from 68 samples that encompassed 19 diverse tissues collected from experimental adult male and female White Leghorn chicken…
View article: A comprehensive prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing
A comprehensive prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing Open
To comprehensively identify and annotate transcript isoforms in the chicken genome, we generated Nanopore long-read sequencing data from a diverse set of 19 chicken tissues comprising 68 samples collected from experimental line 6 × line 7 …
View article: Resetting H3K4me3, H3K27ac, H3K9me3 and H3K27me3 during the maternal-to-zygotic transition and blastocyst lineage specification in bovine embryos
Resetting H3K4me3, H3K27ac, H3K9me3 and H3K27me3 during the maternal-to-zygotic transition and blastocyst lineage specification in bovine embryos Open
It remains poorly understood how histone modifications regulate changes in gene expression during preimplantation development. Using a bovine model, we profiled changes in two activating (H3K4me3 and H3K27ac) and two repressive (H3K9me3 an…
View article: Profiling of open chromatin in developing pig ( <i>Sus scrofa</i> ) muscle to identify regulatory regions
Profiling of open chromatin in developing pig ( <i>Sus scrofa</i> ) muscle to identify regulatory regions Open
There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowle…
View article: Pig genome functional annotation enhances the biological interpretation of complex traits and human disease
Pig genome functional annotation enhances the biological interpretation of complex traits and human disease Open
The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits of economic importance, adaptive evolution and comparative genomics. Here, we provide the most comprehensive …
View article: Large-Scale Multiplexing Permits Full-Length Transcriptome Annotation of 32 Bovine Tissues From a Single Nanopore Flow Cell
Large-Scale Multiplexing Permits Full-Length Transcriptome Annotation of 32 Bovine Tissues From a Single Nanopore Flow Cell Open
A comprehensive annotation of transcript isoforms in domesticated species is lacking. Especially considering that transcriptome complexity and splicing patterns are not well-conserved between species, this presents a substantial obstacle t…
View article: Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research
Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research Open
Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively…
View article: Pig genome functional annotation enhances biological interpretations of complex traits and comparative epigenomics
Pig genome functional annotation enhances biological interpretations of complex traits and comparative epigenomics Open
The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits of economic importance, adaptive evolution and comparative genomics. Here, we provide the most comprehensive …
View article: Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage
Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage Open
Characterizing transcription start sites is essential for understanding the regulatory mechanisms that control gene expression. Recently, a new bovine genome assembly (ARS-UCD1.2) with high continuity, accuracy, and completeness was releas…
View article: Profiling of open chromatin in developing pig (<i>Sus scrofa</i>) muscle to identify regulatory regions
Profiling of open chromatin in developing pig (<i>Sus scrofa</i>) muscle to identify regulatory regions Open
There is very little information about how the genome is regulated in domestic pigs ( Sus scrofa ). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programmes. In order to addres…
View article: Chromatin remodeling in bovine embryos indicates species-specific regulation of genome activation
Chromatin remodeling in bovine embryos indicates species-specific regulation of genome activation Open
The shift from maternal to embryonic control is a critical developmental milestone in preimplantation development. Widespread transcriptomic and epigenetic remodeling facilitate this transition from terminally differentiated gametes to tot…
View article: Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage
Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage Open
Characterizing transcription start sites is essential for understanding the regulatory mechanisms that control gene expression. Recently, a new bovine genome assembly (ARS-UCD1.2) with high continuity, accuracy, and completeness was releas…
View article: A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues
A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues Open
Background Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional …
View article: Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues
Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues Open
The use of Assay for Transposase-Accessible Chromatin (ATAC-seq) to profile chromatin accessibility has surged over the past years, but its applicability to tissues has been very limited. With the intent of preserving nuclear architecture …
View article: Additional file 3 of A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues
Additional file 3 of A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues Open
Additional file 3. Pig ATAC-seq peaks. Genomic locations of ATAC-seq peaks that were called for each tissue in each replicate.
View article: Additional file 2 of A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues
Additional file 2 of A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues Open
Additional file 2. Cattle ATAC-seq peaks. Genomic locations of ATAC-seq peaks that were called for each tissue in each replicate.
View article: Chromatin remodeling in bovine embryos indicates species-specific regulation of genome activation
Chromatin remodeling in bovine embryos indicates species-specific regulation of genome activation Open
The maternal-to-zygotic transition (MZT) is underpinned by wide-spread transcriptomic and epigenomic remodeling that facilitates totipotency acquisition. Factors regulating MZT vary across species and differences in timing of developmental…
View article: Transcript profiling of bovine embryos implicates specific transcription factors in the maternal-to-embryo transition
Transcript profiling of bovine embryos implicates specific transcription factors in the maternal-to-embryo transition Open
Full-grown oocytes are transcriptionally quiescent. Following maturation and fertilization, the early stages of embryonic development occur in the absence (or low levels) of transcription that results in a period of development relying on …
View article: Transcriptome profiling of individual rhesus macaque oocytes and preimplantation embryos†
Transcriptome profiling of individual rhesus macaque oocytes and preimplantation embryos† Open
Early mammalian embryonic transcriptomes are dynamic throughout the process of preimplantation development. Cataloging of primate transcriptomics during early development has been accomplished in humans, but global characterization of tran…